scholarly journals DFT-based investigation of the electronic structure of a double-stranded AC B-DNA dim

2013 ◽  
Vol 16 ◽  
pp. 117-122
Author(s):  
Emerson Rengifo ◽  
Gustavo Murillo
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Computational Cost ◽  
Semiempirical Method ◽  
Basis Sets ◽  
Functional Theory ◽  
One Dimensional ◽  
Exchange Correlation ◽  
Dna Dodecamer ◽  
Low Computational Cost

Calculations of the electronic structure of a stacked dimmer sequence from the D(GCAAACGTTTGC)2 B-DNA dodecamer resolved in a PDB file 1HQ7 are performed within density functional theory. Seeking to understand the minimum level of theory that yields a reliable description for these systems, the basis sets 6-31g*, 6-31g*+BSSE, 6-311g*, 6-311g**, 6-311++g** along with the B3LYP and PBE0 exchange-correlation functionals were employed. These results are then used to implement a one dimensional model of long stacked systems to obtain a new semiempirical method that can be employed at low computational cost.

Fast computation of DFT nuclear gradient with multiresolution*This article is dedicated to Dr. Russell J. Boyd for his distinguished career in chemical research.

2011 ◽  
Vol 89 (6) ◽  
pp. 657-662 ◽  
Author(s):  
Nicholas J. Russ ◽  
Chun-min Chang ◽  
Jing Kong
Keyword(s):  
Density Functional Theory ◽  
Electron Density ◽  
Density Functional ◽  
Density Functional Theory Calculation ◽  
Computational Cost ◽  
Basis Sets ◽  
Local Spin Density Approximation ◽  
Functional Theory ◽  
Exchange Correlation ◽  
The Impact

We present an efficient algorithm for evaluating the exchange-correlation contribution to the nuclear gradients of density-functional theory calculation within the local spin-density approximation. The algorithm is an extension of the multiresolution exchange-correlation (mrXC) method, which treats smooth and compact parts of the electron density separately. The nuclear gradient of the smooth density is calculated on the even-spaced grid while the compact part of the density is handled on the normal atom-centered grid (ACG). The overall formulism is still formally based on the ACG, and thus does not change the results of the existing ACG-based algorithms for all-electron density-functional theory (DFT) calculations. The variation of the positions and weights of ACG owing to the nuclear perturbation is also handled rigorously. Benchmark calculations with different basis sets and sizes of ACG show that mrXC reduces the computational cost by several times without loss of accuracy. It also lessens the impact on the CPU time when the size of the ACG is increased.

Evaluating Transition Metal Barrier Heights with the Latest DFT Exchange–Correlation Functionals – the MOBH35 Benchmark Dataset

2019 ◽  
Author(s):  
Mark Iron ◽  
Trevor Janes
Keyword(s):  
Transition Metal ◽  
Density Functional ◽  
Computational Cost ◽  
Basis Set ◽  
Functional Theory ◽  
Exchange Correlation ◽  
Barrier Heights ◽  
Complete Basis Set ◽  
Complete Basis Set Limit ◽  
Hybrid Functionals

A new database of transition metal reaction barrier heights – MOBH35 – is presented. Benchmark energies (forward and reverse barriers and reaction energy) are calculated using DLPNO-CCSD(T) extrapolated to the complete basis set limit using a Weizmann1-like scheme. Using these benchmark energies, the performance of a wide selection of density functional theory (DFT) exchange–correlation functionals, including the latest from the Truhlar and Head-Gordon groups, is evaluated. It was found, using the def2-TZVPP basis set, that the ωB97M-V (MAD 1.8 kcal/mol), ωB97X-V (MAD 2.1 kcal/mol) and SCAN0 (MAD 2.1 kcal/mol) hybrid functionals are recommended. The double-hybrid functionals PWPB95 (MAD 1.6 kcal/mol) and B2K-PLYP (MAD 1.8 kcal/mol) did perform slightly better but this has to be balanced by their increased computational cost.

