Ab initio MO calculations were carried out at the MP4/6-311++G(3df,3pd)//MP2/6-311++G(3df,3pd) level to investigate the conformational Gibbs energy of a series of methyl ethers CH(3)O-CH(2)-X (X=OH, OCH(3), F, Cl, Br, CN, C triple bond CH, C(6)H(5), CHO). It was found that the Gibbs energy of the gauche conformers is lower in every case than that of the corresponding anti conformers. In the mor...

Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Con...

Gas-phase electronic and structural properties of the room temperature ionic liquid 1-ethyl-3-methylimidazolium tris(perfluoroethyl)trifluorophosphate ([EMIM][FAP]) were studied using density functional theory, and confirmed with results from infrared spectroscopy. A conformational analysis allowed the identification of several plausible conformers of the ion pairs. For the detected conformers,...

Recently available G-protein coupled receptor (GPCR) structures and biophysical studies suggest that the difference between the effects of various agonists and antagonists cannot be explained by single structures alone, but rather that the conformational ensembles of the proteins need to be considered. Here we use an elastic network model-guided molecular dynamics simulation protocol to generat...

Conformation-dependent properties of l-phenylalanine in neutral and radical cations have been studied by using density functional theory (DFT) with a new density functional M05-2X, which is applicable to molecular systems with nonconvalent interactions. Adiabatic and vertical ionization energies and charge distributions in the cationic conformers in addition to optimized geometrical structures ...

A combination of methods, including laser-induced fluorescence excitation, fluorescence-dip infrared ~FDIR! spectroscopy, and UV-UV hole-burning spectroscopy, have been used to study the infrared and ultraviolet spectra of single conformations of two methyl-capped dipeptides: N-acetyl tryptophan amide ~NATA! and N-acetyl tryptophan methyl amide ~NATMA!. Density functional theory calculations pr...

Structures of three cocrystals nootropic racetams were studied. They included two phenylpiracetam (PPA) with 4-hydroxybenzoic acid (HBA) different stoichiometries, PPA·HBA and PPA·2HBA, cocrystal 2-(4-phenyl-2-oxopyrrolidin-1-yl)-N’-isopropylideneacetohydrazide (PPAH) 4-hydroxybenzamide (HBD), PPAH·HBD·(acetone solvate). X-ray study the pure forms PPA PPAH was also carried out to identify varia...

an ab initio and density functional theory (dft) study about conformational analysis of tripeptide model hco−gly−l−ile−gly−nh2 is presented. the tripeptide was scanned about initial, central, and final residues, separately while for every scanning procedure the two other residues had been kept in the β conformation and side chain (sc) dihedral angles were maintained on the gauche− (g‾) state (χ...

Machine-learning analyses enable identifying signatures of peptide conformers in single molecule electron transport experiments.