The Cyclohexasilanes Si6H11X and Si6Me11X with X=F,Cl, Br and I: A Quantum Chemical and Raman Spectroscopic Investigation of a Multiple Conformer Problem

The conformers of the monohalocyclohexasilanes, Si₆H₁₁X (X=F, Cl, Br or I) and the haloundecamethylcyclohexasilanes, Si₆Me₁₁X (X=F, Cl, Br or I) are investigated by DFT calculations employing the B3LYP density functional and 6‐31+G* basis sets for elements up to the third row, and SDD basis sets for heavier elements. Five minima are found for Si₆H₁₁X—the axial and equatorial chair conformers, with the substituent X either in an axial or equatorial position—and another three twisted structures. The equatorial chair conformer is the global minimum for the X=Cl, Br and I, the axial chair for X=F. The barrier for the ring inversion is ～13 kJ mol^?1 for all four compounds. Five minima closely related to those of Si₆H₁₁X are found for Si₆Me₁₁X. Again, the equatorial chair is the global minimum for X=Cl, Br and I, and the axial chair for X=F. Additionally, two symmetrical boat conformers are found as local minima on the potential energy surfaces for X=F, Cl and Br, but not for X=I. The barrier for the ring inversion is ～14–16 kJ mol^?1 for all compounds. The conformational equilibria for Si₆Me₁₁X in toluene solution are investigated using temperature dependent Raman spectroscopy. The wavenumber range of the stretching vibrations of the heavy atoms X and Si from 270–370 cm^?1 is analyzed. Using the van′t Hoff relationship, the enthalpy differences between axial and equatorial chair conformers (H_ax?H_eq.) are 1.1 kJ mol^?1 for X=F, and 1.8 to 2.8 kJ mol^?1 for X=Cl, Br and I. Due to rapid interconversion, only a single Raman band originating from the “averaged” twist and boat conformers could be observed. Generally, reasonable agreement between the calculated relative energies and the experimentally determined values is found.     

Interactions intramoléculaires: XXIII—Constantes de couplage et interactions gauches avec un groupement t-butyle (cyclohexanones disubstituées 3, 4)

The ¹H NMR spectra of a series of cis and trans-3R,4 X-cyclohexanones (-2,2,6,6-d₄) are analysed. By comparison of their ³J coupling constants with those of cyclohexane homologues we obtain information about the chair–chair equilibrium constants for R = CH₃, X = CN, the chair structure of cis isomers with an equatorial t-butyl group, and a conformational heterogeneity with trans (CH₃)₃C and CN groups. This latter situation is analysed by means of a simplified but controlled Karplus relationship, on the basis of a mixture of two conformers; this involves a diequatorial chair and a boat form with a dihedral angle Φ₃₄ of about ?6°.     

Conformational analysis of some 1R,4S‐2‐arylidene‐p‐menthan‐3‐ones by 1H NMR spectroscopy and molecular simulation

Based on ¹H NMR spectral analysis combined with molecular simulation, conformational states of the cyclohexanone ring were studied for some 1R,4S‐2‐(4‐X‐benzylidene)‐p‐menthan‐3‐ones (X = COOCH₃ or C₆H₅) in CDCl₃ and C₆D₆. The co‐existence of chair conformers with an axial orientation of both alkyl substituents and twist‐boat forms was established for the compounds studied at room temperature (22–23° C). The substituent X does not influence appreciably the ratio of these conformers, but the fraction of twist‐boat forms increases noticeably in benzene solutions as compared with CDCl₃ solutions. Rotameric states of the isopropyl fragment were also characterised for the compounds studied. Distinctions in conformational states for the 1R,4S‐2‐arylidene‐p‐menthan‐3‐ones and (?)‐menthone were revealed and are discussed. Copyright © 2002 John Wiley & Sons, Ltd.     

