book of abstracts - vibeslab...day4, thursday 21nd november session viii: 9:00-12:00 chair: julien...
TRANSCRIPT
上海大学国际部
International Center of Quantum and
Molecular Structures Shanghai University
2019 The 2nd
Quantum
International
Frontiers
Book of
Abstracts
1
Welcome
Quantum theories emerged about a century ago with the completely new view of
the Universe then the previously established classical one. However, only very
recently we are really moving to the quantum era with the direct applications of
quantum theories in very diverse disciplines as telecommunication, technology,
material science, bioscience, cryptography, quantum computing and so on. The newly
established Quantum International Frontier series, acts as a platform for exchange of
experience, research directions and techniques, and nexus for new ideas in the
Quantum Sciences by bringing together and encouraging collaboration between
researcher working on different aspects of quantum theories and their applications in
“real life”.
One of the important aspects of the Quantum International Frontiers is its novel
format with Frontier and Pedagogical Invited Lectures in addition to the Standard
Invited Lectures, and a live question submission system, accessible from PCs, laptops
and mobile devices. Such combined lecture format focus on exposure to an
international research environment for the students and young researchers, the
introduction to the quantum theories, highlighting theoretical background, putting
modern research in the historical perspective and allowing for the better
understanding of cutting-edge novel research.
I thank all the speakers and poster presenters for their contributions to the 2nd QIF
conference. I hope that the conference will be a place of many fruitful scientific
discussions and will bring numerous new scientific ideas.
I also hope that you will enjoy your stay in Shanghai, and at the Shanghai
University Baoshan Campus, and bring back home some lasting memories.
We welcome you to Shanghai!
Malgorzata Biczysko
QIF2019 Chair
On behalf of the Organizing and Scientific Committees
2
FURTHER INFORMATION:
http://www.vibes-lab.org/2qif/
2019 2nd QIF WeChat group QR code
WIFI – for conference
Name：Shanghai University
QIF questions system
Wifi for Q-system: QIFRONTIER
Web browse to http://10.0.0.1:3000
Select channel #qifrontiers
(or scan the QR code)
Sign in as an 'anonymous' user to contribute questions and follow the discussion
Use the '...' menu on the right or 'long press' on mobile devices to edit your
contributions
3
Committees:
International Scientific and Honorary Committees
Paul W. Ayers Canada HC
Erkki J. Brändas Sweden ISC
Tucker Carrington Canada HC
Sir David Clary UK ISC
Leticia Gonzalez Austria ISC
Frank E. Harris USA ISC
Kersti Hermansson Sweden HC
Philip Hoggan France HC
Chao-Ping Hsu China (Taiwan) ISC
Samantha Jenkins China ISC
Steven R. Kirk China ISC
Anna Krylov USA ISC
Shuhua Li China HC
Wenjian Liu China ISC
Jian Liu China ISC
Sergei Manzhos Canada ISC
Debashis Mukherjee India HC
Marco Nascimento Brazil HC
Sourav Pal India ISC
Martin J. Paterson UK ISC
Katarzyna Pernal Poland ISC
Piotr Piecuch USA ISC
Martin Quack Switzerland ISC
Markus Reiher Switzerland HC
Jeffrey R. Reimers China HC
Michael A. Robb UK HC
Yasuteru Shigeta Japan ISC
4
Zhigang Shuai China HC
Akitomo Tachibana Japan HC
David Wales UK HC
Yan Alexander Wang Canada ISC
Angela K. Wilson USA ISC
Wei Wu China HC
Weitao Yang USA HC
Local Organizing Committee
Malgorzata Biczysko - Chair
Wei Ren – Co-chair SHU
Michael J Ford – Co-chair UTS
Xiaoyan Gao Hanli Tian
Chong Shu Youjia Liu
Mingzhu Sheng Ping Wang
Ruiqin Xu Hexu Ye
Yage Zhao Xinxing Li
Bo Wang Yaru Wang
Wensong Wang Linlin Qiao
Zhenglong Gong
5
SPONSORS:
6
7
8
Day1, Monday 18th November
15:00-15:30 Conference Opening
Session I: 15:30-17:30
Chair: Malgorzata Biczysko
15:30-16:30 Frontier Invited Lecture: Piotr Piecuch
Approaching Exact Quantum Chemistry by Stochastic Wave Function Sampling and
Deterministic Coupled-Cluster Computations
16:30-17:30 Frontier Invited Lecture: Xiaosong Li
Watch the Dance of Electrons in Molecules – from Time-Dependent Quantum Theory to
Spectroscopy
17:30 – 20:00 Welcome Reception
Day2, Tuesday 19th November
Session II: 9:00-12:00
Chair: Xiaosong Li
9:00-10:00 Frontier Invited Lecture: Julien Bloino
A Quest for Accuracy in the Vibrational World
10:00-10:30 Coffee/Tea break
10:30-11:15 Pedagogical Invited Lecture: Kenneth Ruud
On the calculation of molecular properties
11:15-12:00 Pedagogical Invited Lecture: Xi Chen
Shortcuts to Adiabaticity
12:00-13:30 Lunch
Session III: 13:30-15:00
9
Chair: Jeffrey R. Reimers
13:30-14:15 Pedagogical Invited Lecture: Chao-Ping Hsu
Theories for excited state calculation, and diabatic states for electron/energy transfer.
14:15-15:00 Pedagogical Invited Lecture: llaria Ciofini
Modeling Excited States using Density Functional Theory
15:00-15:30 Coffee/Tea break
Session IV: 15:30-17:30
Chair: Katarzyna Pernal
15:30-16:30 Frontier Invited Lecture: Roland Lindh
On the use of the exact operator for the semiclassical light-matter interaction to evaluate
oscillator and rotatory strengths
16:30-17:30 Frontier Invited Lecture: Michael A Robb
Observing the Motion of Electrons on an Attosecond Timescale: The Ehrenfest method with
Classical and Quantum Dynamics
10
Day3, Wednesday 20th November
Session V: 9:00-12:00
Chair: Piotr Piecuch
9:00-10:00 Frontier Invited Lecture: Angela K. Wilson
Computational Approaches Across the Periodic Table: Predicting Energetics and
Spectroscopic Properties
10:00-10:30 Coffee/Tea break
10:30-11:15 Frontier Invited Lecture: Jeffrey R. Reimers
UV/Visible spectroscopy for molecules and nanophotonics: interpreting and predicting
low-resolution and high-resolution data
11:15-12:00 Frontier Invited Lecture: Marco Nascimento
The nature of the chemical bond
12:00-13:30 Lunch
Session VI: 13:30-15:00
Chair: Sergei Manzhos
13:30-14:00 Invited Lecture: Wanzhen Liang
Multiscale Modeling and Simulation of Plasmon-Exciton Interaction
14:00-14:20 Contributed Talk: William Glover
Fragmentation approach to electronic excitations
14:20-14:40 Contributed Talk: Qin Yang
Accurate vibrational chiroptical spectroscopy simulation beyond the harmonic
approximation: the VPT2 approach
14:40-15:00 Contributed Talk: Igor Ying Zhang
Simultaneous Attenuation of Both Self-Interaction Error and Nondynamic Correlation Error
in Density Functional Theory: A Spin-pair Distinctive Adiabatic-Connection Approximation
11
15:00-15:30 Coffee/Tea break
Session VII: 15:30-17:30
Chair: Michael A Robb
15:30-16:30 Pedagogical Invited Lecture: Ping Ao
Some Problems in Dynamics of Topological Defects, Quantum Computing and
Non-equilibrium Processes
16:30-17:30 Invited Lecture: Ziqiu Chen
High-resolution spectroscopy of small cyclic molecules: Probing large amplitude motions
Day4, Thursday 21nd November
Session VIII: 9:00-12:00
Chair: Julien Bloino
9:00-10:00 Frontier Invited Lecture: Yi Luo
Scanning Raman Microscopy
10:00-10:30 Coffee/Tea break
10:30-11:00 Invited Lecture: Jing Ma
Rational design and fabrications of two-dimensional materials
11:00-11:30 Invited Lecture: Samantha Jenkins
A 3-D Directional Chemical Perspective with Next Generation QTAIM
11:30-12:00 Invited Lecture: Sergei Manzhos
Machine learning for orbital-free DFT
12:00-13:30 Lunch
12
Session IX: 13:30-15:00
Chair: Roland Lindh
13:30-14:00 Invited Lecture: Sai Duan
Theoretical Chemistry under Tips: Raman and STM images
14:00-14:20 Contributed Talk: Alberto Baiardi
Electronic and nuclear quantum dynamics with the Time-Dependent Density Matrix
Renormalization Group
14:20-14:40 Contributed Talk: Pavlo Dral
Quantum Chemistry Assisted by Machine Learning
14:40-15:00 Contributed Talk: Tonghao Shen
Massive-parallel implementation of the resolution-of-identity coupled-cluster approaches in
the numeric atom-center orbital framework for molecular systems
15:00-15:30 Coffee/Tea break
Session X: 15:30-17:30
Chair: Michael J. Ford
15:30-16:30 Frontier Invited Lecture: Katarzyna Pernal
Multiconfiguration DFT with on-top pair density functionals and the long-range correction
energy correction
16:30-17:30 Invited Lecture: Frank E. Harris
Studies of four-body problems using exponential wavefunctions in all the relative
coordinates
13
Friday 22nd November
Session XI: 9:00-10:00
Chair: Lee Burton
9:00-9:30 Invited Lecture: Zhigang Shuai
Time-dependent Matrix Product States for Finite Temperature
9:30-10:00 Invited Lecture: Alessandro Stroppa
Microscopic mechanisms and origins of ferroelectricity in Hybrid Inorganic-Organic
compounds
10:00-10:30 Coffee/Tea break
Session XII: 10:30-12:00
Chair: TBA
10:30-11:00 Invited Lecture: Michael J. Ford
TBA
11:00-11:20 Contributed Talk: Steven Kirk
TBA
11:20-11:40 Contributed Talk: Sergio Sousa
Application of Quantum Mechanics in the Study of Enzymatic Mechanisms
11:40-12:00 Contributed Talk: Tianyu Liu
Nonlinear dynamics of a quantum Cournot duopoly game with Marinatto-Weber model
12:00-13:30 Lunch
Session XIII: 13:30-15:00
Chair: Samantha Jenkins
13:30-14:00 Invited Lecture: Holger Kruse
Computing Accurate Interaction Energies for Stacked Nucleobases
14
14:00-14:30 Invited Lecture: Piotr de Silva
Insights into thermally activated delayed fluorescence (TADF) through the electronic
structure models
14:30-15:00 Closing ceremony
15
Catalogue of abstracts:
LECTURES
Frontier Invited Lectures .......................................................................................... 20
Approaching Exact Quantum Chemistry by Stochastic Wave Function Sampling and
Deterministic Coupled-Cluster Computations (Piotr Piecuch) .................................. 21
Watch the Dance of Electrons in Molecules – from Time-Dependent Quantum Theory to
Spectroscopy (Xiaosong Li) ...................................................................... 23
A Quest for Accuracy in the Vibrational World (Julien Bloino) ................................ 24
On the use of the exact operator for the semiclassical light-matter interaction to evaluate
oscillator and rotatory strengths (Roland Lindh) ................................................. 26
Observing the Motion of Electrons on an Attosecond Timescale: The Ehrenfest method with
Classical and Quantum Dynamics (Michael A. Robb) ........................................... 27
Computational Approaches Across the Periodic Table: Predicting Energetics and Spectroscopic
Properties (Angela K. Wilson) .................................................................... 28
Scanning Raman Microscopy (Yi Luo) ........................................................... 29
Multiconfiguration DFT with on-top pair density functionals and the long-range correlation
energy correction (Katarzyna Pernal) ............................................................. 30
Pedagogical Invited Lectures .................................................................................... 32
Calculating molecular properties: From real-time methods to (quasi-)energy derivatives
(Kenneth Ruud) .................................................................................... 33
Shortcuts to adiabaticity (Xi Chen) ............................................................... 34
Theories for excited state calculation, and diabatic states for electron/energy transfer (Chao-Ping
Hsu) ................................................................................................ 35
Modeling excited states using Density Functional Theory (Ilaria Ciofini) ...................... 36
UV/Visible spectroscopy for molecules and nanophotonics: interpreting and predicting
low-resolution and high-resolution data (Jeffrey R. Reimers) ................................... 37
The nature of the chemical bond (Marco Nascimento) .......................................... 38
Some Problems in Dynamics of Topological Defects, Quantum Computing, and Non-equilibrium
Processes (Ping Ao) ............................................................................... 40
Standard Invited Lectures ........................................................................................ 41
Multiscale Modeling and Simulation of Plasmon-Exciton Interaction (Wanzhen Liang) ..... 42
High-resolution spectroscopy of small cyclic molecules: Probing large amplitude motions (Ziqiu
Chen) ............................................................................................... 43
Rational design and fabrications of two-dimensional materials (Jing Ma) ...................... 44
A 3-D Directional Chemical Perspective with Next Generation QTAIM (Samantha Jenkins) . 46
16
Rectangular collocation for solution of the Schrödinger equation with collocation point set
optimization (Sergei Manzhos) ................................................................... 47
Extended Koopmans’ Theorem at the Second Order Perturbation Theory: From Wave Function
Theory to Density Functional Theory (Xin Xu) (Cancelled) .................................... 48
Studies of four-body problems using exponential wavefunctions in all the relative coordinates
(Frank E. Harris) ................................................................................... 49
Time-dependent matrix product states for finite temperature (Zhigang Shuai) ................. 50
Microscopic mechanisms and origins of ferroelectricity in Hybrid Inorganic-Organic compounds
(Alessandro Stroppa) .............................................................................. 51
Theoretical spectroscopy of semiconductor defects with application to 2D nBN nanophotonics
(Michael J. Ford) .............................................................. ..............52
Computing Accurate Interaction Energies for Stacked Nucleobases. (Holger Kruse) .......... 53
Insights into thermally activated delayed fluorescence (TADF) through the electronic structure
models (Piotr de Silva) ............................................................................ 54
Contributed Talks ...................................................................................................... 55
Fragmentation approach to electronic excitations (William Glover) ........................... 56
Accurate vibrational chiroptical spectroscopy simulation beyond the harmonic approximation:
the VPT2 approach (Qin Yang) ................................................................... 58
Simultaneous attenustion of both self-interaction error and nondynamic correlation error in
Density Functional Theory: a spon-pair distinctive adiabatic-connection approximation (Igor
Ying Zhang) ....................................................................................... 60
Electronic and nuclear quantum dynamics with the Time-Dependent Density Matrix
Renormalization Group (Alberto Baiardi) ........................................................ 61
Quantum Chemistry Assisted by Machine Learning (Pavlo Dral) ............................... 62
Theoretical Chemistry under Tips: Raman and STM Images (Sai Duan) ....................... 63
TBA (Steven KirK) ................................................................................ 65
Application of Quantum Mechanics in The Study of Enzymatic Mechanisms (Sergio Sousa) . 66
Nonlinear dynamics of a quantum Cournot duopoly game with Marinatto-Weber scheme (Tianyu
Liu) ................................................................................................. 67
Massive-Parallel implementation of the resolution-of-identity Coupled-Cluster approaches in the
numeric atom-center orbital framework for molecular systems (Tonghao Shen)………………68
POSTERS
Explanation of the Role of Hydrogen Bonding in the Structural Preferences of Small Molecule
Conformers ........................................................................................ 70
Next Generation QTAIM for the S1/S0 Conical Intersections in Dynamics Trajectories of a
Light-Driven Rotary Molecular Motor ........................................................... 71
17
The Role of the Transition Density in the S0 → S1 (S01) and S0 → S2 (S02) Transitions of Fulvene
with Next Generation QTAIM .................................................................... 72
Multistate density functional theory applied with 3 unpaired electrons in 3 orbitals: the
singdoublet and tripdoublet states of the ethylene cation ........................................ 73
Next-Generation Quantum Theory of Atoms in Molecules for the Ground and Excited State of
the Ring-Opening of Cyclohexadiene (CHD) .................................................... 74
Next-Generation Quantum Theory of Atoms in Molecules for the Ground and Excited State of
DHCL .............................................................................................. 75
Next-Generation QTAIM for the Design of Quinone-based switches ........................... 76
Next-Generation Quantum Theory of Atoms in Molecules for the Ground and Excited States of
the Penta-2,4-dieniminium Cation (PSB3) ....................................................... 77
Next-Generation Quantum Theory of Atoms in Molecules for the Photochemical Ring-Opening
Reactions of Oxirane .............................................................................. 78
The Directional Bonding of [1.1.1]propellane with Next Generation QTAIM ................. 79
Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical Insight .......... 80
Flip Rearrangement in the Water Pentamer: Analysis of Electronic Structure .................. 81
Quinone-based Switches for Candidate Building Blocks of Molecular Junctions with QTAIM
and the Stress Tensor .............................................................................. 82
Halogen and Hydrogen Bonding in Halogenabenzene/NH3 Complexes Compared
UsingNext-Generation QTAIM ................................................................... 83
3-D bond-paths of QTAIM and the Stress Tensor in Small Water Clusters on the Ehrenfest Force
Molecular Graph ................................................................................... 84
Insights into the Mechanism of Fatty Acid Photodecarboxylase: Trimolecular vs. Bimolecular
Photocycle ......................................................................................... 85
Equilibrize photoluminescence quantum yield and charge mobility of organic semiconductor：A
QM/MM study ..................................................................................... 87
Effect of different connection node on the charge transport property for D-A copolymers: a
Computational Study .............................................................................. 89
A periodic DFT investigation of the hybrid perovskite solar cell interface: From structural
features to electron injection through ligand’s connection ....................................... 90
A strategy for predicting crystal engineering to balance exciton coupling and electronic
coupling ............................................................................................ 92
Q|R: Quantum-based Refinement of Biomacromolecules ....................................... 93
Identification of DNA bases and their cations in Astrochemical environments: Computational
Spectroscopy of Thymine as a test case .......................................................... 94
Simulation of fully anharmonic IR spectra for flexible peptides ................................ 95
Effective QM computational models for protein science ........................................ 96
18
Cβ deviation: a metric for the protein structure validation ....................................... 97
Quantum computations for proteins spectroscopic probes ....................................... 98
Structural properties of molecules with disulfide bond: an accurate theoretical study .......... 99
Accurate determination of energies and molecular structures for isolated small peptides ..... 100
Investigation of the hydrogen bonding in serine: a computational spectroscopy study ........ 101
Fragmental Approach to Electronic Excited States: full ab initio description of solvatochromism
of Brooker’s merocyanine dye…………………………………………………………………102
Formation of Na(0) layers between graphene and monolayer NaCl…………………………...103
Map of campus .……………………………………………...104
19
LECTURES
20
Frontier Invited Lectures
21
Approaching Exact Quantum Chemistry by
Stochastic Wave Function Sampling and
Deterministic Coupled-Cluster Computations
Piotr Piecuch1,2, J. Emiliano Deustua1, Jun Shen1, Ilias Magoulas1, Stephen H.
Yuwono1, Arnab Chakraborty1
1Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
2Department of Physics and Astronomy, Michigan State University, East Lansing, MI
48824, USA
One of the main goals of electronic structure theory is to precisely describe
increasingly complex polyatomic systems. It is widely accepted that size extensive
methods based on the coupled-cluster (CC) theory and their extensions to excited
states via the equation-of-motion (EOM) formalism are excellent candidates for
addressing this goal. In this talk, we will examine a radically new way of obtaining
accurate energetics equivalent to high-level CC calculations, such as CCSDT or
CCSDTQ, even when multireference correlation effects become significant, at the
small fraction of the computational cost, while preserving the black-box character of
single-reference computations. The key idea is a merger of the deterministic
formalism, abbreviated as CC (P; Q) [1,2], with the stochastic CI [3,4] and CC [5]
Quantum Monte Carlo (QMC) approaches [6]. We will also demonstrate that one can
take the merger of the stochastic and deterministic ideas to the ultimate level and use
it to extract the exact, full CI (FCI), energetics out of the early stages of FCIQMC
propagations with the help of the relatively inexpensive polynomial steps similar to
CCSD calculations, eliminating exponential complexity of conventional FCI
Hamiltonian diagonalizations altogether [7]. The advantages of the new
methodologies will be illustrated by molecular examples, where the goal is to recover
the nearly exact, CCSDT and CCSDTQ, and exact, FCI, energetics in situations
involving chemical bond dissociations and reaction pathways and many-electron
systems beyond the reach of FCI. Extensions to excited electronic states by a
combination of stochastic CIQMC and deterministic EOMCC computations [8] and
converging FCI energetics in strongly correlated systems, such as those involved in
modeling metal–insulator transitions [9], where the traditional CCSD, CCSDT,
CCSDTQ, etc. hierarchy breaks down, will be discussed as well.
References:
[1] J. Shen, P. Piecuch, Chem. Phys. 401, 180 (2012); J. Chem. Phys. 136, 144104 (2012).
[2] N. P. Bauman, J. Shen, P. Piecuch, Mol. Phys. 115, 2860 (2017).
[3] G. H. Booth, A. J. W. Thom, A. Alavi, J. Chem. Phys. 131, 054106 (2009).
[4] D. Cleland, G. H. Booth, A. Alavi, J. Chem. Phys. 132, 041103 (2010).
22
[5] A. J. W. Thom, Phys. Rev. Lett. 105, 263004 (2010).
[6] J. E. Deustua, J. Shen, P. Piecuch, Phys. Rev. Lett. 119, 223003 (2017); in preparation.
[7] J. E. Deustua, I. Magoulas, J. Shen, P. Piecuch, J. Chem. Phys. 149, 151101 (2018).
[8] J. E. Deustua, S. H. Yuwono, J. Shen, P. Piecuch, J. Chem. Phys. 150, 111101 (2019); S. H.
Yuwono, [9] A. Chakraborty, J. E. Deustua, J. Shen, P. Piecuch, in preparation.
[10] I. Magoulas, J. E. Deustua, J. Shen, P. Piecuch, in preparation.
23
Watch the Dance of Electrons in Molecules – from
Time-Dependent Quantum Theory to Spectroscopy
Xiaosong Li
Department of Chemistry, University of Washington, Seattle, USA
Ultrafast electronic dynamics are foundational to a wide range of chemical processes.
For example, charge transfer and relaxation, crucial processes implicated in the
function of photovoltaic and photocatalytic materials, are driven by electron motions
and their interactions with electromagnetic fields. Research efforts in the Li group
focus on the development of time-dependent many-electron theories and computational
methods to investigate these ultrafast non-equilibrium dynamical processes. This talk
will illustrate the power of quantum electron dynamics by presenting several important
applications in molecular and materials sciences, including the formation and decay of
molecular plasmons, and the coherence of electron waves and spins.
24
A Quest for Accuracy in the Vibrational World
Julien Bloino1
1Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
Computational spectroscopy is nowadays routinely used as a predictive and
interpretative tool to complement and support experiment, providing insights of the
underlying elemen- tary phenomena responsible for the overall band-shape. However,
the reliability of the produced results is strongly correlated to the underlying models.
This aspect can be espe- cially critical in some fields of applications like chiroptical
analysis or astrochemistry, for instance. Such considerations emphasize the need of
carefully setting up computational protocols, in particular by selecting the most
appropriate level of theory available. As a matter of fact, for medium-to-large
molecular systems with possible environmental effects, a trade-off is necessary
between accuracy and computational cost, and several strategies can be devised, with
suitabilities varying depending on the cases.
Thanks to ongoing developments, it is now possible to compute fully anharmonic
vibrational spectra, providing a systematic improvement over the harmonic level of
theory, the latter being in most cases readily available from standard electronic
structure calculations. Among the available methods, second-order vibrational
perturbation theory (VPT2)[1] is particularly appealing for the gain in accuracy it
affords with respect to its computational cost, with well-documented successes in the
interpretation and prediction of IR spectra of molecules of astrochemical interest.[2-4]
With VPT2 calculations becoming more accessible even for medium-to-large
molecular systems of more than a dozen of atoms, a proper assessment of its
limitations and how they can be overcome is necessary. Astrochemical and chiral
molecules will be used to illustrate the main features of VPT2 and the problem of
resonances, their impact on band positions and intensities, and the possible strategies
to identify and correct them to obtain accurate and reliable results. Then, two aspects
beyond the direct application of VPT2 will be discussed. First, we will briefly
consider the presence of large amplitude motions in flexible molecules, which often
require ad hoc, variational treatments to correctly account for their contribution to the
overall spectrum. Then, we will describe available strategies to tune the
computational cost, using hybrid schemes mixing different levels of electronic
structures calculations or reducing the size of the anharmonic problem. Finally, by
choosing a suitable representation, intermediate data produced during simulations can
be exploited to assess the reliability of the results and provide further insights into the
origin of the observed signal. Such possibilities will be illustrated during the
presentation.[7]
References:
[1] H. H. Nielsen, Rev. Mod. Phys. 23, 90 (1951).
[2] J. Bloino, A. Baiardi, M. Biczysko, Int. J. Quantum Chem. 116, 1543 (2016).
[3] M. Biczysko, J. Bloino, C. Puzzarini, WIREs Comput. Mol. Sci. 8 e1349 (2018).
25
[4] N. M. Kreienborg, J. Bloino, T, Osowski, C. H. Pollok, C. Merten, Phys. Chem. Chem. Phys. 21,
6582 (2019).
[5] M. Fusè, F. Egidi, J. Bloino, Phys. Chem. Chem. Phys. 21, 4224 (2019).
26
On the use of the exact operator for the semiclassical
light-matter interaction to evaluate oscillator and
rotatory strengths
Ignacio Fdez. Galván1, Marjan Khamesian1, Lasse Kragh Sørensen2, Mickaël
Delcey3, Roland Lindh 1
1Dept. of Chemistry – BMC, Uppsala University, Uppsala, Sweden 2Dept. of Theoretical Chemistry and Biology, KTH, School of Engineering Sciences in
Chemistry, Biotechnology and Health (CBH), Stockholm, Sweden 3Dept. of Chemistry – Ångström, Uppsala University, Uppsala, Sweden
In this presentation the implementation of the exact semi-classical operator to
compute transitions moments (see Figure 1) in a state specific multiconfigurational
approach is discussed. The presentation will address issues as origin dependence,
merits of using different representations (length v.s. momentum), basis set
convergence, analytical procedures to compute the associated integrals, and the use of
the method in association with X-ray spectroscopy. In the latter case we will
demonstrate that the results can be achieved without the recomputation of the
associated integrals for each transition that is investigated.
A more detailed presentation of the subject can be found in Ref. [1]
Fig. 1: Real and imaginary part of the transition moment projected on the
polarization plane.
References:
[1] Marjan Khamesian, Ignacio Fdez. Galván, Mickaël G. Delcey, Lasse Kragh Sørensen, Roland
Lindh,
Chapter Three - Spectroscopy of linear and circular polarized light with the exact semi-classical light–
matter interaction, Editor(s): David A. Dixon, in Annual Reports in Computational Chemistry, Elsevier,
Volume 15,
2019, Pages 39-76. DOI: https://doi.org/10.1016/bs.arcc.2019.08.004
27
Observing the Motion of Electrons on an Attosecond
Timescale: The Ehrenfest method with Classical and
Quantum Dynamics
Michael A Robb1 Andrew J. Jenkins2, K. Eryn Spinlove3, Morgane Vacher4,
Michael J Bearpark1, Graham A. Worth3 , Thierry Tran3
1Dept. of Chemistry, Imperial College London, 2Department of Chemistry, University
of Washington, Seattle, WA 98195,USA 3Dept. of Chemistry, University College
London, 20, Gordon St., WC1H 0AJ, UK 4Dept. of Chemistry-Ångström, Uppsala
University
Attosecond spectroscopy has opened up the possibility of observing the motion of
electrons (see figure below) on their natural timescale (few attoseconds). We have
been studying such electron dynamics together with coupled nuclear motion, using
our implementation of the Ehrenfest method with both classical and quantized nuclear
motion. 1 The initial electronic wavepacket can be chosen as a superposition of
eigenstates (Ehrenfest ) to model the effects seen in attosecond spectroscopy.
We will review our methodology 1 for the combination of the Ehrenfest method with
both classical and quantum dynamics 2 We will then discuss two types of application
with some examples: 1) electron dynamics, and its subsequent decoherence driven
by nuclear motion and the natural zero point distribution in geometries 3, and 2) the
electronic control of nuclear dynamics 4.
[1].A. Jenkins, K. Spinlove, M. Vacher, G. Worth and M. Robb, J.
Chem Phys149 (2018).
[2]K. G. G. A. Worth, G. W. Richings, I. Burghardt, M. H. Beck, A.
Jäckle, and H.-D. Meyer. The QUANTICS Package, Version 1.1,
(2015), University of Birmingham, Birmingham, U.K., (2015).
[3].M. A. Robb, A. J. Jenkins and M. and Vacher, in Attosecond
Molecular Dynamics edited by M. J. J. Vrakking and F. Lepine (The
Royal Society of Chemistry, 2018), pp. 275-307.
[4]J. Meisner, M. Vacher, M. J. Bearpark and M. A. Robb, Journal of
Chemical Theory and Computation 11 (7), 3115-3122 (2015).
28
Computational Approaches Across the Periodic
Table: Predicting Energetics and Spectroscopic
Properties
Lucas Aebersold, Timothe Melin, Prajay Patel, Brad Welch, Angela K. Wilson
Michigan State University, East Lansing, Michigan, U.S.A.
Much of our group’s efforts are focused upon the development of ab initio approaches
that aim for the accurate prediction of thermochemical properties across the periodic
table. Included in our efforts has been the development of successful and versatile ab
initio composite schemes, called correlation consistent Composite Approaches (ccCA),
that provide reduced computational cost (in terms of computer time, memory, and disk
space) means to achieve energetic predictions. The approaches are useful for
ground-state, excited-state, and transition-state energies, and can be applied to
situations where single-reference wavefunctions or where multireference
wavefunctions (i.e., bond-breaking, diradicals) are necessary. Included in our work is
the development of Gaussian basis sets, providing new additions to the correlation
consistent basis set family, and rigorous evaluation of existing and new basis sets. To
provide context, the performance of methodologies, such as density functional theory,
particularly for situations where there may be few, if any, needed experiments for
comparison, are also discussed. Though our work has expanded the periodic table,
much of the focus here will be upon the lower portion of the periodic table.
29
Scanning Raman Microscopy
Yi Luo
Hefei National Laboratory for Physical Sciences at the Microscale, University of
Science and Technology of China, Hefei, China & Department of Theoretical
Chemistry and Biology, Royal Institute of Technology, Stockholm, Sweden
The determination of the chemical structure of a molecule is of paramount importance
in any molecule-related science, critical for understanding its chemical, physical, and
biological functions. Scanning tunneling microscopy (STM) and atomic force
microscopy (AFM) have shown a remarkable ability to visualize molecular skeletons,
but still lacking sufficient chemical information for precise chemical structure
determinations. The ability to achieve single-molecule Raman mapping with
sub-nanometer spatial resolution (~0.5 nm) provides a powerful means to chemically
resolving the internal structure of a molecule [1]. It has been shown that such high
resolution Raman images are resulted from the spatial confinement of nanocavity
plasmon[2-3]. It was predicted that with Ångström resolution, the Raman images of
individual vibrational modes of a molecule in real space could be obtained [4], which
was verified by a recent experimental work [5]. Very recently, the full images of
individual vibrational modes have been experimentally produced, which enables us to
visually construct the molecular chemical structure through a Lego-like building
process [6]. This marks the birth of a new methodology, named as scanning Raman
microscopy (SRM), for molecular structure determinations. The new features
associated with nanocavity plasmon [7,8] will also be discussed.
References:
[1] R. Zhang, et al., Nature, 498, 82 (2013).
[2] S. Duan, et al., J. Am. Chem. Soc., 137, 9515 (2015).
[3] S. Jiang, et al., Nature Nanotech., 10, 865 (2015).
[4] S. Duan, et al., Angew. Chem. Int. Ed., 128, 1053 (2016).
[5] J. Lee, et al., Nature, 568, 78 (2019).
[6] Y. Zhang, et al., Nat. Sci. Rev. https://doi.org/10.1093/nsr/nwz180, (2019)
[7] S. Duan, et al., J. Am. Chem. Soc., 141, 13795 (2019).
