Modeling of real 20-component protein chains: Determination of the electronic density of states of aperiodic seven-component polypeptide chains containing strongly different amino acid residues

To model a real 20-component protein chain, the results of the electronic density of states (DOS ) of seven-component periodic and aperiodic polypeptide chains calculated on the basis of ab initio matrix block negative factor counting method are presented. The seven amino acid residues taken into account are rather different: glycine, serine, cysteine, asparagine, histidine, aspartic acid, and tryptophane. In the case of aperiodic chains, the energy states are found to be distributed over a much wider range of energy than in the corresponding periodic chains. In the intrinsic state, both periodic and aperiodic polypeptide chains are predicted to be insulators. The effect of the block copolymerization on the DOS distribution and the band gap values of both periodic and aperiodic polypeptide chains has been also investigated. Finally, the methods to calculate from the DOS curves hopping conductivities and the possibilities to compare them with experiment are outlined.     

On the electronic structure and conduction properties of aperiodic DNA and proteins. IV. Electronic structure of aperiodic proteins

The densities of states (DOS) of 4- and 5-component aperiodic polypeptide chains with 300 units are calculated on the ab initio level using the negative factor counting approach. The amino acid residues were glycine, serine, cysteine, asparagine and histidine. The localization of the wavefunctions belonging to the lowest lying energy levels in the conduction band region are investigated and hopping probabilities are calculated. On the basis of these results the possibility for hopping conduction in proteins is discussed under the assumption of charge transfer from DNA to the peptide chain.     

不同边界条件下导电高分子电子结构的研究

用一维复式晶格作为反式聚乙炔的模型 ,在周期与非周期边界条件下 ,考虑链端效应并计及电子的非近邻跳跃 ,数值计算了格点数分别等于N =10、5 0、10 0和 2 0 0时聚乙炔的能谱和态密度 .讨论了不同格点数和结构参数对态密度及带宽的影响 ,并对两种边界条件下的计算结果进行了比较 .计算结果表明 ,当格点数N <5 0时 ,两者相差较大 ,这表明系统的边界将起很大作用 ;当格点数N≥ 5 0时 ,两者相差甚微 ,这时可利用周期性边界条件来研究有限系统问题 .     

Thecis-trans energy difference in bi-1-cyclopro-pen-1-yl and related compounds

Thecis-trans energy difference of bi-1-cyclopropen-1-yl and the fluorosubstituted derivatives are studied byab initio methods in order to establish the stability of the cis andtrans diene isomers.The results of theab initio method STO-3G points toward thetrans bi-1-cyclopropen-1-yl as the most stable isomer (0.2kcal/mol). The energy of the transition state is about 2.5 kcal/mol above that of thetrans isomer. The electronic transitions of the isomers are also reported.Senior Fullbright-Hays Scholar to Uruguay.     

Ab initio simulations of two‐dimensional electronic spectra: The SOS//QM/MM approach

Two‐dimensional electronic spectroscopy (2DES) is a cutting‐edge technique for investigating with high temporal resolution energy transfer, structure, and dynamics in a wide range of systems in physical chemistry, energy sciences, biophysics, and biocatalysis. However, the interpretation of 2DES is challenging and requires computational modeling. This perspective provides a roadmap for the development of computational tools that could be routinely applied to simulate 2DES spectra of multichromophoric systems active in the UV region (2DUV) using state‐of‐the‐art ab initio electronic structure methods within a quatum mechanics/molecular mechanics (QM/MM) scheme and the sum‐over‐states (SOS) approach (here called SOS//QM/MM). Multiconfigurational and multireference perturbative methods, such as the complete active space self‐consistent field and second‐order multireference perturbation theory (CASPT2) techniques, can be applied to reliably calculate the electronic properties of multichromophoric systems. Hybrid QM/MM method and molecular dynamics techniques can be used to assess environmental and conformational effects, respectively, that shape the 2D electronic spectra. DNA and proteins are important biological targets containing UV chromophores. We report ab initio simulation of 2DUV spectra of a cyclic tetrapeptide containing two interacting aromatic side chains, a model system for the study of protein structure and dynamics by means of 2DUV spectroscopy. © 2013 Wiley Periodicals, Inc.     

He++N2 Charge Transfer Reaction: An Ab initio Analysis

An ab initio analysis on the involved potential energy surfaces is presented for the investigation of the charge transfer mechanism for the He⁺+N₂ system. At high collision energy, as many as seven low-lying electronic states are observed to be involved in the charge transfer mechanism. Potential energy surfaces for these low-lying electronic states have been computed in the Jacobi scattering coordinates, applying multireference configuration interaction level of theory and aug-cc-pVQZ basis sets. Asymptotes for the ground and various excited states are assigned to mark the entrance (He⁺+N₂) and charge transfer channels (He+N₂⁺). Nonadiabatic coupling matrix elements and quasi-diabatic potential energy surfaces have been computed for all seven states to rationalize the available experimental data on the charge transfer processes and to facilitate dynamics studies.     

The application of the extended negative factor counting method to deal with the electronic energy levels of pig insulin

The quantum-chemical calculation for pig insulin was done by the ENFC method in which the matrix elements were calculated in the ab initio level with the help of a minimal basis. The aqueous solution surrounding insulin was simulated by putting point charges around the residues that have electric charges. The electronic density of states (DOS) of insulin confirmed the conclusions obtained from aperiodic model peptide chains. It is shown that the frontier orbitals of the insulin were mainly localized on those residues which are involved in the expression of biological activity of insulin.     

Theoretical study of the electronic structure of LiX and NaX (X = Rb,Cs) molecules

Adiabatic potential energy, spectroscopic constants, dipole moments, and vibrational levels have been computed for the lowest electronic states of alkali dimers LiX and NaX (X = Rb, Cs). Calculations have been carried with the use of an ab initio approach with core‐potential potentials and full‐valence configuration. Thus, these systems are treated as two‐electron systems. A good agreement is obtained for some lowest states of the molecules studied with available theoretical works. The existence of numerous avoided crossings between electronic states for ¹Σ symmetries is related to the charge‐transfer process in each molecule between its two ionic systems (Li⁺X^?, Li^?X⁺) and (Na⁺X^?, Na^?X⁺). © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

On the electronic structure and conduction properties of aperiodic DNA and proteins. III. The band structures of periodic polypeptides

In this paper the calculation of the energy band structure of periodic polypeptides using the ab initio Hartree-Fock crystal orbital method is described. Results are discussed for the twenty homopolypeptides in the β-pleated sheet configuration and for several periodic systems assuming the α-helix structure. The negative factor method in its matrix block form is used to provide density of states curve for periodic two-component polypeptides. The resulting properties of the band structure suggest that homopolypeptides and periodic more-component polyamino acids are in themselves insulators, but may become weak semiconductors if free charge carriers are generated in their valence or conduction bands, respectively, through charge transfer.