Infrared, Raman and NMR spectra, conformational stability, normal coordinate analysis and B3LYP calculations of 5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbothioamide

Raman, infrared and NMR spectral analysis, normal coordinate analysis and theoretical calculations of 5-(methylthio)-1,3,4-thiadiazole-2(3H)-thione and its thiol tautomer

Raman (3400-100 cm(-1)) and infrared (4000-200 cm(-1)) spectra of 5-(methylthio)-1,3,4-thiadiazole-2(3H)-thione (C3H4N2S3; MTT) were measured in the solid state, and the (1)H/(13)C NMR spectra were obtained in DMSO-d6. Initially, twelve structures were proposed as a result of thiol-thione tautomerism and the internal rotation about the C-S bonds. The energies and vibrational frequencies of the optimized structures were calculated using the 6-31G(d) basis set with the methods of MP2 and DFT/B3LYP with Gaussian 98 quantum calculations. Additionally, (1)H/(13)C NMR chemical shifts were predicted for the thiol (structure 5) and thione (structure 9) tautomers by means of B3LYP/6-311+G(d,p) calculations utilizing the GIAO approximation and the PCM solvation model. After complete relaxation of twelve candidate isomers, the thione tautomer (structure 9) was favored owing to its low energy and its predicted real spectral frequencies. These results agree with the recorded infrared and Raman results, in addition to the observed/calculated (1)H and (13)C NMR spectra. Aided by normal coordinate analysis and potential energy distributions (PEDs), complete vibrational assignments have been proposed for all observed fundamentals for the thione tautomer. With the aid of MP2/6-31G(d) potential surface scans, CH3, CH3S, and SH barriers to internal rotations were estimated with the optimized structural parameters from the MP2 method with the 6-31G(d) basis set. The results are discussed herein and compared with similar model compounds whenever appropriate.

Structural conformations, tautomerization and vibrational spectral study of 6-amino-1-methylpurine with density functional theoretical calculations

The FT-IR and FT-Raman spectra of 6-amino-1-methylpurine (AMP) have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The optimized geometry, frequency and intensity of the vibrational bands of AMP have been obtained by DFT level of theory using B3LYP method with 6-311++G(d,p) basis set. A complete vibrational assignment aided by the theoretical harmonic frequency analysis has been proposed. Purines, including substituted purines and their tautomers, are the most widely occurring nitrogen-containing heterocyclic in nature. Purines and pyrimidines make up the two groups of nitrogenous bases, including the two groups of nucleotide bases. Two of the four deoxyribonucleotides and two of the four ribonucleotides, the respective building-blocks of DNA and RNA, are purines. The calculated vibrational values are in good agreement when they are compared with IR and Raman experimental data. Amine-imine tautomerism of 6-amino-1-methyl purine is studied in detail. In agreement with experimental results, it was found that imine tautomer is more stable than amine tautomer.

Infrared and NMR spectra, tautomerism, vibrational assignment, normal coordinate analysis, and quantum mechanical calculations of 4-amino-5-pyrimidinecarbonitrile

The infrared (4000-200 cm(-1)) spectrum for 4-amino-5-pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the (1)H and (13)C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the (1)H and (13)C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm(-1) (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.

Vibrational and theoretical analysis of pentyl-4-benzoyl-1-[2,4-dinitrophenyl]-5-phenyl-1H-pyrazole-3-carboxylate

Infrared spectrum of the compound, pentyl-4-benzoyl-1-[2,4-dinitrophenyl]-5-phenyl-1H-pyrazole-3-carboxylate (PBDPPC) has been measured. Conformational search through relaxed scan has been carried out to find the most stable conformational isomer. After the full geometry optimization for the most stable conformer using B3LYP and BLYP hybrid functionals of Density Functional Theory (DFT), vibrational normal modes have been calculated at the same theoretical levels. Potential Energy Distribution (PED) of each normal mode has been calculated by means of VEDA4 to obtain contributions of internal coordinates to the normal modes. Natural Bond Orbital (NBO) analysis has been performed to get insights into the possible hydrogen bonding sites for all the conformational isomers.

Molecular structural, IR and NMR spectroscopic studies on the four isomers of thiotriazinone by DFT and HF calculations

One of the isomers of thiotriazinone, 6-hydroxy-2-methyl-3-thioxo-2H-1,2,4-triazin-5-one, was characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2(1)/c with a=9.5837(19)Å, b=5.7006(11)Å, c=15.065(4)Å, α=90°, β=128.540(19)° and γ=90°. The molecular geometries and vibrational frequencies of the four isomers of thiotriazinone in the ground state have been calculated using the density functional theory (DFT) and Hartree-Fock (HF) methods with 6-311++G(d,p) basis set, and compared with the experimental data. Gauge-including atomic orbital (GIAO) (13)C and (1)H NMR chemical shift values were calculated by DFT/6-311++G(2d,2p) and HF/6-311++G(2d,2p) methods, and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters. The theoretical IR spectra and (13)C and (1)H NMR chemical shift values also show good agreement with experimental data. In addition, frontier molecular orbitals (FMO) and molecular electrostatic potential (MEP) analysis of the four isomers were investigated using theoretical calculations.

Vibrational assignments, normal coordinate analysis, B3LYP calculations and conformational analysis of methyl-5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbodithioate

The Raman and infrared spectra of solid methyl-5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbodithioate (MAMPC, C7H8N4S3) were measured in the spectral range of 3700-100 cm(-1) and 4000-200 cm(-1) with a resolution of 4 and 0.5 cm(-1), respectively. Room temperature 13C NMR and (1)H NMR spectra from room temperature down to -60 °C were also recorded. As a result of internal rotation around C-N and/or C-S bonds, eighteen rotational isomers are suggested for the MAMPC molecule (Cs symmetry). DFT/B3LYP and MP2 calculations were carried out up to 6-311++G(d,p) basis sets to include polarization and diffusion functions. The results favor conformer 1 in the solid (experimentally) and gaseous (theoretically) phases. For conformer 1, the two -CH3 groups are directed towards the nitrogen atoms (pyrazole ring) and CS, while the -NH2 group retains sp2 hybridization and C-CN bond is quasi linear. To support NMR spectral assignments, chemical shifts (δ) were predicted at the B3LYP/6-311+G(2d,p) level using the method of Gauge-Invariant Atomic Orbital (GIAO) method. Moreover, the solvent effect was included via the Polarizable Continuum Model (PCM). Additionally, both infrared and Raman spectra were predicted using B3LYP/6-31G(d) calculations. The recorded vibrational, 1H and 13C NMR spectral data favors conformer 1 in both the solid phase and in solution. Aided by normal coordinate analysis and potential energy distributions, confident vibrational assignments for observed bands have been proposed. Moreover, the CH3 barriers to internal rotations were investigated. The results are discussed herein are compared with similar molecules whenever appropriate.