Potential Energy Surface calculations of Alanine Dipeptide using BVWN Density functional approach and 6-311G basis set
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1219-AA04-08
Potential Energy Surface calculations of Alanine Dipeptide using BVWN Density functional approach and 6-311G basis set 1
Jyoti Singh, 2Subhash C. Singh and 3N.B. Singh*
1.
J.K. institute of Applied Physics and Technology, Department of Computer Science, University of Allahabad, Allahabad-211002, India 2 LNational Centre for Plasma Science and Technology, Dublin City University, Dublin-9, Ireland University of Allahabad, Allahabad-211002, India 3. Plant physiology laboratory, Department of Botany, University of Allahabad, Allahabad-211002 *E-mail: [email protected] ABSTRACT This work is devoted to a study of the conformational properties of alanine dipeptide. We have studied potential energy surfaces of alanine dipeptide molecule using density functional theoretical approach with 6-311G basis set. For this purpose potential energies of this molecule are calculated as a function of Ramachandran angles ϕ and ψ, which are important factors for the characterizations of polypeptide chains. These degrees of freedoms ϕ and ψ are important for the characterization of protein folding systems. Stable conformations, energy barriers and reaction coordinates of this important dipeptide molecule are calculated. Energy required for the transition of one conformation into other are also discussed. INTRODUCTION Proteins consist of amino acids whose number may vary in the range from hundreds up to tens of thousands. Small fragments of proteins are usually called polypeptide chains or polypeptides. Aminoacids are basic building blocks of proteins, DNA, RNA genetic molecules. Study of amino-acids is important due to the investigation, development and modification of proteins and genes. Recently, it became possible to study experimentally fragments of proteins, i.e. chains of amino acids, in a gas phase with the use of the MALDI mass spectroscopy [1,2]. Ab-initio computational calculations of the amino acids have shown great interest now a day with increasing demands [3-6]. Study optical and electronic properties of amino acids became more interesting due to their probable application in the fabrication of biodegradable molecular devices. Present work deals with conformational study of alanine dipeptide using BVWN density functional method with 6-311G basis set. Potential energies are calculated as a function of Ramachandran angles ϕ and ψ with the step of 10 degrees and results are plotted to get its potential energy surface. Stable isomers of alanine dipeptide in terms of their dihedral angles, reaction coordinates, energy level diagram, Homo to Lumo transition energy, Mulliken charges etc. are calculated. THEORETICAL METHODS
Our study for the potential energies of alanine dipeptide at different dihedral angles is based on the density functional theoretical approximation for all electrons in the system. It is difficult to solve Schrödinger equation for the molecules having more than two electrons to get their potential energies and dynamical studies. To overcome this problem Kohn-Sham equation is utilized,
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