S. Manogaran

Conformational effects on vibrational frequencies of cysteine and serine: an ab initio study

Abstract The vibrational frequencies of three conformations of cysteine and serine in the non-ionized form have been evaluated using ab initio methods at the 4-31G ∗ level. The calculated frequencies along with the corresponding potential energy distributions were used to assign the IR spectra of the methyl ester, hydrochloride and zwitterion of cysteine and serine. It was found that the v (C β X) frequency is dependent on the value of X 1 [CC α C β X] torsional angle. The conformational dependence of some of the frequencies have been highlighted.

Ground state vibrational spectra of cysteine and serine zwitterion: a theoretical prediction

Abstract Transferability of scale factors from smaller constituents to a larger one is successfully attempted for two important amino acids cysteine (Cys) and serine (Ser) in zwitterionic form. A complete set of scale factors are generated for alanine (Ala) by fitting the ab initio (HF/6–31++G ∗ ) solvated model force field to the experimental frequencies of five different isotopomers. These scale factors are then used to scale the ab initio force field of both the molecules. Scale factors of the side chain residues of both cysteine and serine are obtained by fitting the ab initio solvated model force field of ethanethiol and ethanol to their respective experimental frequencies at the same level of theory. In both the cases the predicted frequencies and their normal mode descriptions are excellent compared to the size and complexity of the molecules.

An ab initio study of pyruvic acid

Abstract The geometries and vibrational frequencies of two conformers of pyruvic acid have been obtained at the ab initio second order Moller-Plesset level of theory using the 6–311++G∗∗ basis set. While the calculated geometries have been compared to the experimental microwave data, the vibrational frequencies have been assigned, using the experimental gas phase IR spectra of 13 isotopes of pyruvic acid by a recently developed scaling procedure (IRPROG). An attempt has been made to explain the stability of the eclipsed conformation over the staggered conformation of pyruvic acid by taking account of the molecular orbitals.

Conformations and vibrations of dicarboxylic acids. An ab initio study

Abstract The conformations of the higher dicarboxylic acids HOOC(CH 2 ) n COOH, n = 1–4 , the hydroxymalonic acid have been studied at the HF/4-21G level of theory. The conformational characteristics of these acids have been elucidated through potential energy scans at this level. The vibrational frequencies of all the dicarboxylic acids have also been evaluated at this level. Calculations at the HF/6-31G ** level of theory were also carried out on malonic, hydroxymalonic and succinic acids. They have been assigned to the solid state Raman and IR spectra of the dicarboxylic acids. The potential energy distributions, Raman activities and IR intensities calculated at the levels indicated have been used as aids in making the assignments. The calculated frequencies have also been compared with the frequencies evaluated at the MP2/4-31G * level for oxalic acid.

Proline and hydroxyproline zwitterions—an ab initio study

Abstract Ab initio calculations of proline and hydroxyproline zwitterions have been performed at the Hartree-Fock level using the 4-21++G basis set. The evaluated geometries have been compared to the corresponding X-ray parameters. The probable assignments for the experimental solid state vibrational spectra of proline and hydroxyproline based on the calculated ab initio frequencies and intensities were made.

Interpretation and accurate prediction of vibrational spectra—a modified ab initio scaled quantum mechanical approach

Abstract A novel method is described to obtain a scale factor for each force constant in the force constant matrix as a quantitative measure of the systematic error in ab initio methods. These scale factors offer a simple solution to the problem of interpretation and prediction of vibrational spectra using the scaled quantum mechanical (SQM) approach. The advantages of the method are illustrated using benzene, acrolein, pyridine and benzaldehyde as examples. This method also simplifies the traditional, tedious way of performing normal coordinate analysis.

Vibrational frequencies of proline and hydroxyproline An ab initio study

Abstract The vibrational frequencies of two conformations of proline and hydroxyproline in the non-ionized form have been evaluated using the ab initio method at the HF/4-21G level. The barrier heights of the rotation of the carboxy and hydroxy hydrogen atoms have been evaluated at the HF/4-21G level. The calculated frequencies are assigned to the experimental vibrational spectra of proline and hydroxyproline.

Force field calculation of molecules with isotopomers of different symmetries in vibrational spectral analysis

Abstract Under Born–Oppenheimer approximation, the isotopomers of different symmetries of a molecule should have the same potential energy surface and hence the same force constants. A novel method is proposed to obtain the minimum number of unique force constants and the redundancy relations to obtain the other force constants from these unique ones for a given symmetry. Transformation matrices for converting from one symmetry to another are also obtained. For all symmetries of isotopomers, the minimum unique number of force constants is the same as that of the highest symmetry. Benzene and ethylene are used as examples.

Force fields and assignments of the vibrational spectra of acridine and phenazine—an ab initio study

Abstract A complete set of force constants and their corresponding scale factors in non-redundant local coordinates were obtained by fitting the in-plane ab initio Hartree–Fock (HF) vibrational frequencies computed using 4-21G and 6-31G ∗∗ basis sets to the experimental ones. Using these force constants the potential energy distribution (PED) of the normal modes was obtained and based on the PED the earlier empirical assignments were either confirmed or reassigned for all the in-plane fundamentals. The force constants of acridine and phenazine are compared to those of anthracene to study the similarities and differences. Probable assignment is proposed for the out-of-plane fundamentals of acridine based on Durigs simple scaling of the local force constants.

Infrared Spectra of Dimethylquinolines in the Gas Phase: Experiment and Theory

Infrared spectra of atmospherically important dimethylquinolines (DMQs), namely 2,4-DMQ, 2,6-DMQ, 2,7-DMQ, and 2,8-DMQ in the gas phase at 80 degrees C were recorded using a long variable path-length cell. DFT calculations were carried out to assign the bands in the experimentally observed spectra at the B3LYP/6-31G* level of theory. The spectral assignments particularly for the C-H stretching modes could not be made unambiguously using calculated anharmonic or scaled harmonic frequencies. To resolve this problem, a scaled force field method of assignment was used. Assignment of fundamental modes was confirmed by potential energy distributions (PEDs) of the normal modes derived by the scaled force fields using a modified version of the UMAT program in the QCPE package. We demonstrate that for large molecules such as the DMQs, the scaling of the force field is more effective in arriving at the correct assignment of the fundamentals for a quantitative vibrational analysis. An error analysis of the mean deviation of the calculated harmonic, anharmonic, and force field fitted frequencies from the observed frequency provides strong evidence for the correctness of the assignment.