[8] C.K. Xu, et al. Nature Physics, 10, 753 (2014)
30
Multiconfiguration DFT with on-top pair density
functionals and the long-range correlation energy
correction
Katarzyna Pernal1
1Institute of Physics, Lodz University of Technology, Lodz, Poland
Multiconfiguration density functional theory (MC DFT), proposed by A. Savin [1],
rigorously combines DFT with wavefunction theory in such a way that both
approaches to the many-electron problem complement each other. MC DFT takes
advantage of the efficient description of the electron cusp by density functional
approximations by constraining their action to the short-range regime of the
electron-electron interaction. The wavefunction component accounts for description
of static correlation.
Even though MC DFT is an exact theory, in practice its accuracy is limited by
approximate short-range density functionals and adequacy of the wavefunction
model assumed for a given problem. The available semilocal short-range
exchange-correlation functionals are known to suffer from both the self-interaction
and static-correlation, which they inherit from their full-range counterparts. The
usually adopted strategy in MC DFT is to introduce static correlation effects by
limiting the wavefunction to include only a few determinants. On the one hand, this
allows one to keep the computation cost related to the wavefunction calculation at the
minimum. On the other hand, the important part of dynamic correlation – not covered
by the short-range functional part – may be missing. A striking consequence of this
deficiency is the absence of the long-range dispersion component in the interaction
energies.
It has been shown that the long-range correlation energy can be efficiently accounted
for by the multireference adiabatic connection formula [2] rederived and
approximated for the long-range electron interaction operator [3]. Recent
developments in circumventing deficiencies of the semilocal short-range density
functionals assumes turning to on-top pair density functionals [4,5]. We have
proposed to make the short-range functional dependent on the on-top pair density
through the use of auxiliary spin densities to reduce static correlation error without
breaking the spin symmetry [3].
31
In the talk I will present exact MC DFT formalism and limitations of the typically
used approximations, which employ semilocal density functionals. The recent
developments leading to circumventing two main bottlenecks of approximate MC
DFT: static correlation error in the short-range functional part and neglect of the
long-range correlation effects, will be presented. Finally, I will show that the recently
proposed MC DFT approach [3] yields encouraging results for dissociation energies,
noncovalent interactions and excitation energies, competing in accuracy with more
computationally demanding ab initio methods.
References:
[1] A. Savin, in Recent Developments of Modern Density Functional Theory, edited by J. M. Seminario
(Elsevier, Amsterdam, 1996).
[2] K. Pernal, Phys. Rev. Lett. 120, 013001 (2018).
[3] M. Hapka, E. Pastorczak, A. Krzeminska, K. Pernal, J. Chem. Phys. submitted.
[4] A. Ferte, E. Giner, and J. Toulouse, J. Chem. Phys. 150, 084103 (2019).
G. Li Manni, R. K. Carlson, S. Luo, D. Ma, J. Olsen, D. G. Truhlar, and L. Gagliardi, J. Chem.
Theory Comput. 10, 3669 (2014).
32
Pedagogical Invited Lectures
33
Calculating molecular properties: From real-time
methods to (quasi-)energy derivatives
Kenneth Ruud1
1Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry,
University of Tromsø – The Arctic University of Norway, 9037 Tromsø, Norway
In this lecture, I will motivate why we would be interested in computational
spectroscopy, and how the concept of molecular properties allows us to link
observations made in experimental spectroscopic studies to fundamental properties of
the electron density [1].
The focus of the lecture will be on the qualitative principles behind the calculation of
molecular properties, using either exact-state theory or assuming a self-consistent field
approach for the more advanced methods. Two approaches to the calculation of
molecular properties will be emphasized: real-time methods [2] and quasi-energy
derivatives methods [3].
For the latter approach, we will discuss ways of allowing properties of arbitrary order to
be calculated [4,5], and if time allows, introduce the concept of automatic
differentiation [6] as a way of obtaining high-order derivatives of complex functions
without explicitly calculation the derivatives of the functions of interest.
Some examples of the use of both real-time methods (applied to the study of X-ray
spectra using relativistic density-functional theory) and quasi-energy derivative theory
(applied to multidimensional vibrational spectra and multiphoton absorption) will also
be given.
References:
[1] Patrick Norman, Kenneth Ruud, Trond Saue, Principles and Practices of Molecular Properties:
Theory, Modelling and Simulations, Wiley (2018).
[2] Michal Repisky, Lukas Konecny, Marius Kadek, Stanislav Komorovsky, Vladimir G. Malkon,
Olga L. Malkina, Kenneth Ruud, J. Chem. Theory Comput. 11, 980 (2015).
[3] Ove Christiansen, Poul Jørgensen, Christof Hättig, Int. J. Quantum Chem. 68, 1 (1998)
[4] Andreas J. Thorvaldsen, Kenneth Ruud, Kasper Kristensen, Poul Jørgensen, Sonia Coriani, J.
Chem. Phys. 129, 214108 (2008).
[5] Magnus Ringholm, Dan Jonsson, Kenneth Ruud, J. Comp. Chem. 35, 622 (2013).
[6] Ulf Ekström, Lucas Visscher, Radovan Bast, Andreas J. Thorvaldsen, Kenneth Ruud, J. Chem.
Theory Comput. 6, 1971 (2010).
34
Shortcuts to adiabaticity
Xi Chen
International Center of Quantum Artificial Intelligence for Science and Technology
(QuArtist) and Department of Physics, Shanghai University, 200444 Shanghai, China
In this talk we shall first review the techniques of shortcuts to adiabaticity, by focusing
on the experimental progress. Next, we start with Lagrangian variational method for
controlling BECs and soliton in trapping potentials. The fast compression of soliton is
achieved and further applicable to quantum Otto heat engine. Furthermore, we have
insight into the effects of many-body coherence on the quantum speed limit and
shortcuts to adiabaticity in ultracold atomic gases. We conclude that collisions between
the strongly interacting bosons can lead to changes in the coherence which results in
larger speed limits. Finally, we present the work on the fast manipulation of single,
two-interaction spins by using shortcuts to adiabaticity. The optimal control of
nonlinear two-level system, describing the transition between atom and molecular
BECs is also discussed. The talk will end up with some extension of shortcuts to
adiabaticity with the applications in quantum control, quantum information processing,
quantum annealing and quantum sensing.
35
Theories for excited state calculation, and diabatic
states for electron/energy transfer
Chao-Ping Hsu
Academia Sinica, Taipei
In this talk, I’ll review the currently available theories for excited state calculation,
mainly for large systems. Current problems of TDDFT will be discussed, together with
various of newer approaches that can produce better results with similar computational
complexity. I’ll also go on and discuss methods to obtain diabatic states for electron and
energy transfer problems.
36
Modeling excited states using Density Functional
Theory
Ilaria Ciofini
37
UV/Visible spectroscopy for molecules and
nanophotonics: interpreting and predicting
low-resolution and high-resolution data
Jeffrey R. Reimers
38
The nature of the chemical bond
Marco Antonio Chaer Nascimento
Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade
Universitária, CT Bloco A Sala 41, Rio de Janeiro, RJ 21941-909, Brazil
The nature of the chemical bond is perhaps the central subject in theoretical
chemistry. Our understanding of the behavior of molecules developed amazingly in
the last century, mostly with the rise of quantum mechanics (QM) and with
QM-based theories such as valence bond and molecular orbital. Such theories are
very successful in describing molecular properties, but they are not able to explain
the origin of the chemical bond. This problem was first addressed by Ruedenberg [1],
who showed that covalent bonds result from quantum interference between
one-electron states. The generality of this result and its quantification for a large
variety of molecules was made possible through the recent development of the
Generalized Product Function Energy Partitioning method (GPF-EP) [2], which
allows the partition of the electronic density and energy in their interference and
quasi-classical (non-interference) contributions for each bond of a molecule,
separately. This Interference Energy Analysis (IEA) has been applied to a large
variety of molecules with single, double and triple bonds, with different degrees of
polarity, linear or branched, cyclic or not, conjugated and aromatics, to verify the role
played by quantum interference. In all cases, the conclusion was exactly the same:
for each bond of the molecules considered the main contribution to its stability comes
from the interference term.
One-electron two-center (2c1e) bonds are the simplest kind of chemical bonds. Yet
they are often viewed as odd or unconventional cases of bonding. Likewise,
three-centers-two electrons (3c2e) are also thought as some special kind of bond.
But, are they any different from the conventional (2c2e) bonds? If so, what
differences can we expect on the nature of (2c1e) and (3c2e) relative to electron-pair
bonds? In this talk we present the GPF-EP method [3], its extension to describe bonds
involving N electrons in M orbitals (N<M), and application to several (2c1e) and
(3c2e) bonds and, when possible, compare the results with the respective analogous
molecules exhibiting the “conventional” two-electron bond. For all cases the GPF
results show that interference is the dominant effect for the one-electron bonds and,
therefore, (2c1e) bonds should not be considered as special, since they also result
from quantum interference. More recently, the GPF-EP method has also been applied
to three centers-two electrons bonds (3c2e), and the same behavior has been
observed. These results together with the ones already obtained for (2c2e) and (2c1e)
39
bonds clearly indicate that there is no conceptual difference among them and that
quantum interference provides a way for the unification of the chemical bond
concept, turning meaningless the standard way of classifying bonds as pure covalent,
polar or ionic (CNPq, FAPERJ, CAPES).
[1] Ruedenberg, K. Rev. Mod. Phys. 1962, 34 (2), 326–376.
[2] Cardozo, T. M.; Nascimento, M. A. C. J. Chem. Phys. 2009, 130 (10), 104102; ibid., J. Phys.
Chem. A 2009, 113 (45), 12541–12548; Cardozo, T. M.; Nascimento Freitas, G.; Nascimento, M.
A. C. J. Phys. Chem. A 2010, 114 (33), 8798–8805; Fantuzzi, F.; Cardozo, T. M.; Nascimento, M.
A. C. Phys. Chem. Chem. Phys. 2012, 14 (16), 5479–5488; Vieira, F. S.; Fantuzzi, F.; Cardozo,
T. M.; Nascimento, M. A. C.
J. Phys. Chem. A 2013, 117 (19), 4025–4034; Cardozo, T. M.; Fantuzzi, F.; Nascimento,
M. A. C. Phys.Chem. Chem. Phys. 2014, 11024–11030; Fantuzzi, F.; Nascimento, M. A.
C. J. Chem. Theory Comput.
2014, 10 (6), 2322–2332; Fantuzzi, F.; Cardozo, T. M.; Nascimento, M. A. C. J. Phys. Chem. A
2015, 119
(21), 5335–5343; Sousa, D. W. O. de; Nascimento, M. A. C. J. Chem. Theory Comput. 2016, 12
(5), 2234–
2241; Fantuzzi, F.; Cardozo, T. M.; Nascimento, M. A. C. ChemPhysChem 2016, 17 (2), 288–
295; Fantuzzi, F.; de Sousa, D. W. O.; Chaer Nascimento, M. A. Comput. Theor. Chem. 2017,
1116, 225; Fantuzzi, F.; Nascimento, M. A. C. Phys.Chem.Chem.Phys 2017, 19, 19352; Sousa,
D. W. O. de; Nascimento, M. A. C. Acc. Chem, Research 2017, 50, 2264; Fantuzzi, F.; de Sousa,
D. W. O.; M.A. Chaer Nascimento. Chemistry Select 2017, 2, 604; Fantuzzi, F.; Benedikt,
R.;Wolff, W.; Chaer Nascimento, M. A., J. Am. Chem. Soc. 2018, 140, 4288; de Sousa, D. W.
O.;Chaer Nascimento, M.A., J. Phys. Chem. A 2018, 121, 1406; de Sousa, D. W. O.;Chaer
Nascimento, M.A., Phys. Chem. Chem. Phys. 2019, 21, 11319; Fantuzzi, F.; Nascimento, M. A.
C. Phys.Chem.Chem.Phys. 2019 (DOI: 10.1039/C9CP04964A); Chaer Nascimento, M.A., J.
Braz. Chem. Soc. 2008, 19 (2), 245–256.
Sousa, D. W. O. de, M.Sc. Thesis (Instituto de Química da UFRJ, Brazil, 2016)
40
Some Problems in Dynamics of Topological Defects,
Quantum Computing, and Non-equilibrium Processes
Ping Ao
Physics Department and Shanghai Center Quantitative Life Sciences, Shanghai
University, Shanghai, China
In solids and in quantum fluids dynamics of topological defects determines an
important part of physics properties. Nevertheless, such dynamical behaviors in many
situations are a bit counter intuitive. One essential feature is their connection to
nonequilibrium processes without detailed balance. A few examples will be discussed,
along with an introduction to progresses in theory of nonequilibrium processes. A
related quantum computing approach will be discussed, too, on how to achieve 100%
fidelity in a finite time in a quantum process.
References
1) Berry's Phase and the Magnus Force for a Vortex Line in a Superconductor
Ao, Thouless, Phys. Rev. Lett. 70, 2158 (1993)
http://prola.aps.org/abstract/PRL/v70/i14/p2158_1
2) Tunneling of a Quantized Vortex: Roles of Pinning and Dissipation
Ao, Thouless. Phys. Rev. Lett. 72, 132 (1994)
http://prola.aps.org/abstract/PRL/v72/i1/p132_1
3) Transverse Force on a Quantized Vortex in a Superfluid
Thouless, Ao, Niu. Phys. Rev. Lett. 76, 3758 (1996)
http://prola.aps.org/abstract/PRL/v76/i20/p3758_1 ;
4) Escape rate for nonequilibrium processes dominated by strong non-detailed balance
force
Tang, Xu, Ao. The Journal of Chemical Physics 148, 064102 (2018)
http://aip.scitation.org/doi/10.1063/1.5008524 ;
5) Structure of Stochastic Dynamics near Fixed Points
Kwon, Ao, Thouless. Proc. Nat’l Acad. Sci. (USA) 102 (2005) 13029-13033
http://www.pnas.org/content/102/37/13029.full.pdf+html
6) Steering an Eigenstate to Destination
Emmanouilidou, Zhao, Ao, Niu. Phys. Rev. Lett. 85, 1626 (2000)
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.85.1626
41
Standard Invited Lectures
42
Multiscale Modeling and Simulation of
Plasmon-Exciton Interaction
WanZhen Liang
Department of Chemistry, Xiamen University, Xiamen, China
The complex interplay between molecules and plasmonic metal nanoparticles (MNPs)
presents a set of particular characteristics in absorption/scattering spectra such as
excitonic splitting, asymmetric lineshapes, plasmon-induced absorption enhancement
and transparencies, etc. Although the MNPs-molecule systems have been intensively
investigated experimentally and theoretically, the construction of a theoretical
framework which can produce all the disparate experimental observations and account
for the molecular electron-phonon coupling is still in progress. Here I present our
group’s recent efforts on the development of theoretical models to simulate the
plasmon-enhanced phenomena. Additionally, I demonstrate the evolution of linear
and nonlinear optical properties and exciton dynamics with the plasmon-exciton
coupling strength, plasmon damping rate and the detuning energy.
References:
[1] J. Sun, G. Li & W. Z. Liang Phys. Chem. Chem. Phys. 17, 16835 (2015)
[2] P. C. Zhang, J. Wen & W. Z. Liang J. Phys. Chem. C 122, 10545 (2018)
[3] P. C. Zhang & W. Z. Liang Electron. Struct. 1, 044001 (2019)
[4] B. Zhang, Y. Zhao & W. Z. Liang, J. Chem. Phys. 151, 044702 (2019)
[5] B. Zhang & W. Z. Liang, J. Chem. Phys. In version.
43
High-resolution spectroscopy of small cyclic
molecules: Probing large amplitude motions
Ziqiu Chen, Lanzhou University, China
The lowest frequency vibrations of cyclic molecules typically involve motions of
most heavy atoms of the ring skeleton as it flexes, contracts or twists. Understanding
these motions is important as these low-lying energy states are appreciably populated
at room temperature and thus, these vibrations influence the physical and chemical
properties of the rings themselves. The underlying potentials governing these
large-amplitude motions in the ring backbone are often anharmonic and difficult to
model using established theories. High resolution spectroscopy can provide accurate
information about the potential energy surfaces that cannot be matched to the same
degree by any other technique, making it valuable to both experimental and
theoretical studies. In this talk, I will briefly describe the principles of operations of
our experimental techniques employed in the microwave and GHz regions, as well as
the synchrotron-based THz spectroscopy. The specific features in the pure rotational
and rovibrational spectra of prototype small cyclic molecules arising from large
amplitude motions that are only manifested at high resolution will be discussed in
detail. Spectroscopy of small heterocycles of astrochemical interest will also be
included.
