Proteins fold in a time range of microseconds to minutes despite the large amount of possible conformers. Molecular dynamics simulations of a three-stranded antiparallel beta-sheet peptide (for a total of 12.6 microsec and 72 folding events) show that at the melting temperature the unfolded state ensemble contains many more conformers than those sampled during a folding event.

Chiral oligomeric diimides prepared from pyromellitic dianhydride, (R,R)-1,2-diaminocyclohexane and phthalic anhydride fold into M or P helical conformers; trimer 1 folds into the P conformer in the crystal but the M conformer dominates in solution; longer chain oligomers 2 and 3 form preferentially P conformers in solution, as a result of intermolecular interactions.

Three distinct procedures for obtaining the effective Gibbs energies of activation from computed a reaction involving multiple reactant-state (RS) and transition-state (TS) conformers are shown to be equivalent. If Boltzmann-weighted average RS TS evaluated, then energy contribution entropy mixing both must also included in order obtain correct value activation. Application solvolytic 4,4′-dime...

The present study describes the fragmentation under electron ionization (EI) of gas phase serine and threonine amino acids. Ab initio methods were performed to calculate the fragmentation paths and interpret the mass spectra. The six lowest energy conformers of L-serine, L-threonine and L-allo-threonine were obtained with B3LYP, G3MP2 and MP2 methods. The adiabatic and vertical ionizat...

The conformational space of the natural product thymol (2-isopropyl-5-methylphenol) was investigated using quantum chemical calculations at B3LYP and MP2 levels, which revealed existence four types conformers differing in orientation isopropyl hydroxyl groups. Thymol monomers were isolated noble gas (Ar Xe) matrices (at 15 K) characterized by IR spectroscopy. With support harmonic vibrational c...

the present study describes the fragmentation under electron ionization (ei) of gas phase serine and threonine amino acids. ab initio methods were performed to calculate the fragmentation paths and interpret the mass spectra. the six lowest energy conformers of l-serine, l-threonine and l-allo-threonine were obtained with b3lyp, g3mp2 and mp2 methods. the adiabatic and vertical ionization energ...

Mycoplasma fermentans possesses unique α-glycolipid antigens (GGPL-I and GGPL-III) at the cytoplasm membrane, which carry a phosphocholine group at the sugar primary (6-OH) position. This paper describes a practical synthetic pathway to a GGPL-I homologue (C(16:0)) and its diastereomer, in which our one-pot α-glycosylation method was effectively applied. The synthetic GGPL-I isomers were charac...

The gas-phase structures of the disilanes 1,1,2,2-tetrakis(trimethylsilyl)disilane [(Me3Si)2HSiSiH(SiMe3)2] (1) and 1,1,2,2-tetrakis(trimethylsilyl)dimethyldisilane [(Me3Si)2MeSiSiMe(SiMe3)2] (2) have been determined by density functional theoretical calculations and by gas electron diffraction (GED) employing the SARACEN method. For each of 1 and 2 DFT calculations revealed four C2-symmetric c...

Investigations into the conformational behaviour of macrocyclic ligands 5 and 6 derived from (R,R)-1,2-diaminocyclohexane have been undertaken using molecular modelling, single crystal X-ray diffraction and variable temperature 1H NMR spectroscopy. These have revealed that the lowest energy conformers in both cases do not possess the expected C2-element of symmetry, which can only be accessed a...

Most theoretical models for NMR relaxation in liquids assume that overall rotational motion can be described as rotational diffusion with a single diffusion tensor. Such models cannot handle motions (such as between "closed" and "open" states of an enzyme, or between conformers of a partially disordered system) where the shape of the molecule (and hence its rotational diffusion behavior) fluctu...