Self Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Biological Molecules

1998 ◽  
Vol 538 ◽  
Author(s):  
M. Elstner ◽  
D. Porezag ◽  
G. Seifert ◽  
Th. Frauenheim ◽  
S. Suhai
Keyword(s):  
Density Functional ◽  
Tight Binding ◽  
Molecular Complexes ◽  
Biological Molecules ◽  
Small Organic Molecules ◽  
Biologically Relevant ◽  
Dna Base ◽  
Self Consistent ◽  
Dna Base Pair ◽  
Semi Empirical

AbstractWe apply a self-consistent charge tight-binding scheme to biomolecules. This method has been shown to give a reliable description of reaction energies, geometries and vibrational frequencies of small organic molecules. We discuss the performance of this method for model peptides and non-bonding interactions in biologically relevant molecular complexes. A comparison with semi-empirical methods and ab initio calculations will be given for DNA base pair H-bonding and stacking interactions.

GaAs Total Energy Tight Binding Hamiltonians for use in Molecular Dynamics

1990 ◽  
Vol 193 ◽  
Author(s):  
Jeremy Broughton ◽  
Mark Pederson ◽  
Dimitrios Papaconstantopoulos ◽  
David Singh
Keyword(s):  
Density Functional ◽  
Local Density ◽  
Tight Binding ◽  
Large Data ◽  
Matrix Elements ◽  
Energy Matrix ◽  
Self Consistent ◽  
Total Energies ◽  
Local Density Functional ◽  
Semi Empirical

ABSTRACTA self-consistent non-orthogonal semi-empirical tight binding Hamiltonian is proposed for GaAs, or any sp system, which is simple, reliable, transferable, accurate and fast to evaluate. Matrix elements are functions of charges, distances between atoms and simple cosines of angles between s and p-electron densities and interatomic vectors which maintain the simplicity of Slater-Koster parameterizations. The tight binding scheme is fit against a large data base of local density functional derived total energies for systems of differing coordination and geometry. The Hamiltonian fulfills the correct Virial constraint, invokes the physically correct relationship between overlap and kinetic energy matrix elements and defines charges via Mulliken or Löwdin schemes. Such Hamiltonians will allow the reliable simulation of statistical mechanically interesting systems of order hundred or more atoms over physically useful periods of time of order tens to hundreds of thousands of time steps within not unreasonable supercomputer budgets.

scholarly journals Quantum chemical molecular dynamics and metadynamics simulation of aluminium binding to amyloid-β and related peptides

2020 ◽  
Vol 7 (2) ◽  
pp. 191562
Author(s):  
James A. Platts
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
A Priori ◽  
Tight Binding ◽  
Amyloid Β ◽  
Model Systems ◽  
Binding Modes ◽  
Biologically Relevant ◽  
Dynamics Simulations ◽  
Semi Empirical

We report semi-empirical tight-binding simulations of the interaction between Al(III) and biologically relevant peptides. The GFN2-XTB method is shown to accurately reproduce previously reported and density functional theory (DFT)-calculated geometries of model systems. Molecular dynamics simulations based on this method are able to sample peptide flexibility over timescales of up to nanoseconds, but these timescales are insufficient to explore potential changes in metal–peptide binding modes. To achieve this, metadynamics simulations using root mean square deviation as a collective variable were employed. With suitably chosen biasing potentials, these are able to efficiently explore diverse coordination modes, for instance, through Glu and/or Asp residues in a model peptide. Using these methods, we find that Al(III) binding to the N-terminal sequence of amyloid-β is highly fluxional, with all acidic sidechains and several backbone oxygens participating in coordination. We also show that such simulations could provide a means to predict a priori possible binding modes as a precursor to longer, atomistic simulations.

scholarly journals A quantitative evaluation of computational methods to accelerate the study of alloxazine-derived electroactive compounds for energy storage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qi Zhang ◽  
Abhishek Khetan ◽  
Süleyman Er
Keyword(s):  
Energy Storage ◽  
Density Functional ◽  
Tight Binding ◽  
Computational Cost ◽  
Redox Potentials ◽  
Storage Compounds ◽  
Computational Screening ◽  
Chemical Descriptor ◽  
Lowest Unoccupied Molecular Orbital ◽  
Semi Empirical

AbstractAlloxazines are a promising class of organic electroactive compounds for application in aqueous redox flow batteries (ARFBs), whose redox properties need to be tuned further for higher performance. High-throughput computational screening (HTCS) enables rational and time-efficient study of energy storage compounds. We compared the performance of computational chemistry methods, including the force field based molecular mechanics, semi-empirical quantum mechanics, density functional tight binding, and density functional theory, on the basis of their accuracy and computational cost in predicting the redox potentials of alloxazines. Various energy-based descriptors, including the redox reaction energies and the frontier orbital energies of the reactant and product molecules, were considered. We found that the lowest unoccupied molecular orbital (LUMO) energy of the reactant molecules is the best performing chemical descriptor for alloxazines, which is in contrast to other classes of energy storage compounds, such as quinones that we reported earlier. Notably, we present a flexible in silico approach to accelerate both the singly and the HTCS studies, therewithal considering the level of accuracy versus measured electrochemical data, which is readily applicable for the discovery of alloxazine-derived organic compounds for energy storage in ARFBs.

Thermal Properties of Divalent Metal Oxides: CaO as a Prototype

2013 ◽  
Vol 209 ◽  
pp. 190-193
Author(s):  
Nisarg K. Bhatt ◽  
Brijmohan Y. Thakore ◽  
P.R. Vyas ◽  
A.Y. Vahora ◽  
Asvin R. Jani
Keyword(s):  
Density Functional ◽  
Tight Binding ◽  
Mean Field ◽  
Field Potential ◽  
Theoretical Data ◽  
Test Case ◽  
Generalized Gradient ◽  
Core Electrons ◽  
Vibrational Free Energy ◽  
Semi Empirical

Commonly employed quasiharmonic approximation (QHA) is inadequate to account for intrinsic anharmonism such as phonon-phonon interaction, vacancy contribution, etc. Though anharmonic contributions are important at high temperatures and low pressure, complete ab initio calculations are scanty due largely to laborious computational requirements. Nevertheless, some simple semi-empirical schemes can be used effectively to incorporate the anharmonism. In this regards, in the present study we have proposed a simple computational scheme to include the effect of vacancy directly into the description within the mean-field potential approach, which calculates vibrational free energy of ions. Validity of the scheme is verified by taking calcium oxide as a test case. Equilibrium properties at (T,P) = (0,0) condition is obtained within the tight-binding second-moment approximation (TB-SMA), whose parameters were determined through first principles density functional theory. Kohn-Sham equations for core electrons were solved using ultrasoft plane-wave pseudopotential employing the generalized gradient approximation for exchange and correlation. Present findings for thermal expansion and high-T EOS clearly show perceptible improvement over the case when vacancy contribution was not included. Some related thermodynamic properties are also calculated and compared with the available experimental and theoretical data.

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