44
Rational design and fabrications of two-dimensional
materials
Jing Ma1
1 School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of MOE, Nanjing University, Nanjing, China
The functionalized arsenene AsR family (R = F, OH and CH3, etc.), which have quasi
planar structures, exhibit gapless features when excluding the spin-orbit coupling
(SOC). They were predicted to be 2D topological insulators (TIs) with 100-160 meV
bandgap opening when the SOC is switched on.1 Through interlayer interaction, the
electronic structures of 2D layered materials can be effectively modulated. The
change of stacking order could render the bilayered AsF heterostructure to
simultaneously possess Rashba spin splitting and topologically nontrivial electronic
states.2 The introduction of built-in electric field and SOC caused an obvious splitting
of the band structure at K point in the AA-stacked AsF.2 The Rashba parameter αR
was estimated to be 1.67 eV·Å, comparable to that (1.36 eV·Å) of Pt-Si nanowire.
The application of tensile strain and electric field caused variations of band gap
splitting and nontrivial electronic states of the bilayered AsF,2 suggesting potential
usages in novel electronics such as spin field-effect transistors and QSH insulators.3
The interaction between monolayered arsenene and various solvents (or polymers)
was found to be correlated with the extent of charge transfer from arsenene to the
solvents (polymers).4-6 The as-prepared concentrations of the As dispersions vary
monotonically with the calculated adsorption energies and charge transfer per contact
area. Transmission electron microscopy characterization and size distribution analyses
manifested that the lateral size distributions of the exfoliated arsenic nanosheets
ranged from 100 nm to 1050 nm.4
45
References： [1] Zhao, J.; Li, Y.; Ma, J., Nanoscale, 2016, 8, 9657-9666.
[2] Zhao, J.; Guo, W.; Ma, J., 2017, 10, 491-502.
[3] Zhao, J.; Qi, Z.; Xu, Y.; Dai, J.; Zeng, X.; Guo, W.; Ma, J. WIREs Comput. Mol. Sci. 2019,
9(2):e1387.
[4] Qi, Z.; Hu, Y.; Jin, Z.; Ma, J., Phys. Chem. Chem. Phys., 2019, 21(23), 12087-12090.
[5] Hu, Y.; Qi, Z.; Zou, et al., Chem Mater, 2019, 31(12), 4524-4535.
[6] Zhao, J.; Guo, W.; Ma, J., Nanoscale, 2017, 9, 7006-7011.
46
A 3-D Directional Chemical Perspective with Next
Generation QTAIM
Samantha Jenkins
Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and
Key Laboratory of Resource National and Local Joint Engineering Laboratory for New
Petro-chemical Materials and Fine Utilization of
Resources, College of Chemistry and Chemical Engineering, Hunan Normal
University,
Changsha, Hunan 410081, China
The theoretical chemical physics/bio-chemistry that the BEACON research group
undertakes seeks to develop new theory and explanations for chemical observations
whilst also posing questions to be answered by future experiments. Our (next
generation) QTAIM based research pioneers new theoretical tools that provide a new
3-D vector based perspective to solve what was only until recently considered
unsolvable. An example of this was our explanation of chirality using only chemical
measures [1]. By providing new tools based on ignoring previous assumptions in
theoretical chemistry/chemical physics we can currently address new areas such as
isotope separation, excited state dynamics [2], prediction of competitive and
non-competitive ring-opening reactions [3], excited state phenomena [4], physical
properties including the application of E-fields [5] and spectroscopic response.
http://www.beaconresearch.org
References:
[1] Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical
Insight, Journal of the American Chemical Society, 141(13), 5497–5503 (2019). DOI:
10.1021/jacs.9b00823.
[2] QTAIM and Stress Tensor Characterization of Intramolecular Interactions Along
Dynamics Trajectories of a Light-Driven Rotary Molecular Motor, J. Phys. Chem. A
121(25), 4778–4792, (2017). DOI: 10.1021/acs.jpca.7b02347.
[3] A vector-based representation of the chemical bond for predicting competitive and
noncompetitive torquoselectivity of thermal ring-opening reactions, International
Journal of Quantum Chemistry 118(20), e25707 (2018). DOI:10.1002/qua.25707
[4] A 3-D Bonding Perspective of the Factors Influencing the Relative Stability of the
S1/S0 Conical Intersections of the Penta-2,4-dieniminium Cation (PSB3), International
Journal of Quantum Chemistry, 119(11), e25903 (2019).
DOI: 10.1002/qua.25903
[5] The Destabilization of Hydrogen-bonds in an External E-Field for Improved
Switch Performance,
Journal of Computational Chemistry, Early View (2019). DOI: 10.1002/jcc.25843
47
Rectangular collocation for solution of the
Schrödinger equation with collocation point set
optimization
Sergei Manzhos1, Tucker Carrington2
1Centre Énergie Matériaux Télécommunications, Institut National de la Recherche
Scientifique, 1650 boulevard Lionel-Boulet, Varennes QC J3X1S2, Canada 2 Chemistry Department Queen's University Kingston, Ontario K7L 3N6 Canada
The rectangular collocation approach allows solving the Schrödinger equation,
electronic or nuclear, without converging integrals. It is therefore possible to obtain
good solutions from a small number of samples of the potential which could also be
located in a limited volume of space. The rectangular nature of the matrix equation
facilitates basis optimization and, when applying the KEO numerically [1], it is easy
to use any basis functions, even non-integrable [2]. As a result, the method can handle
problems which pose difficulties with the variational approach such as, in the case of
nuclei Schrödinger equation, calculation of vibrational spectra at interfaces, where
potential energy surfaces are usually unavailable and ab initio calculations are costly
[3]. In the case of the electronic Schrödinger equation, singularities of the potential
are dealt with trivially and one can easily use Slater type functions, which are
advantageous in full potential calculations but do not result in analytic integrals [4].
In the case of both the electronic and the vibrational Schrödinger equation, the
absence of the requirement to converge integral allows to reduce the volume of space
sampled by the collocation points and to use relatively small point sets. I will present
recent results of machine learning optimization of the collocation point set when
solving the Kohn-Sham equation as well as results of calculations when sampling
only selected parts of the configuration space when solving the vibrational
Schrödinger equation.
References:
[1] S. Manzhos, T. Carrington, J. Chem. Phys. 145, 224110 (2016).
[2] A. Kamath, S. Manzhos, Mathematics 6, 253 (2018).
[3] S. Manzhos, M. Chan, T. Carrington, J. Chem. Phys. 139, 051101 (2013); Phys. Chem. Chem.
Phys. 15, 10028 (2013).
[4] S. Manzhos, T. Carrington, J. Chem. Phys. 149, 204105 (2018).
[5] arXiv:1904.07122
[6] S. Manzhos, X. Wang, T. Carrington, Chem. Phys. 509, 139 (2018).
48
Extended Koopmans’ Theorem at the Second Order
Perturbation Theory: From Wave Function Theory
to Density Functional Theory
Xin Xu1
(Cancelled)
1Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key
Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for
Computational Physical Science, Department of Chemistry, Fudan University,
Shanghai, 200433, China
Ionization potential (IP) is a fundamental property of atoms, molecules and solids,
which is often associated with the orbital energy via Koopmans’ theorem [1] in wave
function theory (WFT) or Janak theorem [2] in density functional theory (DFT).
However, relaxation and correlation effects are often important in the electron
detachment process, calling for the respective extensions [3-7].The extended
Koopmans’ theorem (EKT) at the level of second order perturbation theory (MP2)
provides a straightforward way to calculate IPs as one electron quantities. Such an
EKT-MP [2] method [4], by taking advantage of the relaxed density matrices, often
suffers from the negative occupation problem, failing to provide the complete IP
spectrum. Here a small positive number approximation is proposed [8] to cure this
problem and the associated unphysical results. As an extension of the EKT formalism
to DFT, a combination of EKT and the doubly hybrid functionals (EKT-DH [9]) is
developed. When EKT-MP2 and EKT-DH are applied to a set of atoms and
molecules, new insights are gained on the roles played by the relaxation and
correlation effects in the IP calculations. In particular, the EKT-XYG3 method [8,9] is
shown to be capable of describing the breakdowns of the quasi-particle
approximations for the inner valence IPs with low computational cost and high
accuracy.
We appreciate the support from National Natural Science Foundation of China (Grant
21688102).
References:
[1] Koopmans, T. Physica 1 104 (1934).
[2] Janak, J.F. Phys. Rev. B18 7165 (1978).
[3] Smith, D.W., Day, O.W. J. Chem. Phys., 62 113 (1975).
[4] Cioslowski, J., Piskorz, P., Liu, G. J. Chem. Phys., 107 6804 (1997).
[5] Su, N.Q., Xu, X. J. Chem. Theory Comput. 11 4677 (2015).
[6] Su, N.Q., Xu, X. J. Chem. Theory Comput. 12 2285 (2016).
[7] Su, N.Q., Xu, X. J. Phys. Chem. Lett. 10 2692 (2019).
[8] Gu, Y.H., Xu, X. to be submitted (2019).
[9] Gu, Y.H., Yan, W.J., Xu, X. to be submitted (2019).
49
Studies of four-body problems using exponential
wavefunctions in all the relative coordinates
Frank E. Harris (a) and Alexei M Frolov (b)
(a) Department of Physics, University of Utah, Salt Lake City, UT (USA) 84112 and
Quantum Theory Project, University of Florida, P. O. Box 118435, Gainesville, FL
(USA) 32611.
(b) Department of Applied Mathematics, University of Western Ontario, London,
Ontario N6H 5B7, Canada
[email protected], [email protected]
Use of the interparticle distances as coordinates in few-body systems permits their
quantum-mechanical description in expansions that are much more rapidly convergent
than formulations based solely upon orbitsls, but this desirable feature is accompanied
by major difficulties in evaluating the integrals needed to describe contributions to the
system energy. An initial analytical solution to the four-body integral evsluation
problem was presented in 1987 by Fromm and Hill, followed in 1997 by a
contribution by the present author. Work on the somewhat more restricted Hylleraas
wavefunctions was reported by Remiddi in 1991; the consistency between Remiddi's
results and those of Fromm and Hill for the same waveunctions demonstrated the
validity of the complicated analyses that characterized the work of both researxh
groups. The present contribution surveys the current status of the integral evaluation
problem, points out its applicability to descriptions of nuclear structure, and presents
some results for various atomic and exotic systems.
50
Time-dependent matrix product states for finite
temperature
Zhigang Shuai
51
Microscopic mechanisms and origins of
ferroelectricity in Hybrid Inorganic-Organic
compounds
Alessandro Stroppa
CNR-SPIN, c/o Dip.to di Scienze Fisiche e Chimiche -
Università degli Studi dell'Aquila - Via Vetoio - 67100 - Coppito (AQ), Italy
In this talk, we will discuss the intriguing origin of ferroelectricity in hybrid
inorganic-organic compounds with perovskite structures. In particular, we will discuss
the hybrid improper mechanism where Jahn-Teller cooperative distortions are subtly
coupled to inversion symmetry breaking giving rise to a switchable electric
polarization. Moreover, symmetry invariants theory permits to predict a
magnetoelectric coupling which has been recently confirmed by experiments. We
discuss further examples of the complex multifunctional behaviour arising from the
organic and inorganic dual nature as well as from the interplay between
ferroelectricity and magnetism in hybrid perovskites.
52
Theoretical spectroscopy of semiconductor defects
with application to 2D hBN nanophotonics
A Sajid1,2, S A Tawfik1, M Fronzi1, R Kobayashi4, J R Reimers1,3 and M J Ford1
1University of Technology Sydney, School of Mathematical and Physical Sciences,
Ultimo, New South Wales 2007, Australia 2Department of Physics, GC University Faisalabad, Allama Iqbal Road, 38000
Faisalabad, Pakistan 3International Centre for Quantum and Molecular Structures and Department of
Physics, Shanghai University, Shanghai 200444, China 4National Computational Infrastructure, The Australian National University,
Canberra, ACT 2600, Australia
The discovery of single-photon emission from hBN [1] has generated considerable
interest and efforts are underway to characterise its spectroscopy [2. However
computational approaches for the determination of excited-state energies for large
periodic systems remains a significant challenge [3].
A widely used approach to this problem are Density Functional Theory (DFT) based
methods offering a good balance between computational expediency and reliability.
The HSE06 functional reproduces bandgaps in semiconductors well and, combined
with methods to constrain orbital occupation, is perhaps the most favoured approach.
Electronic states of defects are often inherently multi-reference open-shell and
closed-shell states that involve broken chemical bonds and charge-transfer. Here, we
assess the performance of DFT by comparing with ab initio wavefunction based
methods such as coupled cluster and multi-reference configuration interaction, along
with time-dependent DFT. We also present an extension of the empirical methods for
estimating energies of low-spin multiplicity to states containing more than 2 open shell
electrons, and a symmetry based methodology for ensuring that constrained DFT
calculations converge to the expected excited state. Our aim is to understand the
reliability of excited state energies calculated using the common approach of
constrained HSE06 DFT. This is an important problem that impacts our understanding
of the nanophotonics of semiconductor in general
This work was supported by the National Computational Infrastructure (NCI), and
Pawsey Supercomputing Centre, Australia. Funding was provided by the Australian
Research Council (DP 150103317 and DP 160101301) and Chinese NSF Grant
#1167040630
[1] T T Tran et al, Nature Nanotech, 11 37-41(2016)
[2] M Abdi et al, ACS Photonics 5 1967 (2018); S A Tawfik et al Nanoscale 9(36) 13575 (2017);
[3] J Reimers et al Chem Theory and Comp (2018) Accepted
53
Computing Accurate Interaction Energies for
Stacked Nucleobases.
Holger Kruse1
1Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65
Brno, Czech Republic
Understanding and accurate modeling of the energetics of stacking interactions of
nucleobases is a key step to describe the formation and stability of DNA and RNA
structural motifs. Recently, highly accurate CCSD(T)-based interaction energies have
been obtained for the stacking of B-DNA base-pair steps [1] and conformations of the
cytosine homodimer (Fig 1) [2]. Key results from these studies are presented. Among
them, SAPT (beyond 2nd order) data for the cytosine dimer show an unexpectedly large
swing in the balance of the individual SAPT components for a combined scan of twist
angle and stacking distance. The accuracy of various quantum chemical methods
(dispersion-corrected DFT, MP2 flavors, local correlation methods, semi-empirics) and
classical force fields (AMBER, CHARMM) is compared to the new high-level
references.
Fig. 1: Different conformations of the cytosine homodimer. [2]
References:
[1] H. Kruse, P. Banáš, J. Šponer, J. Chem. Theory Comput. 15, 95-115 (2019)
[2] H. Kruse, J. Šponer, J. Phys. Chem. A Just Accepted (2019) 10.1021/acs.jpca.9b05940
54
Insights into thermally activated delayed fluorescence
(TADF) through the electronic structure models
Piotr de Silva1
1Department of Energy Conversion and Storage, Technical University of Denmark,
Fysikvej 309, 2800 Kongens Lyngby, Denmark
Organic molecules exhibiting thermally activated delayed fluorescence (TADF) are
currently the most promising class of materials to improve the efficiency of organic
light-emitting diodes (OLED). The emission of light from a bright singlet excited state
is preceded by a thermally-activated up-conversion of triplet excitons. This reverse
intersystem crossing proceeds efficiently thanks to a small singlet-triplet energy gap
and non-vanishing spin-orbit coupling. The detailed mechanism of TADF is still a
subject of a debate, as within the simplest model, efficient reverse intersystem crossing
and high quantum yields appear to be competing properties. The role of both, charge
transfer (CT) and locally excited (LE) states, as well as non-adiabatic effects has been
recently extensively studied to explain the phenomenon.
In this contribution we propose a simple quantum-mechanical model for TADF, which
is based on representation of a Hamiltonian in the basis of four spin-mixed diabatic
states representing pure CT and LE excitations [1]. The model can explain the
coexistence of fast T1→S1 intersystem crossing and S1→S0 radiative decay. We show
that the parameter space of the model can be largely explored through conformational
fluctuations. The analysis enables to formulate new guidelines for optimization of
TADF emitters.
