NOTE ON HYDROGENIC ATOMIC ORBITALS TO EVALUATE SENSITIVE PROPERTIES OF MOLECULES: AN EXAMPLE OF NMR CHEMICAL SHIFTS

2004 ◽  
Vol 03 (02) ◽  
pp. 163-168 ◽  
Author(s):  
P. E. HOGGAN
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Chemical Shifts ◽  
Geometry Optimization ◽  
Basis Sets ◽  
Slater Type ◽  
Slater Type Orbital ◽  
Dft Methods ◽  
Type Orbital ◽  
Nuclear Shielding

Now that the problems surrounding ab initio calculations over a Slater Type Orbital basis have been solved, it is available in several software packages. For general structures the STOP package (Slater Type Orbital Package) has offered ab initio SCF molecular properties since 1996, the requisite integrals all being evaluated analytically, including the four center term available since 1994. SMILES (Slater Molecular Integrals for Large Electronic Systems) has offered various basis sets, geometry optimization and CI since 2001. For density functional work, ADF, the Amsterdam Density Functional suite of programs, is a project dating from the 1970s with a 2003 edition. In this work the preferred ETOs (Exponential Type Orbitals) will be shown to be the hydrogenic orbitals and similar Coulomb Sturmians. Slater Type Functions (STFs) will be compared to them and suitable equivalent combinations, which are rarely used, given. The correct shielding of the nucleus, resulting from radial factors of hydrogenic orbitals is shown to be essential in the evaluation of precise nuclear shielding tensors for NMR spectroscopy of molecules using ab initio or DFT methods. The case study of benzothiazoles using natural abundance 15N is re-examined and compared with previous work including measurements.

A theoretical study of the 77Se NMR and vibrational spectroscopic properties of SenS8–n ring molecules

2002 ◽  
Vol 80 (11) ◽  
pp. 1435-1443 ◽  
Author(s):  
J Komulainen ◽  
R S Laitinen ◽  
R J Suontamo
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Chemical Shifts ◽  
Atomic Orbital ◽  
Geometry Optimization ◽  
Spectroscopic Properties ◽  
Basis Sets ◽  
Orbital Method ◽  
Hybrid Functional ◽  
Ring Molecules

The structures and spectroscopic properties of SenS8–n ring molecules have been studied by the use of ab initio molecular orbital techniques and density functional techniques involving Stuttgart relativistic large core effective core potential approximation with double zeta basis sets for valence orbitals augmented by two polarization functions for both sulfur and selenium. Full geometry optimizations have been carried out for all 30 isomers at the Hartree-Fock level of theory. The optimized geometries and the calculated fundamental vibrations and Raman intensities of the SenS8–n molecules agree closely with experimental information where available. The nuclear magnetic shielding tensor calculations have been carried out by the Gauge-independent atomic orbital method at the DFT level using Becke's three-parameter hybrid functional with Perdew/Wang 91 correlation. The isotropic shielding tensors correlate well with the observed chemical shift data. The calculated chemical shifts provide a definite assignment of the observed 77Se NMR spectroscopic data and can be used in the prediction of the chemical shifts of unknown SenS8–n ring molecules.Key words: selenium sulfides, ab initio, DFT, effective core potentials, geometry optimization, energetics, fundamental vibrations, 77Se chemical shifts.

A density functional approach toward structural features and properties of C20…N2X2 (X = H, F, Cl, Br, Me) molecules

2014 ◽  
Vol 13 (04) ◽  
pp. 1450023 ◽  
Author(s):  
Reza Ghiasi ◽  
Morteza Zaman Fashami ◽  
Amir Hossein Hakimioun
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Geometry Optimization ◽  
Structural Features ◽  
Nbo Analysis ◽  
Basis Set ◽  
Basis Sets ◽  
Basis Set Superposition Error ◽  
Homo And Lumo ◽  
Lowest Unoccupied Molecular Orbitals

In this work, the interaction of C 20 with N 2 X 2 ( X = H , F , Cl , Br , Me ) molecules has been explored using the B3LYP, M062x methods and 6-311G(d,p) and 6-311+G(d,p) basis sets. The interaction energies (IEs) obtained with standard method were corrected by basis set superposition error (BSSE) during the geometry optimization for all molecules at the same levels of theory. It was found C 20… N 2 H 2 interaction is stronger than the interaction of other N 2 X 2 ( X = F , Cl , Br , Me ) with C 20. Highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) levels are illustrated by density of states spectra (DOS). The nucleus-independent chemical shifts (NICSs) confirm that C 20… N 2 X 2 molecules exhibit aromatic characteristics. Geometries obtained from DFT calculations were used to perform NBO analysis. Also, 14 N NQR parameters of the C 20… N 2 X 2 molecules are predicted.

Theoretical Study of the Vertical Electronic Spectra, Electron-Spin g-Factors and Hyperfine Coupling Constants of the (C2v) Cyclic Radicals C3+, Si3+, C3− and Si3−

2003 ◽  
Vol 217 (3) ◽  
pp. 265-288 ◽  
Author(s):  
P. J. Bruna ◽  
F. Grein
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Bound States ◽  
Hyperfine Coupling ◽  
Coupling Constants ◽  
Basis Sets ◽  
Dft Methods ◽  
Functional Theory ◽  
Hyperfine Coupling Constants ◽  
Vertical Transition

