Standard normal mode analysis (NMA) method is able to calculate vibrational entropy of proteins, but it is computationally intensive, especially for large proteins. To evaluate vibrational entropy efficiently and accurately, we, here, propose computation schemes based on coarse-grained NMA methods. This can be achieved by rescaling coarse-grained results with a specific factor that is derived o...

Vibrational transitions contain some of the richest fingerprints of molecules and materials, providing considerable physicochemical information. Vibrational transitions can be characterized by different spectroscopies, and alternatively by several imaging techniques enabling to reach sub-microscopic spatial resolution. In a quest to always push forward the detection limit and to lower the numbe...

Metformin is one of the important anti-diabetic drugs to treat non-insulin dependent diabetes mellitus (NIDDM). Fourier transform infrared (FTIR) and Fourier transform Raman (FTR) spectra of metformin have been used for the molecular study. A satisfactory band assignment has been made on the fundamental modes of vibration. Employing the molecular mechanics method using MM3 force field, the theo...

The vibrational modes of three solid AlF3 phases (alpha, beta, and amorphous high surface area AlF3) are investigated. Calculations have been performed using hybrid exchange correlation functionals to determine the equilibrium geometries and Gamma-point phonon frequencies for the alpha-AlF3 and beta-AlF3 phases. The calculated optical modes are in excellent agreement with experiment. The IR abs...

We have found that tri-L-alanine (Ala3) can crystallize in a parallel-chain beta structure in addition to the previously known antiparallel-chain beta structure. Although the chain conformations in each structure are essentially similar, the ir and Raman spectra are distinctively different. We have calculated the normal modes of each structure, and can account in significant detail for these di...

Structure, dynamics, and coupling involving single-molecules determine function in catalytic, electronic or biological systems. While vibrational spectroscopy provides insight into molecular structure, rapid fluctuations blur the molecular trajectory even in single-molecule spectroscopy, analogous to spatial averaging in measuring large ensembles. To gain insight into intramolecular coupling, s...

The methodology for a vibrational analysis within the nuclear–electronic orbital ~NEO! framework is presented. In the NEO approach, specified nuclei are treated quantum mechanically on the same level as the electrons, and mixed nuclear–electronic wave functions are calculated variationally with molecular orbital methods. Both electronic and nuclear molecular orbitals are expressed as linear com...

Geometry optimization and vibrational spectra (infrared and Raman spectra) calculations of proteins are carried out by a quantum chemical approach using the EE-GMFCC (electrostatically embedded generalized molecular fractionation with conjugate caps) method (J. Phys. Chem. A, 2013, 117, 7149). The first and second derivatives of the EE-GMFCC energy are derived and employed in geometry optimizat...

Hot carriers at metal surfaces can drive nonthermal reactions of adsorbates. Characterizing nonequilibrium statistics among various degrees of freedom in an ultrafast time scale is crucial to understand and develop hot carrier-driven chemistry. Here we demonstrate multidimensional vibrational dynamics of carbon monoxide (CO) on Cu(100) along hot-carrier induced desorption studied by using time-...

Vibrational absorption (VA) and vibrational circular dichroism (VCD) spectroscopy was applied in the analysis of vibrational and low lying electronic transitions of a triplet ground state cobalt(III) coordination compound. The spectroscopic measurements were performed on the tetrabutylammonium salt of (6S,7S)-1,3,5,8,10,12-hexaaza-2,4,9,11-tetraoxo-6,7-diphenyl-dodecanato(4-)cobaltate(III) in D...