Conformational analysis of spiro-epoxides by principal component analysis of molecular dynamics trajectories

Abstract

A new procedure for full conformational analyses comprising the statistical analysis of molecular dynamics trajectories was developed and applied. This method included a coordinate space for sampling using molecular dynamics simulations, reduction of dimensionality using tensor decomposition tools, determination of probability distributions in a reduced space, and finally the search for all of the strict extrema points of probability distributions. These extracted extrema points formed an initial guess for geometry optimization and clustering of conformers. A complete conformational space of 1-oxaspiro[2,5]octane and its cis- and trans-4-, 5- and 6-methyl substituted derivatives was also determined. In each case, eight conformers were found with two chair-like conformers predominant at room temperature. It was found that chair-like conformers with an epoxide ring oxygen atom in the pseudo-axial position had less strain, as well as all of their conformers with the methyl substituent in an equatorial position on a cyclohexane moiety.

New and Potent Quinuclidine-Based Antimicrobial Agents

“…First, a full conformational analysis for all compounds was performed. Conformers were determined by using the recently developed approach consisting of ab initio molecular dynamics and probability search in reduced space [23]. The example of conducted conformational analysis is presented on Figure 6.…”

“…Conformational analysis for all compounds was performed by using the tensor decomposition of ab initio molecular dynamics trajectories using the previously published procedure [23]. Ab initio molecular dynamics were performed using on-the-fly calculations of forces in each point of the simulation and integration with the velocity Verlet algorithm.…”

Conformational Analysis of Cinhonine and Cinhonidine by Tensor Decomposition of Molecular Dynamics Trajectories

“…A set of structures determined from probability distributions was used as an initial guess for the full conformational analysis. [31] All structures from the initial guess were optimized and subsequently clustered. Optimizations of these structures were performed using the B3LYP-D3 functional and 6-311++G(d,p) basis set.…”

Effective methods for the synthesis of hydrazones, quinazolines, and Schiff bases: reaction monitoring using a chemometric approach

“…PCA enables one to nd the best linear projections for a high dimensional set of data in the least-squares sense. Scores t i represent projections of the original points on the principal component (PC) direction and can be used for classication or building of probability distributions, 49 whereas loadings 56 represent the eigenvectors of data covariance (or correlation) matrix and can be used for the identication of variability among the data. 51 whereas the name was introduced by Hotelling.…”