AbstractThe vertical transition energies and Δg-values of cyclic C3+, Si3+ (X2B2), C3− (12A1, metastable) and Si3− (X2A1) are studied with ROHF MOs, multireference (MRDCI) wavefunctions and 6-311+G(2d) basis sets. Si3− has at least eight bound states. For each radical, the in-plane components of the g shift, Δgyy and Δgzz (with gii = ge + Δgii), have similar negative values (about −1200 ppm for C3+, C3− and about −8000 ppm for Si3+, Si3−). The Δgxx’s are larger in magnitude, negative for C3+, Si3+ (−11000 and −72000 ppm) but positive for C3−, Si3− (8000 and 165000 ppm). The hyperfine coupling constants Aiso, Adip are evaluated with ab initio CISD, QCISD, CCD, MP4SDQ methods as well as with density functional theory (DFT) methods (SVWN, B3LYP, B3PW91, PW91PW91), using a spin-unrestricted formalism; several basis sets are considered. Both approaches give internally consistent Aiso’s and Adip’s for each X3− center, with the (positive) s-spin-density at each basal atom (average Aiso (MHz) = 75 for C3− and −25 for Si3−) being smaller than at the apical center (275 and −95 MHz). The results are less satisfactory for X3+. All treatments agree, more or less, in a larger (positive) s-density at the basal atoms (Aiso(MHz) from 300 to 700 for C3+, and −80 to −150 for Si3+), whereas the s-contribution at the apical center depends on the method: for C3+, it is positive with ab initio but negative with DFT, whereas for Si3+ the opposite trend is found; as well, Adip(X3+) shows unusually large discrepancies for each center. For these radicals, literature values of Aiso and Adip are not available, either from experimental or multireference ab initio studies, to allow for comparisons with our results.

A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

2018 ◽  
Author(s):  
Danilo Carmona ◽  
David Contreras ◽  
Oscar A. Douglas-Gallardo ◽  
Stefan Vogt-Geisse ◽  
Pablo Jaque ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Hydroxyl Radical ◽  
Ab Initio ◽  
Fenton Reaction ◽  
Basis Set ◽  
Basis Sets ◽  
Dft Methods ◽  
Elementary Steps ◽  
Oxygen Oxygen ◽  
Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

BAND NN: A Deep Learning Framework For Energy Prediction and Geometry Optimization of Organic Small Molecules

2019 ◽  
Author(s):  
Siddhartha Laghuvarapu ◽  
Yashaswi Pathak ◽  
U. Deva Priyakumar
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Computational Cost ◽  
Geometry Optimization ◽  
Dft Methods ◽  
Energy Prediction ◽  
Machine Learning Model ◽  
Equilibrium Structures ◽  
High Level ◽  
Non Equilibrium

Recent advances in artificial intelligence along with development of large datasets of energies calculated using quantum mechanical (QM)/density functional theory (DFT) methods have enabled prediction of accurate molecular energies at reasonably low computational cost. However, machine learning models that have been reported so far requires the atomic positions obtained from geometry optimizations using high level QM/DFT methods as input in order to predict the energies, and do not allow for geometry optimization. In this paper, a transferable and molecule-size independent machine learning model (BAND NN) based on a chemically intuitive representation inspired by molecular mechanics force fields is presented. The model predicts the atomization energies of equilibrium and non-equilibrium structures as sum of energy contributions from bonds (B), angles (A), nonbonds (N) and dihedrals (D) at remarkable accuracy. The robustness of the proposed model is further validated by calculations that span over the conformational, configurational and reaction space. The transferability of this model on systems larger than the ones in the dataset is demonstrated by performing calculations on select large molecules. Importantly, employing the BAND NN model, it is possible to perform geometry optimizations starting from non-equilibrium structures along with predicting their energies.

Quantum-Chemical Ab Initio Calculations on Inda- and Thallabenzene (C5H5In and C5H5Tl) and their Structural Isomers η5-C5H5In and η5-C5H5Tl

2018 ◽  
Vol 71 (3) ◽  
pp. 102
Author(s):  
Emma Persoon ◽  
Yuekui Wang ◽  
Gerhard Raabe
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Density Functional ◽  
Single Point ◽  
Normal Modes ◽  
Dft Method ◽  
Basis Sets ◽  
Triplet States ◽  
Structural Isomers ◽  
Td Dft

Quantum-chemical ab initio, time-independent, as well as time-dependent density functional theory (TD-DFT) calculations were performed on the so far elusive heterocycles inda- and thallabenzene (C5H5In and C5H5Tl), employing several different methods (MP2, CISD, CCSD, CCSD(T), BD, BD(T), QCISD, QCISD(T), CASSCF, DFT/B3LYP), effective core potentials, and different basis sets. While calculations on the MP2 level predict the ground states of the title compounds to be singlets with the first triplet states between 13 and 15 kcal mol−1 higher in energy, single point calculations with the QCISD(T), CCSD(T), and BD(T) methods at CCSD-optimized structures result in energy differences between the singlet and the triplet states in the range between 0.3 and 2.1 kcal mol−1 in favour of the triplet states. According to a CASSCF(8,8) calculation the triplets are also more stable by about 2.5–2.9 kcal mol−1. Calculations were also performed for the C5v-symmetric η5 structural isomers (cyclopentadienylindium, CpIn, and cyclopentadienylthallium, CpTl, Cp = C5H5) of the title compounds. At the highest level of theory employed in this study, C5H5In is between 79 and 88 kcal mol−1 higher in energy than CpIn, while this energy difference is even larger for thallabenzene where C5H5Tl is energetically between 94 and 102 kcal mol−1 above CpTl. In addition we report on the UV/vis spectra calculated with a TD-DFT method as well as on the spectra of the normal modes of C5H5In and C5H5Tl. Both types of spectra might facilitate identification of the title compounds eventually formed in photolysis or pyrolysis experiments.

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