Some periodic trends,molecular structure,normal coordinate analysis of 1,3,5-trioxane, -trithiane and -triselenane: computational and vibrational studies

The Raman (3200–100 cm⁻¹) and infrared spectra (3200–200 cm⁻¹) of solid C₃H₆O₃ (TO) and C₃H₆S₃ (TS) have been recorded and only the chair conformation is present. Furthermore, utilizing the CH stretching bands at the infrared spectrum of the gaseous phase, the CH_ax and CH_eq distances are found to be 1.088 and 1.107 Å, respectively. The structural parameters and conformational stabilities for 1,3,5-C₃H₆X₃ series (where X=O, S and Se atoms) have been obtained from density functional theory at the Becke3-LYP gradient-corrected functional (DFT-B3LYP) and from MP2 level with full electron correlation. These calculations have been extended up to 6-311++G(d,p) basis set to include polarization and diffusion functions. All computational results and vibrational analysis are in favor of the chair conformation (C_3v), whereas the boat (C₁) and Planar (D_3h) forms have been excluded owing to the predicted imaginary wavenumber(s). According to 6-311++G(d,p) basis set, the ring size and the tendency of the ring to undergo flattening is found to be directly proportional to the atomic size of the substituted hetero atoms (X) of the chair. The calculated DFT-B3LYP scaled quantum chemistry (QC) force fields at 6-31G(d) basis set lead to a number of revised assignments for certain vibrational modes and it appears to give quite accurate Raman spectra for the investigated chalcogenanes. The estimated bond lengths, bond angles, rotational constants, Raman activities dipole moment and unscaled force constants are compared with either theoretical and/or experimental results whenever possible.     

A force-field study of the conformational characteristics of the iduronate ring

Methods of molecular mechanics were applied to investigate the conformation of the (methyl 2-O-sulfate-4-methyl-α-L-idopyranose) uronic acid (DMIS), in order to correlate the peculiar vicinal proton coupling constants observed in polysaccharides containing the iduronate ring to the conformational characteristics of this sugar ring. We found three conformers with comparable energies, namely the two chair forms ¹C₄ and ⁴C₁ and the skew-boat form ²S₀(L); the latter is separated from each chair form by a barrier of about 9 kcal/mol. Along the pseudorotational path three additional minima (³S₁, ¹S₃, and ¹S₅) were found, yet at least 4 kcal/mol higher than ²S₀. The results obtained for the relative energies of the three conformers and the conformation of the side groups were affected by the inclusion of the electrostatic term and, in particular, by the charge assigned to the ionic groups of DMIS. However, the conformational properties of the idopyranosidic ring in DMIS (and in related compounds) should still be interpreted in terms of equilibrium among these three conformers only.     

Conformational effects in compounds with 6-membered rings—XIII : Detection of twist conformers using 13C NMR chemical shifts

¹³C NMR spectra of derivatives of cyclohexane, piperidine, and thian in chair and twist eonformers, and of model compounds, lead to estimates of deshielding (Δδ = 3.6 ± 0.2 ppm) for axial C$\text{Me}$₃ on a cyclohexane ring and shielding (Δδ = ?0.2 to ?0.6 ppm) for ψe-C$\text{Me}$₃ in twist conformers, relative to equatorial C$\text{Me}$₃. Ring carbon atoms are considerably shielded in twist conformers relative to chair eonformers. The value of ¹³C chemical shifts in the study of chair-twist equilibria is exemplified by variable temperature measurements on diastereomeric pairs of compounds (11 and 13; 38 and 50).     

Gas-phase conformations and exciton couplings in 5,6,11,12-tetrahydrodibenzo[a,e]cyclooctene

The conformations and exciton couplings in 5,6,11,12-tetrahydrodibenzo[a,e]cyclooctene (THDC) have been studied using resonance-enhanced two-photon ionization spectroscopy in a supersonic jet expansion. It has been estimated from the spectral analysis that 90% of THDC exists in the twist-boat (TB) conformation; the chair (C) conformer constitutes the remaining 10%. Most of the vibronic activity in the spectrum of THDC is associated with the symmetric flapping of the aromatic rings of the TB conformer. The observed S₁/S₂ exciton splitting of the TB conformer is 100 cm^?1. The S₁/S₂ transition of the C conformer is found to be forbidden. The exciton splittings of the C and TB conformers were estimated by the spectral analysis of two deuterated isotopomers of THDC. The estimated exciton splittings of the C and TB conformers are 14.7 and 101.9 cm^?1, respectively. The supramolecular model of bichromophores with identical chromophores at the CIS/6-31+G(d)//HF/6-31+G(d) level of theory predicted electronic coupling energies that are very close to the experimental exciton coupling energies.     

