Electronic and vibrational polarizabilities of the twenty naturally occurring amino acids

Abstract

The geometries, relative energies, gas-phase static and dynamic dipole polarizabilities of the two most stable neutral forms and of the zwitterionic form of the twenty naturally occurring amino acids have been obtained by Density Functional and conventional ab initio HatreeFock theories using correlation consistent basis sets. Mean electronic polarizabilities (<α e >s) are encompassed in the 40-160 a.u. range and are little dependent on the amino acid framework conformation, structure and conformation. The relation between <α e > and the number of electrons in the molecule makes to classify the amino acids as one of the most polarizable family of compounds. Calculated <α e > values of the neutral forms linearly relate to the molecular volume and molecular hardness as well as, rather unexpectedly, with the experimental values in water solution, where amino acids are known to be in a zwitterionic form. Vibrational polarizabilities amount to 15-45 a.u.. They come essentially from the lowfrequency angular deformation modes of the -OH and -NH 2 groups.

Formation of Peptide Radical Cations (M+·) in Electron Capture Dissociation of Peptides Adducted with Group IIB Metal Ions

“…Theoretically, the energetic of the electron transfer reaction is governed by: [57], it is obvious that electron transfer from the peptide moiety to any of the monovalent Group IIB metal ions is energetically feasible. In the literature, the phenomenon of electron transfer from gas phase organic molecules to monovalent metal ions has been examined extensively [58][59][60][61].…”

Calculations of the binding affinities of protein-protein complexes with the fast multipole method

“…rot =20 cm −1 is used for this calculation which is typical rotational frequency of molecules. 29 Other properties are listed in Table I based on the calculated results from Millefiori et al 17 An accurate parametrization of the dielectric function ͑i͒ of water based on the experimental data is taken from Parsegian's work. 30 In order to present a simple argument to show that our model indeed captures the dispersion interaction, a Drude model in one dimension can be used to illustrate the basic physics of the dispersion interaction.…”

“…For each residue there is also a polarizable dipole at the center of the sphere, whose nuclear polarizability had been determined from our recent work 16 and the electronic polarizability is estimated from optical dielectric constants augmented with quantum chemistry calculations. 17 There are three kinds of interactions in this model: the electrostatic interaction due to electric double layer effect, the van der Waals attraction due to the polarizable dipoles, and a short range correction term to account for the short range interactions such as the desolvation energy, hydrophobic interaction, and so on. In this report, we consider the electrostatic interactions which give the most contribution to the protein-protein interaction, 18,19 and the van der Waals interactions, which are the major contributors to the binding affinity calculations.…”

Calculations of the second virial coefficients of protein solutions with an extended fast multipole method

“…[22]. Other properties listed in Table I from Kim et al [29] are based on the calculated results from Millefiori et al [23] An accurate parametrization of the dielectric function ε(iω) of water based on the experimental data is taken from Parsegian's work [35].…”

“…Alternatively experimental or calculated pK a values of residues can be used to account for the local environments as it was done in this paper. For each residue there is also a polarizable dipole at the center of the sphere, whose nuclear polarizability had been determined from our recent work [22] and the electronic polarizability is estimated from optical dielectric constant augmented with quantum chemistry calculations [23]. There are three kinds of interactions in this model: the electrostatic interaction due to the electric double layer effect, the van der Waals attraction due to the polarizable dipoles and a short-range correction term to account for the short-range interactions such as the desolvation energy, hydrophobic interaction, and so on.…”