Ab Initio Study of the Conformational and Geometrical Isomerism in Heteroallyl and Heteropropenyl Systems

Conformational isomerism has been studied by ab initio methods (RHF/6-31+G*, MP2/6-31+G*) for CH₂=CHCH₂X heteroallyl and CH₃CH=CHX heteropropenyl systems (X = H, Me, NMe₂, OMe, PMe₂, SMe, ONCH₂). In 3-heteroprop-1-enes, substituents preferably occupy the AC position relative to the C=C double bond. The E isomers of 1-methylthio- and 1-methoxyprop-1-enes, which are thermodynamically more stable, have two stable forms, SP and AC; for 1-dimethylamino- and 1-imethylphosphinoprop-1-enes, the stable forms are AP and SC. The molecule of the E isomer of formoxime propenyl ether exists in two stable rotamer forms, SC and AP, the latter being predominant. The Z isomers preferably exist in the form of AC (X = CH₃O, CH₃S) and AP (X = (CH₃)₂N, (CH₃)₂P, CH₂=NO) conformations. Migration of the double bond toward an heteroatom in formoxime allyl ether, forming the E and Z isomers, is energetically favorable, the Z isomer being thermodynamically preferable.     

Infrared and Raman Spectra,Conformational Stability,Ab Initio Calculations,and Vibrational Assignments for Cyclopropyldifluorosilane

The infrared (3200–30 cm^–1) spectra of gaseous and solid Cyclopropyldifluorosilane, c-C₃H₅SiF₂H, and the Raman spectra (3200–20 cm^–1) of the liquid with quantitative depolarization values and the solid have been recorded. Both the syn (cis) and skew (gauche) conformers have been identified in the fluid phases, but only the syn conformer remains in the solid. Variable temperature (–55 to –100°C) studies of the infrared spectra of the sample dissolved in liquid xenon have been carried out. From these data, the enthalpy difference has been determined to be 73 ± 10 cm^–1 (209 ± 29 cal mol^–1), with the syn conformer being the more stable rotamer, which is at variance with the predictions from ab initio calculations. A complete vibrational assignment is proposed for both conformers based on infared band contours, relative intensities, depolarization values, and group frequencies. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G* calculations. Utilizing the frequencies of the silicon–hydrogen sketch, the rm Si—H bond distances of 1.474 and 1.472 Å have been obtained for the syn and skew conformers, respectively. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing the 6-31G* and 6-311 +G** basis sets at levels of restricted Hartree-Fock (RHF) and/or Moller–Plesset (MP) to second order. The potential energy terms for the conformer interconversion have been obtained from the MP2/6-31G* calculation. The results are discussed and compared to those obtained for some similar molecules.     

Conformational Analysis of Planar Enol Rotamers of 2,4-Pentanedione: an Ab Initio Study

All conformations among different planar enol conformers (rotamers) of 2,4-pentanedione were studied by means of the Hartree-Fock method using the STO-3G** basis set. The calculations were carried out with the Gaussian-98 program. For each conformation, stationary points with the highest energy on the energy curve were found graphically. Several conformations have low energy barriers and correspond to rotations around single bonds. They describe the spatial motion of only one (in most cases, hydrogen) atom or a small molecular fragment. All low energy barriers are in the interval 13-59 kJ·mol^-1. As would be expected, the lowest energy barrier is exhibited by the conformation that leads to the formation of an enol rotamer having an intramolecular H-bond (so-called -shaped form). On the other hand, conformations in which rotation around a bond leads to a break of the intramolecular hydrogen bond have the highest energy barriers. Conformations in which rotation occurs around the double bond have high energy barriers. The influence of the solvents CHCl₃ and CH₃CN on the intramolecular H-bond has also been studied by means of IPCM at the HF/6-31G** level.     

Crystal Structure and Quantum Chemical Ab Initio Calculations of Ibotenic Acid,an Excitatory Amino Acid Receptor Agonist

Ibotenic acid, a constituent of Amanita muscaria, is a potent NMDA receptor agonist. The structure of the ibotenic acid zwitterion monohydrate in the crystalline state has been determined by X-ray crystallography. The crystal structure has two ibotenic acid monohydrate formula units in the asymmetric unit and features an extensive hydrogen bond network. The ibotenic acid zwitter-ions in the crystalline state are compared to the in vacuo structure calculated by quantum chemical ab initio calculations at the HF/6-31+G* level and the effects of the hydrogen bond network on the structures in the solid state are discussed. The calculated potential energy curve with respect to side-chain orientation displays a single energy minimum. The conformations corresponding to the solid-state conformations are calculated to be ca. 2 kcal/mol higher in energy than the minimum-energy conformation in vacuo.     

An Ab Initio Study of the Relative Stabilities and Molecular Structures of 3-Substituted 2,5-Dihydrofurans and 4-Substituted 2,3-Dihydrofurans

The geometry optimized structures and total energies of 3-substituted (R) 2,5-dihydrofurans (a) and their isomers, 4-substituted 2,3-dihydrofurans (b), have been determined by ab initio calculations at the MP2/6-31G^*//HF/6-31G^* level. The nature of the moiety R has a marked effect on the relative total energies of the isomeric forms: at the calculation level cited, the reaction enthalpies for the a b isomerization range from +4.7 kJ mol^–1 for R = MeO to –30.5 kJ mol^–1 for both R = COOMe and R = NO₂. The reaction enthalpies appear to be controlled by the electronic effect of R on the strength of p- conjugation in b. The a isomer has a planar ring, independent of R (excluding NH₂), whereas the planarity of b depends on the electronic nature of R: the 2,3-dihydrofuran ring is planar for both R = COOMe and R = NO₂, but nonplanar for less conjugation-enhancing substituents.     

Molecular Structure of ortho-Fluoronitrobenzene Studied by Gas Electron Diffraction and Ab Initio MO Calculations

The molecular structure of ortho-fluoronitrobenzene (o-FNB) has been investigated by gas-phase electron diffraction and ab initio MO calculations. The geometrical parameters and force fields of o-FNB were calculated by ab initio and DFT methods. The obtained force fields were used to calculate vibrational amplitudes required as input parameters in an electron diffraction analysis. Within the experimental error limits, the geometrical parameters obtained from the gas-phase electron diffraction analysis are mostly in agreement with the results obtained from the ab initio calculations. The main results are: the molecular geometry of o-FNB is nonplanar with a dihedral angle about C–N of 38(3)°. The r _g (C–F) bond is shortened to 1.307(13) Å in comparison with r _g (C–F) = 1.356(4) Å in C₆H₅F.     

Cyclohexanone Dimethyl Acetals: A 13C NMR, Thermodynamic, and Ab Initio Study

The spatial structures of a number of mono- and disubstituted 1,1-dimethoxycyclohexanes (cyclohexanone dimethyl acetals) were studied by ¹³C NMR spectroscopy. In the monosubstituted acetals, substituents (Me, Et, i-Pr, and MeO) on C-2 are axially oriented, contrary to their normal, equatorial orientation on C-3 and C-4. Besides the spectroscopic study, the relative thermodynamic stabilities of the cis-trans isomers of a few 2,X-dialkyl (X = 3, 4, 5, or 6) derivatives of the parent cyclohexanone dimethyl acetal were determined by acid-catalyzed chemical equilibration in MeOH solution. In the most stable isomeric form, the 2-substituent is axial and the other equatorial. In the less stable isomer, both substituents are equatorial, excluding the cis-2,6-dimethyl derivative, where the ¹³C NMR shift data point to a predominance of the diaxial form. In general, the enthalpy difference between the isomeric forms is ca. 9 kJ mol^–1, while the entropy term favors the less stable isomer by 4 to 16 J K^–1 mol^–1. In the 2,6-dimethyl derivatives, however, the trans form is favored by only 0.8 kJ mol^–1 in G _m at 298.15 K. The main findings of the experimental work are in good agreement with ab initio calculations.     

Ab Initio Calculation of the Structure of 5-Chloro-1,2,4-triazole

Three tautomeric forms of 5-chloro-1,2,4-triazole were calculated using the Hartree-Fock (ab initio) and Meller-Plesset methods in the 6-31G(d) basis. The ³⁵Cl NQR parameters were calculated using the occupancies of the 3p-components of the valence p-orbitals of the chlorine atom. The structure of this triazole was derived from the data obtained.     

Molecular Structures and Thermodynamic Stabilities of Cycloalkadienes and Their Methoxy Derivatives: An Ab Initio and DFT Study

The geometry-optimized molecular structures and total energies of 4- to 6-membered cycloalkadienes, and of a number of their monoand dimethoxy derivatives, have been calculated by ab initio (HF/6-31G^*, MP2/6-31G^*//HF/6-31G^*) and DFT (B3LYP/6-31G^*) methods. By comparison with available experimental data, the reliability of these computational methods for an estimation of the relative stabilities (enthalpies) of the isomeric forms of the title compounds was tested. The experimental enthalpies of isomerization proved to agree best with the respective theoretical data based on the mean of the HF/6-31G^* and B3LYP/6-31G^* energies. The theoretical calculations were then extended to several isomeric methoxy-substituted cycloalkadienes, for which no previous thermodynamic data exist. Some structural features of the title dienes were also discussed.     

Far-Infrared Spectra, Conformational Stability, Barriers to Internal Rotation, Ab Initio Calculations, r0 Structural Parameters, and Vibrational Assignment of Ethyl Methyl Ether

The far-infrared spectra (350–35 cm^–1) of gaseous ethyl methyl ether-d ₀ and ethyl methyl-d ₃-ether have been recorded at a resolution of 0.10 cm^–1. For the d ₀ species, the fundamental asymmetric torsion of the more stable trans conformer (two methyl moieties are trans to one another) has been observed at 115.40 cm^–1 with four upper state transitions falling to lower frequency, whereas, for the gauche form, it has been observed at 93.56 cm^–1 with two excited states falling to lower frequency. the corresponding series for the d ₃ species start from 106.00 and 87.10 cm^–1, respectively. From these data, the asymmetric torsional potential coefficients for the d ₀ species have been determined to be: V ₁ = 572 ± 30; V ₂ = 85 ± 8; V ₃ = 619 ± 30; V ₄ = 175 ± 18, and V ₆ = –28 ± 3 cm^–1. The trans to gauche and gauche to gauche barriers were calculated to be 958 cm^–1 (11.5 kJ/mol) and 631 cm^–1 (7.55 kJ/mol), respectively, with an energy difference of 550 ± 6 cm^–1 (6.58 ± 0.07 kJ/mol). Utilizing three conformer pairs, variable temperature studies (–105 to –150°C) of the infrared spectra of the d ₀ sample dissolved in liquid krypton gave an enthalpy difference of 547 ± 28 cm^–1 (6.54 ± 0.33 kJ/mol) with the trans conformer the more stable rotamer. It is estimated that there is only 4% of the gauche conformer present at ambient temperatures. The structural parameters, conformational stabilities, barriers to internal rotation, and fundamental vibrational frequencies, which have been determined experimentally, are compared to those obtained from ab initio gradient predictions from RHF/6-31G* and with full electron correlation at the MP2 level with three different basis sets. The adjusted r ₀ structural parameters have been obtained for the trans conformer from combined ab initio MP2/6-311+G** predictions and previously reported microwave rotational constants. The reported distances should be accurate to 0.003 Å and the angles to 0.5°. These results are compared to the corresponding quantities obtained for some similar molecules.     

Conformational Stability from Variable-Temperature Infrared Spectra of Krypton Solutions, Ab Initio Calculations, and r o Structural Parameters of Chlorocyclopentane

The infrared spectra (3500–400 cm^–1) of krypton solutions of chlorocyclopentane, c-C₅H₉Cl, at variable temperatures (–101 to –150°C) have been recorded and the fundamental vibrations of the axial conformer and several of those for the equatorial form have been assigned. Utilizing two pairs of fundamentals for the two conformers in the krypton solution, an enthalpy difference of 145±15 cm^–1 (1.73±0.18 kJ-mol^–1) has been obtained with the axial conformer the more stable form. It is estimated that there is 67±2% of the axial conformer present at ambient temperature. Convincing spectroscopic evidence shows that a significant percentage of the chlorocyclopentane molecules are undergoing pseudorotation at ambient temperature. The conformational stabilities, harmonic force constants, fundamental frequencies, infrared intensities, and Raman activities have been obtained from MP2/6-31G(d) calculations with full electron correlation and these quantities have been compared to the experimental values when appropriate. The optimized geometries and conformational stabilities have also been obtained from ab initio MP2 calculations as well as by density functional theory (DFT) by the B3LYP method with several different basis sets. The adjusted r ₀ structural parameters have been obtained for both conformers by combining the ab initio data with the previously reported microwave rotational constants. These new values of the structural parameters for both conformers are compared to those previously reported from electron diffraction and microwave studies. These results are compared to the corresponding quantities of some similar molecules.     

Ab Initio Study of the Nonequivalence of Adsorption of D- and L-Peptides on Clay Mineral Surfaces

Ab initio geometry optimizations were performed of the structures of the L and D enantiomers of the model dipeptide, N-formyl alanine amide (L-Ala and D-Ala, respectively) adsorbed on the mineral surface in the interlayer space of the 2:1 clay, nontronite. Density functional procedures were used as implemented in the ab initio program CASTEP, in fully periodic calculations in which the properties of a model unit cell are determined by including the effects of its neighboring cells in an infinite crystal. Geometry optimization included the atomic positions of the mineral and the adsorbates within the unit cell, in addition to unit cell lengths and angles, achieving full optimization of the entire crystal system. In agreement with previous studies of the adsorption of organic compounds on clay mineral surfaces, in the most stable arrangement of L-Ala and D-Ala found here, the two molecules reside flat on the mineral basal plane, forming a parallel monolayer. The resulting L-Ala/mineral cocrystal is more stable, by 6 kcal/mol, than D-Ala. A characteristic structural difference exists for the enantiomers in that, in the optimized structure of L-Ala, the C()–C() bond is directed away from one of the mineral basal planes toward the dioctahedral cavity of the other, while the side group of D-Ala is parallel to the mineral basal plane and pointing to the nearest neighbor in an adjacent unit cell. As expected, the reverse results are obtained for the adsorption of L-Ala and D-Ala on a nontronite surface that is the enantiomer of the one used above. The geometry optimizations illustrate the structural compatibility of clay mineral lattices with peptide structures. That is, balance of adsorption energies and peptide interaction energies, and mineral lattice structure and periodicity allow for adsorption structures, which involve the entire backbone of a single peptide molecule and can, at the same time, immobilize the adsorbates in such a way that stabilizing intermolecular interactions occur across unit cell boundaries. Compatibility of the repeat distances on the clay surface with repeat distances of peptides should be an important property when clay minerals serve as templates for protein synthesis.     

Conformational stability of peroxynitric acid molecule and the barriers to internal rotation about the O−O and N−O bonds

The structure of conformers and potential curves of the internal rotation (PCR) about the O?O and N?O bonds in peroxynitric acid (PNA) were calculated by the unrestricted Hartree-Fock-Roothaan method. The standard valence-split 6–31G and 6–31G^* basis sets were used. The presence of two maxima on every curve has been shown. To refine the values of barriers to the internal rotation in the regions of minima and maxima of PCR, calculations taking into account the electron correlation energy have been carried out at the second- and fourth-order Møller-Plesset level of perturbation theory (MP2 and MP4, respectively). At the MP4/6-61G^* level of approximation, the barriers to the rotation about the O?O bond are equal to 8.6 kJ mol^?1 and 14.7 kJ mol^?1, and both barriers to the rotation about the N?O bond are equal to 33.5 kJ mol^?1. The results are compared with those published for PCR in hydrogen peroxide and peroxynitric acid.     

The Molecular Structure and the Puckering Potential Function of Octamethylcyclotetrasilane,Si4Me8, Determined by Gas Electron Diffraction and Relaxation Constraints from Ab Initio Calculations

Gas electron diffraction data are applied to determine the geometrical parameters of the octamethylcyclotetrasilane molecule using a dynamic model in which the ring puckering is treated as a large amplitude motion. The structural parameters and parameters of the potential function were refined, taking into account the relaxation of the molecular geometry estimated from ab initio calculations at the Hartree–Fock level of theory using a 6-311G** basis set. The potential function has been described as V() = V ₀[(/ _e )² – 1]² with V ₀ = 1.0 ± 0.5 kcal/mol and _e = 28.3 ± 1.9°, where is the puckering angle of the ring. The geometric parameters at the minimum of V() (r _a in Å, in degrees and errors given as three times the standard deviations including a scale error) are as follows: r(Si—C)_av = 1.894(3), r(Si—Si) = 2.363(3), r(C—H) = 1.104(3), CSiC = 109.5(6), SiSiSi = 88.2(2), SiCH = 111.7(6), C = 4.1, where the tilt C was estimated from ab initio constraints. The structural parameters are compared with those obtained for related compounds.     

Molecular Conformation of 2,2'-Dinitrodiphenylamine According to Dielectric Studies and Ab Initio Quantum Chemical Calculations

According to the results of ab initio calculations employing the HF/6-31G* approach, the isolated 2,2'-dinitrodiphenylamine molecule exists as an sc, sc conformer stabilized by a symmetric intramolecular bifurcated (three-center) hydrogen bond. In protophilic solvents (1,4-dioxane), the conformational equilibrium is also shifted in the direction of this rotational isomer.     

Molecular Structure of 1-Substituted Bicyclo[2.2.0]hexanes: A Combined X-Ray Structural and Ab Initio Study

The synthesis and X-ray crystal structure of the p-bromoanilide derivative of bicyclo[2.2.0]hexane-l-carboxylic acid (1), N-(4-bromophenyl)-bicyclo[2.2.0]hexane-l-carboxamide (2), is reported. N-(4-Bromophenyl)-bicyclo[2.2.0]hexane-l-carboxamide is synthesized in good yield via the DCC coupling of bicyclo[2.2.0]hexane-l-carboxylic acid (1) with p-bromoaniline. Low-temperature X-ray analysis of 2 reveals that the bonds of the bicyclo[2.2.0]hexane skeleton vicinal to the amide group show a slight lengthening due to conjugative interaction with the -accepting amide group. Ab initio calculations at the 6-31G* level of theory on bicyclo[2.2.0]hexane-l-carboxamide, a model for 2, and for other 1-substituted bicyclo[2.2.0]hexanes are also reported.     

Conformational flexibility and aromaticity of azanaphthalenes

Conformational flexibility of naphthalene and its different mono-and diaza analogues has been studied by MP2/6-31G(d, p) quantum chemical computations. It is shown that all molecules possess a considerable conformational flexibility. The out-of-plane deformation energy of both a bicyclic π-system on the whole and separate rings directly depends on the degree of aromaticity of the conjugated system. Effects of the amount and arrangement of nitrogen atoms on conformational features and aromaticity of the molecules considered were analyzed.     

Ab initio calculations of methionines and their protonated forms

Ab initio calculations of molecular and electronic structures of neutral molecules and protonated forms of methionine and its derivatives in the gaseous phase were carried out by the Hartree-Fock method using the 6–31G^* basis set with full geometry optimization. Proton affinities of methionine (1), methionine sulfoxide (2), and methionine sulfone (3) were calculated for different modes of coordination of the proton. The results of calculations demonstrated that in protonated forms of 1 and 3, bonding between the proton and the N atom is most favorable, while in protonated form of 2, bonding between the proton and the O atom of the SO group is most favorable. The proton affinities of the amino acids are as follows: 223.2 (1), 241.2 (2), and 221.5 (3) kcal mol⁻¹,i.e., methionine sulfoxide 2 exhibits the highest proton affinity in the series of the amino acids under consideration. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1487–1490, August, 1998.     

Ab initio study of the ground state and conformational stability of peroxyacetyl nitrate in internal rotation about the peroxide bond

The molecular and electronic structure of the ground state of peroxyacetyl nitrate (PAN) was calculated by the unrestricted Hartree-Fock-Roothaan method with the use of the standard 3–21G and 6–31G basis set. The potential curve of the internal rotation about the peroxide bond of PAN was calculated with the 6–31G basis set. The curve contains two maxima. The ground state of PAN is characterized by a structure in which groups of atoms adjacent to the peroxide bond lie in planes that are perpendicular to each other (the dihedral angle ϱ(COON) is 89.9°). The calculated barriers to rotation are 19.6 and 66.8 kJ mol⁻¹. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 600–604, April, 1998.     

Ab Initio Studies on the Molecular Conformation of Lignin Model Compounds I. Conformational Preferences of the Phenolic Hydroxyl and Methoxy Groups in Guaiacol

Summary. The conformational preferences of the lignin guaiacyl structural unit were studied at the MP2/6-311G(d,p) level of theory using guaiacol (2-methoxyphenol) as model compound. The potential energy surface of guaiacol was investigated by the ab initio method with full geometry optimization by varying the torsion angles of the guaiacol functional groups (hydroxyl and methoxy). An overall of nine stationary points were located, four of which were found to be minima and the other five transition structures between them. The energy minima of guaiacol can adopt one cisoid and three transoid conformations for the hydroxyl and methoxy groups. The transoid structures differ by the orientation of the methoxy group inside and outside of the aromatic plane. The most stable cisoid conformer has an intramolecular hydrogen bond between phenolic hydrogen and methoxy oxygen with a binding energy of 18.09–18.51 kJ/mol as calculated with the second-order (MP2) and fourth-order (MP4SDQ) M?ller-Plesset methods and with larger polarized basis sets including diffuse functions. When comparing the geometrical parameters of the global energy structure with relevant experimental data from crystallographic structures good agreement between the data was found. The saddle points, the effect of calculation level on the energy relative stability, the rotational barrier heights, and the relative concentrations of the conformers are also discussed.