scholarly journals Comparison of Molecular Geometry Optimization Methods Based on Molecular Descriptors

Mathematics ◽  
2021 ◽  
Vol 9 (22) ◽  
pp. 2855
Author(s):  
Donatella Bálint ◽  
Lorentz Jäntschi
Keyword(s):  
Density Functional ◽  
Geometry Optimization ◽  
Principal Component ◽  
Optimization Procedure ◽  
Molecular Geometry ◽  
Optimization Methods ◽  
Hartree Fock ◽  
Pubchem Database ◽  
Semi Empirical ◽  
The Relationship

Various methods (Hartree–Fock methods, semi-empirical methods, Density Functional Theory, Molecular Mechanics) used to optimize a molecule structure feature the same basic approach but differ in the mathematical approximations used. The geometry optimization procedure calculates the energy at an initial geometry of a molecule and then proceeds to search a new geometry with a lower energy. Using the 3D structures collected from the PubChem database, 20 amino acid geometry optimization calculations were performed with several methods. The purpose of the study was to analyze these methods (39) to find the relationship between them and to determine which to use under different circumstances. Cluster analysis and principal component analysis were performed to evaluate the similarities between the different methods. The results after the analysis can classified into three main groups and can be selected accordingly to solve different types of problems.

scholarly journals Density functional tight binding: values of semi-empirical methods in an ab initio era

2014 ◽  
Vol 16 (28) ◽  
pp. 14368-14377 ◽  
Author(s):  
Qiang Cui ◽  
Marcus Elstner
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Tight Binding ◽  
Empirical Methods ◽  
Functional Theory ◽  
Hartree Fock ◽  
Semi Empirical

Semi-empirical (SE) methods are derived from Hartree–Fock (HF) or Density Functional Theory (DFT) by neglect and approximation of electronic integrals.

Density Functional Theory Studies of Electronic Structures and Hyperfine Interactions of Muonium in Imidazole

2015 ◽  
Vol 749 ◽  
pp. 134-138 ◽  
Author(s):  
Pek Lan Toh ◽  
Shukri Sulaiman ◽  
Mohamed Ismail Mohamed Ibrahim ◽  
Lee Sin Ang
Keyword(s):  
Density Functional Theory ◽  
Electronic Structures ◽  
Density Functional ◽  
Hyperfine Interactions ◽  
Geometry Optimization ◽  
Optimization Procedure ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Total Energies ◽  
Structure Calculations

We carried out ab initio electronic structure calculations in the frameworks of the Density Functional Theory (DFT) to study the electronic structures and hyperfine interaction of muonium (Mu) in imidazole (C3H4N2) and 1–methylimidazole (CH3C3H3N2). The local energy minima and hyperfine interactions of the Mu trapped at the three studies sites were determined by performing geometry optimization procedure. The results show the total energies for all three studied sites are close to one another. The Mu hyperfine interactions were also determined, with the corresponding values vary from 343.00 MHz to 471.28 MHz for the imidazole–Mu cluster, and from 380.21 MHz – 465.57 MHz to 475.93 MHz for the cluster of 1–methylimidazole–Mu, respectively.

scholarly journals Quantum chemical studies on the molecular structure, spectroscopic and electronic properties of (6-Methoxy-2-oxo-2H-chromen-4-yl)-methyl pyrrolidine-1-carbodithioate

2016 ◽  
Vol 34 (4) ◽  
pp. 886-904 ◽  
Author(s):  
Meryem Evecen ◽  
Hasan Tanak
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Electronic Absorption Spectra ◽  
Chemical Shifts ◽  
Density Functional Theory Calculations ◽  
Molecular Geometry ◽  
Basis Set ◽  
Functional Theory ◽  
Hartree Fock ◽  
Chemical Studies

AbstractIn this paper, the molecular geometry, vibrational frequencies and chemical shifts of (6-Methoxy-2-oxo-2H-chromen-4-yl)methyl pyrrolidine-1-carbodithioate in the ground state have been calculated using the Hartree-Fock and density functional methods with the 6-311++G(d,p) basis set. To investigate the nonlinear optical properties of the title compound, the polarizability and the first hyperpolarizability were calculated. The conformational properties of the molecule have been determined by analyzing molecular energy properties. Using the time dependent density functional theory, electronic absorption spectra have been calculated. Frontier molecular orbitals, natural bond orbitals, natural atomic charges and thermodynamical parameters were also investigated by using the density functional theory calculations.

scholarly journals Computational Study of some Double Headed Acyclo-C-Nucleosides

