Molecular structure and vibrational spectra of lepidine and 2-chlorolepidine by density functional theory and ab initio Hartree–Fock Calculations

The molecular geometry and vibrational frequencies of lepidine and 2-chlorolepidine in the ground state have been calculated by using the Hartree–Fock and density functional methods (B3LYP) with 6-31G (d) as the basis set. The optimized geometric bond lengths obtained by using B3LYP and bond angles obtained by HF that correspond to the experimental values of 2-cl-lepidine molecule were given. Comparison of the observed fundamental vibrational frequencies of lepidine and 2-chlorolepidine, and calculated results by density functional B3LYP and Hartree–Fock methods indicates that B3LYP is superior to the scaled Hartree–Fock approach for molecular vibrational problems.     

Molecular structure and vibrational spectra of indole and 5-aminoindole by density functional theory and ab initio Hartree–Fock calculations

The molecular geometry and vibrational frequencies of indole and 5-aminoindole in the ground state have been calculated by using the Hartree–Fock and density functional method with 6-311++G(d,p) basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of indole and 5-aminoindole with the calculated results by density functional and Hartree–Fock methods indicates that B3LYP is superior to the scaled Hartree–Fock approach for molecular vibrational problems. The theoretical spectrograms for FT-IR spectrum of 5-aminoindole have been constructed.     

Molecular structure and vibrational spectra of N-mesylhydroxylamin and N-mesyl-O-methylhydroxylamin by density functional theory and ab initio Hartree–Fock calculations

The molecular geometry and vibrational frequencies of N-mesylhydroxylamin (N-MHN) and N-mesyl-O-methylhydroxylamin (N-MMHN) in the ground state have been calculated using the Hartree–Fock and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric band lengths and bond angles obtained by using HF and DFT (B3LYP) show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of N-MHN and N-MMHN and calculated results by density functional B3LYP and Hartree–Fock methods indicate that B3LYP is superior to the scaled Hartree–Fock approach for molecular vibrational problems.     

Vibrational spectra and potential energy distributions for 3-cyclopropenecarboxaldehyde by density functional and normal coordinate calculations

The structural stability and internal rotation in 3-cylopropenecarboxaldehyde were investigated by ab initio calculations with 6-311++G^** basis set. The calculations were carried out at the restricted Hartree–Fock (HF) and the Density Functional B3LYP levels. The vibrational frequencies were computed at HF and DFT-B3LYP levels. Normal coordinate calculations were carried out and potential energy distributions were calculated for the cis and the trans conformers of the molecule.     

Infrared, and Raman spectra, conformational stability, normal coordinate analysis, ab initio calculations, and vibrational assignment of 1-chlorosilacyclobutane

The infrared spectra (3500–40 cm⁻¹) of gaseous and solid and the Raman spectra (3500–30 cm⁻¹) of liquid and solid 1-chlorosilacyclobutane, c-C₃H₆SiClH, have been obtained. Both the axial and equatorial conformers with respect to the chlorine atom have been identified in the fluid phases. Variable temperature (−105 to −150°C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data, the enthalpy difference has been determined to be 211±17 cm⁻¹ (2.53±0.21 kJ/mol), with the equatorial conformer being the more stable form and the only conformer remaining in the annealed solid. At ambient temperatures, approximately 26% of the axial conformers are present in the vapor phase. A complete vibrational assignment is proposed for the equatorial conformer, and many of the fundamentals of the axial conformers have also been identified. The vibrational assignments are supported by normal coordinate calculations utilizing ab initio force constants. Complete equilibrium geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities, and depolarization ratios have been determined for both rotamers by ab initio calculations employing the 6-31G(d) basis set at the levels of restricted Hartree–Fock (RHF) and/or Moller–Plesset (MP) to second order. Structural parameters have also been obtained using MP2/6-311+G(d,p) ab initio calculations. The r₀ parameters for both conformers are obtained from a combination of the ab initio predicted values and the twelve previously reported microwave rotational constants. The results are discussed and compared to those obtained for some similar molecules.     

