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...

Photoelectron spectra of the cis and trans isomers of HCOH were computed using vibrational wave functions calculated by diagonalizing the Watson Hamiltonian, including up to four mode couplings. The full-dimensional CCSD(T)/cc-pVTZ potential energy surfaces were employed in the calculation. Photoionization induces significant changes in equilibrium structures, which results in long progressions...

Optical pulses at THz and mid-infrared frequencies tuned to specific vibrational resonances modulate the lattice along chosen normal mode coordinates. In this way, solids can be switched between competing electronic phases and new states are created. Here, we use vibrational modulation to make electronic interactions (Hubbard-U) in Mott-insulator time dependent. Mid-infrared optical pulses exci...

The normal mode spectrum of the deuteron in the Skyrme model is computed. We find a bound doublet mode below the pion mass, which can be related to the wellknown 90◦ scattering of two skyrmions. We also find a singlet ‘breather’ mode and another doublet above the pion mass. The qualitative pattern of the spectrum is similar to that recently found for the B = 4 multiskyrmion. The symmetries of a...

Vibrational modes and their interactions affect numerous physical processes in condensed-matter systems. In the present work, hydrogen vibrations in Se-doped AlSb were investigated with first-principles calculations. Vibrational frequencies were calculated for the longitudinal, transverse, wag (bending), and stretch modes of the Al-H complex. The Al-H stretch mode interacts with a combination m...

FOX-7 (1,1-diamino-2,2-dinitroethylene) recently is expected as a relatively new energetic material with high-performance and low sensitivity. The RHF and MP2 levels and DFT method with B3LYP functional with aug-cc-pVDZ basis set have been used for obtaining equilibrium geometry and Rho function (electron density distribution). By the aid of fundamental physical theorems implemented in the ...

The vibrational energy relaxation of dissociated carbon monoxide in the heme pocket of sperm whale myoglobin has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the delta- and epsilon-tautomers of the distal histidine, His64. Vibrational population relaxation times wer...

Recent calculations on the formation of self-trapped amide group vibrational states in -helical polypeptides J. Chem. Phys. 124, 134907 2006 are extended to the amide N–H normal mode vibrations. First, the adiabatic N–H vibrational singleand two-exciton states are examined by treating the longitudinal chain coordinates as parameters. Then, in using the multiconfiguration time-dependent Hartree ...

Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer pro...

The vibrational energy relaxation of carbon monoxide in the heme pocket of sperm whale myoglobin was studied by using molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the delta- and epsilon-tautomers of the distal His-64. Vibrational population relaxation times of 335 +/- 115 ps for the delta-tautome...