Car–Parrinello molecular dynamics simulations of infrared spectra of crystalline imidazole

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

Conformations of n-butyl imidazole: matrix isolation infrared and DFT studies

Conformations of n-butyl imidazole (B-IMID) were studied using matrix isolation infrared spectroscopy by trapping in argon, xenon and nitrogen matrixes using an effusive nozzle source. The experimental studies were supported by DFT computations performed at the B3LYP/6-311++G(d,p) level. Computations identified nine unique minima for B-IMID, corresponding to conformers with tg(±)tt, tg(±)g(∓)t, tg(±)g(±)t, tg(±)tg(±), tg(±)tg(∓), tg(±)g(∓)g(∓), tg(±)g(±)g(±), tg(±)g(∓)g(±) and tg(±)g(±)g(∓) structures, given in order of increasing energy. Computations of the transition state structures connecting the higher energy conformers to the global minimum, tg(±)tt structure were carried out. The barriers for the conformer inter-conversion were found to be ∼2 kcal/mol. Natural Bond Orbital (NBO) analysis was performed to understand the reasons for conformational preferences in B-IMID.

Investigation of hydrogen bonds properties in the terephthalic acid crystal, using molecular dynamics method

The aim of this study was to perform calculations using the method of Car-Parrinello molecular dynamics, leading to the optimized geometry of the molecules of 1,4-benzenedicarboxylic acid (terephthalic acid) in crystals, for the hydrogen form and three variants of substitution of deuterium atoms inside a carboxyl group. Based on the results, trajectories and dipole moments were calculated, what makes possible to simulate vibrations in different systems, and to make calculation of theoretical infrared spectra and atomic power spectra. Theoretical results were compared with the experimental spectra, which verifies the correctness of the method and also was compared with the results obtained by quantum-mechanical calculations using DFT for the isolated dimer. Comparison of the spectra of different forms, allowed for in-depth analysis of the effect of isotopic substitution on the frequency of vibrations and shapes of bands, and confirm the presence of possible coupling effects and intra- and intermolecular interactions. Comparison with the DFT results for the dimer show influence of the crystal structure on the spectra.

H/D isotopic recognition in hydrogen bonded systems: H/D isotopic self-organization effects in the IR spectra of the hydrogen bond in 2-methylimidazole crystals

Polarized IR spectra of H12(3)45 2-methylimidazole and of its H1D2(3)45, D1H2(3)45 and D12(3)45 deuterium derivative crystals are reported and interpreted within the limits of the "strong-coupling" theory. The spectra interpretation facilitated the recognition of the H/D isotopic "self-organization" phenomenon, which depends on a non-random distribution of protons and deuterons in the lattices of isotopically diluted crystal samples. The H/D isotopic "self-organization" mechanism engaged all four hydrogen bonds from each unit cell. These effects basically resulted from the dynamical co-operative interactions involving adjacent hydrogen bonds in each hydrogen bond chain. A weaker exciton coupling involved the closely spaced hydrogen bonds; each belonging to a different chain of associated 2-methylimidazole molecules. The high intensity of the narrow band at ca. 1880cm(-1) was interpreted as the result of coupling between the γ(N-H⋯N) proton bending "out of plane" vibration overtone and the ν(N-H) proton stretching vibration.