Are donor–acceptor self organised aromatic systems NLO (non-linear optical) active?

This contribution to the understanding of non-linear optical (NLO) properties of organic systems is concentrated on donor–acceptor aromatic systems such as [2]catenanes. We report accurate ab initio quantum chemical calculations of the first static hyperpolarizability (β) of donor–acceptor aromatic systems containing naphthalene and anthracene as electron donors and pyromellitimide and naphthadiimide as electron acceptors. We investigate the NLO effect when the donor acceptor units are not connected through a bridge. In this kind of system the electronic communication between donor and acceptor is solely due to through space charge transfer mechanism. Geometries of all molecular systems were optimised at the Hartree–Fock level with STO-3G minimal basis set and with the 3-21G split valence basis and finally with 6-31G basis set using GAUSSIAN 98W. The first static hyperpolarizabilities of these molecular systems were calculated using Hartree–Fock level using 6-31G basis set using GAUSSIAN 98W. To understand the possibility of developing these systems as NLO materials we have also calculated the linear and nonlinear optical properties of bridged donor–acceptor systems. The study suggested that these unconnected donor–acceptor systems equivalent to some [2]catenanes reported in literature in general have little influence on the first static hyperpolarizability, however, the linked macro cyclic systems may have potential applications in the development of non-linear optical materials.     

The effect of electron correlation on the conformational space of melatonin

The pineal gland hormone melatonin regulates several physiological processes including circadian rhythm and also alleviates oxidative stress‐induced degenerative diseases. In spite of its important biological roles, no high level ab initio conformational study has been conducted to reveal its structural features. In this work, the conformational flexibility of melatonin was investigated using correlated ab initio calculations. Conformers, obtained previously at the Hartree‐Fock level (HF/6‐31G*), were fully optimized using second order Møller‐Plesset perturbation theory applying the frozen core approximation (MP2(FC)/6‐31G*). Furthermore, single‐point MP4(SDQ,FC)/6‐31G*//MP2(FC)/6‐31G* computations were performed to investigate the effect of higher order perturbation terms. The HF and MP2 conformational spaces are considerably different: the initial 128 structures converged into 102 different local minima as confirmed by frequency calculations; 28 new minima appeared and 26 previous HF local minima disappeared; no “all‐trans” C3 side chain conformations are seen at the MP2(FC) level. The MP2 global minimum conformation is stabilized by an aromatic‐side chain interaction. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008     

Conformational and structural studies of ethyl fluorosilane from temperature dependent FT-IR spectra of krypton solutions and ab initio calculations

The infrared spectra (3200–30 cm⁻¹) of gaseous and solid ethyl fluorosilane, CH₃CH₂SiH₂F, have been recorded. Additionally, the Raman spectra (3200–30 cm⁻¹) of the liquid and solid have been recorded and quantitative depolarization values obtained. Both the gauche and trans conformers have been identified in the fluid phases but only the gauche conformer remains in the solid. Variable temperature (−105 to −150°C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data, the enthalpy difference has been determined to be 54±16 cm⁻¹ (646±191 J/mol) with the gauche conformer the more stable form. This is consistent with the predictions from ab initio, MP2/6-311+G(2d,2p), calculation as well as those with smaller basis sets with full electron correlations. A complete vibrational assignment is proposed for both the trans and gauche conformers based on infrared band contours, relative intensities, depolarization values, and group frequencies, which are supported by normal-coordinate calculations utilizing the force constants from MP2/6-31G(d) ab initio calculations. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing a variety of basis sets up to 6-311+G(2d,2p) at levels of restricted Hartree–Fock (RHF) and/or Moller Plesset to the second order (MP2) with full electron correlation. The adjusted r₀ parameters have been obtained for both conformers from a combination of the previously reported rotational constants with ab initio predicted values. All results are compared to similar quantities of some corresponding molecules.     

Infrared-induced conformational isomerization and vibrational relaxation dynamics in melatonin and 5-methoxy-N-acetyl tryptophan methyl amide

The conformational isomerization dynamics of melatonin and 5-methoxy N-acetyltryptophan methyl amide (5-methoxy NATMA) have been studied using the methods of IR-UV hole-filling spectroscopy and IR-induced population transfer spectroscopy. Using these techniques, single conformers of melatonin were excited via a well-defined NH stretch fundamental with an IR pump laser. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were re-cooled into their zero-point levels, partially re-filling the hole created in the ground state population of the excited conformer, and creating gains in population of the other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion via an UV probe laser. The isomerization quantum yields for melatonin show some conformation specificity but no hint of vibrational mode specificity. In 5-methoxy NATMA, no isomerization was observed out of the single conformational well populated in the expansion in the absence of the infrared excitation. In order to study the dependence of the isomerization on the cooling rate, the experimental arrangement was modified so that faster cooling conditions could be studied. In this arrangement, the pump and probe lasers were overlapped in space in the high density region of the expansion, and the time dependence of the zero-point level populations of the conformers was probed following selective excitation of a single conformation. The analysis needed to extract isomerization quantum yields from the timing scans was developed and applied to the melatonin timing scans. Comparison between the frequency and time domain isomerization quantum yields under identical experimental conditions produced similar results. Under fast cooling conditions, the product quantum yields were shifted from their values under standard conditions. The results for melatonin are compared with those for N-acetyl tryptophan methyl amide.     

DFT studies on endohedral fullerene C@C60: C centers the C60 cage

Structural and electronic properties of C@C₆₀ were studied via Hartree–Fock self-consistent field (SCF) and density functional B3LYP levels of theory with the STO-3G, 6-31G(d) and 6-31G(d, p) basis sets. Both singlet and triplet were considered. The triplet structure with C on the center of the C₆₀ cage was proved to be global minimum on the C@C₆₀ molecular potential energy surface. The calculated HOMO-LUMO gaps as well as the electron affinity (EA) and the ionization potential (IP) were also presented as an indicator of the kinetic stability.     

Incoherent scattering of 59.54 keV γ-rays at small momentum transfers

Whole atom differential incoherent scattering cross sections for 59.54 keV γ-rays were measured for a number of elements in the region 29Z82 at scattering angles 90, 60, 45 and 30° employing a reflection geometry set up and a graded shielding arrangement. A 6 cm³ HPGe detector was used to detect the scattered γ-rays. All the 49 cross sections reported in this paper constitute the first experimental measurement and serve to fill the existing gaps in the cross-section data. The comparison of the measured cross sections with Klein–Nishina theory shows electron binding effects becoming significantly large at small scattering angles and for high Z elements. Incoherent scattering functions S(x, Z), corresponding to momentum transfer values 3.395, 2.4, 1.84 and 1.242 Å⁻¹ were extracted from the measured cross sections and were compared with the theoretical predictions. The non-relativistic Hartree–Fock theory is found to be comparatively better than the Thomas–Fermi model. At small momentum transfer values and for high Z elements experimental values deviate more from Hartree–Fock theory also suggesting the need for a more rigorous second-order S-matrix calculations.     

Molecular modelling of some para-substituted aryl methyl telluride and diaryl telluride antioxidants

Quantum mechanical calculations using the 3-21G(d) basis-set were performed on some p-substituted diaryl tellurides and aryl methyl tellurides, and the corresponding cationic radicals of these compounds. Calculated relative radical stabilization energies (RSE:s) were shown to correlate with experimentally determined peak oxidation potentials (R=0.93) and ¹²⁵Te-NMR chemical shifts (R=0.91). A good correlation was also observed between the RSE:s and the Mulliken charge at the tellurium atoms (R=0.97). The results showed that Hartree–Fock calculations using the 3-21G(d) basis set was sufficiently accurate for estimating the impact of p-substituents in aryl tellurides on experimentally determined properties such as peak oxidation potentials and ¹²⁵Te-NMR chemical shifts.     

Structure and vibrational spectra of the salts of mononitroalkanes

The molecular geometries of the anions of nitromethane and 2-nitropropane were optimised and their harmonic force fields were calculated by the RHF/6-311G(d,p), MP2/6-311G(d,p) and B3LYP/6-311G(d,p) methods. The force fields obtained made it possible to reliably interpret the IR and Raman spectra of the Na⁺ salt of nitromethane, d₂-nitromethane and 2-nitropropane. The assignment proposed significantly improves the interpretation of vibrational spectra known so far. Some general conclusions on geometry and vibrational spectra of the salts of mononitroalkanes studied are made. The hybrid density functional method used (B3LYP) is shown to be in better agreement with experimental data available than the Hartree–Fock methods.     

Theoretical determination of molecular structure and conformation : Part 12. Puckering of 1,3,5-cycloheptatriene, 1H-azepine, oxepine and their norcaradienic valence tautomers

Restricted Hartree—Fock calculations have been carried out for 1,3,5-cycloheptatriene, norcaradiene, 1H-azepine, benzenimine (azanorcardiene), oxepine and benzene oxide (oxanorcaradiene) employing the STO—3G, 4—31G and 6—31G^* basis sets. Theoretical geometries, conformations and barriers to ring inversion have been obtained and compared with the available experimental structural data. It has been found that the cyclotrienes possess a boat conformation with a constant admixture of 22% chair character leading to a flattening of the triene part and π-electron delocalization typical for a planar polyene. The structural data obtained in this work suggest that cyclic delocalization of either 6π (homoaromaticity) or 8π electrons (antiaromaticity) is not present in the three cyclotrienes. The former possibility, however, cannot be excluded in the case of the three norcaradienes.     

A full conformational space analysis of bilirubin

Ab initio methods were utilized in a gas-phase systematic conformational search of bilirubin conformers. The whole molecule was divided into four fragments. Most stable conformers of them were employed to build 196 conformers of the complete bilirubin molecule. Initial geometries were optimized using HF/3-21G level of theory and the minimum energy conformers were then reoptimized at B3LYP/6-31G(d) level. Ridge-tile conformer was the most stable one, in perfect agreement with X-ray data. We found that while tetrapyrrole backbone shows some flexibility, propionic acid side chains have a greater influence in bilirubin conformation because they can interact through different hydrogen bond patterns with the backbone and between them.     

Theoretical study on infrared vibrational spectra of boric-acid in gas-phase using density functional methods

Density functional theory (DFT) methods with various exchange-correlation functionals such as SVWN, BVWN, BVWN5, BLYP, B1LYP, B3LYP, B3PW91, and BH and H are employed in a theoretical study of molecular boric-acid in gas-phase. In the calculations, the split valence 6-311++G** and 6-31G* basis sets were used. The geometry, zero-point vibrational energies (ZPVEs), and harmonic infrared vibrational (IR) frequencies are predicted. The calculated C_3h-symmetry geometrical parameters are compared with Hartree–Fock (HF) calculation results and experimental data. IR frequencies predicted by the BLYP, B3LYP, and B3PW91 calculations are in good agreement with experimental data. The frequency calculations presented here also suggest that the C_3h-symmetrical structure corresponds to a minimum in the potential energy surface, but neither is D_3h- or C₃-symmetrical structure.     

Conformational analysis of polymethylated derivatives of piperidine by the method of molecular mechanics

The conformational (steric) energies of different conformers and thus the type of dominant conformation were determined by the method of molecular mechanics for polysubstituted derivatives of piperidine. The chair conformation dominates for polymethylated 4-piperidines. The half-chair conformation is preferred for 1-methyl-3-methylene-4-piperidone, and the sofa conformation is preferred for analogous polymethylated enones.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 1, pp. 91–97, January, 1991.     

On the difference between hydrogen fluoride and hydrogen chloride crystals

The geometrical and energetical parameters of hydrogen fluoride and hydrogen chloride crystals are calculated using the periodic Hartree–Fock method with 6-31G and 6-31G(d,p) basis sets. The comparison of the stabilisation energies reveals that HCl crystals are about 75% less stable than HF crystals. The activation energy for collective proton movements are computed and discussed in view of data of isolated infinite chains. The barriers of 13.1 and 40.0 kcal mol⁻¹ at 6-31G(d,p) level are found for HF and HCl crystals.     

Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium

The conformational properties of the diphosphate linkage have been studied with ab initio methods using the dimethyl diphosphate dianion (1) and magnesium dimethyl diphosphate (2) as models. The ab initio energy and geometry of the conformers around the P-O bonds have been determined at the self-consistent-field (SCF) using the 6-31G* and the tzp basis sets; whereas, the 6-31G* basis set alone has been used for 2. In addition, the adiabatic connection method (ACM) of density functional theory (DFT) using the dzvp basis set has been employed for 1. The optimization of all possible staggered conformers assumed for the four P-O bonds, led to nine minima for 1. In agreement with the general anomeric effect, the sc conformation about the P-O bonds is clearly preferred over the ap one. Vibrational frequencies were calculated at the SCF level using the 6-31G* basis set and used to evaluate zero-point energies, thermal energies, and entropies for all minima of 1. The effect of zero-point energies and thermal energies is quite small. However, the effect of entropies, mainly resulting from a multiplicity contribution, changes the stability of the conformers. For each minimum of 1, up to six different arrangements of the Mg²⁺ were used to determine minima of 2. This procedure led to 21 distinct minima. The presence of the magnesium counter-ion appeared to completely change the structure and relative energy of the conformers. The preferred structures of the complex exhibit the (sc, ap) orientation around the two central P–O bonds and an arrangement in which the magnesium cation is coordinated by three phosphoryl oxygen atoms. The results of this work clearly demonstrate that interactions with the metal counter-ion can induce conformational changes in the overall 3D-shape adopted by molecules containing diphosphate linkages. The PM3 and MNDO quantum semi-empirical methods and molecular mechanics methods using the CVFF force field were tested and large differences in the minimum structures, as well as in the conformational energies between these and ab initio methods, are discussed.     

Infrared and Raman spectra, conformational stability, ab initio calculations, and vibrational assignments for methylaminothiophosphoryl difluoride

Infrared spectra (4000–50 cm⁻¹) of the vapor, amorphous and crystalline solids and Raman spectra (3600–10 cm⁻¹) of the liquid with qualitative depolarization data as well as the amorphous and crystalline solids of methylaminothiophosphoryl difluoride, CH₃N(H)P(=S)F₂, and three deuterated species, CD₃N(H)P(=S)F₂, CH₃N(D)P(=S)F₂, and CD₃N(D)P(=S)F₂, have been recorded. The spectra indicate that in the vapor, liquid and amorphous solid a small amount of a second conformer is present, whereas only one conformer remains in the low temperature crystalline phase. The near-infrared spectra of the vapor confirms the existence of two conformers in the gas phase. Asymmetric top contour simulation of the vapor shows that the trans conformer is the predominant vapor phase conformer. From a temperature study of the Raman spectrum of the liquid the enthalpy difference between the trans and near-cis conformers was determined to be 368±15 cm⁻¹ (4.41±0.2 kJ/mol), with the trans conformer being thermodynamically preferred. Ab Initio calculations with structure optimization using the 6-31G(d) and 6-311+G(d,p) basis sets at the restricted Hartree–Fock (RHF) and/or with full electron correlation by the perturbation method to second order (MP2) support the occurrence of near-trans (5° from trans) and near-cis (20° from cis) conformers. From the RHF/6-31G(d) calculation the near-trans conformer is predicted to be the more stable form by 451 cm⁻¹ (5.35 kJ/mol) and from the MP2/6-311+G(d,p) calculation by 387 cm⁻¹ (4.63 kJ/mol). All of the normal modes of the near-trans rotamer have been assigned based on infrared band contours, depolarization values and group frequencies and the assignment is supported by the normal coordinate calculation utilizing harmonic force constants from the MP2/6-31G(d) ab initio calculations.