We will also demonstrate what are the necessary conditions for the inversion of the
singlet-triplet gap, i.e. a situation where the first excited singlet is energetically below
the first excited triplet. Molecules with such an inverted structure have a potential to be
very efficient harvesters of triplet excitons. We will show that gap inversion is possible
but requires a significant contribution of double excitations and that commonly used
methods like adiabatic TD-DFT fail to capture this effect [2].
References:
[1] P. de Silva, C. A. Kim, T. Zhu, T. Van Voorhis, Chem. Mater. 31, 17, 6995-7006 (2019).
[2] P. de Silva, J. Phys. Chem. Lett. 10, 5674-5679 (2019).
55
Contributed Talks
56
Fragmentation approach to electronic excitations
Xingpin Li1, Xinsheng Jin,2 Xiao He,2,3 William J. Glover1,3,4
1NYU Shanghai, 1555 Century Avenue, Shanghai, China 2Shanghai Engineering Research Center of Molecular Therapeutics and New Drug
Development, School of Chemistry and Molecular Engineering, East China Normal
University, Shanghai, China 3NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 North
Zhongshan Road, Shanghai, China 4Department of Chemistry, New York University, New York, New York, USA
Electronic excitations correspond to a rearrangement of the electrons in a molecule in
response to absorption of electromagnetic radiation and are important in a wide range
of systems of technological and biological interest, such as fluorescent proteins,
photoswitches, and dye molecules. Unfortunately, the large size and complexity of
these systems precludes the application of standard ab initio electronic structure
methods such as time-dependent density functional theory to the full system,
particularly when combined with excited-state dynamic simulations. Based on the
Many-Body Expansion (MBE), and its extension to covalently bonded systems with
Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps
(EE-GMFCC), we have developed a fragmentation approach for electronic excited
states (ES-MBE) that is able to treat localized electronic excitations and excited-state
properties in systems of thousands of atoms.[1,2] We find ES-MBE converges rapidly
for electronic excitations, justifying a low-order truncation of the expansion that
rigorously achieves linear scaling and trivial parallelization, while remaining
quantitatively accurate with full-system reference calculations. We demonstrate the
ES-MBE approach on a diverse range of systems, including solvatochromism in dyes,
and color tuning in Fluorescent Proteins (FP). Furthermore, the ES-MBE allows us to
understand, on a per-molecule basis, how the environment (be it solvent or protein)
modulates the excitation energy of a solute. This information is expected to be valuable
in the rational design of FPs with tailored properties.
Full system TD -D FT excitations at linear scaling cost
57
References:
[1] J. Liu, H. Sun, W. J. Glover, X. He, J. Phys. Chem. A 123, 5407 (2019)
[2] X. Jin, W. J. Glover, X. He, Under Review (2019)
58
Accurate vibrational chiroptical spectroscopy
simulation beyond the harmonic approximation:
the VPT2 approach
Qin Yang, J. Bloino
Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
The biological activity of organic molecules is strongly dependent on their chirality.
Understanding this property is thus of critical importance in pharmaceutical
industries, as well as in technological applications. Chiral spectroscopy, in particular
Vibrational Circular Dichroism (VCD) and Raman Optical Activity (ROA), are the
methods of choice to probe and analyzing the dynamic and structural characteristic of
such molecules. [1] The wealth of information contained in experimental spectra
cannot be fully exploited through phenomenological studies, and theoretical
simulations are now systematically used to support and complement observations.
While the harmonic approximation is often used to assign absolute configurations, it
has inherent limitations, which can hinder a detailed analysis of the vibrational
properties of a system, like the overestimation of transition energies or the
impossibility to reproduce the non-fundamental bands. Such issues are often
exacerbated by the sensitivity of chiroptical spectroscopies. Significant improvements
are obtained by proper inclusion of anharmonic effects. However, the computational
cost of such methods has confined them to small molecular systems.
Thanks to hardware improvements and good cost-accuracy ratio of vibrational
second-order perturbation theory (VPT2)[2], the applicability of anharmonic
simulation to medium-to-large molecular systems, has become possible.[3,4]
Nevertheless, the increase in problem size and structural complexity also worsen the
well-known issue of resonance which can seriously hinder the accuracy and reliability
of VPT2 results. Because a manual identification of resonances becomes unpractical,
robust automatic procedures are necessary, which require extensive studies on small-
to medium-sized molecules. In this contribution, the importance of a correct
identification and treatment of resonances will be illustrated.[5] The impact of the
quality of the harmonic approximation, and the underlying electronic structure
calculation method will also be considered. The design of a reliable protocol will
build the path to systematic application of VPT2 to larger systems, here represented
by pinene and artemisinin.
References:
[1] L. A. Nafie, Annu. Rev. Chem. 48, 357 (1997).
[2] N.H. Nielsen, Rev. Mod. Phys. 23, 90 (1951).
59
[3] V. Barone, J. Chem. Phys. 122, 014108 (2005).
[4] J. Bloino and V. Barone V, J. Chem. Phys. 136, 124108 (2012).
[5] J. Bloino, A. Baiardi and M. Biczysko Int. J. Quantum Chem. 116, 1543 (2016).
60
Simultaneous attenustion of both self-interaction
error and nondynamic correlation error in Density
Functional Theory: a spon-pair distinctive
adiabatic-connection approximation
Igor Ying Zhang
Department of Chemistry, Fudan University, Shanghai 200433, China
We present a spin-pair distinctive algorithm in the context of adiabatic-connection
fluctuation-dissipation (ACFD) theorem[1], which enables to quantify the
self-interaction error (SIE) and the nondynamic/strong correlation error (NCE) in the
direct random-phase approximation (dRPA)[2]. Using this knowledge, we propose a
spin-component scaled dRPA (scsRPA) correlation model with simultaneous
attenuation of both the SIE and the NCE. Along with the exact exchange, scsRPA is
shown to present a comprehensive improvement over dRPA, as well as the
well-established PBE and PBE0 functionals, for bonding energies of pronounced
multi-reference characters and transition-metal complexes of strongly correlated
systems, while consistently provide an accurate description for reaction energies,
reaction barriers, and non-covalent bond interactions of weakly correlated systems.
References:
[1] IY Zhang and X Xu, J. Phys. Chem. Lett. 10 2617 (2019);
[2] AJ Cohen et al., Chem. Rev. 112 289 (2011).
61
Electronic and nuclear quantum dynamics with the
Time-Dependent Density Matrix Renormalization
Group
Alberto Baiardi1, Markus Reiher1
1ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093
Zürich, Switzerland
Thanks to the design of increasingly more accurate ultrafast spectroscopic techniques,
it is nowadays possible to resolve the dynamics of a molecule on the natural time scales
of both its electronic and nuclear motions, therefore allowing to track its time evolution
under non-equilibrium conditions. In principle, methods that rely on a configuration
interaction (CI)-like parametrization of the wave function, such as the
multi-configurational time-dependent Hartree method [1] or time-dependent CI [2],
provide the exact propagation of a molecule within a given basis. However, the
exponential scaling of their computational cost with the system size hiders their
application to large systems with more than 10-20 atoms. In the present contribution,
we show how this unfavorable scaling can be limited by expressing the wavefunction as
a matrix product state during the whole propagation. The MPS parametrizaton is
employed in the well-known density matrix renormalization group algorithm (DMRG)
[3] and allows for a compact representation of CI wave functions. The resulting
equation of motion, that are broadly defined as time-dependent DMRG (TD-DMRG),
can be integrated efficiently based on so-called tangent-space methods [4]. In the
present contribution, we apply the tangent-space based formulation of TD-DMRG to
simulate electronic [5] and vibrational [6-7] dynamics, possibly coupled together, of
molecules with several dozens of degrees of freedom [8]. We assess the accuracy of the
simulations by comparison with state-of-the-art experimental measurements obtained
from time-resolved techniques. Moreover, we show that TD-DMRG outperforms its
time-independent parallel in the calculation of high-order molecular properties and in
the simulation of spectra in regions with a high density of excited states. Finally, we
discuss how quantum information-based measures can be exploited to increase the
efficiency of TD-DMRG to target even larger systems.
References:
[1] H.D. Meyer, WIRES Comp. Mol. Sci. 2, 351 (2011).
[2] T. Sato, K.L. Ishikawa, Phys. Rev. A, 88, 023402 (2013).
[3] A. Baiardi, M. Reiher, arXiv, 1910.0013 (2019).
[4] J. Haegeman, C. Lubich, I. Oseledets, B. Vandereycken, F. Verstraete, Phys. Rev. B, 94, 165116
(2016).
[5] S. Keller, M. Dolfi, M. Troyer, M. Reiher, J. Chem. Phys., 143, 244118 (2015).
[6] A. Baiardi, C.J. Stein, V. Barone, M. Reiher, J. Chem. Theo. Comput., 13, 3764 (2017).
[7] A. Baiardi, C.J. Stein, V. Barone, M. Reiher, J. Chem. Phys., 150, 094113 (2019).
[8]. A. Baiardi, M. Reiher {\it J. Chem. Theo. Comput.} {\bf 15} (2019), 3481.
62
Quantum Chemistry Assisted by Machine Learning
Pavlo O. Dral
State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key
Laboratory of Theoretical and Computational Chemistry, and College of Chemistry
and Chemical Engineering, Xiamen University, Xiamen 361005, China
Machine learning (ML) becomes a useful tool for assisting quantum chemical research in a variety
of ways. First, machine learning can be used to improve the accuracy of low-level quantum
chemical (QC) method either by explicitly correcting their predictions as in Δ-learning approach[1]
or by improving the semiempirical QC Hamiltonian as in parameter learning technique.[2] Second,
ML can be used for very accurate representation of potential energy surfaces, e.g. to drastically cut
the number of high-level QC calculations required for predicting rovibrational spectra with
spectroscopic accuracy[3] or to perform excited-state nonadiabatic dynamics simulations at very
low computational cost[4-5]. For carrying out this research I develop MLatom[6-7] program
package optimized for efficient and user-friendly use of kernel ridge regression-based ML in
atomistic simulations.
Fig. 1: ML significantly improves semiempirical QC Hamiltonian.[2]
References:
[1] R. Ramakrishnan, P. O. Dral, M. Rupp, O. A. von Lilienfeld, J. Chem. Theory Comput. 11, 2087–
2096 (2015).
[2] P. O. Dral, O. A. von Lilienfeld, W. Thiel, J. Chem. Theory Comput. 11, 2120–2125 (2015).
[3] P. O. Dral, A. Owens, S. N. Yurchenko, W. Thiel, J. Chem. Phys. 146, 244108 (2017).
[4] P. O. Dral, M. Barbatti, W. Thiel, J. Phys. Chem. Lett. 9, 5660–5663 (2018).
[5] W.-K. Chen, X.-Y. Liu, W. Fang, P. O. Dral, G. Cui, J. Phys. Chem. Lett. 9, 6702–6708 (2018).
[6] P. O. Dral, MLatom: A Package for Atomistic Simulations with Machine Learning,
http://MLatom.com (2013–2019).
[7] P. O. Dral, J. Comput. Chem. 40, 2339–2347 (2019).
63
Theoretical Chemistry under Tips: Raman and STM
Images
Sai Duan1
1Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key
Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory
of Computational Physical Sciences, Department of Chemistry, Fudan University,
Shanghai 200433, P. R. China
Take the advantage of piezoelectric controlled scanners, the amazingly spatial
resolution of probing tips has been achieved, which provides a perfect investigating
framework for single molecule. In this context, the optical and electric perturbations
accompanied the tips are facilitating external stimuli-source for molecular probing (Fig.
1), resulting in the high-resolution Raman and scanning tunneling microscope (STM)
images, respectively. This talk will focus on the recent development of the entirely new
theoretical framework for Raman images[1-3] as well as the simulations of the
high-resolution STM images at the first-principles level[4-6]. The new theory of
Raman images not only quantitatively reproduced the state-of-the-art experimental
observations[1] but also proposed a practical protocol for visualization of molecular
vibrations in real space[2]. The breakdown of conventional spectral selection rules by
the optical fields under the tips will be also discussed[3]. For STM images, the in-situ
configurations for an azo-based molecular switcher[4], water hexamer[5], and
1,3,5-tribromobenzene[6] were identified by our simulations, which revisits the surface
chemistry of these important systems.
Fig. 1: Schematic of optical and electric response of a single molecule under the top.
References:
[1] Sai Duan, Guangjun Tian, Yongfei Ji, Jiushu Shao, Zhenchao Dong, and Yi Luo. J. Am. Chem.
Soc., 137, 9515−9518 (2015).
[2] Sai Duan, Guangjun Tian, and Yi Luo. Angew. Chem. Int. Ed., 55, 1041–1045 (2016).
64
[3] Sai Duan, Zilvinas Rinkevicius, Guangjun Tian, and Yi Luo. J. Am. Chem. Soc., 141,
13795−13798 (2019).
[4] Zhen Xie, Sai Duan, Chuan-Kui Wang, and Yi Luo. To be submitted.
[5] Sai Duan, Igor Ying Zhang, Zhen Xie, and Xin Xu. In perpetration.
Shichao Li, Zeqi Zha, Sai Duan, Jinliang Pan, Ke Deng, Mengxi Liu, Xiaohui Qiu. In perpetration.
65
TBA
Steven Kirk
66
Application of Quantum Mechanics in The Study of
Enzymatic Mechanisms
Sérgio F. Sousa
UCIBIO@REQUIMTE – BioSIM, Departamento de Biomedicina, Faculdade de
Medicina da Universidade do Porto, Portugal (email: [email protected])
Quantum mechanics (QM) has become an important tool in computational chemistry
for the study of the reactivity of molecules. When combined with molecular
mechanics (MM), quantum mechanics can be applied to the study of the reactivity of
larger molecules and more complex systems. In fact, hybrid QM/MM methods offer a
very appealing option for the computational study of enzymatic reaction mechanisms,
by separating the problem into two parts that can be treated with different
computational methods [1].
Hence, in a QM/MM formalism, the part of the system in which catalysis actually
occurs and that involves the active site, substrates and directly participating amino
acid residues is treated at an adequate quantum mechanical level to describe the
chemistry taking place. Often DFT is used, with the B3LYP density functional as the
most common choice. For the remaining of the enzyme, which does not participate
directly in the reaction, but that typically involves a much larger number of atoms,
molecular mechanics is employed, traditionally through the application of a
biomolecular force field.
When applied with care, QM/MM methods can be used with great advantage in
comparing, at a structural and energetic level, different mechanistic proposals,
discarding mechanistic alternatives and proposing new mechanistic pathways that are
consistent with the available experimental data.
Here, we illustrate some recent applications of QM/MM methods in the study of
enzymatic reactions based on our recent studies [2-4], illustrating the typical choices
made for the treatment of the QM region, in terms of quantum method, basis sets,
number of atoms, level of interaction with the MM region, etc. Present challenges and
future priorities for development are discussed.
Acknowledgments: This work has been supported by the Fundação para a Ciência e a Tecnologia
(FCT) UID/Multi/04378/2019
References:
[1] SF Sousa et. al, WIREs Comput Mol Sci 7:e1281(2017)
[2] P Paiva, SF Sousa, PA Fernandes, MJ Ramos, ChemCatChem 11, 3853 (2019)
[3] CSS Teixeira, MJ Ramos, SF Sousa, N Cerqueira, ChemCatChem (2019) Doi:
10.1002/cctc.201901505
[4] JF Rocha, AF Pina, SF Sousa, N Cerqueira, Cat Sci Technol 9, 4864 (2019)
67
Nonlinear dynamics of a quantum Cournot duopoly
game with Marinatto-Weber scheme
Tianyu Liu1, Hao Sun1
1 School of Science, Northwestern Polytechnical University, Xi’an 710129, China
In this paper, a dynamic quantum Cournot duopoly game with Marinatto-Weber (MW)
scheme is proposed. We analyze the influence of the input with different initial states on
stability and dynamics behavior of the system. What’s more, we also propose Cournot
duopoly games with quantity-setting firms use nolinear demand function. The result
shows that: (i) The corresponding classical Cournot duopoly game is a special case of the
dynamic quantum Cournot duopoly game with MW. (ii) The locally asymptotic stability
of equilibrium points are analyzed. (iii) Numerical simulations show that the complicated
dynamics behaviors of quantum Cournot game, and the relationship of several groups of
variables.