N16-oxides of sparteine, 2-methylsparteine and 2-phenylsparteine as ligands; spectroscopic and DFT studies of complexes with ZnX2 (X=Cl,Br)

Six new ZnX₂ (X=Cl, Br) complexes with N16-oxides of sparteine, 2-methylsparteine and 2-phenylsparteine as ligands have been synthesized and characterized by MS, IR, NMR and DFT methods. All complexes have 1 : 1 stoichiometry. Complexation with N16-oxides involves inversion of the configuration at N16, converting ring C from a boat into a chair with the oxygen engaged in coordination. All complexes investigated are of composition [(L–H)⁺(ZnX₃)^?] (where L is N-oxide). The structures of the complexes obtained have been compared with those of the monoperchlorate salts of the N-oxides.     

Conformational Studies of Marine Polyhalogenated α-Chamigrenes Using Temperature-dependent NMR spectra inverted-chair and twist-boat cyclohexane moieties in the presence of an axial halogen atom at C(8)

α-Chamigren-3-one (+) -8 bearing an axial CI-atom at C(8) exists as a largely dominant conformer with Me—C(5) at the envelope-shaped enone ring pointing away from CI_ax?C(8) at the cyclohexane ring (= B) in the ‘normal’ chair conformation, as shown by ¹H-NMR. In contrast, the α-chamigren-3-ols (+) -9 and (+) -10 , obtained from hydride reduction of (+) -8 , show a temperature-dependent equilibrium of conformers where the major conformers have ring B in the inverted-chair (and twist-boat for (+) -9 ) conformation to avoid repulsions between Me?C(5) and CI_ax–C(8) (Scheme 1). This is in agreement with the conformation of the epoxidation product (+) -12 of (+) -9 where Me–C(5) is pushed away from CI_ax–C(8) in a ring-B chair similar to that of (+) -8 (Scheme 2). Introduction of a pseudoequatorial Br-atom at C(2) of (+) -8 , as in enone (+) -15 (Scheme 3), does not affect the conformation; but a pseudoaxial Br? C(2) experiences repulsive interactions with H_eq–C(7), as shown by the ¹H-NMR data of the isomeric enone (+) -16 where the ‘normal’-chair conformer Cβ -16 is in an equilibrium with the inverted chair conformer ICβ -16 (Scheme 3). These results and the accompanying paper allow a unifying view on the conformational behavior of marine polyhalogenated α-chamigrenes. This view is supported by the acid-induced isomerization of α-chamigrene (+) -9 (inverted chair) to β-chamigrene (+) -17 (‘normal’ chair; Scheme 4), the driving force being the lesser space requirement of CH₂?C(5) than of Me–C(5). This explains why β-chamigrenes are so common in nature.     

Conformational stability and force field of chloromonophosphazenes: MNDO calculations,vibrational spectra and normal coordinate analyses of Cl3PNP(X)Cl2 (X = O,S) and [Cl3PNPCl3][Y] (Y = Cl,PCl6)

The potential energy around the PN bonds for the Cl₃PNP(X)Cl₂ (X = O, S) molecules and [Cl₃PNPCl₃]⁺ cation have been derived from MNDO (modified neglect of diatomic overlap) calculations. The most stable conformations are two s-trans isomers in nearly eclipsed forms. The calculated structural parameters agree well with the X-ray experimental data. Barriers of 6 and 1.5 kJ/mol for the rotations of the POCl₂ and PCl₃ groups are predicted. In addition, the Raman spectra and the qualitative depolarization measurements for these molecules in the liquid phase have been obtained. All the data indicate that the molecules exist as a mixture of two rotamers in the molten phase. These two conformers are stabilized in the crystal packing of Cl₃PNP(O)Cl₂. The observed frequencies are in good agreement with the calculated values obtained by normal coordinate analysis. The MNDO calculation of the harmonic force field is in reasonable agreement with the experimental values. The force-constant values assigned to the torsional modes around the PN bonds correspond to low barriers for the internal rotations. These easy internal rotations around the PN and PN bonds can explain the flexibility of the phosphazene backbone and the elastomeric properties of the polyphosphazene polymers.     

