An ab initio structural and vibrational analysis of gauche,trans,trans- and gauche,cis,trans-hexa-1,3,5-trienes

The results of complete geometry optimizations of the high energy stable gauche,Trans,trans- and gauche,Cis,trans- rotamers of hexa-1,3,5-trienes are reported at the RHF/6-31G//RHF/B-31G level. The angles of rotation around one of the single C-C bonds are found to be 33.7° and 45.5°, respectively. The corresponding harmonic force fields of these molecules are also reported at this level and corrected using scale factors transferred from buta 1,3-diene. Aspecial scale factor was used for the central C=C double bond stretching coordinate to take into account vibronic coupling. The theoretical vibrational frequencies, calculated with the scaled quantum mechanical (SQM) force fields, allow a complete interpretation of the experimental vibrational spectra of these molecules.Preliminary results were reported at the Austin XII Symposium on Molecular Structure, Austin, TX, February 28 through March 3, 1988, S 18, p. 111 (USA) and at the XIXth European Congress on Molecular Spectroscopy, Dresden, September 4 through September 8, 1989, p. 226 (GDR).     

Modelization of vibrational spectra beyond the harmonic approximation from an iterative variation–perturbation scheme: the four conformers of the glycolaldehyde

This paper presents the computed anharmonic frequencies and IR intensities in the mid-infrared region for the four conformers of glycolaldehyde (Cis cis, Trans trans, Trans gauche and Cis trans forms). The fundamental transitions and their connected overtones and combination bands through strong anharmonic couplings (Fermi resonances) are provided. The results are stemmed from an iterative variational–perturbational resolution of the vibrational problem implemented in the VCI-P code. The four potential electronic surfaces are built as a Taylor series truncated to the fourth order around each minimum geometry. The second derivatives with respect to the normal coordinates were computed at the CCSD(T)/cc-pVTZ level, while the third and fourth derivatives were estimated with the B3LYP/6-31 + G(d,p) model chemistry. For the most stable Cc form, an average deviation of about 10 cm⁻¹ is obtained with respect to the unambiguous experimental values. Furthermore, some of the transitions observed in the CH stretchings region were reassigned. The theoretical values calculated for the Tt and Tg forms are compared to the experimental data obtained from the irradiation of the Cc conformer isolated in Ar matrix with an IR source.     

从头计算研究乙酰胆碱构象和分子静电势

在Hartree－Fock和二级Moller－Plesset微扰理论MP2水平，用6－31G对乙酰胆碱进行了从头计算研究，发现了旁式和反式两种稳定构象．经零点振动能校正后，在Hartree－Fock级别旁式较反式稳定0．24kJ·mol~(-1)；而在MP2级别，反式较旁式稳定2．07kJ·mol~(-1).谐振动频率在HF／6－31G水平计算.还给出了两种构象的MP2分子静电势图.     

The structure of the singlet tetramethylene diradical intermediate

Ab initio MC SCF geometry optimizations of the gauche and trans conformers of the singlet tetramethylene diradical have been carried out using MC SCF gradients with a minimal (STO-3G) and extended (4-31G) basis set. At both computational levels, it has been found that the tetramethylene diradical exists as a stable species in two different conformations, a gauche and a trans.     

Vitamin E models. Conformational analysis and stereochemistry of tetralin, chroman, thiochroman and selenochroman

Tetralin, chroman as well as its' S and Se containing congeners were subjected to ab initio (RHF/3-21G and RHF/6-31G(d)) and DFT (B3LYP/6-31G(d)) computation. Molecular geometries and the activation energies for ring inversions were determined with full geometry optimizations.     