Electronic structure of cubic BaTbO3 from first-principles pseudopotential calculations

2006 ◽  
Vol 84 (2) ◽  
pp. 115-120 ◽  
Author(s):  
G Y Gao ◽  
K L Yao ◽  
Z L Liu
Keyword(s):  
Electronic Structure ◽  
First Principles ◽  
Density Functional ◽  
First Principles Calculations ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Exchange Correlation ◽  
Pseudopotential Calculations ◽  
Correlation Potential ◽  
Density Contour

First-principles calculations of the electronic structure are performed for cubic BaTbO3 using the plane-wave pseudopotential method within the framework of density functional theory and using the generalized gradient approximation for the exchange-correlation potential. Our calculations show that cubic BaTbO3 is metallic, and that this metallic character is mainly governed by the Tb 4f electrons and the hybridization between the Tb 5d and O 2p states. From the analysis of the density of states, band structure, and charge density contour, we find that the chemical bonding between Tb and O is covalent while that between Ba and TbO3 is ionic. PACS Nos.: 71.15.Mb, 71.20.-b

THEORETICAL STUDIES ON BOND DISSOCIATION ENERGIES FOR SOME THIOL COMPOUNDS BY DENSITRY FUNCTIONAL THEORY AND CBS-Q METHOD

2008 ◽  
Vol 07 (05) ◽  
pp. 943-951 ◽  
Author(s):  
XIAO-HONG LI ◽  
ZHENG-XIN TANG ◽  
ABRAHAM F. JALBOUT ◽  
XIAN-ZHOU ZHANG ◽  
XIN-LU CHENG
Keyword(s):  
Density Functional ◽  
Computational Cost ◽  
Basis Set ◽  
Basis Sets ◽  
Q Method ◽  
Bond Dissociation Energies ◽  
Functional Theory ◽  
Thiol Compounds ◽  
Bond Dissociation ◽  
Dissociation Energies

Quantum chemical calculations are used to estimate the bond dissociation energies (BDEs) for 15 thiol compounds. These compounds are studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86, PBE0) methods and the complete basis set (CBS-Q) method together with 6-311G** basis set. It is demonstrated that B3P86 and CBS-Q methods are accurate for computing the reliable BDEs for thiol compounds. In order to test whether the non-local BLYP method suggested by Fu et al.19 is general for our study and whether B3P86 method has a low basis set sensitivity, the BDEs for seven thiol compounds are also calculated using BLYP/6-31+G* and B3P86 method with 6-31+G*, 6-31+G**, and 6-311+G** basis sets for comparison. The obtained results are compared with the available experimental results. It is noted that B3P86 method is not sensitive to the basis set. Considering the inevitable computational cost of CBS-Q method and the reliability of the B3P86 calculations, B3P86 method with a moderate or a larger basis set may be more suitable to calculate the BDEs of the C–SH bond for thiol compounds.

scholarly journals NMR and Theoretical Studies on the Conformational Preferences of Some Non-metal Coordinated N-Enoyl Systems Attached to Common Chiral Auxilaries

2017 ◽  
Vol 58 (2) ◽  
Author(s):  
Rosmarbel Morales-Nava ◽  
Alejandro Ramírez-Solís ◽  
Mario Fernández-Zertuche
Keyword(s):  
Density Functional ◽  
Vibrational Analysis ◽  
Basis Sets ◽  
Chiral Auxiliaries ◽  
Nmr Studies ◽  
Stable Conformation ◽  
Functional Theory ◽  
Exchange Correlation ◽  
H Nmr ◽  
Conformational Preferences

<p>We report a systematic study of a series of N-enoyl systems attached to common oxazolidin-2-ones, oxazolidine-2-thiones and thiazolidine-2-thiones chiral auxiliaries in order to determine the most stable conformation of these compounds. <sup>1</sup>H NMR studies show an <em>anti</em>-<em>s</em>-<em>cis</em> structure as the most stable conformation for these series of compounds. Density Functional Theory geometry optimizations and vibrational analysis using the b3lyp exchange-correlation functional with the standard 6-31g** basis sets were done, including solvent effects (chloroform and toluene). Gibbs free energy differences show that the <em>anti</em>-<em>s</em>-<em>cis</em> structures are the most stable conformers lying, on average, ca. 6 kcal/mol lower in energy than the <em>syn</em>-<em>s</em>-<em>cis</em> conformers, widely used to explain the structure and reactivity of <em>N</em>-enoyl systems.</p>

