crystal and molecular structures of 3-[1-(2-hydroxyethylamino)-ethylidene]-chroman-2,4-dione and...

Chemical Physics 297 (2004) 235–244

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Crystal and molecular structures of3-[1-(2-hydroxyethylamino)-ethylidene]-chroman-2,4-dione

and 2-methoxy-3-[1-(benzylamino)-ethylidene]-2,3-dihydro-2,4-dioxo-2k5-benzo[e][1,2]oxaphosphinane and DFT study

of intramolecular H-bonds of related compounds

Magdalena Małecka a, Sławomir J. Grabowski a,*, El _zbieta Budzisz b

a Department of Crystallography and Crystal Chemistry, University of Ł�od�z, Pomorska 149/153, 90-236 Ł�od�z, Polandb Department of Bioinorganic Chemistry, Faculty of Pharmacy, Medical University, Muszy�nskiego 1, 90-151 Ł�od�z, Poland

Received 22 July 2003; accepted 20 October 2003

Abstract

The crystal and molecular structures of 3-[1-(2-hydroxyethylamino)-ethylidene]-chroman-2,4-dione and 2-methoxy-3-[1-(ben-

zylamino)-ethylidene]-2,3-dihydro-2,4-dioxo-2k5-benzo[e][1,2]oxaphosphinane determined by single crystal X-ray diffraction are

presented. Inter- and intramolecular H-bonds for these structures are analyzed. Additionally DFT calculations at B3LYP/6-311+G*

level of theory are performed for similar model species. The results of calculations show that tautomeric forms with N–H � � �Ointramolecular H-bonds are more stable than tautomers with O–H � � �N H-bonds. The Bader theory is also used to characterize that

kind of interactions. Bond critical points are analyzed in terms of electron densities and their Laplacians.

� 2003 Elsevier B.V. All rights reserved.

Keywords: X-ray diffraction; Crystal and molecular structures; Intramolecular H-bonds; The Bader theory; Bond critical points

1. Introduction

Coumarin and chromone derivatives are of great in-

terest due to their biological properties [1], particularly

owing to their physiological [2], bacteriostatic [3] and

antitumor activity [4–6]. On the other hand the amino-

phosphonic acid derivatives have been identified as

biologically active compounds [7].We investigated the reaction of 2-methyl-4-oxo-

4H-chromene-3-carboxylic acid methyl ester (1) with

hydroxyethylamine and dimethyl 2-methyl-4-oxo-

4H-chromen-3-yl-phosphonate (2) with benzylamine

(Scheme 1).

The reactions products 3 and 4 exist in ketoenamine

form. This is in contrary to the iminoenol-type structure

* Corresponding author. Tel.: +42-635-57-37; fax: +048+42-679-04-

47.

E-mail address: [email protected] (S.J. Grabowski).

0301-0104/$ - see front matter � 2003 Elsevier B.V. All rights reserved.

doi:10.1016/j.chemphys.2003.10.029

for analog of 3 which was suggested by Strakov [8]. The

evidence that keto-enol equilibrium of 3 is shifted toward

its ketoenemine form is confirmed by the presence in 1H

NMR spectrum of the signal of N–H proton with the

chemical shift of 14 ppm. The cytotoxic effects and

alkylating activity of 3-[1-(2-hydroxyethylamino)-ethyli-

dene]-chroman-2,4-dione (3) and 2-methoxy-3-[1-(benzyl-

amino)-ethylidene]-2,3-dihydro-2,4-dioxo-2k5-benzo[e][1,2]oxaphosphinane (4) on the two HL-60 and NALM-6

leukaemia cell lines have been determined [9].

The aim of this paper is to study the crystal and

molecular structures of 3-[1-(2-hydroxyethylamino)-

ethylidene]-chroman-2,4-dione (3) and 2-methoxy-3-

[1-(benzylamino)-ethylidene]-2,3-dihydro-2,4-dioxo-2k5-benzo[e][1,2]oxaphosphinane (4) which will be named in

the further analyses as ChD and OxP, respectively. Theinteractions influencing arrangement of molecules in

crystals are described here. For the similar, model spe-

cies DFT calculations are performed to get the more

mail to: [email protected]

Scheme 1.

236 M. Małecka et al. / Chemical Physics 297 (2004) 235–244

precise insight into the nature of such interactions. The

�atoms in molecules� (AIM) theory of Bader is also ap-

plied here to characterize H-bond interactions [10].

Fig. 1. Molecular drawing of 3-[1-(2-hydroxyethylamino)-ethylidene]-

chroman-2,4-dione and 2-methoxy-3-[1-(benzylamino)-ethylidene]-2,

3-dihydro-2,4-dioxo-2k5-benzo[e][1,2]oxaphosphinane compounds.

Dis- placement ellipsoids are drawn at the 30% probability level. The

short contacts, possible H-bonds, are shown with dotted lines.

2. Results and discussion

2.1. Crystal and molecular structures

Fig. 1 presents the molecular structures of ChD and

OxP. Fig. 2 shows unit cell contests for both crystal

structures (crystallographic details are given in Table 1).The designations of atoms of Fig. 1 are the same as

those of Table 2 where selected bond lengths and angles

are presented. We see possible intramolecular H-bonds

indicated in Fig. 1 as dotted lines. There are N15–

H15 � � �O12, N15–H15 � � �O18 intramolecular contacts

for ChD and N13–H13 � � �O9 contact for OxP. Table 3

presents the intermolecular and intramolecular contacts

which may be classified as hydrogen bonds. We see thatonly the existence N15–H15 � � �O18 intramolecular H-

bond is problematic since the geometrical criteria for H-

bonding interaction [11] are hardly satisfied; H � � �Odistance is slightly less than the sum of corresponding

van der Waals radii and the N–H � � �O angle is far from

linearity )103�. For the remaining intramolecular H-

bonds, the short H � � �O contacts, 1.84 and 1.87 �A for

ChD and OxP, respectively suggest that they are of amedium strength.

The more detailed insight into the molecular struc-

tures of ChD and OxP shows that N15–H15 � � �O12 and

N13–H13 � � �O9 may be classified as resonance assisted

hydrogen bonds (RAHBs). Such RAHBs have been

described earlier [12,13] for homonuclear O–H � � �O in-

teractions and later for heteronuclear N–H � � �ORAHBs [14]. For these systems there is the equalization

of the corresponding covalent bonds within the ring

created owing to the intramolecular H-bond formation.It may be explained as an effect of the p-electron delo-

calization within the system. For example, for the H15–

N15–C13@C9–C8@O12 ring of ChD crystal structure,

we should observe the equalization of C13@C9 and C9–

C8 bond lengths. Table 2 shows that they are practically

equal, even C13–C9 bond (should be double) is slightly

longer than C9–C8 (should be single). For the OxP

crystal structure the equalization is not very evident butit is observable. We should also observe for N–H � � �ORAHBs analyzed here the elongation of C@O bonds

and the shortening of C–N bonds within the ring; this

effect is not clear for ChD and OxP crystal structures.

Such effect is clear for homonuclear O–H � � �O RAHBs

[15] for which there is the equalization of C–O and C@O

bonds. Table 2 shows that for ChD and OxP C@O

bonds are of the similar length, 1.253 and 1.258 �A, re-spectively. They are longer than the C@O bonds not

Fig. 2. Unit cell contests of 3-[1-(2-hydroxyethylamino)-ethylidene]-

chroman-2,4-dione and 2-methoxy-3-[1-(benzylamino)-ethylidene]-2,3-

dihydro-2,4-dioxo-2k5-benzo[e][1,2]oxaphosphinane compounds.

M. Małecka et al. / Chemical Physics 297 (2004) 235–244 237

involved in H-bond interaction [16]. The corresponding

C–N bonds are equal 1.308 and 1.320 �A showing that

for ChD the p-electron delocalization effect is stronger.

It has been pointed out that for RAHBs the greater isthe p-electron delocalization thus the greater is the bond

lengths equalization and the stronger is H-bond [13,15].

The results presented in Tables 2 and 3 suggest that the

intramolecular H-bond for the ChD structure is slightly

stronger than the corresponding H-bond of OxP. The

similar N–H � � �O RAHBs existing for crystal structures

of chromones have been also studied recently [17].

Table 3 also presents the intermolecular H-bonds,

mainly weak C–H � � �O interactions, only for ChD there

is the stronger intermolecular O–H � � �O hydrogen

bond. Fig. 3 presents the O–H � � �O motifs existing in

this crystal structure.

2.2. DFT calculations

To explain the interactions existing for the ChD and

OxP crystal structures, mainly intramolecular RAHBs

described in the previous section, the calculations on

model systems similar to ChD and OxP molecules have

been performed here. The optimizations have beenperformed at the B3LYP/6-311+G* level of theory and

the wave functions for optimized species were further

applied to find critical points. Figs. 4 and 5 show the

molecular graphs of the species analyzed here.

The following model moieties have been considered:

3-aminomethylene-pyran-2,4-dione (designated later as

A1) as the system similar to ChD molecule and con-

taining the intramolecular N–H � � �O hydrogen bond;the tautomeric form of A1 containing the intramolecular

O–H � � �N H-bond – 4-hydroxy-3-iminomethyl-pyran-2-

one (designated as A2); the molecular analog of OxP

molecule – 3-aminomethylene-2-hydroxy-2-oxo-2,3-

dihydro-2k5-[1,2]oxaphosphinin-4-one (B1) with N–

H � � �O intramolecular H-bond and its tautomeric form

containing O–H � � �N bond – 3-iminomethyl-2-oxo-2H-

2k5-[1,2]oxaphosphinine-2,4-diol (B2). Additionally, forcomparison, the molecules containing homonuclear O–

H � � �O bonds instead of N–H � � �O or O–H � � �N ones

were optimized; 3-hydroxymethylene-pyran-2,4-dione

(designated as C1 and being the analog of A1), 4-hy-

droxy-2-oxo-2H-pyran-3-carbaldehyde (C2 as the ana-

log of A2), 2-hydroxy-3-hydroxymethylene-2-oxo-2,

3-dihydro-2k5-[1,2]oxaphosphinin-4-one (D1 – the ana-

log of B1) and 2,4-dihydroxy-2-oxo-2H-2k5-[1,2]oxa-phosphinine-3-carbaldehyde (D2 as the analog of B2).

For all mentioned species the stable systems were found

after optimizations since no imaginary frequencies were

detected.

It was described previously that for the crystal

structures of chromone derivatives the tautomeric forms

with N–H � � �O and O–H � � �N intramolecular H-bonds

are observable but the later are not as common as theprevious ones [17]. The high level ab initio calculations

on simple molecular analogs of chromones show that

the systems containing N–H � � �O bonds are energeti-

cally more stable than corresponding tautomers con-

taining O–H � � �N bonds [17]. For the model systems

analyzed here the transition states for the proton

transfer N–H � � �O () N � � �H–O and O–H � � �O ()O � � �H–O reactions were found. For A1 and A2 tau-tomers there is the transition state designated later as

AT, for B1 and B2–BT. For C1 and C2 tautomers the

transition state is designated as CT and there is DT

Table 1

Crystallographic data and structure refinement

ChD OxP

Formula C13H13NO4 C18H18NO4P

M 247.24 343.30

Crystal system Monoclinic Triclinic

Space group P21=n P�1a (�A) 7.123(3) 10.929(2)

b (�A) 9.680(9) 13.403(3)

c (�A) 16.678(3) 6.113(3)

a (�) 96.97(3)

b (�) 95.27(2) 98.64(3)

c (�) 70.28(2)

V (�A3) 1145.0(1) 830.9(4)

Z 4 2

Dx (g cm�3) 1.434 1.372

l (mm�1) 0.896 1.661

T (K) 293(2) 293(2)

k (�A) 1.54178 1.54178

Index ranges 06 h6 8; 06 k6 11; �196 l6 19 �76 h6 13; �156 k6 15; �76 l6 7

No. of data collected 2141 3035

No. of unique data 1970 2869

Rint 0.0226 0.0237

No. of I > 2rðIÞ data 990 1584

No. of parameters 166 220

R1 (all data)a 0.0865 0.1058

wR2 (all data)b 0.1178c 0.1527d

R1 [I > 2rðIÞ]a 0.0430 0.0561

wR2 [I > 2rðIÞ]b 0.1131c 0.1451d

Dqmin (e �A�3) )0.157 )0.328Dqmax (e �A�3) 0.177 0.275

aR1 ¼P

ðjFo � FcjÞ=P

jFoj.bwR2 ¼ ½

PwðjFo � FcjÞ2=

PjFoj2�1=2.

cw ¼ expð3:0 sin2 h=kÞ=½r2ðF 2o Þ þ ð0:0593PÞ2�.

dw ¼ 1=½r2ðF 2o Þ þ ð0:0886P Þ2� where P ¼ ½ðF 2

o Þ þ 2ðF 2c Þ�=3.


transition state for D1 and D2 tautomeric forms. For

optimized molecular structures of AT, BT, CT and DT

one imaginary point was detected showing that they are

really transition states. The molecular graphs of them

are also present at Figs. 4 and 5.

Table 4 presents the energies of the described species,

the differences in energies between tautomeric forms and

the activation energies for the proton transfer reactions.We see that for systems containing N–H � � �O or O–

H � � �N bonds those are more stable which contain N–

H � � �O H-bonds that is keto forms. It is in agreement

with the previous investigations [17] and it explains why

such tautomeric forms exist for ChD and OxP crystal

structures. For the systems with O–H � � �O bonds the

more stable are enol forms than keto ones.

Table 5 shows the geometrical parameters of intra-molecular H-bonds. We see that the H � � �N intramo-

lecular contacts are shorter than H � � �O contacts for

corresponding tautomeric forms. The H � � �N and

H � � �O contacts are shortest for transition states and H-

bridges are closest to linearity. These results are in line

with the previous investigations [17] where for model

systems it was found that O–H � � �N bonds are stronger

than N–H � � �O bonds for corresponding tautomeric

forms; however the tautomeric forms with O–H � � �Nbonds are energetically less stable than those forms

which contain N–H � � �O bonds. The clear explanation

of such a situation was given recently by Gilli et al. [18]

in the study on N–H � � �O/O–H � � �N tautomeric forms.

The authors explain that the less stable tautomeric form

contains the stronger hydrogen bond since it is closer tothe transition state and it more participates in TS

structure. Such an explanation is in line with the Ham-

mond Postulate [19]. And there is the similar explana-

tion that the more stable tautomer contains weaker

H-bond because it is farther from the transition state.

Table 6 shows bond lengths of the ring created owing

to the intramolecular H-bond formation. It is well

known that for the resonance assisted H-bonds the H-bond strength correlates with the equalization of bonds

inside such a ring [13,14]. For pairs of tautomers with

N–H � � �O and O–H � � �N interactions such equalization

is comparable only for CC bonds; we see that the

equalization of C@C and C–C bonds is greater for

systems containing stronger O–H � � �N bonds. For spe-

cies with O–H � � �O intramolecular interactions the

Table 2

(a) Selected bond lengths (�A) and angles (�) (ChD)

O1–C10 1.376(3) C8–C9 1.430(3)

O1–C2 1.377(3) C9–C13 1.437(3)

C2–C7 1.381(3) C9–C10 1.437(3)

C2–C3 1.392(3) C10–O11 1.219(3)

C3–C4 1.360(4) C13–N15 1.308(3)

C4–C5 1.385(4) C13–C14 1.493(3)

C5–C6 1.374(3) N15–C16 1.460(3)

C6–C7 1.390(3) C16–C17 1.514(3)

C7–C8 1.467(3) C17–O18 1.409(3)

C8–O12 1.253(3)

C10–O1–C2 122.5(2) C9–C8–C7 117.9(2)

O1–C2–C7 121.2(2) C8–C9–C13 120.7(2)

O1–C2–C3 116.8(2) C8–C9–C10 119.7(2)

C7–C2–C3 122.0(3) C13–C9–C10 119.5(2)

C4–C3–C2 118.6(3) O11–C10–O1 112.8(2)

C3–C4–C5 120.9(3) O11–C10–C9 128.0(2)

C6–C5–C4 119.9(3) O1–C10–C9 119.2(2)

C5–C6–C7 120.7(3) N15–C13–C9 118.6(2)

C2–C7–C6 117.8(2) N15–C13–C14 117.7(2)

C2–C7–C8 119.5(2) C9–C13–C14 123.7(2)

C6–C7–C8 122.7(2) C13–N15–C16 126.9(2)

O12–C8–C9 123.7(2) N15–C16–C17 109.4(2)

O12–C8–C7 118.4(2) O18–C17–C16 112.3(2)

(b) Selected bond lengths (�A) and angles (�) (OxP)

P1–O100 1.464(2) C9–C10 1.445(5)

P1–O200 1.573(2) C10–C11 1.413(5)

P1–O2 1.601(3) C11–N13 1.320(4)

P1–C10 1.739(3) C11–C12 1.500(5)

O2–C3 1.401(4) N13–C14 1.469(4)

C3–C8 1.382(5) C14–C15 1.499(5)

C3–C4 1.385(5) C15–C20 1.369(5)

C4–C5 1.383(6) C15–C16 1.372(5)

C5–C6 1.370(5) C16–C17 1.383(6)

C6–C7 1.379(5) C17–C18 1.374(6)

C7–C8 1.384(5) C18–C19 1.345(7)

C8–C9 1.494(5) C19–C20 1.388(6)

C9–O9 1.258(4) O200–C201 1.450(4)

O100–P1–O200 114.7(2) C10–C9–C8 119.9(3)

O100–P1–O2 107.6(2) C11–C10–C9 120.6(3)

O200–P1–O2 104.3(2) C11–C10–P1 122.8(3)

O100–P1–C10 120.7(2) C9–C10–P1 116.5(3)

O200–P1–C10 103.4(2) N13–C11–C10 120.5(3)

O2–P1–C10 104.5(2) N13–C11–C12 116.2(3)

C3–O2–P1 118.9(2) C10–C11–C12 123.2(3)

C8–C3–C4 122.2(4) C11–N13–C14 127.0(3)

C4–C3–O2 116.9(3) N13–C14–C15 110.2(3)

C5–C4–C3 118.5(4) C20–C15–C16 118.4(4)

C6–C5–C4 120.3(4) C20–C15–C14 120.7(4)

C5–C6–C7 120.3(4) C16–C15–C14 120.8(4)

C6–C7–C8 120.9(4) C15–C16–C17 120.7(4)

C3–C8–C7 117.7(3) C18–C17–C16 120.0(5)

C3–C8–C9 122.2(3) C19–C18–C17 119.7(5)

C7–C8–C9 119.9(3) C18–C19–C20 120.5(5)

O9–C9–C10 122.9(3) C15–C20–C19 120.7(4)

O9–C9–C8 117.2(3) C201–O200–P1 119.9(2)


stronger H-bonds correspond to more stable enol tau-

tomeric forms for which we observe shorter H � � �Ocontacts (Table 5) and greater equalization of CC and

CO bonds (Table 6).

The presented above geometrical results are in

agreement with the topological parameters (Table 7). It

is known that the electron density at the bond criti-

cal point corresponding to H � � �A contact within

Table 3

D–H H � � �A D � � �A D–H � � �A

(a) Hydrogen bonding geometry (�A, �) (ChD)

*N15–H15 � � �O12 0.86 1.84 2.561(3) 140(3)

*N15–H15 � � �O18 0.86 2.51 2.844(3) 103(2)

**O18–H18 � � �O11a 0.82 2.03 2.838(3) 167(2)

Non-conventional

*C14–H14B � � �O11 0.96 2.29 2.754(3) 109(2)

**C16–H16A � � �O18b 0.97 2.55 3.507(3) 166(2)

**C17–H17A � � �O12b 0.97 2.51 3.341(3) 143(3)

(b) Hydrogen bonding geometry (�A, �) (OxP)

*N13–H13 � � �O9 0.86 1.87 2.576(4) 139(3)

Non-conventional

*C12–H12B � � �O100 0.96 2.28 3.100(5) 143(2)

**C7–H7 � � �O9c 0.93 2.51 3.305(5) 143(2)

**C14–H14A � � �O100d 0.97 2.56 3.515(3) 167(2)

*Intramolecular H-bonds. **Intermolecular H-bond.a 1=2þ x; 3=2� y; 1=2þ z.b 1=2� x; 1=2þ y; 1=2� z.c 2� x;�y; 2� z.d 1� x; 1� y; 2� z.

Fig. 3. Unit cell contest of 3-[1-(2-hydroxyethylamino)-ethylidene]-

chroman-2,4-dione; intermolecular O–H � � �O H-bonds are shown.


D–H � � �A H-bond (qH��A) correlates with its strength

[20,21]. Table 7 shows that qH��NðOÞ are greatest for

transition states, next for H � � �N contacts within O–

H � � �N bonds and are smallest for corresponding BCPs

within N–H � � �O bonds. There are similar observations

for Laplacians of these electron densities. For transitionstates the values of Laplacians for H � � �N and H � � �Ocontacts are negative indicating partly their covalent

nature. The partly covalent nature of contacts for very

strong RAHBs was reported by Gilli and co-workers

[13] and it was also supported by AIM theory in later

studies [17,18].

These findings show that the topological and geo-

metrical parameters may be applied as measures of thestrength of intramolecular hydrogen bonding, especially

for homogeneous samples. Fig. 6 shows the correlation

between H � � �A (A¼N, O) distance and the electron

density at H � � �A BCP. The second order correlation

coefficient is equal to 0.994 for all contacts: H � � �O and

H � � �N, for stable structures and for transition states.

However if we take into account the homogeneous

sample, for example only H � � �O contacts without those

of transition states thus the correlation is excellent and

linear. The linear correlation coefficient amounts to

0.999.

3. Summary

Two crystal structures with intramolecular N–H � � �OH-bonds are discussed in terms of X-ray crystal struc-

ture determinations. Additionally DFT calculations are

performed for simpler than those of solid state but very

similar model species. The results show that the systemswith N–H � � �O bonds are energetically more stable than

those containing O–H � � �N bonds in spite of the fact

that O–H � � �N bonds are stronger than N–H � � �O ones.

It is in line with the study of Gilli and co-workers [18] as

well as with the Hammond postulate [19]. The findings

based on the Bader theory support the experimental and

DFT results on the nature of intramolecular interac-

tions. It is stated that the topological parameters such asthe electron density at HA BCP are good measures for

intramolecular H-bond strength.

4. Experimental

4.1. Synthesis

2-Methyl-4-oxo-4H-chromene-3-carboxylic acid me-

thyl ester (1) was prepared according to the proce-

Fig. 4. The molecular graphs of the model systems with N–H � � �O and O–H � � �N intramolecular H-bonds. Small circles correspond to critical points

(red – BCPs; yellow – RCPs) while the big ones to attractors (grey – hydrogen atoms, red – oxygen atoms, black – carbon atoms, blue – nitrogen

atoms, dark red – phosphorus atoms). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of

this article.)


dure described earlier [22], similarly dimethyl 2-methyl-

4-oxo-4H-chromen-3-yl-phosphonate (2) [23] and 2-

m e t h o x y - 3-[1-(benzylamino)ethylidene]-2,3-dihydro-2,

4-dioxo-2k5-benzo[e][1,2]oxaphosphinane (4) [24].

2-Hydroxyethylamine or benzylamine (20 mmol) in

methanol (0.5 ml) was added at room temperature to a

solution of 2-methyl-4-oxo-4H-chromene-3-carboxylic

Fig. 5. The molecular graphs of the modelled systems with O–H � � �O intramo

yellow – RCPs) while the big ones to attractors (grey – hydrogen atoms, red

(For interpretation of the references to colour in this figure legend, the read

acid methyl ester (1) or dimethyl 2-methyl-4-oxo-4H-

chromen-3-yl-phosphonate (2) (20 mmol) in methanol (5

ml). The solid crude product (3 or 4 – ChD or OxP),

which precipitated after several minutes, was filtered off,

dried, and crystallized from methanol.

Yield: 3.75 g (76%) m.p. 183–185 �C (3); 6.03 g (88%)

m.p. 130–132 �C (4).

lecular H-bonds. Small circles correspond to critical points (red – BCPs;

– oxygen atoms, black – carbon atoms, dark red – phosphorus atoms).

er is referred to the web version of this article.)

Table 4

Energies (in hartrees) of the model systems optimized at B3LYP/6-

311+G* level of theory and analyzed here, the energies of transition

states are also given and the differences in energies (in kcal/mol)

Molecule Energy Energy difference

A1 )512.2131524A2 )512.1985115 9.19a

AT )512.1957647 10.91/1.72b

B1 )891.3689925B2 )891.3562047 8.02a

BT )891.3538669 9.49/1.47b

C1 )532.076888C2 )532.0810198 2.59a

CT )532.0724721 2.77/5.36b

D1 )911.233659D2 )911.2405657 4.33a

DT )911.2330798 0.36/4.70b

aDifferences in energies between both tautomeric forms.bActivation energies for the proton transfer reactions; from keto

form to enol form and reverse.


4.2. X-ray measurements

Transparent, colorless crystals of both compounds

(ChD and OxP) suitable for single-X-ray diffraction

were obtained after the recrystallization from methanol

and grown by slow evaporation of solutions at room

Table 5

The geometrical parameters (�A, �) of intramolecular H-bonds of the model

Molecule D–H � � �A D–H H

A1 N–H � � �O 1.019 1

A2 O–H � � �N 1.012 1

AT N � � �H � � �O 1.330 1

B1 N–H � � �O 1.016 1

B2 O–H � � �N 1.013 1

BT N � � �H � � �O 1.338 1

C1 O–H � � �O 1.004 1

C2 O–H � � �O 0.996 1

CT O � � �H � � �O 1.192 1

D1 O–H � � �O 0.997 1

D2 O–H � � �O 0.996 1

DT O � � �H � � �O 1.204 1

Table 6

Geometrical parameters for modelled systems within rings of intramolecular

Molecule C@C C–C

A1 1.387 1.461

A2 1.398 1.447

AT 1.428 1.418

B1 1.382 1.464

B2 1.394 1.446

BT 1.415 1.426

C1 1.378 1.462

C2 1.400 1.448

CT 1.406 1.433

D1 1.373 1.468

D2 1.398 1.445

DT 1.434 1.403

temperature. Single crystals were mounted on glass fi-

bers. Data were collected at room temperature on a

Rigaku AFC5S diffractometer [25] using graphite

monochromated Cu Ka radiation. The unit cell dimen-

sions were determined from a least-squares fit to settingangles of set reflections 25 for both ChD and OxP. Three

standard reflections monitored after collection every 150

reflections showed no significant decays. All data were

corrected for Lorentz and polarization factors. Analyt-

ical [26] absorption corrections were applied.

The methods of solving and refinement of the struc-

tures were the same. The structures were solved by direct

methods using SHELXS86 [27] and refined by full-ma-trix least-squares method on F2 using SHELXL97 [28].

After the refinement with isotropic displacement pa-

rameters, refinement was continued with anisotropic

displacement parameters for all non-hydrogen atoms.

Positions of hydrogen atoms were found on difference

Fourier map and were treated as riding atoms with O–H

distances of 0.82 �A, N–H distances of 0.86 �A and C–H

distances in the range 0.93–0.98 �A. In the final step ofrefinement procedure, all non-hydrogen atoms were re-

fined with anisotropic thermal displacement parameters.

A summary of crystallographic relevant data is given in

Table 1.

systems investigated here

� � �A D. . .A D–H � � �A angle

.913 2.672 128.8

.667 2.570 146.2

.171 2.421 150.8

.954 2.695 127.4

.652 2.560 146.7

.159 2.416 150.7

.668 2.561 145.7

.709 2.592 145.5

.249 2.384 155.2

.704 2.581 144.4

.692 2.580 146.2

.232 2.380 155.2

H-bonds (in �A)

C–N(O) C@N(O)

1.326 1.242

1.317 1.289

1.300 1.291

1.332 1.240

1.320 1.291

1.295 1.302

1.303 1.246

1.318 1.234

1.272 1.277

1.310 1.244

1.321 1.236

1.280 1.273

Table 7

The topological parameters (in a.u.) of the modelled systems investigated here

Molecule D–H � � �A qDH r2qDH qH��A r2qH��A

A1 N–H � � �O 0.3237 )1.708 0.0303 0.1172

A2 O–H � � �N 0.3020 )1.902 0.0581 0.1233

AT N � � �H � � �O 0.1336 )0.0364 0.1862 )0.3569B1 N–H � � �O 0.3266 )1.716 0.0276 0.1088

B2 O–H � � �N 0.3007 )1.884 0.0600 0.1242

BT N � � �H � � �O 0.1306 )0.0208 0.1921 )0.4174C1 O–H � � �O 0.3106 )2.019 0.0525 0.1518

C2 O–H � � �O 0.3194 )2.118 0.0476 0.1454

CT O � � �H � � �O 0.1754 )0.2548 0.1505 )0.0547D1 O–H � � �O 0.3182 )2.104 0.0480 0.1474

D2 O–H � � �O 0.3186 )2.107 0.0494 0.1493

DT O � � �H � � �O 0.1700 )0.2022 0.1573 )0.0990

Fig. 6. The relationship between the electron density at H � � �A BCP

and H � � �A distance, the circles correspond to H � � �O contacts and the

squares to H � � �N ones; empty circles and squares are those of tran-

sition states.


The molecular geometry was calculated by

PARST97 [29] and PLATON [30]. Selected bond dis-tances and angles of ChD and OxP are summarized in

Table 2. The drawings were made by PLATON. Fur-

ther experimental details, coordinates and displacement

parameters have been deposited at the Cambridge

Crystallographic Data Centre; CCDC 209345 and

CCDC 209344 reference numbers for ChD and OxP,

respectively.

4.3. Computational details

The calculations have been performed using Gaussian

98 set of codes [31]. The full DFT [32] geometry opti-

mizations for model species described earlier in the text

have been done, using the B3LYPmethod which consists

of Becke�s three parameter hybrid exchange functional

[33] plus the non-local correlation functional of Lee et al.

[34]. For proper treatment of hydrogen bonding, we

chose the 6-311+G* basis set as a reasonable compr-

omize between size and reliability. The transitions states

of the proton transfer reactions were identified by the

QST2 method and further checked with the use of QST3

method [35].

The B3LYP/6-311+G* wave functions were used forAIM2000 program [36] which allows to apply the Bader

theory [10]. Thus using AIM2000 program bond critical

points (BCPs) and ring critical points (RCPs) were

found. Their characteristics were analyzed in terms of

electron densities and their Laplacians.

Acknowledgements

This work was financially supported by the Univer-

sity of Ł�od�z (Grant No. 505=675 2003). The authors

wish to acknowledge Academic Computer center Cyfr-

onet AGH Krak�ow for computational facilities. Finan-

cial support from Medical University of Ł�od�z (Grant

No. 502-13-755 to E. Budzisz) is gratefully acknowl-edged. We thank Mrs. Agnieszka Zdolska for skilful

experimental assistance.

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crystal and molecular structures of 3-[1-(2-hydroxyethylamino)-ethylidene]-chroman-2,4-dione and...

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