Hugo J. Bohórquez

QTAIM Study of an α-Helix Hydrogen Bond Network

The structures of 19 alpha-helical alanine-based peptides, 13 amino acids in length, have been fully optimized using density functional theory and analyzed by means of the quantum theory of atoms in molecules. Two types of N-H...O bonds and one type of C-H...O bond have been identified. The value of the electron density at hydrogen bond critical points corresponding to N-H...O interactions is higher than that of C-H...O interactions. The effect of amino acid substitution at the central position of the peptide on the hydrogen bond network of the alpha-helix has been assessed. The strength of the hydrogen bond network, measured as the summation of the electron density over the hydrogen bond critical points, may be used to explain experimental relative helix propensities of amino acids in cases where solvation and entropic effects cannot.

On the local representation of the electronic momentum operator in atomic systems

The local quantum theory is applied to the study of the momentum operator in atomic systems. Consequently, a quantum-based local momentum expression in terms of the single-electron density is determined. The limiting values of this function correctly obey two fundamental theorems: Katos cusp condition and the Hoffmann-Ostenhof and Hoffmann-Ostenhof exponential decay. The local momentum also depicts the electron shell structure in atoms as given by its local maxima and inflection points. The integration of the electron density in a shell gives electron populations that are in agreement with the ones expected from the Periodic Table of the elements. The shell structure obtained is in agreement with the higher level of theory computations, which include the Kohn-Sham kinetic energy density. The average of the local kinetic energy associated with the local momentum is the Weizsacker kinetic energy. In conclusion, the local representation of the momentum operator provides relevant information about the electronic properties of the atom at any distance from the nucleus.

Molecular Model with Quantum Mechanical Bonding Information

The molecular structure can be defined quantum mechanically thanks to the theory of atoms in molecules. Here, we report a new molecular model that reflects quantum mechanical properties of the chemical bonds. This graphical representation of molecules is based on the topology of the electron density at the critical points. The eigenvalues of the Hessian are used for depicting the critical points three-dimensionally. The bond path linking two atoms has a thickness that is proportional to the electron density at the bond critical point. The nuclei are represented according to the experimentally determined atomic radii. The resulting molecular structures are similar to the traditional ball and stick ones, with the difference that in this model each object included in the plot provides topological information about the atoms and bonding interactions. As a result, the character and intensity of any given interatomic interaction can be identified by visual inspection, including the noncovalent ones. Because similar bonding interactions have similar plots, this tool permits the visualization of chemical bond transferability, revealing the presence of functional groups in large molecules.

Constructing a useful tool for characterizing amino acid conformers by means of quantum chemical and graph theory indices.

The aim of this work is to construct a tool to assist in the prediction of peptidic properties resulting from the exchange of two amino acids in a proteic chain. In the past others have used experimental properties for this purpose. However, the nature of these data sets severely limits their access to important properties pertaining to secondary structure, and hence the indices used cannot characterize different backbone conformers like alpha helix and beta strands, or side-chain conformations like gauche +, gauche - and trans. In this study we explore the importance of backbone and side-chain angles with regard to conformer similarity measured with theoretical properties calculated in an ab initio manner. For each of the 20 genetically encoded amino acids, we studied five conformers that correspond to alpha helical and beta strand structures, with three different side chain conformations for each, defined solely by their angles phi, psi and chi1. This methodology allowed each of the 108 conformers to be represented by a mathematical object without ambiguity. The peptidic chain was emulated using two capping models to simulate the effect of nearest neighbors. These are OHC-Xaa-NH2 and Ala-Xaa-Ala, where Xaa is the conformer of interest. We then calculated 40 ab initio quantum chemical and graph theory indices for each backbone-side-chain conformer to obtain a characterization and classification scheme. We found that: (1) while backbone structure is very important to conformer similarity, side-chain conformations do not cluster together in a top-level manner; (2) amino acids with pi electrons group together independent of backbone conformation.

Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements

Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn ↔ Asp, Phe ↔ Tyr, Lys ↔ Arg, Gln ↔ Glu, Ile ↔ Val, Met → Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation (

The Kernel energy method: Application to graphene and extended aromatics

\overline{R}

Is the size of an atom determined by its ionization energy

R¯ = 0.85) between thirty amino acid mutability scales and the mutational inertia (IX), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions.