Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model

Author(s):  
C.R. Legler ◽  
N.R. Brown ◽  
R.A. Dunbar ◽  
M.D. Harness ◽  
K. Nguyen ◽  
...  
Clay Minerals ◽  
2008 ◽  
Vol 43 (3) ◽  
pp. 351-361 ◽  
Author(s):  
J. Ortega-Castro ◽  
N. Hernández-Haro ◽  
A. Hernández-Laguna ◽  
C. I. Sainz-Díaz

AbstractThe low-charge dioctahedral 2:1 phyllosilicates are an important group of clay minerals that have a low degree of cation substitution and very weak interlayer interatomic interactions which are difficult to reproduce with quantum mechanical calculations. In order to study the crystallographic properties of these compounds with density functional theory (DFT) quantum-mechanical methods, an optimization of norm-conserving pseudopotentials of Al, Si, O, H and Na atoms has been carried out, and an optimization of the cutoff radii of the basis sets has been accomplished. Crystallographic properties and vibrational stretching frequencies of the OH groups, ν(OH), have been calculated, being consistent with previous computational and experimental results. All frequencies can be related to the different molecular environment of the OH groups. The effect of octahedral Fe3+ substitution on the ν(OH) frequency is reproduced. Several configurations of cation substitutions and interlayer cation (IC) positions are studied in low-charge dioctahedral 2:1 phyllosilicates, such as Al4(Si7–xAlx)O20(OH)4Nax, with x = 0.25, 0.50 and 0.75, indicating that the IVAl3+ is highly dispersed and the IC tends to be in the substituted ditrigonal hole. For the Al4(Si7Al)O20(OH)4Na composition, the trans-vacant form is more stable than the cis-vacant one.


2020 ◽  
Vol 2 ◽  
pp. e8 ◽  
Author(s):  
Jitnapa Sirirak ◽  
Narin Lawan ◽  
Marc W. Van der Kamp ◽  
Jeremy N. Harvey ◽  
Adrian J. Mulholland

To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol−1, respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol−1), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol−1). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.


1999 ◽  
Vol 77 (1) ◽  
pp. 24-27 ◽  
Author(s):  
Germán Cavigliasso ◽  
Delano P Chong

Our procedure for calculating core-electron binding energies (CEBEs), based on the unrestricted generalized transition state model using B88/P86 functional, was extended to boron-containing molecules. Both unscaled (cc-pVTZ, cc-pVQZ, cc-pV5Z) and scaled (scaled-pVTZ and scaled-pVQZ) basis sets were used. The average absolute deviation from experiment for boron CEBEs with the scaled-pVTZ basis set was found to be 0.24 eV, compared to 0.23 eV for the much larger cc-pV5Z basis set.Keywords: DFT, boron, core-electron binding energies.


2018 ◽  
Vol 3 (6) ◽  
Author(s):  
M. Alcolea Palafox

Abstract The performance of ab initio and density functional theory (DFT) methods in calculating the vibrational wavenumbers in the isolated state was analyzed. To correct the calculated values, several scaling procedures were described in detail. The two linear scaling equation (TLSE) procedure leads to the lowest error and it is recommended for scaling. A comprehensive compendium of the main scale factors and scaling equations available to date for a good accurate prediction of the wavenumbers was also shown. Examples of each case were presented, with special attention to the benzene and uracil molecules and to some of their derivatives. Several DFT methods and basis sets were used. After scaling, the X3LYP/DFT method leads to the lowest error in these molecules. The B3LYP method appears closely in accuracy, and it is also recommended to be used. The accuracy of the results in the solid state was shown and several additional corrections are presented.


Author(s):  
Vikas Samvedi ◽  
Vikas Tomar

Atomistic analyses of thermal conduction across ZrB2/SiC based nanocomposite interface are performed using first principles density functional theory (DFT) with plane-wave basis sets. The changes in the thermal properties of nanocomposites have been analyzed under the effect of straining and temperature and compared for their phononic and electronic dependence.


2015 ◽  
Vol 8 (2) ◽  
pp. 2122-2134
Author(s):  
Sarvendra Kumar ◽  
Rajesh Kumar ◽  
Jayant Teotia ◽  
M. K. Yadav

In the present work, UV- Visible spectra of 2-Chloro-3,4-Dimethoxybenzaldehyde (2,3,4-CDMB) compound  have been carried out experimentally and theoretically. The ultraviolet absorption spectrum of title compound in three solvents (Acetone, Diethyl Ether, CCl4) of different polarity were examined in the range of 200–500 nm. The structure of the molecule was optimized and the structural characteristics were determined by HF and DFT (B3LYP) methods with 6-31+G(d,p) and 6-311++G(d,p) as basis sets. The excitation energy, wavelength corresponds to absorption maxima () and oscillator strength (f) are calculated by Time-Dependent Density Functional Theory (TD-DFT) using B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) as basis sets. The electric dipole moment (μ), polarizability (α) and the first hyperpolarizability (β ) have been computed to evaluate the non-linear optical (NLO) response of the investigated compound by HF and DFT (B3LYP) with already mentioned basis sets. Thermodynamic functions of the title compound at different temperatures were also calculated.


2018 ◽  
Author(s):  
Oscar A. Douglas-Gallardo ◽  
David A. Sáez ◽  
Stefan Vogt-Geisse ◽  
Esteban Vöhringer-Martinez

<div><div><div><p>Carboxylation reactions represent a very special class of chemical reactions that is characterized by the presence of a carbon dioxide (CO2) molecule as reactive species within its global chemical equation. These reactions work as fundamental gear to accomplish the CO2 fixation and thus to build up more complex molecules through different technological and biochemical processes. In this context, a correct description of the CO2 electronic structure turns out to be crucial to study the chemical and electronic properties associated with this kind of reactions. Here, a sys- tematic study of CO2 electronic structure and its contribution to different carboxylation reaction electronic energies has been carried out by means of several high-level ab-initio post-Hartree Fock (post-HF) and Density Functional Theory (DFT) calculations for a set of biochemistry and inorganic systems. We have found that for a correct description of the CO2 electronic correlation energy it is necessary to include post-CCSD(T) contributions (beyond the gold standard). These high-order excitations are required to properly describe the interactions of the four π-electrons as- sociated with the two degenerated π-molecular orbitals of the CO2 molecule. Likewise, our results show that in some reactions it is possible to obtain accurate reaction electronic energy values with computationally less demanding methods when the error in the electronic correlation energy com- pensates between reactants and products. Furthermore, the provided post-HF reference values allowed to validate different DFT exchange-correlation functionals combined with different basis sets for chemical reactions that are relevant in biochemical CO2 fixing enzymes.</p></div></div></div>


2019 ◽  
Author(s):  
Kamal Batra ◽  
Stefan Zahn ◽  
Thomas Heine

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>


Author(s):  
Kenneth G. Dyall ◽  
Knut Faegri

This book provides an introduction to the essentials of relativistic effects in quantum chemistry, and a reference work that collects all the major developments in this field. It is designed for the graduate student and the computational chemist with a good background in nonrelativistic theory. In addition to explaining the necessary theory in detail, at a level that the non-expert and the student should readily be able to follow, the book discusses the implementation of the theory and practicalities of its use in calculations. After a brief introduction to classical relativity and electromagnetism, the Dirac equation is presented, and its symmetry, atomic solutions, and interpretation are explored. Four-component molecular methods are then developed: self-consistent field theory and the use of basis sets, double-group and time-reversal symmetry, correlation methods, molecular properties, and an overview of relativistic density functional theory. The emphases in this section are on the basics of relativistic theory and how relativistic theory differs from nonrelativistic theory. Approximate methods are treated next, starting with spin separation in the Dirac equation, and proceeding to the Foldy-Wouthuysen, Douglas-Kroll, and related transformations, Breit-Pauli and direct perturbation theory, regular approximations, matrix approximations, and pseudopotential and model potential methods. For each of these approximations, one-electron operators and many-electron methods are developed, spin-free and spin-orbit operators are presented, and the calculation of electric and magnetic properties is discussed. The treatment of spin-orbit effects with correlation rounds off the presentation of approximate methods. The book concludes with a discussion of the qualitative changes in the picture of structure and bonding that arise from the inclusion of relativity.


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