N-Acetyl-L-alanine N′-methylamide: a density functional analysis of the vibrational absorption and vibrational circular dichroism spectra

Towards the Determination of the Absolute Configuration of Complex Molecular Systems: Matrix Isolation Vibrational Circular Dichroism Study of (R)‐2‐Amino‐1‐propanol

“…As suggested earlier by Suhai et al [4] and is demonstrated in the study herein, the combined use of VCD with matrix isolation (MI-VCD) enables the determination of the absolute configuration in the complicated cases mentioned above. To the best of our knowledge MI-VCD has, until now, been applied only to a rigid, single-conformer molecule, apinene.…”

Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in π-stacking and hydrogen-bonding behavior

“…The continuum solvent model performs adequately for the determination of geometries as has been done in this work. However, for the calculation of spectra of molecules in a solvent, it is essential to take into account the first shell of solvent molecules explicitly [63][64][65][66][67][68][69]. For instance, Nicu et al [63] showed that the VCD spectrum of 2-benzoic acid is influenced by the hydrogen bonding with the solvent due to the donor-acceptor interaction (which of course is not taken into account by continuum solvent models).…”

Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation

“…Imagine that we "position" (i.e., we write the corresponding Z-matrix row) every atom up to the hydrogen denoted by H 9 , and that we are now prepared to position the hydrogens in the side chain (H 10 , H 11 , and H 12 ) via one bond length, one bond angle, and one dihedral for each one of them. We will denote by (i, j) the bond length between atoms i and j; by (i, j, k), the bond angle between the vectors r jk and r ji ; and by (i, j, k, l) the dihedral angle between the plane defined by the atoms i, j, and k and the one defined by j, k, and l. A choice to position the atoms that is frequently seen in the literature 1,2,[21][22][23] is the one shown in Table 1. If we now perform the gedanken experiment that consists of taking a typical conformation of the molecule and slightly moving each internal coordinate at a time while keeping the rest constant, we find that any one of the three dihedrals in the previous definition is a hard coordinate, because moving one of them while keeping the other two constant distorts the internal structure of the methyl group.…”

“…For related documents and references, see http://www.chem.qmul.ac.uk/iupac/jcbn/.) The main difference with other Z-matrix-like coordinates normally used in the literature 1,2,[21][22][23] is that, instead of positioning each atom with a bond length, a bond angle, and a dihedral angle, we use normal dihedral angles (called, from now on, "principal dihedrals") only to fix the orientation of whole groups and a different type of dihedrals, termed "phase dihedrals" by Abagyan and coworkers [14][15][16] (see Fig. 1), to describe the covalent structure inside a group.…”