2015 ◽  
Vol 61 ◽  
pp. 1-11
Author(s):  
Sarah Amara ◽  
Noureddine Tchouar ◽  
Salah Belaidi
Keyword(s):  
Electronic Properties ◽  
Ground State ◽  
Density Functional ◽  
Computational Study ◽  
Experimental Studies ◽  
Functional Theory ◽  
Hartree Fock ◽  
Structural And Electronic Properties ◽  
Semi Empirical

In the present paper we have a focus in a study of theoretical characterization of three double headed acyclo-C-nucleosides, which are a recent target of experimental studies. The structural and electronic properties of double headed acyclo-C-nucleosides, 1,4-bis (3-mercapto-1H-1,2,4-triazol-5-yl) butane-1,2,3,4-tetrol, 1,4-bis (4-amino-5-mercapto-4H-1,2,4-triazol-3-yl) butane-1,2,3,4-tetrol and 5,5'-(1,2,3,4-tetrahydroxybutane-1,4-diyl) bis (1,3,4-oxadiazole-2(3H)-thione), have been investigated theoretically by performing semi-empirical molecular orbital, ab initio Hartree-Fock (HF) and Density Functional Theory (DFT) calculations. Geometries of the three molecules are optimized at the level of Austin Model 1 (AM1). The electronic properties and relative energies of the molecules have been calculated by HF and DFT in the ground state.

Calculations of Surface Structure for SrTiO3 Perovskite

2001 ◽  
Vol 672 ◽  
Author(s):  
E. Heifetsa ◽  
R.I. Eglitisb ◽  
E.A. Kotomin ◽  
G. Borstelb
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Dipole Moments ◽  
Surface Relaxation ◽  
Surface Layers ◽  
Functional Theory ◽  
Near Surface ◽  
Hartree Fock ◽  
Semi Empirical

ABSTRACTWe present and discuss results of the calculations for SrTiO3 (100) surface relaxation with different terminations (SrO and TiO2) using a semi-empirical shell model (SM) as well as abinitio methods based on Hartree-Fock (HF) and Density Functional Theory (DFT) formalisms. Using the SM, the positions of atoms in 16 near-surface layers placed atop a slab of rigid ions are optimized. This permits us determination of surface rumpling and surfaceinduced dipole moments (polarization) for different terminations. We also compare results of the ab initio calculations based on both HF with the DFT-type electroncorrelation corrections, several DFT with different exchange-correlation functionals, and hybrid exchange techniques. OurSM results for the (100) surfaces are in a good agreement with both our ab initio calculations and LEED experiments.

scholarly journals How do the Hückel and Baird Rules Fade away in Annulenes?

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 711 ◽  
Author(s):  
Irene Casademont-Reig ◽  
Eloy Ramos-Cordoba ◽  
Miquel Torrent-Sucarrat ◽  
Eduard Matito
Keyword(s):  
Density Functional ◽  
Geometry Optimization ◽  
Ring Structure ◽  
Orbital Method ◽  
Triplet States ◽  
Molecular Orbital Method ◽  
Geometrical Structures ◽  
Hartree Fock ◽  
Aromatic Character ◽  
Singlet And Triplet States

Two of the most popular rules to characterize the aromaticity of molecules are those due to Hückel and Baird, which govern the aromaticity of singlet and triplet states. In this work, we study how these rules fade away as the ring structure increases and an optimal overlap between p orbitals is no longer possible due to geometrical restrictions. To this end, we study the lowest-lying singlet and triplet states of neutral annulenes with an even number of carbon atoms between four and eighteen. First of all, we analyze these rules from the Hückel molecular orbital method and, afterwards, we perform a geometry optimization of the annulenes with several density functional approximations in order to analyze the effect that the distortions from planarity produce on the aromaticity of annulenes. Finally, we analyze the performance of three density functional approximations that employ different percentages of Hartree-Fock exchange (B3LYP, CAM-B3LYP and M06-2X) and Hartree-Fock. Our results reveal that functionals with a low percentage of Hartree-Fock exchange at long ranges suffer from severe delocalization errors that result in wrong geometrical structures and the overestimation of the aromatic character of annulenes.

scholarly journals Restricted-Variance Molecular Geometry Optimization Based on Gradient-Enhanced Kriging

2020 ◽  
Author(s):  
Gerardo Raggi ◽  
Ignacio Fernández Galván ◽  
Christian L. Ritterhoff ◽  
Morgane Vacher ◽  
Roland Lindh
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Geometry Optimization ◽  
Arbitrary Point ◽  
Molecular Geometry ◽  
Second Order ◽  
Machine Learning Techniques ◽  
Stationary Points ◽  
Molecular Geometry Optimization ◽  
Test Suites

Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional - step-restricted second-order truncated expansion - molecular optimization methods. In particular, the surrogate model given by GEK can have multiple stationary points, will smoothly converge to the exact model as the number of sample points increases, and contains an explicit expression for the expected error of the model function at an arbitrary point. Machine learning is, however, associated with abundance of data, contrary to the situation desired for efficient geometry optimizations. In the paper we demonstrate how the GEK procedure can be utilized in a fashion such that in the presence of few data points, the surrogate surface will in a robust way guide the optimization to a minimum of a potential energy surface. In this respect the GEK procedure will be used to mimic the behavior of a conventional second-order scheme, but retaining the flexibility of the superior machine learning approach. Moreover, the expected error will be used in the optimization to facilitate restricted-variance optimizations (RVO). A procedure which relates the eigenvalues of the approximate guessed Hessian with the individual characteristic lengths, used in the GEK model, reduces the number of empirical parameters to optimize to two - the value of the trend function and the maximum allowed variance. These parameters are determined using the extended Baker (e-Baker) and part of the Baker transition-state (Baker-TS) test suites as a training set. The so-created optimization procedure is tested using the e-Baker, the full Baker-TS, and the S22 test suites, at the density-functional-theory and second order Møller-Plesset levels of approximation. The results show that the new method is generally of similar or better performance than a state-of-the-art conventional method, even for cases where no significant improvement was expected.

scholarly journals Restricted-Variance Molecular Geometry Optimization Based on Gradient-Enhanced Kriging

2020 ◽  
Author(s):  
Gerardo Raggi ◽  
Christian L. Ritterhoff ◽  
Ignacio Fernández Galván ◽  
Morgane Vacher ◽  
Roland Lindh
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Geometry Optimization ◽  
Arbitrary Point ◽  
Molecular Geometry ◽  
Second Order ◽  
Machine Learning Techniques ◽  
Stationary Points ◽  
Molecular Geometry Optimization ◽  
Test Suites

Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional - step-restricted second-order truncated expansion - molecular optimization methods. In particular, the surrogate model given by GEK can have multiple stationary points, will smoothly converge to the exact model as the number of sample points increases, and contains an explicit expression for the expected error of the model function at an arbitrary point. Machine learning is, however, associated with abundance of data, contrary to the situation desired for efficient geometry optimizations. In the paper we demonstrate how the GEK procedure can be utilized in a fashion such that in the presence of few data points, the surrogate surface will in a robust way guide the optimization to a minimum of a potential energy surface. In this respect the GEK procedure will be used to mimic the behavior of a conventional second-order scheme, but retaining the flexibility of the superior machine learning approach. Moreover, the expected error will be used in the optimization to facilitate restricted-variance optimizations (RVO). A procedure which relates the eigenvalues of the approximate guessed Hessian with the individual characteristic lengths, used in the GEK model, reduces the number of empirical parameters to optimize to two - the value of the trend function and the maximum allowed variance. These parameters are determined using the extended Baker (e-Baker) and part of the Baker transition-state (Baker-TS) test suites as a training set. The so-created optimization procedure is tested using the e-Baker, the full Baker-TS, and the S22 test suites, at the density-functional-theory and second order Møller-Plesset levels of approximation. The results show that the new method is generally of similar or better performance than a state-of-the-art conventional method, even for cases where no significant improvement was expected.

Computational Studies of Electronic Structures and Hyperfine Interactions of Muonium in Tetraphenylgermane

2012 ◽  
Vol 620 ◽  
pp. 418-423
Author(s):  
Pek Lan Toh ◽  
Shukri Sulaiman ◽  
Mohamed Ismail Mohamed-Ibrahim
Keyword(s):  
Density Functional ◽  
Hyperfine Interactions ◽  
Geometry Optimization ◽  
Optimization Procedure ◽  
Dft Method ◽  
Equilibrium Structure ◽  
Coupling Constants ◽  
Local Energy Minimum ◽  
Phenyl Rings ◽  
Principle Density Functional Theory

The equilibrium structure of muoniatedtetraphenylgermane (GePh4Mu) was studied using the first principle Density Functional Theory (DFT) method. Three muonium (Mu) trapping sites were considered, namelyortho,meta, andparapositions on one of the phenyl rings. Geometry optimization procedure was utilized to determine the local energy minimum for all the systems. The total energies corresponding to Mu at the three positions are very similar to each other. For themetacase, the corresponding energy is higher than the other two sites by only about 0.03 eV. The hyperfine parameters of Mu were also calculated. The Mu isotropic hyperfine coupling constants were found to be 441.85 MHz, 449.80 MHz, and 439.01 MHz for theortho,meta, andparacases, respectively. The anisotropic value was calculated to be very small.

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