References:
[1] S.Askar, Common. Nonlinear Sci Numer Simular 19, 1918-1925 (2014).
[2] L. Shi, F. Xu, Quantum Inf. Process.18, 227 (2019).
68
Massive-Parallel Implementation of the
Resolution-of-Identity Coupled-Cluster Approaches
in the Numeric Atom-center Orbital Framework for
Molecular systems
Tonghao Shen
69
POSTERS
70
Explanation of the Role of Hydrogen Bonding in the
Structural Preferences of Small Molecule Conformers
Liling Wang, Alireza Azizi, Tianlv Xu, Steven R. Kirk* and Samantha Jenkins*
Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and
Key Laboratory of Resource National and Local Joint Engineering Laboratory for New
Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and
Chemical Engineering, Hunan Normal University,Changsha, Hunan 410081, China
Next generation QTAIM was used to explain the structural preferences and
differences of a series phenolic esters and nitrogen analogues. The planarity of the
nitrogen analogue structures was explained by a resistance to torsion of the N-linking
bond. Conversely, a resistance to planarity of the O-linking bond in the phenolic
esters explained the twisted geometries. Hydrogen bonding that linked the aromatic
ring with the rest of the molecule was only found to be present for the nitrogen
analogues. Confirmation of the findings was provided by a stress tensor analysis.
71
Next Generation QTAIM for the S1/S0 Conical
Intersections in Dynamics Trajectories of a
Light-Driven Rotary Molecular Motor
LiLing Wang1, Alireza Azizi1, Roya Momen1, Tianlv Xu1, Steven R. Kirk1*, Michael
Filatov1,2 and Samantha Jenkins1*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and
Key Laboratory of Resource National and Local Joint Engineering Laboratory for New
Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and
Chemical Engineering, Hunan Normal University,Changsha, Hunan 410081, China 2Department of Chemistry, Ulsan National Institute of Science and Technology
(UNIST), 50 UNIST-gil, Ulsan44919, Korea
Next generation QTAIM was applied to analyze, along an entire bond-path,
intramolecular interactions known to influence the photo-isomerization dynamics of a
light-driven rotary molecular motor. The 3-D bond-path framework set B0,1,
constructed from the least and most preferred directions of electronic motion, provided
new insights into the bonding leading to different S1 state lifetimes including the first
quantification of covalent character of a closed-shell intramolecular bond-path. We
undertook the first use of the stress tensor trajectory Tσ(s) analysis on selected
non-adiabatic molecular dynamics trajectories with the electron densities obtained
using the ensemble density functional theory method. The stress tensor Tσ(s) analysis
was found to be well suited to follow the dynamics trajectories that included the S0 and
S1 electronic states through the conical intersection and also provided to a new measure
to assess the degree of purity of the axial bond rotation for the design of rotary
molecular motors.
72
The Role of the Transition Density in the S0 → S1 (S01)
and S0 → S2 (S02) Transitions of Fulvene with Next
Generation QTAIM
LiLing Wang1, Alireza Azizi1, Tianlv Xu1, Michael Filatov2, Steven R. Kirk1*, Martin
J. Paterson3 and Samantha Jenkins1*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and
Key Laboratory of Resource National and Local Joint Engineering Laboratory for New
Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and
Chemical Engineering, Hunan Normal University,Changsha, Hunan 410081, China 2Department of Chemistry, Ulsan National Institute of Science and Technology
(UNIST), 50 UNIST-gil, Ulsan44919, Korea 3Institute of Chemical Sciences, School of
Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS,
UK
We present, for the first time the S0 → S1 (S01) and S0 → S2 (S02) transition densities
for fulvene, using the 3-D next generation QTAIM that is constructed using the
preferred direction of electronic charge density accumulation. A symmetrization of the
position of the bond critical point (BCP) of the torsional C2-C6 BCP along the
bond-path associated with the presence of a conical intersection (CI) for the first
excited state (S1). The corresponding transition density S0 → S1 (S01) displays
hindered BCP motion that is associated with a large rearrangement of the properties
of the total electronic charge density in the form of a 3-D bond-path. The reaction
pathway for second excited state does not have an associated CI and the BCP for the
S0 → S2 (S02) transition density, or symmetrization of the BCP position or hindered
motion or large deviation in the 3-D bond-path. We hypothesize that the
symmetrization of the position of the torsional C2-C6 BCP along a bond-path for an
excited state pathway is associated with a CI, where the transition density BCP is
hindered and as consequence undergoes a large rearrangement.
73
Multistate density functional theory applied with 3
unpaired electrons in 3 orbitals: the singdoublet and
tripdoublet states of the ethylene cation Likun Yanga, Adam Grofeb, Jeffrey R Reimersac, Jiali Gaodef
a International Centre for Quantum and Molecular Structures and the Department of
Physics, Shanghai University, Shanghai, 200444, China b Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical
Chemistry, Jilin University, Changchun, Jilin Province 130023, China c School of Mathematical and Physical Sciences, University of technology Sydney,
NSW, 2007, Australia d Shenzhen Bay Laboratory, Shenzhen 518055, China
e Peking University Shenzhen Graduate School, Shenzhen 518055, China f Department of Chemistry and Supercomputing Insitute, University of Minnesota,
Minneapolis, Minnesota 55455, United States.
Multistate density functional theory (MSDFT) is extended to facilitate treatment of
situations involving more than two open-shell electrons. The method is applied to
determine energies for the two doublet state (tripdoublet and singdoublet) and the
quartet-state components that arise when two electrons of one spin type and one
electron of the other singly occupy three orbitals. A test system, the (,*)
excitation of the ethylene cation, is utilized, with MSDFT delivering energies that are
numerically superior to those from time-dependent density-functional theory
(TD-DFT) and states free from spin contamination.
74
Next-Generation Quantum Theory of Atoms in
Molecules for the Ground and Excited State of the
Ring-Opening of Cyclohexadiene (CHD)
Tian T.1, Xu T.1, Kirk S. R.1*, Filatov M.1,2, Jenkins S.1*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan 410081, China 2Department of Chemistry, Ulsan National Institute of Science and Technology
(UNIST), 50 UNIST-gil, Ulsan 44919, Korea
The factors underlying the experimentally observed branching ratio (70:30) of the
(1,3-cyclohexadiene) CHD→HT (1,3,5-hexatriene) photochemical ring-opening
reaction are investigated. The ring-opening reaction path is optimized by a high-level
multi-reference DFT method and the density along the path is analyzed by the
QTAIM and stress tensor methods. The performed density analysis suggests that, in
both S1 and S0 electronic states, there exists an attractive interaction between the ends
of the fissile σ-bond of CHD that steers the ring-opening reaction predominantly in
the direction of restoration of the ring. It is suggested that opening of the ring and
formation of the reaction product (HT) can only be achieved when there is a sufficient
persistent nuclear momentum in the direction of stretching of the fissile bond. As this
orientation of the nuclear momentum vector can be expected relatively rare during the
dynamics, this explains the observed low quantum yield of the ring-opening reaction.
75
Next-Generation Quantum Theory of Atoms in
Molecules for the Ground and Excited State of DHCL
Tian T.1, Xu T.1, Kirk S. R.1*, Filatov M.1,2, Jenkins S.1*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan 410081, China 2Department of Chemistry, Ulsan National Institute of Science and Technology
(UNIST), 50 UNIST-gil, Ulsan 44919, Korea
The factors underlying two possible pathways for the Dihydrocostunolide (DHCL)
photochemical ring-opening reaction were investigated; the first pathway returned to
the ring-closed conformation of the reactant and the second pathway progressed to the
ring-opened product. High-level multi-reference DFT methods were used to optimize
the two pathways and the density was analyzed using QTAIM and the stress tensor.
Oscillations in the chemical character of the fissile bond were found for the first
pathway before and after the conical intersection that steered the reaction back to
reactant. Conversely, this behavior was absent for the second pathway that led
forward to the product.
76
Next-Generation QTAIM for the Design of
Quinone-based switches
Tian T.1, Xu T.1, Mourik T.2, Früchtl H.2,Kirk S. R.1*, Jenkins S.1*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan 410081, China 2EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St
Andrews, Fife KY16 9ST, Scotland, United Kingdom.
Investigation of the hydrogen transfer tautomerization process yielded metallic
hydrogen bonds in the benzoquinone-like core of the switch. Bond-path framework
sets B and Bσ, comprising a three stranded, non-minimal 3-D bond, which included the
familiar QTAIM bond-path and two additional paths defining the least and most
preferred directions of electron density motion, were used with QTAIM and the
stress-tensor respectively. The B and Bσ were visualized and uncovered the
destabilizing effects on the hydrogen bond of the presence of an Fe atom. The length
of B and Bσ quantified this effect and the dependence on the position of a fluorine
substituent.
77
Next-Generation Quantum Theory of Atoms in
Molecules for the Ground and Excited States of the
Penta-2,4-dieniminium Cation (PSB3)
Xin Bin1,2, Tianlv Xu1,2, Steven R. Kirk1,2, Michael Filatov1,2,3, Samantha Jenkins1,2
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan 410081, China 2Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan, China 3Department of Chemistry, Ulsan National Institute of Science and Technology
(UNIST), 50 UNIST-gil, Ulsan44919, Korea
A 3-D vector-based representation of the chemical bond recently introduced, the
bond-path frame-work set B, is applied to analysis of the minimum energy pathways
corresponding to deactivation of the first excited singlet state of PSB3 and occurring
through torsion about the three double bonds of PSB3 combined with other
intramolecular degrees of freedom, such as the bond length alternation. Using the
bond-path framework set B analysis we elucidate the importance of a balanced
treatment of the covalent and ionic contributions to the ground and excited state
originating from torsion about various double bonds, which is known to be strongly
dependent on the presence of dynamic electron correlation. Therefore, we present a
more sophisticated method of determination of the degree of covalent and ionic
contributions known to be responsible for altering the relative stability of the S1/S0
conical intersections. The presented results suggest that the commonly used simplified
multi-reference methodologies that omit the dynamic correlation are to be avoided as
they often result in incorrect predictions for the excited state deactivation reaction
mechanism.
78
Next-Generation Quantum Theory of Atoms in
Molecules for the Photochemical Ring-Opening
Reactions of Oxirane
Xin Bin1, Alireza Azizi1, Tianlv Xu1, Steven R. Kirk1, Michael Filatov1,2, Samantha
Jenkins1
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan 410081, China 2Department of Chemistry, Ulsan National Institute of Science and Technology
(UNIST), 50 UNIST-gil, Ulsan44919, Korea
The conical intersections corresponding to the C-O and C-C ring opening were
optimized and the reaction paths traversing these intersections were obtained.
Investigation of the C-O ring opening revealed that when traversing the lowest energy
conical intersection, the reaction path returns to the closed ring geometry. The C-O
path traversing the intersection featuring torsion of terminal CH2 group however, led
to a ring-opened geometry, an H-shift and the formation of acetaldehyde that can
undergo further dissociation. The observation of different reaction paths was
explained by the 3-D paths from quantum theory of atoms in molecules (QTAIM) that
defined the most preferred direction of electronic motion that precisely tracked the
mechanisms of bond breaking and formation throughout the photo-reactions. The size,
orientation, and location of these most preferred 3-D paths indicated the extent and
direction of motion of atoms, bonds, and the degree of torsion or planarity of a bond
indicating a predictive ability.
79
The Directional Bonding of [1.1.1]propellane with
Next Generation QTAIM
Xin Bin, Tianlv Xu, Steven R. Kirk, Samantha Jenkins*
Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and
Key Laboratory of Resource National and Local Joint Engineering Laboratory for
New Petro-chemical Materials and Fine Utilization of Resources, College of
Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan
410081, China
We investigated the [1.1.1]propellane molecule using the 3-D bond-path framework
set B and the stress tensor Bσ within the quantum theory of atoms in
molecules(QTAIM). The controversial axial bond was determined to be a charge-shift
bond comprising significant bond metallicity that correlated with values of the bond
stiffness S < 1. The influence of the axial bond on the neighboring bonding is
quantified in terms of unexpectedly low bond stiffness S values and a new measure of
charge-shift bonding, the polarizability P. Consistency of these results was found at
the MP2, CCSD and B3LYP theory levels.
80
Chirality-Helicity Equivalence in the S and R
Stereoisomers: A Theoretical Insight
Xu T.1, Li J.1, Kirk S. R.1*, Jenkins S.1*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan 410081, China
We located the unknown chirality–helicity equivalence in molecules with a chiral
center, and as a consequence, the degeneracy of the S and R stereoisomers of lactic
acid was lifted. An agreement was found with the naming schemes of S and R
stereoisomers from optical experiments. This was made possible by the construction
of the stress tensor trajectories in a non-Cartesian space defined by the variation of the
position of the torsional bond critical point upon a structural change, along the torsion
angle, θ, involving a chiral carbon atom. This was undertaken by applying a torsion θ,
−180.0° ≤ θ ≤ +180.0° corresponding to clockwise and counterclockwise directions.
We explain why scalar measures can at best only partially lift the degeneracy of the S
and R stereoisomers, as opposed to vector-based measures that can fully lift the
degeneracy. We explained the consequences for stereochemistry in terms of the ability
to determine the chirality of industrially relevant reaction products.
81
Flip Rearrangement in the Water Pentamer: Analysis
of Electronic Structure
Xu T.1, Li J.1, Kirk S. R.1*, Jenkins S.1*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan 410081, China
In this investigation we consider a degenerate rearrangement of the (H2O)5 lowest
energy structure, where a degenerate rearrangement is one in which the two minima
differ only by permutations of atoms of the same element. The profile of the variation
of the relative energy ∆E of the (H2O)5 permutation isomerization reaction pathway
with the intrinsic reaction coordinate (IRC) is asymmetrical. The preferred route, from
the transition state to either the reverse or forward minimum cannot be determined
from the relative energy ∆E. Consequentially, further investigation of the (H2O)5
permutation isomerization reaction pathway requires an approach beyond scalar
measures and we will therefore use Next generation Quantum Theory of Atoms in
Molecules within the framework of conventional QTAIM.
82
Quinone-based Switches for Candidate Building
Blocks of Molecular Junctions with QTAIM and the
Stress Tensor
Xu T.1, Wang L.1, Kirk S. R.1*, Jenkins S.1*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan
Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal
University, Changsha, Hunan 410081, China
The current work investigates candidate building blocks based on molecular junctions
from hydrogen transfer tautomerization in the benzoquinone-like core of an
azophenine molecule with QTAIM and the recently-introduced stress tensor trajectory
analysis. We find that in particular the stress tensor trajectories are well suited to
describe the mechanism of the switching process. The effects of an Fe-dopant atom
coordinated to the quinone ring, as well as F and Cl substitution of different
ring-hydrogens, are investigated and the new QTAIM and stress tensor analysis is
used to draw conclusions on the effectiveness of such molecules as molecular
switches in nano-sized electronic circuits. We find that the coordinated Fe-dopant
greatly improves the switching properties, both in terms of the tautomerisation barrier
that has to be crossed in the switching process and the expected conductance behavior,
while the effects of hydrogen substitution are more subtle. The absence of the
Fe-dopant atom led to impaired functioning of the switch 'OFF' mechanism as well as
coinciding with the formation of closed-shell H---H bond critical points that indicated
a strained or electron deficient environment. Our analysis demonstrates promise for
future use in design of molecular electronic devices.
83
Halogen and Hydrogen Bonding in
Halogenabenzene/NH3 Complexes Compared
UsingNext-Generation QTAIM
Shuman Li 1, Tianlv Xu1, Tanja van Mourik2,* , Herbert Früchtl2,
Steven R. Kirk1,* and Samantha Jenkins1,*
1Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource; National and Local Joint Engineering Laboratory
for New Petro-chemical Materials and Fine Utilization of Resources, College of
Chemistry and Chemical Engineering, Hunan Normal, Changsha 410081, Hunan,
China 2EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews,
Fife KY16 9ST, Scotland, UK *Correspondence: [email protected] (T.v.M.);
[email protected] (S.R.K.); [email protected] (S.J.)
