This paper highlights the relevance of including the high-energy conformational states sampled by Born-Oppenheimer molecular dynamics (BOMD) in the calculation of time-averaged NMR chemical shifts. Our case study is the very flexible glycerol molecule that undergoes interconversion between conformers in a nonrandom way. Along the sequence of structures from one backbone conformer to another, tr...

The proton NMR spectra of n-pentane orientationally ordered in two nematic liquid-crystal solvents are studied over a wide temperature range and analysed using covariance matrix adaptation evolutionary strategy. Since alkanes possess small electrostatic moments, their anisotropic intermolecular interactions are dominated by short-range size-and-shape effects. As we assumed for n-butane, the ani...

A new calixarene-based donor-acceptor system, cone conformer 1, was prepared for the first time. In this compound, the calix[4]arene serves to juxtapose a tri-chloroquinone acceptor near the porphyrin photo-donor plane. As to the conformational control, the cone conformer 1 gave two peaks of phenolic OH groups at 8.40 and 8.43 ppm. This shows that cone conformer 1 is stabilized by intramolecula...

Ionization of equatorial and axial conformational isomers of the chair-bromocyclohexane is investigated with use of the vacuum ultraviolet mass-analyzed threshold ionization (MATI) spectroscopic technique. Two distinct ionization energies of 9.8308 ± 0.0025 and 9.8409 ± 0.0025 eV are determined for equatorial or axial conformers, respectively. From the conformer-selective vibrational analysis, ...

Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the substrate in solution and in the active site of chorismate mutase are reported. Two nonreactive conformers of chorismate are found to be more stable than the reactive pseudodiaxial chair conformer in s...

Previously we have shown that the fluorescence of the dihydropyridine calcium antagonist felodipine provides an accurate means of monitoring the formation of an allosterically potentiated conformer of calmodulin (Mills, J. S., and Johnson, J. D., (1985) Biochemistry 24, 4897-4903). Characteristic of this conformer is the abolition of cooperativity among the two felodipine-binding sites on calmo...

Here, we present the algorithm and validation for OMEGA, a systematic, knowledge-based conformer generator. The algorithm consists of three phases: assembly of an initial 3D structure from a library of fragments; exhaustive enumeration of all rotatable torsions using values drawn from a knowledge-based list of angles, thereby generating a large set of conformations; and sampling of this set by ...

Far-infrared conformer-specific signatures of small aromatic molecules of biological importance

Different conformers of many aliphatic compounds such as ethane, butane, cyclohexane and their derivatives have been studied to find the most reactive well stable conformer. For first time, two p-xylene were found using theoretical DFT calculation vibrational modes, Raman activity, other spectra each conformer also studied. The significant data that clearly distinguished both was depolarization...

We introduce the MacroConf dataset, a collection of cyclic peptide solution structures. The dataset was used to benchmark performance molecular dynamics and cheminformatics-based conformer generators.