Chirality Measures of α-Amino Acids

Abstract

To measure molecular chirality, the molecule is treated as a finite set of points in the Euclidean R(3) space supplemented by k properties, p(1)((i)), p(2)((i)), ..., p(k)((i)) assigned to the ith atom, which constitute a point in the Property P(k) space. Chirality measures are described as the distance between a molecule and its mirror image minimized over all its arbitrary orientation-preserving isometries in the R(3) × P(k) Cartesian product space. Following this formalism, different chirality measures can be estimated by taking into consideration different sets of atomic properties. Here, for α-amino acid zwitterionic structures taken from the Cambridge Structural Database and for all 1684 neutral conformers of 19 biogenic α-amino acid molecules, except glycine and cystine, found at the B3LYP/6-31G** level, chirality measures have been calculated by a CHIMEA program written in this project. It is demonstrated that there is a significant correlation between the measures determined for the α-amino acid zwitterions in crystals and the neutral forms in the gas phase. Performance of the studied chirality measures with changes of the basis set and computation method was also checked. An exemplary quantitative structure–activity relationship (QSAR) application of the chirality measures was presented by an introductory model for the benchmark Cramer data set of steroidal ligands of the sex-hormone binding globulin.

α-Amino Acids In Water: A Review Of VCD And ROA Spectra

“…In that work, the 2d correlation spectroscopy (2d-CoS) was coupled to vCd and IR spectra in multiple spectral regions. In addition, the excellent one-dimensional vCd and IR spectra of L-alanine in d 2 ) as a function of pd (Fig. 5.1).…”

“…the electric dipole-electric dipole polarisability derivatives α 2 αβ are used to form two Raman tensor invariants. α 2 αβ, g' αβ and A αβγ are defined in terms of sum-over-states expressions for exact wave functions; see Ref. [104].…”

“…despite the significant nonrigidity of amino acid molecules [2], the calculations were based on single structures available from a database [158]. A fair agreement between the calculated and experimental spectra was declared; however, for the IR spectra, the generalising conclusions were similar to those that could be drawn by inspection of the classical correlation tables [159,160].…”

“…Indeed, for neutral valine, 19 structures have been found to be stable, yet, for lysine and arginine, as many as 391 and 520 conformers have been found, respectively [2]. therefore, even for small amino acids, the interpretation of vibrational spectra requires quantum chemical analysis.…”

SCRAMBLE’N’GAMBLE: a tool for fast and facile generation of random data for statistical evaluation of QSAR models

“…HOMO/LUMO energies) (Karelson et al 1996 ) or be derived from other theoretical bases (e.g. chemical graph theory, (Balaban 1985 ; Helguera et al 2008 ) theory of quantitative chirality (Ostrowski et al 2012 ; Jamróz et al 2012 etc.). The number of currently available descriptors is enormous (Dearden 2016 ).…”