2-丁基-四氢噻吩亚砜13C-NMR的理论研究

在RHF/6-31G和B3LYP/6-31G水平上对顺式(Cis-)与反式(Trans-)2-丁基-四氢噻吩亚砜(BTHTO)进行几何优化,应用规范不变原子轨道法(GIAO)在6-31G、6-31+G、6-31++G和6-31+G(2d,p)水平上计算了Cis-和Trans-BTHTO的13C-NMR,对13C-NMR谱进行了归属。结果表明,BTHTO噻吩五元环的稳定构象呈半椅式,Cis-和Trans-BTHTO中与硫原子直接碳原子13C-NMR的显著差异主要是由于空间构型不同引起分子的静电势场对相应碳原子的屏蔽作用不同所致。     

Spectra and structure of silicon containing compounds

The Raman (50 to 3200 cm^–1) and infrared (50 to 3500 cm^–1) spectra of chlorodimethylmethoxysilane, Cl(CH₃)₂SiOCH₃, in the vapor and solid phases have been recorded. Raman spectra of the liquid including depolarization ratios have also been recorded. Optimized geometries and conformational stabilities have been obtained from ab initio calculations utilizing the RHF/3–21G* and RHF/6–31G* basis sets. The calculations from both of these basis sets indicated the gauche conformer to be significantly more stable than the trans conformer. Since the gauche has twice the multiplicity of the trans form it is unlikely that the trans conformer will be detected in the fluid phases at room temperature. This is supported by the fact that no infrared or Raman bands were found to vanish in the spectra of the crystalline solid. The vibrational frequencies have been calculated using appropriate scaling factors, and the vibrational spectra are interpreted in detail. The results have been compared with those obtained for some related molecules.Dedicated to Professor Dr. H. Kriegsmann on the occasion of his 70th birthdayFor part XX, see J Raman Spectrosc 26:in press (1995)Analytical R/D Department, Organic Products Division, Miles Inc., Bushy Park Plant. Charleston, SC 9411, USAChemistry Department, Mu'tah University, P.O.Box 7, Mu'tah-Karak, JordanDepartment of Chemistry, Moscow State University, Moscow, B-234, RussiaDepartment of Ceramic Engineering, Inha University, Nam-Ku, Incheon 160, KoreaDepartment of Chemistry, University of Oslo, P.O.Box 1033, 0315 Oslo, Norway     

Conformational stability, vibrational assignmenents, barriers to internal rotations and ab initio calculations of 2-aminophenol (d 0 and d3)

The Raman (3700-100 cm(-1)) and infrared (4000-400 cm(-1)) spectra of solid 2-aminophenol (2AP) have been recorded. The internal rotation of both OH and NH2 moieties produce ten conformers with either Cs or C1 symmetry. However, the calculated energies as well as the imaginary vibrational frequencies reduce rotational isomerism to five isomers. The molecular geometry has been optimized without any constraints using RHF, MP2 and B3LYP levels of theory at 6-31G(d), 6-311+G(d) and 6-31++G(d,p) basis sets. All calculations predict 1 (cis; OH is directed towards NH2) to be the most stable conformation except RHF/6-31++G(d,p) basis set. The 1 (cis) isomer is found to be more stable than 8 (trans; OH is away from the NH2 moiety and the NH bonds are out-of-plane) by 1.7 kcal/mol (598 cm(-1)) as obtained from MP2/6-31G(d) calculations. Aided by experimental and theoretical vibrational spectra, cis and trans 2AP are coexist in solution but cis isomer is more likely present in the crystalline state. Aided by MP2 and B3LYP frequency calculations, molecular force fields, simulated vibrational spectra utilizing 6-31G(d) basis set as well as normal coordinate analysis, complete vibrational assignments for HOC6H4NH2 and DOC6H4ND2 have been proposed. Furthermore, we carried out potential surface scan, to determine the barriers to internal rotations of NH2 and OH groups. All results are reported herein and compared with similar molecules when appropriate.     

Ab initio molecular orbital calculations for 3,6-dihydro-1,2-dithiin and 3,6-dihydro-1,2-dioxin

Optimized geometries and total energies for the conformers of 3,6-dihydro-1,2-dithiin ( 2 ) and 3,6-dihydro-1,2-dioxin ( 3 ) were calculated at several ab initio MO levels: RHF/3-21G(*), RHF/6-31G*, MP2/6-31G*, and MP2/6-31G*/ /RHF/3-21G(*). For the dioxin, in addition to the above levels the corresponding nonextended basis sets ab initio methods were also carried out. The dithiin results are compared with those of simple disulfanes, HSSH and (CH₃)₂S₂, whose optimized geometries agree closely with the observed structures, which is the gauche (C₂ symmetry). For the disulfanes, the gauche geometries from RHF/3-21G(*) are in good agreement with the observed structure while the RHF/3-21G results best fit the dioxin. Pertinent structural data at the RHF/3-21G(*) for the half-chair (C₂) dithiin are: bond lengths, ? SS? , ? CS? , ? CC?, and ? C?C? , 2.050, 1.817, 1.515, and 1.317 Å, respectively; bond angles, CSS, ?CCS, and C?CS, 98.0, 114.2, and 127.8°, respectively; CSSC dihedral angle of 63.2°; and twist angle of 36.5°. The total energy for half-chair dithiin at MP2/6-31G*//RHF/3-21G(*) is less than the planar (C_2v) and the half-boat (C_s) structures by 69.67 and 29.05 kJ/mol, respectively. The calculated structural data (vs. observed) at RHF/3-21G for the half-chair dioxin are: bond lengths, ? OO? , ? CO? , ? CC?, and C?C, 1.464 (1.463), 1.454, 1.509, and 1.313 Å (1.338 Å), respectively; bond angles, COO, ?CCO, and C?CO, 105.0, 109.8 (110.3), and 120.7° (119.9°), respectively; COOC dihedral angle of 79.7° (80 ± 2°); and twist angle of 39.0 (38.3°). The total energy for half-chair dioxin at MP2/6-31G//RHF/3-21G is less than the planar and the half-boat structures by 70.35 and 42.85 kJ/mol, respectively. The total energies calculated at the extended basis sets (*) ab initio levels for the C₂ symmetry dioxin are much lower than those of the nonextended basis sets. © John Wiley & Sons, Inc.     

Theoretical Studies of Distyrylbenzene and its Optical Properties

The electronic and geometrical properties of distyrylbenzene (DSB) are investigated by using chemistry theoretical calculation methods. Specifically, the excited state properties are studied by performing ab initio correlation interaction singlet (CIS) and time‐dependent density functional theory; the ground state and Raman activities are computed by density functional theory with the B3LYP method. Eight conformers of distyrylbenzene are found and they are derived from three isomers which are cis, cis‐, cis, trans‐, and trans, trans‐, respectively. The relative energy shows that each isomer of three types is separated with a large energy barrier, but a small energy difference of each conformer is found if they are in the same type. The transition state also shows the barrier between conformers is lower than isomers. The computed excited transition energies using ZINDO/S based on the optimized geometries at a DFT/B3LYP level with 6–31+G show an excellent agreement with experimental absorption spectra.     

Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods

Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*.     

Conformational stability and vibrations of aminopropylsilanol molecule

Density functional theory (DFT), using the B3-LYP/6-31G(d,p) method have been used to investigate the conformation and vibrational spectra of aminopropylsilanetriol (APST) NH2CH2CH2CH2Si(OH)3. The potential function for CCCSi torsion gives rise to two distinct conformers trans and gauche. The predicted energy of the more stable trans conformer is 337 cm-1 less than the energy of gauche conformer. The calculated barriers to the conformation interchange are: 1095, 2845 and 438 cm-1 for the trans to gauche, gauche to gauche and gauche to trans conformers, respectively. For the trans conformer the potential energy curve for the Si(OH)3 groups torsion in APST has been calculated changing the HOSiC dihedral angle. The barrier for the internal rotation of 3065 cm-1 has been obtained. The optimized molecular structure of APST dimer calculated for trans conformer has a SiOSi angle of 143.2 degrees, and a SiOSi bond length of 0.164 nm. A complete vibrational assignment for both conformers as well as for trans-dimer is supported by the normal coordinate analysis, calculated IR intensities as well as Raman activities. On the basis of the results, the vibrational spectra of APST aqueous solution and APST polymer have been analyzed. The average error between the observed and calculated frequencies is 14 cm-1.     

OPLS all-atom force field for carbohydrates

The OPLS all-atom (AA) force field for organic and biomolecular systems has been expanded to include carbohydrates. Starting with reported nonbonded parameters of alcohols, ethers, and diols, torsional parameters were fit to reproduce results from ab initio calculations on the hexopyranoses, α,β-d -glucopyranose, α,β-d -mannopyranose, α,β-d -galactopyranose, methyl α,β-d -glucopyranoside, and methyl α,β-d -mannopyranoside. In all, geometry optimizations were carried out for 144 conformers at the restricted Hartree–Fock (RHF)/6–31G* level. For the conformers with a relative energy within 3 kcal/mol of the global minima, the effects of electron correlation and basis-set extension were considered by performing single-point calculations with density functional theory at the B3LYP/6–311+G** level. The torsional parameters for the OPLS-AA force field were parameterized to reproduce the energies and structures of these 44 conformers. The resultant force field reproduces the ab initio calculated energies with an average unsigned error of 0.41 kcal/mol. The α/β ratios as well as the relative energies between the isomeric hexopyranoses are in good accord with the ab initio results. The predictive abilities of the force field were also tested against RHF/6–31G* results for d -allopyranose with excellent success; a surprising discovery is that the lowest energy conformer of d -allopyranose is a β anomer. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1955–1970, 1997     

Intramolecular interaction effects and the structure of N2OS and N2O2: An Ab initio study

An ab initio study of O?N? N?S with full geometry optimization has been carried out to corroborate the presence of an interaction between the terminal atoms in this type of structure, which, in O?N? N?O, apparently stabilizes the cis conformer. Using the unscaled 4–31G basis set with a full set of d functions on the sulfur, there is a potential minimun at the trans but not the cis geometry. A gauche conformer with a torsional angle of 77.2° is the most stable. With N₂O₂ this basis set gives potential minima at both the cis and trans geometries, but the trans conformer is slightly more stable, contrary to experiment and the results of (7,3) basis-set calculations reported in the literature in which Gaussian lobe functions were employed. Using a (9,5) basis set there is no longer a potential minimum at the cis geometry, and a gauche structure is more stable than the cis conformer as in the case of N₂OS with the less-extended basis set. Force constants (harmonic and anharmonic), compliance constants, relaxed force constants, and interaction-displacement coordinates for both molecules are compared for key structural elements.     

Aziridinyl ketones and their heteroanalogs. 5. Synthesis and structures of 2-aryl-3-aroylaziridines

A number of trans- and cis-isomeric 1-R-2-aryl-3-aroylaziridines were synthesized, and their IR spectra were studied. Intramolecular hydrogen bonding is realized in the trans isomers when R = H, and they exist in the only possible conformation (intermediate between a gauche and a cisoid conformation). cis-Isomers II (R = alkyl) exist in solutions in the form of two conformers, viz., gauche and cisoid conformers, and the gauche conformer is thermodynamically preferable.See [1] for Communication A.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No, 11, pp. 1489–1494, November, 1980.     

Effect of basic set quality and electron correlation on the scale factors of a harmonic force field

The completely optimized structure and harmonic force field of s-trans-buta-1,3-diene are reported at the MP2/6-31G and MP2/6-31G* levels of computation. Sets of empirical scale factors for the calculated force fields are derived and compared with the corresponding values computed at the RHF/4-31G and RHF/6-31G levels. Changes in the scale factors for this series of force fields are discussed. The vibrational frequencies are also reported for thirteen isotopomers of s-trans-buta-1,3-diene using the MP2/6-31G* force field. Some characteristics of the gauche and cis forms of buta-1,3-diene are also given.     

A systematic study of minima in alanine dipeptide

The alanine dipeptide is a standard system to model dihedral angles in proteins. It is shown that obtaining the Ramachandran plot accurately is a hard problem because of many local minima; depending on the details of geometry optimizations, different Ramachandran plots can be obtained. To locate all energy minima, starting from geometries from MD simulations, 250,000 geometry optimizations were performed at the level of RHF/6-31G*, followed by re-optimizations of the located 827 minima at the level of MP2/6–311++G**, yielding 30 unique minima, most of which were not previously reported in literature. Both in vacuo and solvated structures are discussed. The minima are systematically categorized based on four backbone dihedral angles. The Gibbs energies are evaluated and the structural factors determining the relative stabilities of conformers are discussed. © 2018 Wiley Periodicals, Inc.     

Conformational stability, optimized geometries, vibrational and electronic spectra of methacryloyl bromide in ground and excited electronic states

In order to understand conformational isomerism in methacryloyl bromide (MABR) in the ground (S(0)) and the first excited (S(1)) electronic states and to interpret the vibrational and electronic spectra of its conformers in the S(0) state, quantum mechanical calculations using Density Functional Theory (DFT) and RHF methods with extended basis sets 6-31G, 6-31G** and 6-311+G(d,p) have been conducted. In RHF calculations, electron correlation effects have been included at the M?ller-Plesset MP2 level. It is inferred that in both the electronic states the molecule may exist in two isomeric forms-s-trans and s-cis; the former being more stable than the later by about 1.629 kcal mol(-1) in the S(0) state and by about 2.218 kcal mol(-1) in the S(1) state. Electronic transition tends to increase the s-trans/s-cis and s-cis/s-trans, rotational barriers from 7.059 kcal mol(-1) (2468.1 cm(-1)) and 5.428 kcal mol(-1) (1897.8 cm(-1)) in S(0) state to 23.594 kcal mol(-1) (8249.4 cm(-1)) and 21.376 kcal mol(-1) (7473.9 cm(-1)) in the S(1) state. Completely optimized geometries of the two conformers in S(0) state reveal that while there is no significant difference in their bond lengths, some of the bond angles associated with COBr group are appreciably different. Electronic excitation tends to change both the bond lengths and bond angles. Based on suitably scaled DFT and RHF results obtained from the use of 6-31G** and 6-311+G(d,p) basis sets, a complete assignment is provided to the fundamental vibrational bands of both the s-trans and s-cis conformers in terms of frequency, form and intensity of vibrations and potential distribution across the symmetry coordinates in the S(0) state and a comparison has been made with experimental assignments. A theoretical prediction of the electronic transitions in the near UV-region in the two conformers and their tentative assignment has been provided on the basis of CI level calculations using 6-31G basis set.     

Infrared and Raman spectra, conformational stability, ab initio calculations and vibrational assignments for trans-3-chloropropenoyl chloride

The infrared (3500-30 cm(-1)) spectra of gaseous and solid and the Raman (3500-200 cm(-1)) spectra of the liquid with quantitative depolarization ratios and solid trans-3-chloropropenoyl chloride (trans-ClCHCHCClO) have been recorded. These data indicate that both the anti (carbonyl bond trans to the carbon-carbon double bond) and syn conformers are present in the fluid states but only the anti conformer is present in the crystalline state. The mid-infrared spectra of the sample dissolved in liquid xenon as a function of temperature (-55 to -100 degrees C) have been recorded. Utilizing conformer pairs at 870 and 725 cm(-1), 1215 and 1029 cm(-1), and 1215 and 1228 cm(-1), the enthalpy difference has been determined to be 136+/-5 cm(-1) (389+/-14 cal mol(-1)) with the anti conformer the more stable form. Optimized geometries and conformational stabilities were obtained from ab initio calculations at the levels of RHF/6-31G(d), MP2/6-31G(d), MP2/6-311 + + G(d,p), MP2/6-311 + + G(2d,2p) and MP2/6-311 + + G(2df,2pd) with only the latter two calculations predicting the anti rotamer to be the more stable form. The vibrational frequencies, harmonic force constants and infrared intensities were obtained from the MP2/6-31G(d) calculations, whereas the Raman activities and depolarization values were obtained from the RHF/6-31G(d) calculations. The spectra are interpreted in detail and the results are compared with those obtained for some related molecules.     

Ab initio studies on polymers. VI. Torsional potential in regular polyethylene chains

Ab initio crystal orbital calculations have been performed on regular polyethylene chains applying basis sets of minimal and double-zeta quality. Relative stabilities of periodic all-trans, all-gauche, and alternating trans–gauche conformers have been evaluated, including extensive geometry optimization. Potential curves for a simultaneous rotation around C? C single bonds from the all-trans to the all-gauche conformation have been computed applying the rigid-rotor approximation, the flexible-rotor approximation, and an additional reoptimization of C? C distances. A rigid-rotor potential curve from the all-trans to the alternating trans-gauche conformation has been computed as well. Results obtained are compared with ab initio calculations on butane and pentane and with semiempirical and empirical force-field studies on polyethylene.