Application of J(C,H) coupling constants in conformational analysis

Conformational equilibria for a number of methyl substituted 1,3-dioxanes 1, 1,3-oxathianes 2 and 1,3-dithianes 3 were calculated at the HF and DFT levels of theory. In addition to the chair conformers also the energetically adjacent twist conformers were considered and the positions of the corresponding conformational equilibria estimated. On the basis of the global energy minima of conformers, participating in the conformational equilibria, the ¹J_C,Hax,equ coupling constants were calculated using the GIAO method and compared with the experimental values obtained from ¹³C,¹H coupled ¹³C NMR spectra. The Perlin effect, the influence of the solvent and the suitability of this NMR parameter for assigning the conformational equilibria present are critically discussed.     

Powder X‐ray study of racemic (2RS,3RS)‐5‐amino‐3‐[4‐(3‐methoxyphenyl)piperazin‐1‐yl]‐1,2,3,4‐tetrahydronaphthalen‐2‐ol

The structure of the title benzovesamicol analogue, C₂₁H₂₇N₃O₂, an important compound for the diagnosis of Alzheimer's disease, has been determined by X‐ray powder diffraction. The title compound was firstly synthesized and characterized by spectroscopic methods (FT–IR, and ¹³C and ¹H NMR). The compound is a racemic mixture of enantiomers which crystallizes in the monoclinic system in a centrosymmetric space group (P2₁/c). Crystallography, in particular powder X‐ray diffraction, was pivotal in revealing that the enantio‐resolution did not succeed. The piperazine ring is in a chair conformation, while the cyclohexene ring assumes a half‐chair conformation. The crystal packing is dominated by intermolecular O—H...N hydrogen bonding which links molecules along the c direction.     

A Theoretical Study of the Interaction Between Cytosine and BX<Subscript>3</Subscript> (X = F,Cl) Systems

The B3LYP method of DFT and HF theories of ab initio with 6-311+G^** basis sets were used to predict the geometries of the cytosine-BX₃ (X,=F, Cl) complex systems. Four conformers were obtained with no imaginary frequencies, respectively. The binding energies, enthalpies and Gibbs energies of cytosine-BX₃ have been obtained. The analyses of the combinations between cytosine and BX₃ using the natural bond orbital (NBO) method and thermodynamics indicate that the complexes (a) and (e), which depend on the proton affinities of the oxygen on the cytosine and boron in BX₃, are the most stable ones with their combination energies of −234.21 and −228.23 kJ.mol⁻¹ (B3LYP method, BSSE corrected). Based on the calculation results, a reasonable method was employed to calculate the change in the enthalpies and Gibbs energies to form eight complexes in the gaseous state at 298.15K and 101.325 kPa. It can be shown that the conformers (a) and (e) are the most stable and form readily.     

A Computational Study of Chair–Twist Energy Differences and the Chair–Chair Conformational Interconversion in Tetrahydro-2H-thiopyran (Thiacyclohexane,Thiane)

Ab initio molecular orbital theory with the LANL2DZ, 3-21G, 6-31G(d), 6-31+G(d), 6-31+G(d,p), 6-311+G(d,p),6-31G(2d), 6-31G(3d), and 6-311G(d,p) basis sets and density functional theory (B3P86, B3LYP, B3PW91) have been used to calculate the structures, relative energies, enthalpies, entropies, and free energies of the chair, 1,4-twist, and 2,5-twist conformers of tetrahydro-2H-thiopyran (tetrahydrothiopyran, thiacyclohexane, thiane, pentamethylene sulfide). All levels of theory calculated similar energy values and the effect of basis sets on the calculated energies was small. The chair conformer of tetrahydro-2H-thiopyran was 5.27 kcal/mol more stable than the 1,4-twist conformer, which was slightly more stable (0.81 kcal/mol) than the 2,5-twist conformer. The chair–1,4-twist and chair–2,5-twist free energy differences ( G°_{c – t}) were 5.44 and 5.71 kcal/mol, respectively. Intrinsic reaction coordinate [IRC, minimum-energy path (MEP)] calculations connected the transition state between the chair and the 2,5-twist conformers. This transition state is 9.73 kcal/mol higher in energy than the chair conformer and the energy differences between the chair and the 1,4-boat and 2,5-boat transition states were 8.07 and 6.38 kcal/mol, respectively. Stereoelectronic hyperconjugative interactions were observed in the chair, 1,4-twist, and 2,5-twist conformers of tetrahydro-2H-thiopyran. The stereoelectronic hyperconjugative effects in the chair conformer of tetrahydro-2H-thiopyran have been compared to those in the respective chair conformers of tetrahydro-2H-pyran, tetrahydro-2H-selenane, and tetrahydro-2H-tellurane.     

Raman spectra,conformational stability,structural parameters,vibrational assignment,and ab initio calculations for epifluorohydrin

The Raman spectra (3200–100 cm⁻¹) of epifluorohydrin, OCH₂CH(CH₂F), in variable solvents, as well as that of the gas have been recorded and several of the bands due to the two less stable conformers have been identified. The variable solvent studies were inconclusive on the relative conformer stabilities. The conformational energy differences and optimized geometries for all three conformers have been obtained from ab initio calculations with the 3–21G, 4–31G and 6–31G* basis sets. A normal coordinate analysis has also been performed for each conformer with a force field determined from the 3–21G basis set. Assignment of the vibrational fundamentals observed in the Raman spectra of the fluid phases is proposed based on the normal coordinate calculations. In the liquid phase, one of the conformers with a large dipole moment predominates and it appears to be the gauche-I form which is the only one found in the solid. Utilizing the three rotational constants previously reported for each conformer, along with restricted relative distances for several of the structural parameters among the conformers from ab initio calculations, r₀ structural parameters for the heavy atoms have been determined.     

Computational study of conformations and of sulfinyl oxygen-induced pentacoordination at silicon in 4-chloro-4-silathiacyclohexane 1-oxide and 4,4-dichloro-4-silathiacyclohexane 1-oxide

Second-order Møller-Plesset theory (MP2) and density functional theory (B3LYP) with the 6-311G(d,p) and 6-311+G(d,p) basis sets have been used to calculate the equilibrium geometries and relative energies of the chair, twist, and boat conformations of 4-chloro-4-silathiacyclohexane 1-oxide and 4,4-dichloro-4-silathiacyclohexane 1-oxide. The chair conformers of the axial sulfoxides are lower in energy than the chair conformers of the corresponding equatorial sulfoxides. MP2/6-311+G(d,p) predicted the chair conformer of axial trans-4-chloro-4-silathiacyclohexane 1-oxide (4a) to be 6.12, 0.44, and 0.45 kcal/mol, respectively, more stable than the corresponding 1,4-twist (4b), 2,5-twist (4c) and 1,4-boat (4d) conformers and 6.93 kcal/mol more stable than the 2,5-boat transition state ([4e]^‡). Structures 4c and 4d are stabilized by intramolecular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The 1,4-boat conformer (7d) of axial 4,4-dichloro-4-silathiacyclohexane 1-oxide is also stabilized by transannular coordination of the sulfinyl oxygen with silicon. The energy difference (E_rel = 4.23 kcal/mol) between the chair conformer (7a) and 7d is larger than that between 4a and 4d. The relatively lower stability of the 1,4-boat conformer (7d) of axial 4,4-dichloro-4-silathiacyclohexane 1-oxide (7a) may be due to repulsive interactions of the axial halogen and sulfinyl oxygen atoms. The relative energies and structures of the conformers and transition states of cis- and trans-4-chloro-4-silathiacyclohexane 1-oxide and 4,4-dichloro-4-silathiacyclohexane 1-oxide are discussed in terms of hyperconjugative interactions, orbital interactions, nonbonded interactions, and intramolecular sulfinyl oxygen-silicon coordination.     

Exploring potential energy hypersurfaces for triple symmetric inversion in 3-azabicyclo[3.3.1]nonan-9-one and its N-methyl derivative

The potential energy hypersurfaces for the triple inversion, from chair to boat and α to β conformations, are explored theoretically in 3-azabicyclo[3.3.1]nonan-9-one and its N-methyl derivative, by using ab initio quantum-mechanical calculations. Both compounds are precursors of rigid analogs of the potential GABA_A and GABA_B receptor antagonists. In contrast to results from semiempirical calculations, the chair–chair β conformers are found to be, by far, the most stable structures for both the nonmethylated and N-methylated compounds. The inversion barriers are found to be relatively low, so that the conformers could be expected to exist in thermodynamic equilibrium at room temperature. A population analysis reveals, however, that, in the ab initio approach, the molecules seem to exist practically only in the chair–chair–β conformation. The theoretical results compare well with the available experimental data. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1567–1574, 1998     

Theoretical study of structure,vibrational and electronic spectra of isomers of methyl-3-methoxy-2-propenoate

A systematic quantum mechanical study of the possible conformations, their relative stabilities, vibrational and electronic spectra and thermodynamic parameters of methyl-3-methoxy-2-propenoate has been reported for the electronic ground (S₀) and first excited (S₁) states using time-dependent and time-independent Density Functional Theory (DFT) and RHF methods in extended basis sets. Detailed studies have been restricted to the E-isomer, which is found to be substantially more stable than the Z-isomer. Four possible conformers c′Cc, c′Tc, t′Cc, t′Tc, of which the first two are most stable, have been identified in the S₀ and S₁ states. Electronic excitation to S₁ state is accompanied with a reversal in the relative stability of the c′Cc and c′Tc conformers and a substantial reduction in the rotational barrier between them, as compared with the S₀ state. Optimized geometries of these conformers in the S₀ and S₁ states are being reported. Based on suitably scaled RHF/6-31G^** and DFT/6-311G^** calculations, assignments have been provided to the fundamental vibrational bands of both these conformers in terms of frequency, form and intensity of vibrations and potential energy distribution across the symmetry coordinates in the S₀ state. A complete interpretation of the electronic spectra of the conformers has been provided.     

Conformational equilibria in 7-membered ring metal chelate complexes

Bis(diphosphine)metal and (diphosphine)(diene)metal (M = Rh, Ir) cationic complexes containing 7-membered chelate rings have been studied by low temperature ³¹P and ¹H NMR spectroscopy. For cyclooctadiene-1,4-bis(diphenylphosphino)butane- and -DIOP-rhodium, and cyclooctadiene-1,4-bis(diphenylphosphino)butane-iridium complexes, boat and chair conformations may be distinguished at low temperature. ¹H NMR spectra of these and analogous complexes suggest that both boat and chair conformers are significantly populated at room temperature. Bis(diphosphine) complexes of rhodium and iridium show very complex dynamic behaviour.     

Experimental and theoretical study of N-(2-hydroxyethyl)morpholine betaine

N-(2-hydroxyethyl)morpholine betaine (HEMB) has been characterized by a single crystal X-ray analysis, FTIR spectroscopy and DFT calculations. The crystals are monoclinic, space group P2₁/c with a=10.273(2), b=9.360(2), c=9.447(2) Å and β=104.72(3)Å. Two molecules of HEMB form a centrosymmetric dimer (X2) connected by a pair of hydrogen bonds between the CH₂CH₂OH and COO⁻ groups, with the O?O distance of 2.672(2) Å. The morpholine ring adopts a chair conformation with the CH₂CH₂OH group in the axial and the CH₂COO⁻ group in the equatorial position. The structures of the dimer, B2, and two monomers, B1a and B1b, have been optimized by the B3LYP approach using the 6-31G(d,p) basis set. The computed structure of B2, agrees well with the experimental X2. From two stable monomeric conformers the more favored is B1a, with the intramolecular hydrogen bond with the O-H?O distance of 2.566 Å. The effects of hydrogen bonding and electrostatic interactions on the conformation of the molecules investigated have been discussed. The FTIR spectrum shows a broad absorption in the 3300-2600 cm⁻¹ region, typical of moderate O-H?O hydrogen bonds.