Conformational analysis of some substituted silatranyl-carboxylic acids produced by computational study and NMR spectroscopy

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MOLECULAR ELSEVIER

STRUCTURE

Journal of Molecular Structure 372 (1995)249-256

Conformational analysis of some substituted silatranyl-carboxylic acids produced by computational study and NMR spectroscopy Xiaodong Zhang a, Shizen Mao a, Lianfang Shen a'*, Chaohui Ye a, Renxi Zhengrong L u b, G.A. Webb c

Z h u o b,

aLaboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan blstitute of Physics, the Ch#1ese Academy of Sciences, P.O. Box 71010, Wuhan 430071, China bDepartment of Chemistry, Wuhan UniversiO,, Wuhan 430072, China CDepartment of Chemistry, University of Surrey, Guildford, G U2 5XH, UK

Received 31 January 1995; accepted 8 June 1995

Abstract

The structures of four silatrane compounds, silatranyl-carboxylic acid and its derivatives (I, II, III, IV), are studied with molecular mechanics and NMR methods. The geometrical conformations of the molecules are calculated using full geometry optimization methods with MM2 and CNDO/2. The conformations obtained are in agreement with results in the literature and with our X-ray and NMR experiments. However, there are some differences between the solid state, gas phase, and solution structures. The influence of the substituents (-COOH, -CH 3, - C H = C H 2 , -CH3) is discussed. It has been found that substitution by the carboxyl group in the silatrane framework plays a more important role in influencing the transannular structure than does substitution in the equatorial position. The calculated and experimental results are presented and discussed in detail.

I. Introduction

Silat.ranes, silicon-containing organic compounds, have been reported to show some biological activities, and have received much attention for their important and special S i - N transannular structures in recent years. Many kinds of silatrane compounds have been synthesized and studied by Molecular Orbital theory, X-ray diffraction (XRD), electron diffraction, N M R spectroscopy, etc. [ I - 17]. In these silatrane compounds, the central silicon is bonded to a nitrogen through three oxo bridges * Corresponding author.

and via a dative bond to the nitrogen lone pair electrons. Because the ethoxy links are flexible and the energy cost for constraining the S i - N bond length is modest [14], the framework of the atrane is flexible, and the conformation and S i - N bond character seem to be special in various situations. Most studies are based on silatrane derivatives with axial and equatorial substitutions. Few studies are devoted to the silatranes with non-equatorial substitutions in the atrane framework. The silatrane compounds I, lI, III and IV, substituted silatranyl-4-carboxylic acids (Fig. 1), have been synthesized [1]. The model for these compounds is substituted with a carboxyl group

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Xiaodong Zhang et al./Journal of Molecular Structure 372 (1995) 249-256

250

°~c(

°5

c4

,c,o:

I

R 1c7, c8) I

R'=H

R=-CH3

II

Ul

R'=H

R=-CH=CH2

IV R'=-CH3

R'=-CH3

R=-CH=CH2

V

R'=H

R=H

Vl

R=H

R'=-CH3

R=-CH3

Fig. 1. The chemical structure of silatrane-4-carboxylic acids (compounds 1, I1, II1, IV are synthesized ones, V and VI are model compounds).

in the non-equatorial position of the atrane framework. The crystal structure of l-vinyl-3methylsilatranyl-4-carboxylic acid (IV) was determined by X-ray diffraction [1], but the geometrical conformations of compounds I, II and III have not been previously determined. This paper reports the geometrical conformations of the four substituted silatranes studied with MM2 moleculap mechanics and CNDO/2 semiempirical MO methods [19]. The effects of axial, equatorial, and non-equatorial substitutions were studied by means of MO calculations and N M R results. The theoretical results are found to be consistent with the experimental observations.

2. Methods

The MM2(87) and modified CNDO/2 programs were used to perform all of the calculations reported in the present studies. The calculations were carried out on an AST Premium 486DX computer. During the geometry optimization calculations, no special constraints were imposed on the structures. The initial geometrical conformation model was sketched using the standard bond lengths and bond angles employed with the ALCHEMY program (Tripos Associates, Inc.). Then the MM2 method

was used to make a primitive geometry optimization. The conformation obtained was used as the original input structure for further optimization with the CNDO/2 method. The general chemical structure of the four silatranes is given in Fig. 1. Compounds I, II, III and IV are the synthesized ones, while V, VI are model compounds that are introduced for comparison purposes only. The JH, 13C and 29Si N M R chemical shifts of I, II, III and IV have been reported in Ref. [1]. In order to investigate the geometric conformation of the silatranes, the proton N M R parameters are listed in detail. These are obtained by means of assistance from spectrum simulation performed by the PANIC [17] program. The experimental and simulated IH N M R spectra of compound I are presented in Fig. 2 and the corresponding IH N M R parameters for compounds I, II, III and IV are reported in Table 1.

3. Results and discussion

Since MM2 molecular mechanics theory does not consider the existence of a Si-N dative bond, the calculated geometrical parameters of the ring structure show comparable deviation from the experimental results. However, the substituted groups' positions are predicted well with MM2, while the CNDO/2 calculations present good structural results on the frame conformation (Table 2). Based upon these reasons, both MM2 and CNDO/2 are used in combination to estimate the geometrical conformations. From Table 2, it is found that the calculated conformation results are in agreement with the X R D experimental data. The calculated conformational parameters of compounds I, II, III, and IV are listed in Table 3. For compound IV, some calculated and X R D conformational parameters are listed in Table 2. Obviously, the transannular structure of IV is not well predicted by the MM2 calculations, but the geometric positions for the substituents (-COOH, -CH3, - C H = C H 2 ) seem to be comparable with the X R D results. It is known, that, in the gas phase, the Si-N bond length for silatranes is longer than that in

251

Xiaodong Zhang et al./Journal of Molecular Structure 372 (1995) 249-256

'

'

'

'

31S

'

' PPM

'

'

310

'

'

'

'

Fig. 2. The mH 400M NMR spectrum (bottom) and its simulated spectrum (top) of compound I (the coupling constant unit in Hz) ABC: 6 = 1450, 1509, 1521 Jab = --10.0, Jac = 8.0, Jbc = 8.0;ABCDI: 6 = 1068, 1150, 1430, 1455J,b = -12.0, Jac = 7.0, Jad = -12.0, J~ = 0, Jbd = 3.5, Jca = -12.0; ABCD2:/5 = 1113, 1238. 1446, 1479 Jab = --12.0, Jae = 7.0, Jad = --12.0 Jbc = 0, Jt~ = 4.0, J~ = -12.0. the solid phase, for 1-methyl-silatrane, the difference is a b o u t 0.28 ,~ [2]. Because all o f the c a l c u l a t i o n s r e p o r t e d here are b a s e d on the m o d e l o f a single m o l e c u l e in a v a c u u m , the e s t i m a t e d results are c o m p a r a b l e with a m o l e c u l e in the gas phase. Thus, using the value o f 0.28 ,~ as c o m p e n sation, o r a d j u s t m e n t , we can derive the S i - N b o n d length o f IV to be a b o u t 2.18 ,~ in the solid phase.

This value is in g o o d a g r e e m e n t with the X - r a y result (2.169 A). Therefore, the c o m b i n e d M M 2 a n d C N D O / 2 c a l c u l a t i o n m e t h o d is suitable for the e s t i m a t i o n o f the silatrane g e o m e t r y conformation. T h e c o n f o r m a t i o n a l p a r a m e t e r s o f the related silatranes are listed in T a b l e 3, the perspective a n d p r o j e c t i o n views o f the p r e d i c t e d silatranes

Xiaodong Zhang et al./Journal of Molecular Structure 372 (1995) 249-256

252

Table 1 I H NMR parameters of compounds 1, il, III, IV Parameter a

I

CH3(C10) b CH3(C7) CH(C7) 3j CH2(C8)

-

_

3j

_

H(C2) 3j NCH2

? _

2J(OCH2CH2) 3J(OCH2CH2)

1.19 -0.35

3j H(CI)

OCH2

II

3.78

2.67, 2.78, 3.60, 3.69, -12.5 7, 0,

2.87 3.09 3.62 3.79 12.5

III

IV

-

-

1.21 5.74 14, 20 5.49 5.53 5 3.86

3.85 10, 6 3.14 10 3.11, 2.7-2.8 m 3.59, 3.69

5.74 5.49 5.55 3.89 10, 6 3.23 10 2.79 m, 3.17

? 2.73, 2.91 2.84, 3.14 3.6-3.9 m

-12.5 7, 0, 12.5

3.64, 3.75

-12.5 7, 0, 12.5

-12.5 7, 0, 12.5

a Chemical shift in p.p.m, and coupling constant in Hz. b The atoms numbering is shown in Fig. 1. a r e p l o t t e d i n Fig. 3. O b v i o u s l y , t h e c o m p o u n d s a r e s i m i l a r in t h e i r g e o m e t r i c a l c o n f o r m a t i o n s . Nevertheless, they are characterized by different s u b s t i t u t i o n effects. S o m e d i f f e r e n c e s e x i s t a l s o between the XRD, theoretical calculation, and NMR r e s u l t s , i.e. t h e m o l e c u l a r c o n f o r m a t i o n s a r e d i f f e r e n t in t h e s o l i d s t a t e , g a s p h a s e , a n d in solution.

3.1. Influence of non-equatorial substitution in the framework The simple silatrane skeleton has been found to h a v e a p p r o x i m a t e C3 s y m m e t r y i n t h e s o l i d s t a t e . Because of the flexibility of the atrane framework, the conformation could be varied easily upon substitution. For the silatranes I-IV, a carboxyl

Table 2 The CNDO/2, MM2, MM2+CNDO/2 calculated geometrical parameters and XD result of IV a Bond angle

CNDO/2

MM2

MM2+CNDO/2

X-ray b

O5-C9-C2 C1-C2-C9 N-C2-C9 O4-C9-C2 O4-C9-O5 O2-Si-C7 O3-Si-C7 N-Si-C7 Si-C7-C8 O 1- S i - C 7 C2-CI-CI0 O1-CI-CI0 N -Si-C7-C8 Si-N

118.7 109.9 119.7 124.9 109.2 109.5 105.2 177.4 125.3 107.2 113.1 111.0 173.9 2.492

110.8 112.8 110.1 127.1 122.6 107.5 106.2 178.3 123.4 107.1 111.6 105.5 48.1 2.958

105.6 117.3 102.9 121.4 112.1 109.5 109.5 177.7 126.8 106.9 113.4 105.2 21.54 2.479

110.9 112.8 112.1 124.9 124.5 96.2 96.2 178.4 128.3 96.9 111.9 109.4 169.7 2.169

a The atom number is shown in Fig. 1. Units: ~ngstr6ms and degrees. b From Ref. [1].

253

Xiaodong Zhang et al./Journal of Molecular Structure 372 (1995) 249-256

Table 3 The calculated geometrical parameters for silatranes I-VI Parameter

I

II

III

IV

V

VI

C4-N-C2 a C6-N-C2 C6-N-C4

84.4 122.0 117.9

82.5 121.7 117.3

84. I 121.9 117.8

84.0 121.5 117.4

85.2 121.9 117.9

86.7b 121,6 117.3

O2-Si-O3 Ol-Si-O3 O l-Si-O2

109.6 112.2 109.6

108.7 112.4 109.8

109.7 112.3 109.4

108.7 112.6 109.5

111.0 112.4 110.2

110.1 112.4 110.6

C6-C5-O3-Si C4-C3-O2-Si C2-C 1-O 1-Si

-52.5 -49.7 56.0

-52.8 -49.8 55.5

-52.8 -49.6 55.7

-~i3.6 -50.1 54.5

-52.8 -50.0 54.9

-53.6 -49.9 53.8

O1-Si-N-C2 O2-Si-N-C4 O3-Si-N-C6

18.2 -9.7 3.7

18.0 -9.9 3.4

16.4 - 10.8 2.8

17.9 -9.1 3.0

16.9 -9.2 2.7

O1-O2-O3-Si C2-C4-C6-N

-33.2 -41.7

-33.1 -40.9

-33.2 -41.9

-33.0 -41.0

-32.3 -42.0

-

-

86.9

174.3 -

178.4 86.0

-

-

179.4

178.4

179.2

179.7

-

-

2.436

2,443

O 1-Si-C7-C8 C9-C2-C1-C10 N-Si-C7 Si-N

2.457

17.32 -9.5 3.6

2.465

2.454

2.460

a The atoms numbering is shown in Fig. I. b Units: angle in degrees and distance in ~ngstr6ms. g r o u p is introduced in the non-equatorial position (4S) o f the f r a m w o r k , and the c o n f o r m a t i o n o f the f r a m e w o r k shows some difference. A c c o r d i n g to the M O calculation results (Table 3), the s y m m e t r y has been seriously distorted in the gas phase. The C 4 - N - C 2 b o n d angle is a b o u t 84 ° when C2 is substituted, this is less than the other two C - N - C b o n d angles 122 ° and 117 ° (two unsubstituted chains). The three O - S i - N - C chains are different also. W h e n the molecules exist in the solid state, according to the X R D result [1], the f r a m e w o r k retains a p p r o x i m a t e C3 symmetry. This m a y be because crystal forces are responsible for the structure observed in the solid state [14]. In solution, c o m p a r i n g c o m p o u n d s 2 and I (Table 4), it is shown that the 13C N M R chemical shifts o f the non-equatorial position (C2, C4, C6) m o v e to high frequency and that o f the equatorial position (C3, C5) scarcely changes when a - C O O H g r o u p is present. Because o f the solvent effect and m o v e m e n t o f the - C O O H group, the substituting

g r o u p effect is too weak to detect the difference o f the unsubstituted chains with the 13C N M R experiment. But if two substituents are introduced ( c o m p o u n d s II, IV), the c a r b o n atoms o f the two unsubstituted chains are distinguished because o f steric hindrance. C o m p a r i n g c o m p o u n d s 2 and I, 3 and I I I o f Table 4, the 29Si chemical shift increases a b o u t 11.0 p p m with the C O O H g r o u p ' s presence (Table 4). The increase is m u c h more noticeable than when the substitution occurs in the equatorial position [15]. This implies that the former is m o r e effective in enhancing the dative b o n d than the latter. Referring to the charge distribution data derived from C N D O / 2 calculations (Table 5), when one - C O O H g r o u p substitutes in the 4S position, charge transfer between Si and N increases, and the S i - N b o n d length is shortened. The theoretical results are in agreement with the N M R experiment. Based u p o n the IH N M R parameters o f the silatranes I - I V (Table 2), the p r o t o n s o f the two

Xiaodong Zhang et al./Journal of Molecular Structure 372 (1995) 249-256

254

I

TI

"r'rI

IV

Fig. 3. The geometrical conformations of silatranes l-IV: (bottom) the perspective view; (top) the projection view down Si-N axis. -OCH2CH2- chains of the atrane form an ABCD spin s y s t e m at r o o m t e m p e r a t u r e . F o r c o m p o u n d s I a n d I I I , the s u b s t i t u t e d c h a i n f o r m s a n A B C spin system. T h e I H 400 M H z N M R s p e c t r u m a n d s i m u l a t i o n s p e c t r u m o f c o m p o u n d I is s h o w n in

Fig. 2. A c c o r d i n g to T a b l e 1, o n e o f the t h r e e vicinal c o u p l i n g c o n s t a n t s 3J(OCH2CH2) is a l w a y s e q u a l to zero. R e f e r r i n g to t h e K a r p l u s f o r m u l a [18], ']vie = j 0 , c o s 2

Table 4 UC, 15N and 29Si NMR parameters of some substituted silatranes Compounds

R'

R

6(UC) (p.p.m.) C1 a

C3(C5)

C2

C4(C6)

6(15N)

6(29Si)

Reference

Ib 2 3 4 5 6

H H H O H Me

H Me Vinyl Me Ph Ph

57.57 58.33 58.03 169.9 58.3 64.3

57.57 58.33 58.03 58.2 58.3 58.3

51.51 51.55 51.55 55.7 51.6 58.6

51.51 51.55 51.55 53.6 51.6 52.6

-356.3 -354.2 -344.3 -

-83.6 -64.8 -81.6 -73.6 -80.5 -81.3

[7] [7] [7] [7] [15] [15]

I II III IV

H Me H Me

Me Me Vinyl Vinyl

67.2 65.8 67.2 65.8

57.2 57.2 57.2 57.1

58.7 64.7 58.7 64.7

54.1 49.4 48.3 54.1 49.5 48.5

-

-55.8 -74.2 -70.6 -89.5

[1] [1] [1] [1]

a The atom numbering is shown in Fig. 1. b Compounds 1-6 are substituted without a -COOH group.

Xiaodong Zhang et aL/Journal of Molecular Structure 372 (1995) 249-256

the related dihedral angle is nearly 90 ° . This implies that, with the presence of the - C O O H group, the two unsubstituted chains are distorted, and the - C H 2 - C H 2 - chains form two staggered gauche conformers. 3.2. Influence o f equatorial and axial substitutions

Literature reports on axial substitution are much more common than on the equatorial substitution of the atrane framework. In the present work with the existence of the - C O O H group in the 4S position, the equatorial and axial substitution effects are discussed. The calculated result is in agreement with the previously published results in that the electrondonor axial substituent R will decrease the electron density on the Si atom and thus the S i - N bond becomes weaker. Because - C H 3 performs a stronger electron-donating effect than does - C H = C H 2 , if R = -CH3, the increase in the S i - N bond length is larger. Especially, for the - C H = C H 2 group, the plane of the group is nearly parallel with that of the substituted chain atoms Si-O1-C1. If one - C H 3 group is substituted in the equatorial position in the gas phase, as indicated by the MO calculation (Table 5), the charge transfer between the Si and N atoms decreases, and the S i - N bond becomes weaker, but the effect is very slight. Referring to Table 4, it is found that the equatorial substituents in the framework will cause a low frequency shift of the Si resonance signal in solution. This theoretical result (Table 5)

is not in agreement with the N M R experiment [1,15].

4. Conclusions The following conclusions can be obtained from the study of the silatranes I, II, III and IV. (1) The silatrane conformation is seriously distorted by substitution of'the - C O O H group. Its substitution effect on the S i - N bond is much stronger than is that of the equatorial substitution in the framework of the above silatranes. In the presence of the electron-withdrawing group ( - C O O H ) , the S i - N dative bond becomes stronger, and the two - C H 2 C H 2 - groups of the unsubstituted chains are distorted into the gauche conformer. (2) The length of the dative bond S i - N is mainly affected by axial substitution, and hardly influenced by equatorial substitution in the atrane framework. If one methyl group is introduced in the equatorial position of the atrane framework, the S i - N bond will become slightly weaker. When one carboxyl group appears in the 4S position of the simple silatrane, the introduction of the methyl group in the 3R position will weaken the dative bond in the gas phase also.

Acknowledgement The project was supported by the National Natural Science Foundation of China.

Table 5 Charge distributions of the substituted silatranes I-IV derived from CNDO/2 calculations Compoundsa

R'

R

tr(Si)

a(N)

r(Si-N)

I II 111 IV

H Me H Me

Me Me Vinyl Vinyl

0.842 0.828 0.827 0.814

-0.179 -0.175 -0.178 -0.176

2.457 2.465 2.454 2.460

V VI

H Me

H H

0.875 0.860

-1.178 -0.175

2.436 2.443

¢r

H Me

H H

0.858 0.846

-0.151 -0.153

2.508 2.515

a

Compounds ¢r and .ACtare substituted without a -COOH group.

255

256

Xiaodong Zhang et al./Journal of Molecular Structure 372 (1995) 249-256

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