Evaluating Transition Metal Barrier Heights with the Latest DFT Exchange–Correlation Functionals – the MOBH35 Benchmark Dataset

2019 ◽  
Author(s):  
Mark Iron ◽  
Trevor Janes
Keyword(s):  
Transition Metal ◽  
Density Functional ◽  
Computational Cost ◽  
Basis Set ◽  
Functional Theory ◽  
Exchange Correlation ◽  
Barrier Heights ◽  
Complete Basis Set ◽  
Complete Basis Set Limit ◽  
Hybrid Functionals

A new database of transition metal reaction barrier heights – MOBH35 – is presented. Benchmark energies (forward and reverse barriers and reaction energy) are calculated using DLPNO-CCSD(T) extrapolated to the complete basis set limit using a Weizmann1-like scheme. Using these benchmark energies, the performance of a wide selection of density functional theory (DFT) exchange–correlation functionals, including the latest from the Truhlar and Head-Gordon groups, is evaluated. It was found, using the def2-TZVPP basis set, that the ωB97M-V (MAD 1.8 kcal/mol), ωB97X-V (MAD 2.1 kcal/mol) and SCAN0 (MAD 2.1 kcal/mol) hybrid functionals are recommended. The double-hybrid functionals PWPB95 (MAD 1.6 kcal/mol) and B2K-PLYP (MAD 1.8 kcal/mol) did perform slightly better but this has to be balanced by their increased computational cost.

scholarly journals EFFECT OF DISORDER ON THE INTERACTING FERMI GASES IN A ONE-DIMENSIONAL OPTICAL LATTICE

2008 ◽  
Vol 22 (25n26) ◽  
pp. 4500-4510 ◽  
Author(s):  
XIANLONG GAO ◽  
M. POLINI ◽  
M. P. TOSI ◽  
B. TANATAR
Keyword(s):  
Density Functional ◽  
Cold Atoms ◽  
Local Density ◽  
Fermi Gases ◽  
Functional Theory ◽  
One Dimensional ◽  
Exchange Correlation ◽  
Site Disorder ◽  
Interesting Compound ◽  
Main Effects

Interacting two-component Fermi gases loaded in a one-dimensional (1D) lattice and subjected to a harmonic trapping potential exhibit interesting compound phases in which fluid regions coexist with local Mott-insulator and/or band-insulator regions. Motivated by experiments on cold atoms inside disordered optical lattices, we present a theoretical study of the effects of a correlated random potential on these ground-state phases. We employ a lattice version of density-functional theory within the local-density approximation to determine the density distribution of fermions in these phases. The exchange-correlation potential is obtained from the Lieb-Wu exact solution of Fermi-Hubbard model. On-site disorder (with and without Gaussian correlations) and harmonic trap are treated as external potentials. We find that disorder has two main effects: (i) it destroys the local insulating regions if it is sufficiently strong compared with the on-site atom-atom repulsion, and (ii) it induces an anomaly in the inverse compressibility at low density from quenching of percolation. For sufficiently large disorder correlation length the enhancement in the inverse compressibility diminishes.

scholarly journals Basis Set Extrapolations for Density Functional Theory

2020 ◽  
Author(s):  
Peter Kraus
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Cost ◽  
Basis Set ◽  
Basis Sets ◽  
Density Functionals ◽  
Functional Theory ◽  
Common Basis ◽  
Basis Set Extrapolation

Improving results of correlated wavefunction theory calculations by extrapolating from successive basis sets is nowadays a common practice. However, such approaches are uncommon in density functional theory, especially due its faster convergence towards the basis set limit. In this work I present approaches for basis set extrapolation in density functional theory that enable users to obtain results of 4-zeta quality from 3- and 2-zeta calculations, i.e. at a fraction of the computational cost. The extrapolation techniques work well with modern density functionals and common basis sets.<br>

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