Next generation QTAIM was used to investigate the competition between hydrogen
bonding and halogen bonding for the recently proposed (Y = Br, I, At):
halogenabenzene: NH3 complex. Differences between using the SR-ZORA
Hamiltonian and effective core potentials (ECPs) to account for relativistic effects
with increased atomic mass demonstrated that Next-generation QTAIM is a much
more responsive tool than conventional QTAIM. Subtle details of the competition
between halogen bonding and hydrogen bonding were observed, indicating a mixed
chemical character shown in the 3-D paths constructed from the bond-path framework
set B. The use of SR-ZORA indicated that ECPs overestimate the topological stability
of the halogen bonding and for (X = Cl): 1-methyluracil: H2O this resulted in the
Cl--O halogen bond being replaced by a Cl--H hydrogen bond. In addition, the use of
SR-ZORA reduced or removed entirely spurious features of B on the site of the
halogen atoms.
84
3-D bond-paths of QTAIM and the Stress Tensor in
Small Water Clusters on the Ehrenfest Force
Molecular Graph
Shuman Li1, Alireza Azizi, Steven R. Kirk* and Samantha Jenkins*
1 Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
and Key Laboratory of Resource National and Local Joint Engineering Laboratory
for New Petro-chemical Materials and Fine Utilization of Resources, College of
Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan
410081, China *Correspondence: [email protected] (T.v.M.);
[email protected] (S.R.K.); [email protected] (S.J.)
We have investigated the donation of covalent character from covalent (sigma) to
hydrogen-bonds, by calculating the eigenvector coupling properties of QTAIM, stress
tensor σ(r) and Ehrenfest Force F(r) on the F(r) molecular graph. We present all the
corresponding next generation 3-D bond-path framework sets and find that only the
F(r) bond-path framework sets reproduce the earlier finding on the coupling between
covalent (sigma) and hydrogen-bonds, that possess a degree of covalent character. The
morphology of the covalent (sigma) and hydrogen-bonds 3-D bond-path framework
sets for the F(r) is characteristically different to the results from QTAIM and stress
tensor σ(r).
85
Insights into the Mechanism of Fatty Acid
Photodecarboxylase: Trimolecular vs. Bimolecular
Photocycle
Pan Hong, Anan Wu, Kai Tan, Xin Lu*
State Key Laboratory of Physical Chemistry of Solid Surface & Fujian Provincial Key
Laboratory for Theoretical and Computational Chemistry, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005,
China
Recently a new photoenzyme, fatty acid photodecarboxylase (FAP), was reported by
Beisson et al. that can catalyze fatty acid decarboxylation to afford n-alkanes or
n-alkenes in blue light.1 A trimolecular photocycle mechanism involving an
unidentified proton donor HX was proposed, which is seemingly incompatible with
the observed high quantum yield (> 80%), as the quantum yields of trimolecular
photoreactions reported thus far are extremely poor.2-3 Herein, we propose an
alternative bimolecular mechanism, in which the photoactive part of FAD cofactor in
FAP, i.e., the lumiflavin (FI) fragment (Fig.1), can be protonated to work as proton
donor. Our molecular model-based density functional calculations disclosed that the
bimolecular photocycle can proceed smoothly in five steps, i.e., photoexcitation of
FAD, proton transfer from carboxylic acid to the excited state of FAD, electron
transfer from carboxylate anion to the protonated FAD*, decarboxylation and
hydrogen abstraction, energetically more favorable than the previously proposed
trimolecular mechanism. The present study indicates that the light-capturing organic
molecule, lumiflavin (FI) of FAD, can act as a metal-free photocatalyst for the
photodecarboxylation of fatty acids to afford hydrocarbons, which is yet relatively
rare in organic synthesis.4-7
Fig. 1: Comparison of two photodecarboxylation mechanisms of fatty acid photodecarboxylase
References:
[1] Sorigué, D., Légeret, B., Science, 357, 903 (2017).
86
[2] M. Borja, P. Dutta, Nature, , 362, 43 (1993).
[3] J. Chen, K. Wu, J. Am. Chem. Soc., 138, 884 (2016)
[4] K. Nishikawa, T. Ando, K. Maeda, Org. Lett., 15, 636 (2013).
[5] S. Cai, Y. Xu, Org. Lett., 18, 2990 (2016).
[6] M.-J. Zhang, G. M. Schroeder, RSC Adv., 6, 96693 (2016).
[7] C. Yang, J. D. Yang, J. Org. Chem., 81, 12357 (2016).
87
Equilibrize photoluminescence quantum yield and
charge mobility of organic semiconductor：A
QM/MM study
Yuling Wei1，Meihui Liu1，Xiaoqian Wu1，Yuan Liang1，Ying Lv1，Xiaoxiao Xiao1，
Yanan Sun1, Tiantian Xiao1，Wen Wang1, Geng Hua1,*, Guo Wang1,*，Yuai Duan1,*, Yi
Liao1,*
Department of Chemistry, Capital Normal University, Beijing 100048, China.
*Email: [email protected], [email protected]
Abstract: The new green organic semiconductor BDPV2T1 could equilibrize
photoluminescence quantum yield (PLQY) and charge mobility of organic
semiconductor, while DPVBi2 a classical blue emitter has high photoluminescence
quantum yield but low charge mobility. Particularly they has similar structure. A
quantum mechanics/molecular mechanics (QM/MM) method is adopted to investigate
the photophysical properties, the Marcus equation is used to describe hole and
electron transfer rates, and kinetic Monte Carlo simulation is performed to obtain
charge mobility. In both solution and solid phase, the vertical excitation energy (VEE),
oscillator strength (f), electric transition dipole moment (EDM) and PLQY of
BDPV2T and DPVBi are calculated. In solid phase, the charge mobility and the
Intermolecular interaction effffect is analyzed. The aggregation induced enhancement
emission (AIEE) is thus revealed for this emitter from the tetrahydrofuran (THF)
solution to the solid phase. The calculated mobility of the hole for BDPV2T is larger
than DPVBi. Furthermore, in the BDPV2T found π-π interaction while
CH-πinteraction can be found in DPVBi. Our study demonstrates that Intermolecular
interaction of organic semiconductors has an important effect on their photophysical
and charge transfer properties.
88
Fig.1 Chemical structure of BDPV2T (a) and DPVBi (b). QM/MM model for BDPV2T (c) and DPVBi
(d): the single centered molecule is treated as the high layer and its surrounding molecules are regarded
as the low layer
[1] Ma, S.; Zhou, K.; Hu, M.; Li, Q.; Liu, Y.; Zhang, H.; Jing, J.; Dong, H.; Xu, B.; Hu, W.; Tian, W.,
Integrating Efficient Optical Gain in High-Mobility Organic Semiconductors for Multifunctional
Optoelectronic Applications. Advanced Functional Materials 2018, 28 (36).
[2] Hosokawa, C.; Higashi, H.; Nakamura, H.; Kusumoto, T., Highly efficient blue electroluminescence
from a distyrylarylene emitting layer with a new dopant. Applied Physics Letters 1995, 67 (26),
3853-3855.
89
Effect of different connection node on the charge
transport property for D-A copolymers: a
Computational Study
Xiaoqian Wu1, Hua Geng,* Yuai Duan,* Guo Wang,* Yi Liao,*
Department of Chemistry, Capital Normal University, Beijing 100048, China.
*Email: [email protected], [email protected]
In dithiophenyldiketopyrrolopyrrole (DTDPP)-based copolymers[1], we found that
when diketopyrrolopyrrole (DPP) is linked to the ortho, meta and para positions of
thiophene, the charge transport polarity and mobility of the corresponding
copolymers are significantly different. Based on the super-exchange coupling model [2], we have carried out theoretical calculations and analysis. It is found that the
different connection positions lead to different symmetry and charge distribution of
the end groups, which have a great influence on the charge transport properties.
References:
[1] Feifei He, Changli Cheng, Hua Geng, Yuanping Yi and Zhigang Shuai . J.Mater. Chem.
[2] Changli Cheng, Hua Geng,Yuanping Yi b and Zhigang Shuai . J.Mater. Chem. C,2017,5, 3247.
90
A periodic DFT investigation of the hybrid perovskite
solar cell interface: From structural features to
electron injection through ligand’s connection
Jun Su1, Tao Zhu2, Thierry Pauporté2, Frédéric Labat1, Ilaria Ciofini1
1Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life
and Health Sciences (i-CLeHS), 11 rue P. et M. Curie, F-75005 Paris, France 2Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie
Paris (IRCP), 11 rue P. et M. Curie, F-75005 Paris, France
Recently, perovskite solar cells (PSC) gain a lot of research interests due to its
potentiality to produce clean energy, and advantages like easy fabrication and
relatively high-power conversion efficiency.[1] The general structure of a PSC
consists of a perovskite compound as the light-absorbing material together with hole
and electron transfer layers (H/ETL) and electrodes. Recent research also indicates
that using self-assembled monolayers (SAMs) to engineer the interface can boost the
performance of PSC.[2] Based on this, we conducted a period DFT-based
computational strategy to model the interface properties of PSC.[3] We focused on the
interaction between the perovskite compound methylammonium lead iodide
(CH3NH3PbI3, referred to as MAPI) and TiO2 as an ETL, which are bound to each
other via SAM. In particular, 4-chlorobenzoic acid (CBA) was chosen as the SAM.[4]
The periodic model of the interface was built based on a (4x2) supercell model of the
TiO2-(101) surface and MAPI with (110) surface orientation and MAI-termination,
with CBA binding the two blocks. The relaxed structure shows that the interface
obtained between MAPI, CBA, and TiO2 is mainly ensured by both Ti-O and Pb-Cl
bonds. The computed density of states indicate that MAPI contributes to the top of the
valence band while TiO2 contributes to the bottom of the conduction band with a
bandgap of 2.16 eV. The possibility of electron transfer process from MAPI to TiO2 is
confirmed by the computed spin density of the reduced MAPI/CBA/TiO2 system.
Overall, the proposed DFT-based computational protocol therefore indicates that CBA
can be envisaged to lead to better stability of such PSC systems, together with
improved band alignment and electron injection. The modeling of such interfaces can
shed light on the working principles of such cells, potentially leading to their
improvement.
91
Fig. 1: Schematic drawing of the MAPI/CBA/TiO2 interface unit cell. The solid yellow line represents
the unit cell. Red, light grey, white, green, purple, dark grey, blue and grey spheres correspond to O, Ti,
H, Cl, I, Pb, N and C atoms, respectively.
References:
[1] M. A. Green, A. Ho-Baillie and H. J. Snaith, Nature Photonics 8(7), 506 (2014).
[2] R. Dovesi, A. Erba, R. Orlando, et al., Comput. Mol. Sci. 8(4), 1360 (2018).
[3] C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999).
[4] T. Zhu, J. Su, J. Alvarez, G. Lefèvre, F. Labat, I. Ciofini and T. Pauporté, Adv. Func. Mater.
1903981 (2019).
92
A strategy for predicting crystal engineering to
balance
exciton coupling and electronic coupling
Meihui Liu1, Geng Hua* and Yi Liao*
1Department of Chemistry, Capital Normal University, Beijing 100048, China.
Organic semiconductors integrating excellent charge transport with efficient solid
emission are very challenging to be attained in the construction of light emitting
transistors and even for realization of electrically pumped organic lasers. One of the
key reasons is the limitation of high mobility emissive organic semiconductors, which
is crucial for achieving high density excitons in the conducting channels and thus
high-efficiency. However, because compact packing with strong and plentiful
intermolecular interactions usually not only give rise to excellent charge transporting
property but also quench terribly the solid state luminescence. This contradiction
severely hinders the advancement of OLETs and the realization of electrically
pumped organic lasers. How to modulate the aggregation structure and design organic
optoelectronic materials with high charge mobility and high luminescent efficiency
are the key scientific issues to be solved. In our work, we find a new method to
predict and adjust aggregate structures by balancing the relationship between exciton
coupling and electronic coupling, and this method can be confirmed in recent high
charge mobility and high luminescence efficiency organic optoelectronic materials.
References:
[1] J. Liu, W. Zhu, J. Mater. Chem. C, 2016, 4, 3621–3627.
[2] Li W Q, Peng Q, Chemistry of Materials, 2017, 29, 2513-2520.
[3] Z. Qin, H. Gao, Adv. Mater, 2019, 31, 1903175.
93
Q|R: Quantum-based Refinement of
Biomacromolecules
Min Zheng1,2, Malgorzata Biczysko1, Yanting Xu1, Nigel W. Moriarty3, Holger
Kruse4, Mark P. Waller5, Pavel V. Afonine3
1Shanghai University, China
2Münster University, Germany 3MBIB, Lawrence Berkeley National Laboratory, USA
4Institute of Biophysics of the Czech Academy of Sciences, Czech Republic 5Pending AI Pty Ltd., Australia
Protein structure determination is largely reliant on crystallography (X-ray, neutron or
electron), electron cryo-microscopy or NMR experiments. Refinement is the final step
in obtaining accurate three-dimensional atomic model based on experimental data.
Since the quality of the data (e.g., resolution) is rarely sufficient to utilize these data
alone, this step has traditionally relied on parameterized libraries that describe
stereochemistry of the molecules in question. The libraries used in major refinement
packages do not describe unusual local arrangements of protein residues in
Ramachandran space, novel ligands, or non-covalent interactions such as stacking,
halogen, hydrogen or salt bridges. In particular, structures obtained using
low-to-medium resolution data are biased by simple harmonic geometry restraints
derived from these libraries. Quantum chemical computations can yield accurate
geometries for standard protein or RNA/DNA molecules as well as novel ligands.
The methods we are developing in the Q|R project [1-3], which is our next generation
open-source software package (http://github.com/qrefine), combine experimental data
with chemical restraints derived from quantum-chemical methods. These procedures
have proven to better describe non-covalent interactions, and are expected to yield
more accurate information on the protein structures, e.g. better description of ligand
binding.
References:
[1] M. Zheng, J. R. Reimers, M. P. Waller, P. V. Afonine, Acta Cryst. D 73, 45 (2017)
[2] M. Zheng, N. W. Moriarty, Y. Xu, J. R. Reimers, P. V. Afonine, M. P. Waller, Acta Cryst. D 73,
1020 (2017)
[3] M. Zheng, M. Biczysko, Y. Xu, N. W. Moriarty, H. Kruse, A. Urzhumtsev, M. P. Waller, P. V.
Afonine, Acta Cryst. D, accepted, bioRxiv 827170; doi: https://doi.org/10.1101/827170 (2019)
94
Identification of DNA bases and their cations in
Astrochemical environments: Computational
Spectroscopy of Thymine as a test case
Yage Zhao1, Malgorzata Biczysko1
International Center for Quantum and Molecular Structures, College of science,
Shanghai University, Shanghai, China
Spectroscopic techniques are widely used to infer information about molecular
structure and thermodynamics. In particular, they play a crucial role in the
investigation of planetary atmosphere and the interstellar medium. Astrochemistry
laboratory simulations have shown that complex organic molecules (COMs) can be
formed from the simple species by the vacuum ultraviolet (VUV) or X-ray irradiation.
This expands interest in searching for organic compounds of biological and prebiotic
interests such as DNA and RNA in the astrochemical environments [1].
Thymine is an important component of DNA and RNA, which can be applied as test
case to introduce computational spectroscopy methodologies of interest for
astrochemistry studies [2,3]. We consider the IR spectrum of neutral and cation
ground state, and the photoelectron spectrum in the 8.7eV~9.6eV[4], which shows
abundant vibrational structure that has been assigned with help of vibronic
computations.
References:
[1]. M. Biczysko, J. Bloino, C. Puzzarini, Computational challenges for astrochemistry” WIREs
Comput Mol Sci 8, e1349, 2018
[2] Barone, V.; Biczysko, M.; Bloino, J., Fully anharmonic IR and Raman spectra of medium-size
molecular systems: accuracy and interpretation. Physical Chemistry Chemical Physics 2014, 16 (5),
[3] J Bloino, A Baiardi, M Biczysko “Aiming at an accurate prediction of vibrational and electronic
spectra for medium‐to‐large molecules: An overview” International Journal of Quantum Chemistry,
116, 1543–1574, 2016
[4]. Hochlaf, M.; Pan, Y.; Lau, K.-C.; Majdi, Y.; Poisson, L.; Garcia, G. A.; Nahon, L.; Al Mogren, M.
M.; Schwell, M., Vibrationally resolved photoelectron spectroscopy of electronic excited states of DNA
bases: Application to the à state of thymine cation. The Journal of Physical Chemistry A 2015,
95
Simulation of fully anharmonic IR spectra for flexible
peptides
Ruiqin Xu1, Malgorzata Biczysko1, Bin Yan2, Sjors Bakels2, Robbert C. Ouwersloot2,
Dennis W. P. M. Löwik2 and Anouk M. Rijs2
1 Shanghai University, 99 Shangda Lu, Shanghai 200444, China
2 Radboud University Nijmegen, FELIX Laboratory, The Netherlands.
The conformational preference of the capped tripeptide EAR (Glu-Ala-Arg-NH2) is
complicated due to the high flexibility and presence of several weak interactions.
Among the various types of investigations spectroscopies are the most powerful tools,
allowing direct detection of different binding schemes and three-dimensional (3D)
conformation via microwave (MW) measurements or indirect analysis through
finger-print vibrational features in infrared (IR), Raman, Resonance Raman, UV-vis
or fluorescence spectra, including also their chiral counterparts. These sophisticated
experiments call for accurate and reliable theoretical support in order to link the rich
experimental data to the desired information on the structure and properties of
complex molecular systems. In this work the structural assignment of EAR was
performed via the comparison between the calculated fully anharmonic spectra with
the experimental one, in the NH stretching region (3150-3700 cm-1). The latter was
acquired by employing IR-UV ion dip spectroscopy under laser-desorbed jet cooling
conditions. The conformational search includes three different families depending on
the form of the Arginine side chain: two non-zwitterionic types (canonical and
tautomeric structures) and one zwitterionic type with a deprotonated Glu and
protonated Arg side chain (abbreviated as Z). Their relative energies were determined
by single point energy computations at the B2PLYP-D3/maug-cc-pVTZ level of
theory, and for the close-lying most stable structures (Z1 and Z2) followed by fully
anharmonic B3LYP-D3/6-31G(d) GVPT2 computations, employing also the reduced
dimensionality schemes and hybrid scheme. The computed spectrum of the lowest
energy conformer Z1 shows many more features, some due to the non-fundamental
transitions, in good agreement with the experimental results.
References:
[1] J. Bloino, A. Baiardi, M. Biczysko, Int. J. Quantum Chem. 116, 1543 (2016)
[2] A. M. Rijs, J. Oomens, J., Eds. Gas-Phase IR Spectroscopy and Structure of Biological Molecules;
Topics in Current Chemistry; Springer International Publishing, 2015; Vol. 364
96
Effective QM computational models for protein
science
Zhenlong Gong, Malgorzata Biczysko
Shanghai University, China
Majority of protein structures, usually deposited in the Protein Data Bank (PDB),
have been obtained from crystallography, electron cryo-microscopy or NMR
experiments. Traditionally all these experimental studies have been analyzed based on
some “prior knowledge”. In particular the low-to-medium resolution structures are
obtained with the aid of protein structure refinement tools, which use geometry
restraints typically obtained from high resolution PDB structures for the energetically
favored minima in the Ramachandran (ϕ, ψ) plots. This is because these are the most
common arrangements for which increased number of examples improves the
accuracy of the statistical sampling of structural parameters. This reference data is
used to guide and validate structure building and refinement in the X-ray
crystallography field, which works very well for typical situations but may be not
reliable for new “unknown” situations.
Quantum-based refinement (Q|R) [1-3] uses information directly from
quantum-mechanical (QM) calculations, and is a promising alternative to standard
refinement that uses static (library-based) parameterized restraints. These procedures
have proven to better describe non-covalent interactions, and are expected to yield
more accurate information on the protein structures, e.g. better description of ligand
binding.
Quantum chemical QM restraints have the ability to provide more accurate
bio-macromolecular structures but at the cost of requiring far more computational
resources. The main goal of the present project is definition of reliable, yet
inexpensive, QM methodologies which can support structural and spectroscopic
studies of proteins. In this respect, we will choose high-accuracy experimental
structures with interesting bonding patterns to test cost/accuracy of the most promissing
QM methodologies.
I this work we focus on the accuracy of hydrogen bonding description in the -helix by
recently proposed GFN-xTB method [4-6].
References:
[1] M. Zheng, J. R. Reimers, M. P. Waller, P. V. Afonine, Acta Cryst. D 73, 45 (2017)
[2] M. Zheng, N. W. Moriarty, Y. Xu, J. R. Reimers, P. V. Afonine, M. P. Waller, Acta Cryst. D 73,
1020 (2017)
[3] M. Zheng, M. Biczysko, Y. Xu, N. W. Moriarty, H. Kruse, A. Urzhumtsev, M. P. Waller, P. V.
Afonine, Acta Cryst. D, accepted, bioRxiv 827170; doi: https://doi.org/10.1101/827170 (2019)
[4] S. Grimme, C. Bannwarth, P. Shushkov, J. Chem.Theory Comp. 13, 1989 (2017)
[5] J. Seibert, C. Bannwarth, S. Grimme, J. Am. Chem. Soc. 139, 11682 (2017)
[6] C. Bannwarth, J. Seibert, S. Grimme, J. Chem. Theory Comput. 15, 1652 (2019)
97
Cβ deviation: a metric for the protein structure
validation
Ping Wang1, Malgorzata Biczysko1, Nigel W. Moriarty2
1International Center for Quantum and Molecular Structures, College of science,
Shanghai University, Shanghai, China
2Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley
National Laboratory, Berkeley, CA, USA
The Cβ positions in the proteins are used to validate the geometrical arrangements
around the Cα. The deviation of the observed Cβ atom position from the predefined
ideal position provides a single measure encapsulating the major structure-validation
information contained in bond angle distortions. Cβ deviation (Cβdev) is sensitive to
incompatibilities between sidechain and backbone caused by misfit conformations or
inappropriate refinement restraints. Cβdev serves as a validation metric for protein
structure. However, there is not enough information defining ideal and allowed Cβdev
taking into account also dependence on the other structural parameters.
In this work we consider specific position of residue in the Ramachandran space, and
the variations of the angle τ (N-C-C) by optimizing the model dipeptide structure
using quantum mechanical computations.
References:
[1] Simon C. Lovell, Ian W. Davis, W. Bryan Arendall III, Paul I. W. de Bakker, J. Michael
Word, Michael G. Prisant, Jane S. Richardson, and David C. Richardson, Structure Validation by Cα
Geometry: φ,ψ, and Cβ Deviation. PROTEINS: Structure, Function, and Genetics. 50:437– 450
(2003).
[2] Terwilliger, T. C. & Zwart, P. H. (2010). Acta Crystallogr. Sect. -Biol. Crystallogr. 66, 213–221.
[3] Hintze, B. J., Lewis, S. M., Richardson, J. S. & Richardson, D. C. (2016). Proteins-Struct. Funct.
Bioinformatics. 84, 1177–1189.
[4] Moriarty, N. W., Adams, P. D. & Karplus, P. A. (2014). Comput. Crystallogr. Newsl. 5, 42–49.
98
Quantum computations for proteins spectroscopic
probes
Youjia Liu, Malgorzata Biczysko, Nigel W. Moriarty
1International Centre of Quantum and Molecule Structure, Shanghai University,
Shanghai, China 2Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley
National Laboratory, Berkeley, CA, USA
Nitroxide radicals are characterized by the long-lived spin-unpaired electronic ground
state and molecular character strongly sensitive to the chemical surroundings.
Combined with electron spin resonance (ESR) spectroscopy, these electronic features
have led to wide-spread application of nitroxide derivatives as spin labels used in
studying protein structure and dynamics.
Studies of structure and dynamics of proteins using site-directed spin labelling rely on
explicit modelling of spin label conformations. However, for the protein
crystallography refinement codes Nitroxides represent unusual ligands, with not well
defined or unknown structural parameters. That situation leads to less accurate or
even erroneous description of their structural information provided in PDB Database,
as for instance hydrogens can be added on radical O terminus, the N-O bond length
distance is not correct, as well as the stereochemistry around radical moiety.
In this work, we aim at refining proteins which contain a typical example from
nitroxide family – the MTN ligand by defining its ideal structural parameters based on
the quantum chemical calculations. The refinement results shows that the MTN ligand
parameters get improved by this procedure, at the same time retaining higher
agreement with experimental electron densities.
Reference
[1]. Michele Pavone, Malgorzata Biczysko, Nadia Rega, and Vincenzo Barone. J. Phys. Chem. B. 114,
11509–11514 (2010)
[2]. Alfonso Pedone, Malgorzata Biczysko, and Vincenzo Barone. ChemPhysChem. 11, 1812-1832
(2010).
[3]. Gunnar Jeschke. Progress in Nuclear Magnetic Resonance Spectroscopy 72, 42–60 (2013)
99
Structural properties of molecules with disulfide
bond: an accurate theoretical study
Hexu Ye, Malgorzata Biczysko
Department of Physics, and International Center of Quantum and Molecular
Structures, Shanghai University, Shanghai 200444, China
The covalent disulfide bond between the sulfur atoms is a structural element
important for biochemistry as well as astrochemistry. Although there is a large amount
of available data about disulfide bond molecules, much less information is available
for accurate gas-phase equilibrium structure. Therefore, we use hydrogen disulfide
(HSSH) as test model, which is the simplest molecule contain disulfide bond and high
level theoretical methods can be easily applied to it.
At first for purely quantum-chemical computations we employed the CCSD(T)
method, which is often referred to as the “gold standard of quantum chemistry”. To
reach higher accuracy, composite methods have been applied to HSSH. The so-called
composite schemes take into account simultaneously corrections for basis set effects,
core-valence correlation effects and eventually also higher excitations. Composite
schemes involving CCSD(T) computations can be exploited either at a gradient level
or a geometric-parameter level. While almost all studies about composite schemes
only contain molecules with first-row atoms (in addition to hydrogens) or one
second-row atom, the disulfide bond molecules with two second-row nucleus will be
first studied by the composite scheme. Then because of the available experimental
data for a set of isotopologues, semi-experimental (SE) method has been adopted to
obtain equilibrium geometries (reSE) from nonlinear least squares fit (NLSF) of
experimental rotational constants (B0) for the ground vibrational state corrected by
vibrational contributions (ΔBvib) from a quantum chemical anharmonic force field.
This methodology is considered one of the best approaches to obtain accurate
equilibrium structures for isolated molecules and the semi-experimental results can be
directly compared with equilibrium structures deriving from quantum chemical
calculations.
References:
[1] C. Puzzarini, J. Phys. Chem. A, 113, 14530 (2009).
[2] C. Puzzarini, Int. J. Quantum Chem, 116, 1513 (2016).
[3] E. Penocchio, M. Mendolicchio, N. Tasinato, V. Barone,
Can. J. Chem, 94, 12 (2016).
[4] M. Mendolicchio, E. Penocchio, D. Licari, N. Tasinato,
V. Barone, J. Chem. Theory Comput, 13, 3060 (2017).
100
Accurate determination of energies and molecular
structures for isolated small peptides
Chong Shu, Zhongming Jiang, Malgorzata Biczysko
International Center for Quantum and Molecular Structures, Shanghai University,
China
Among biomolecules building blocks amino acids and polypeptides represents the
highly flexible molecular systems with several possible structural arrangements. This
flexibility is related to the presence of single bonds allowing for conformational
freedom. Even for the isolated amino acids, many conformers are possible and several
of them can be observed in experiment. Properties of amino acids oligomers depend
on their supra-molecular structure, which can be additionally complicated by
combination of weak inter- and intra-molecular interactions, as for example hydrogen
bonding and dispersion. From just twenty canonical amino acids it is possible to
build very different molecular architectures showing specific functionalities, as
demonstrated by the number of already known protein structures.
Understanding and prediction of three-dimensional (3D) conformation, important for
detection of simplest amino-acids in the interstellar space, prebiotic molecules
evolution toward more complex species, polypeptides self-assembly or
structure-function relations in proteins, requires reliable theoretical support. Highly
accurate methodologies are applicable to small amino acids and polypeptides. These
results can be used to check accuracy of less expensive ones, which can be applied to
larger and more complex molecular systems. For the latter, the challenging aspects are
related not only due to the increasing system size but also the description of all types
of weak molecular interactions, and exploration of conformational space which are
needed for the correct description of the related three-dimensional structures.
Step-by-step strategy can start from comparison of dispersion-corrected DFT
approaches with highly accurate theoretical results of CCSD(T)/CBS quality and
state-of-the-art experimental laser ablation molecular beam Fourier transform
microwave (LA-MB-FTMW) spectroscopy results for amino acids and small
polypeptides.
101
Investigation of the hydrogen bonding in serine: a
computational spectroscopy study
Mingzhu Sheng, Malgorzata Biczysko
International Center for Quantum and Molecular Structures, Shanghai University,
China
A comprehensive analysis of the properties of amino acids oligomers and the detailed
characterization of their supra-molecular structure, orientation and dynamics is the
basic requirement for understanding the structure-function relationships, which
further allow designing specific macromolecular architectures with desired micro- and
macroscopic properties. However, it is currently not possible to predict
supramolecular behaviour from sequence alone because molecular organization
usually depends on the synergistic combination of specific and nonspecific
interactions, e.g., ionic, covalent, van der Waals, hydrogen bonding, etc. Among the
various types of investigations, spectroscopic techniques are the most powerful tools,
thus allowing the direct detection of different binding schemes via microwave (MW)
measurements or indirect analysis through ‘finger-print’ vibrational features in
infrared (IR), Raman, Resonance Raman, UV-vis or fluorescence spectra, also
including their chiral counterparts. In this respect, the most stable conformers of
serine represents an interesting case with a structure governed by three or two
different type hydrogen bond interactions, namely, O-H…N, O-H…O=C and
N-H…O-H, for which both microwave and IR spectra have been measured
experimentally. These conformers of serine represent an interesting test case for the
determination of improved spectroscopic parameters by means of composite schemes.
The present computational study aims at a more accurate determination of the
hydrogen-bond characteristics from which the various conformations depend on.
Moreover, highly accurate theoretical results of CCSD(T)/CBS quality and available
spectroscopic data stand as a reference for benchmarking of DFT approaches,
focusing on dispersion-corrected and double-hybrid DFT models.
102
Fragmental Approach to Electronic Excited States:
full ab initio description of solvatochromism of
Brooker’s merocyanine dye
Xingpin Li1,4, Xinsheng Jin2, Xiao He2,3, William J. Glover1, 3, 4
1NYU Shanghai, 1555 Century Avenue, Shanghai, 200122, China 2State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular
Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and
New Drug Development, East China Normal University, Shanghai, 200062, China 3NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai,
200062, China 4Department of Chemistry, New York University, New York, New York, 10003,
USA
Electronic excited states play an important role in a variety of systems including
radiation damage to biological molecules, acid-base indicators, dye molecules and
molecular switches. However, the computational cost of calculating excited states with
standard quantum chemical methods scales steeply with the number of atoms. To
address this problem, we have developed a fragmental approach to achieve linear
scaling (shown in Fig. 1) while retaining near quantitative accuracy with full-system
QM calculations.
Fig. 1: Comparison of the aggregate GPU time of MOED-CHCl3 between ES-MBE and full cluster
excitation energy calculations at the TD-ωB97X/6-31G* level using Terachem on one NVIDIA GTX
1080 Ti GPU.
We apply our method to study the solvatochromism of brooker’s merocyanine dye
(MOED) with 3 different solvents (water, methanol, and chloroform) at the
time-dependent density functional theory level. We show that expansion order of
ES-MBE of the excitation energy converges rapidly at two-body level with quantitative
accuracy compared to full QM calculation. Furthermore, ES-MBE reproduces relative
solvatochromic shifts with near quantitative accuracy compared to experiments.
103
Formation of Na(0) layers between graphene and
monolayer NaCl
Musen Li
Shanghai University
Nowadays, Wu’s group reported the unconventional Na2Cl and Na3Cl nanocrystals.
Many relevant problems arise from these findings: what stabilises these compounds
and what determines their stoichiometries? In Wu’s work, the most impressive fact is
that Na2Cl and Na3Cl growth under ambient pressure in undersaturated solutions of
sodium chloride. It shows the potential of Sodium Chloride used as the sodium-ion
batteries (NIB). However, it is necessary to reveal the reactions during the formation
of unconventional nanocrystal should.
In this poster, we suggest a possible formation routine of such unconventional
nanocrystal. The understanding of such reactions would arise the usage of NaxCl in
the area of NIB and the development of new 2D nanocrystal.
104
Map of campus: