Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-mercaptopropanoic acid

2-(4-Fluorobenzylideneamino)-3-mercaptopropanoic acid (4-FC) was synthesized through the reaction of 4-fluorobenzaldehyde and l-cysteine in refluxing EtOH. Its structure was verified by (1)H NMR, FT-IR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains, respectively. The vibrational wavenumbers of 4-FC were calculated at same level. The scaled theoretical spectra using B3LYP methods, which are in a good agreement with the experimental ones, are superior to those using HF methods.     

Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid

2-(4-Fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid (4-FT) was synthesized through the reaction of 4-fluorobenzaldehyde and l-tyrosine in refluxing EtOH. The structure of 4-FT was verified by measuring 1H NMR, FTIR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains. The vibrational wavenumbers of 4-FT were calculated at same levels. The scaled spectra using B3LYP methods, which are in a good agreement with the measured spectra, are superior to those calculated using HF methods.     

Ab initio Hartree-Fock and density functional theory study on molecular structures, energies, and vibrational frequencies of conformations of 2-hydroxy-3-nitropyridine and 3-hydroxy-2-nitropyridine

The optimized molecular structures, vibrational frequencies and corresponding vibrational assignments of conformations of 2-hydroxy-3-nitropyridine and 3-hydroxy-2-nitropyridine molecules have been investigated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d,p) basis set. The comparison of the experimental and calculated spectra of the molecules have shown that they exist in two conformations with the two OH bond angles (110 degrees and 250 degrees ) respective to the CO bond in the ground state and their energy curves having two minimums have been drawn.     

Ab initio and density functional theory based studies on collagen triplets

An understanding of the amino acid sequence dependent stability of polypeptides is of renowned interest to biophysicists and biochemists, in order to identify the nature of forces that stabilize the three-dimensional structure of proteins. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed. It is found from this study that proline can stabilize the collagen triplet only when other residues are also in the polyproline II conformation. Solvation studies of various triplets indicate that the presence of polar residues increases the free energy of solvation. Especially the triplets containing arginine residues displays a higher solvation free energy. The chemical hardness of all the triplets in collagen-like conformation has been found to be higher than that in the extended conformation. Studies on Gly–X–Y, Gly–X–Hyp, and Gly–Pro–Y triplets confirm that there will be local variations in the stability of collagen along the entire sequence.     

Molecular structures and vibrational frequencies of 2-, 3- and 4-pyridine carboxaldehydes by ab initio Hartree-Fock and density functional theory calculations

The optimised molecular structures, vibrational frequencies and corresponding vibrational assignments of the cis and trans conformers of 2-, 3- and 4-pyridine carboxaldehydes have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d, p) basis set. The calculations were adapted to the C(S) symmetries of all the molecules. The mean vibrational deviations between the vibrational frequency values of the two conformers of all the compounds have been seen to increase while the relative energies increase and it was concluded the more different the molecular structure of the two conformers is the higher the relative energy is between them, and thus a bigger mean vibrational deviation.     

Ab initio benchmark calculations on Ca(II) complexes and assessment of density functional theory methodologies

A set of benchmark results for the geometries, binding energies, and protonation affinities of 24 complexes of small organic ligands with Ca(II) is provided. The chosen level of theory is CCSD(T)/CBS obtained by means of a composite procedure. The performance of four density functionals, namely, PW91, PBE, B3LYP, and TPSS and several Pople-type basis sets, namely, 6-31G(d), 6-31+G(d), 6-31+G(2d,p) and 6-311+G(d) have been assessed. Additionally, the nature of the metal ligand bonding has been analyzed by means of the Symmetry Adapted Perturbation Theory (SAPT). We have found that the B3LYP hybrid functional, in conjunction with either the polarized double-ζ 6-31+G(2d,p) or the triple-ζ 6-311+G(d) basis sets, yields the closest results compared to the benchmark data. The SAPT analysis stresses the importance of induction effects in the binding of these complexes and suggests that consideration of classical electrostatic contributions alone may not be reliable enough for the prediction of relative binding energies for Ca(II) complexes.     

Hartree-Fock and density functional theory study of alpha-cyclodextrin conformers

Herein, we report the geometry optimization of four conformers of alpha-cyclodextrin (alpha-CD) by means of PM3, HF/STO-3G, HF/3-21G, HF/6-31G(d), B3LYP/6-31G(d), and X3LYP/6-31G(d) calculations. The analysis of several geometrical parameters indicates that all conformers possess bond lengths, angles, and dihedrals that agree fairly well with the crystalline structure of alpha-CD. However, only three of them (1-3) resemble the polar character of CDs and show intramolecular hydrogen-bonding patterns that agree with experimental NMR data. Among them, conformer 3 appears to be the most stable species both in the gas phase and in solution; therefore, it is expected to be the most suitable representative structure for alpha-CD conformation. The purpose of selecting such a species is to identify an appropriate structure to be employed as a starting point for reliable computational studies on complexation phenomena. Our results indicate that the choice of a particular alpha-CD conformer should affect the results of ab initio computational studies on the inclusion complexation with this cyclodextrin since both the direction and the magnitude of the dipole moment depend strongly on the conformation of alpha-CD.     

Conformational study on indoline compounds. Structures of 2-phenyl-3-arylimino-3H-indole 1-Oxide, 1,2-dihydro-2-phenyl-2-benzyl- and 2-tert-Butyl-3-phenylimino-3H-indole 1-oxyls

Reacting 1-hydroxy-2-phenylindole with nitrosobenzene, 2-phenyl-3-phenylimino-3H-indole 1-oxide (1) is produced in only one of the two possible diastereomers. The latter reacts with tert-butylmagnesium chloride and benzylmagnesium chloride giving, after oxidation, the corresponding aminoxyls which show the same configuration of the phenylimino group at C-3 as in 1 . This has been demonstrated by means of nmr spectros-copy and X-ray crystal structure and represents an unexpected stereospecific reaction.     

Molecular structure and vibrational assignment of 2-,4-,6-methylquinoline by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments of 2-,4-,6-methylquinoline (2-,4-,6-mq) in the ground state were performed by HF and DFT/B3LYP levels of theory using the 6-31++G(d,p) basis set. Harmonic and anharmonic vibrational frequencies were calculated. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method by using parallel quantum mechanic solutions program. The general agreements between the observed and calculated frequencies are shown.     

Vibrational spectra and molecular structure of chiral and racemic 4-phenyl-1,3-oxazolidin-2-one by density functional theory and ab initio Hartree-Fock calculations

The vibrational frequencies and molecular geometry of (R)- and (rac)-4-phenly-1,3-oxazolidin-2-one (4-POO) 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 bond lengths are described better by HF while bond angles are reproduced more accurately by DFT (B3LYP). Comparison of the observed fundamental vibrational frequencies of (R)-POO and (rac)-4-POO 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.     

Ab initio density functional study of MgO (001) surface with topological defects

Magnesium oxide (MgO) is a useful material because of its catalytical properties. Moreover, surface defects have been found to play a crucial role in determining the activity and selectivity of catalytic surfaces. We present the results of a theoretical investigation of the electronic structure of the MgO (001) surface with three different topological defects. Our calculations are based on density functional theory (DFT) and the pseudopotential method. Slab geometry and periodic boundary conditions have been included with occupied orbitals expanded in plane waves. We compare the obtained results of the (001) MgO clean surface with those containing topological defects. The density of states DOS is analyzed in each case, as well as the chemical nature of the atoms belonging to the defects. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Vibrational spectrum and assignments of 2-(4-methoxyphenyl)-1H-benzo[d]imidazole by ab initio Hartree-Fock and density functional methods

The room temperature attenuated total reflection Fourier transform infrared spectrum of the 2-(4-methoxyphenyl)-1H-benzo[d]imidazole has been recorded with diamond/ZnSe prism. The conformational behaviour, structural stability of optimized geometry, frequency and intensity of the vibrational bands of the title compound were investigated by utilizing ab initio calculations with 6-311G** basis set at HF, B3LYP, BLYP, B3PW91 and mPW1PW91 levels. The harmonic vibrational frequencies were calculated and scaled values have been compared with experimental IR spectrum. The observed and the calculated frequencies are found to be in good agreement. The theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions using VEDA 4 program. Furthermore, the optimal uniform scaling factors calculated for the title compound are 0.9120, 0.9596, 0.9660, 0.9699, and 0.9993 for HF, mPW1PW91, B3PW91, B3LYP and BLYP methods, respectively.     

Ab initio/density functional theory and multichannel RRKM study for the ClO + CH2O reaction

The potential energy surface for the CH(2)O + ClO reaction was calculated at the QCISD(T)/6-311G(2d,2p)//B3LYP/6-311G(d,p) level of theory. The rate constants for the lower barrier reaction channels producing HOCl + HCO, H atom, OCH(2)OCl, cis-HC(O)OCl and trans-HC(O)OCl have been calculated by TST and multichannel RRKM theory. Over the temperature range of 200-2000 K, the overall rate constants were k(200-2000K) = 1.19 x 10(-13)T(0.79) exp(-3000.00/T). At 250 K, the calculated overall rate constant was 5.80 x 10(-17) cm(3) molecule(-1) s(-1), which was in good agreement with the experimental upper limit data. The calculated results demonstrated that the formation of HOCl + HCO was the dominant reaction channel and was exothermic by 9.7 kcal/mol with a barrier of 5.0 kcal/mol. When it retrograded to the reactants CH(2)O + ClO, an energy barrier of 14.7 kcal/mol is required. Furthermore, when HOCl decomposed into H + ClO, the energy required was 93.3 kcal/mol. These results suggest that the decomposition in both the forward and backward directions for HOCl would be difficult in the ground electronic state.     

Ab initio density functional theory investigation of Li-intercalated zinc oxide nanotube bundles

We have investigated the energetic, and geometric and electronic structure of Li-intercalated (5,5) zinc oxide nanotube (ZnONT) bundles via density functional theory as implemented in the code WIEN2k. Our results showed that the most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the ZnONTs. All the Li-intercalated (5,5) ZnONT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial spaces are susceptible for intercalation. The present calculations suggest that the single-walled zinc oxide nanotube (SwZnONT) bundle is a promising candidate for the anode material in battery applications.     

Density functional and Ab initio study of Cr(CO)n (n = 1-6) complexes

Cr(CO)n (n = 1-6) systems were studied for all possible spin states using density functional and high-level ab initio methods to provide a more complete theoretical understanding of the structure of species that may form during ligand dissociation of Cr(CO)6. We carried out geometry optimizations for each system and obtained vibrational frequencies, sequential bond dissociation energies (BDE), and total CO binding energies. We also compared the performance of various DFT functionals. Generally, the ground states of Cr(CO)6, Cr(CO)5, and Cr(CO)4, whose spin multiplicity is a singlet, are in good agreement with both previous theoretical results and currently available experimental data. Calculations on Cr(CO)3, Cr(CO)2, and CrCO provide new findings that the ground state of Cr(CO)3 might be a quintet with C2v symmetry instead of a singlet with C3v symmetry, and the ground state of Cr(CO)2 is not a linear quintet, as suggested by previous DFT calculations, but rather a linear septet. We also found that nonet states of Cr(CO)2 and CrCO display partial C-O bond breakage.     

Vibrational spectra and assignments of 2-amino-5-iodopyridine by ab initio Hartree-Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra of 2-amino-5-iodopyridine were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) methods with the 6-31G(d,p) basis set for C, N, H and LANL2DZ pseudopotential for I. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of 2-amino-5-iodopyridine is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.     

Molecular structure and vibrational assignment of melaminium phthalate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

The molecular geometry, the normal mode frequencies and corresponding vibrational assignment of melaminium phthalate (C₃H₇N₆⁺·C₈H₅O₄⁻) in the ground state were performed by HF and B3LYP levels of theory using the 6-31G(d) basis set. The optimized bond length numbers with bond angles are in good agreement with the X-ray data. The vibrational spectra of melaminium phthalate which is calculated by HF and B3LYP methods, reproduces vibrational wave numbers with an accuracy which allows reliable vibrational assignments. The title compound has been studied in the 4000–100 cm⁻¹ region where the theoretical evaluation and assignment of all observed bands were made.     

Synthesis and properties of 1-methyl-2-phenyl-5-(2-furyl)- and 1-methyl-2-phenyl-5-(2-thienyl)imidazoles

2-Phenyl-5-(2-furyl)- and 2-phenyl-5-(2-thienyl)imidazoles were synthesized by condensation of 2-furoylmethyl and 2-thenoylmethyl acetates with benzaldehyde under the conditions of Weidenhagen reaction. The products were converted to N-methyl derivatives in the KOH-acetone system. The electrophilic substitution reactions of the products (acylation, bromination, nitration, sulfonation, hydroxymethylation) were studied.     

Structure of 1(5)-aryl-3-phenyl-5(1)-(2-benzothiazolyl)formazanes

1,3-Diphenyl-5-(2-benzothiazolyl)formazane exists in its crystalline state (based on x-ray crystal structure data) in the E ^1,2 Z ^2,3 Z ^3,4-conformation, which is stabilized by intramolecular hydrogen bonding (IMHB); the proton is localized on the nitrogen atom which is bound to the heterocycle. In chloroform solutions 1(5)-aryl-3-phenyl-5(1)-(2-benzothiazolyl)formazanes exist in the form of equilibrium mixtures of their chelate and open E ^1,2 Z ^2,3 Z ^3,4-forms, in which the first of these forms predominates. Based on their ¹³ C-NMR spectral data the tautomeric equilibrium involving these forms is shifted in favor of the benzothiazolylhydrazone form. The amount of tautomer containing the benzothiazolidene fragment structure increases in DMSO solution.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1268–1274, September, 1991.     

Ab initio and density functional study of the conformational space of 1C4 α-L-fucose

The conformational space of ¹C₄ α-L-fucose was searched by the MM2^*-SUMM molecular mechanics conformational search technique. The molecular geometries of the first 17 structures of lowest energy were analyzed at the HF/3-21G, 6-31G(d), and generalized gradient approximation (GGA) DFT levels of theory. © 1997 by John Wiley & Sons, Inc.