scholarly journals On the Relevance of Considering the Intermolecular Interactions on the Prediction of the Vibrational Spectra of Isopropylamine

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Ana M. Amado ◽  
Sónia M. Fiuza ◽  
Luis A. E. Batista de Carvalho ◽  
Paulo J. A. Ribeiro-Claro
Keyword(s):  
Hydrogen Bonding ◽  
Weak Interactions ◽  
Vibrational Frequencies ◽  
Basis Set ◽  
Vibrational Modes ◽  
Dft Methods ◽  
Torsional Mode ◽  
Computational Costs ◽  
Donor And Acceptor ◽  
The Comparative Study

The effects of implicitly considering the effects of hydrogen bonding on the molecular properties, such as vibrational frequencies, were inferred on the basis of DFT calculations. Several clusters of isopropylamine were assembled and theoretically characterized. The results showed that maximum H-bond cooperativity is achieved when the amine group acts simultaneously as donor and acceptor. The effect of H-bond cooperativity manifests itself in the relative cluster stability and on the structural and vibrational frequency predictions. Referring to the vibrational frequencies it was found that theNH2stretching and torsion vibrational modes are the most affected by the amine involvement in hydrogen bonding. Both stretching modes were found to be significantly redshifted relative to the monomer. TheNH2torsional mode, on the other hand, was found to be blueshifted up to 350 cm-1. Finally, the comparative study between the theory levels performed allows to conclude that the small 6-31G* basis set is able to stabilize weakC–H⋯Ninteractions as long as the new dispersion corrected DFT methods are considered. The impairments observed with conventional DFT methods for describing weak interactions may be overcome with the improvement of basis set, but the associated increase of computational costs may turn the calculations unfeasible.

THEORETICAL STUDIES OF HYDROGEN BONDING INTERACTION BETWEEN TRIMETHYLAMINE AND SUBSTITUTED PHENOLS, INFLUENCE OF THE SUBSTITUENTS ON THE HYDROGEN BOND PROPERTIES AND THE VIBRATIONAL SPECTRUM

2008 ◽  
Vol 07 (06) ◽  
pp. 1171-1186 ◽  
Author(s):  
SALMA PARVEEN ◽  
SUBOJIT DAS ◽  
ASIT K. CHANDRA ◽  
THERESE ZEEGERS-HUYSKENS
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Structural Changes ◽  
Structural Parameters ◽  
Basis Set ◽  
Bond Properties ◽  
Substituted Phenols ◽  
Hydrogen Bond Formation ◽  
Donor And Acceptor

Hydrogen bonding interactions between trimethylamine (TMA) and a series of para substituted phenols (X– C 6 H 4 OH , X = H , CH 3, NH 2, Cl , CN , and NO 2) are studied by using density functional theory with the hybrid B3LYP functional and the 6-31++G(d,p) basis set. Both electron donor and acceptor substituents (X) are chosen to study systematically the relation between the proton donor ability of the phenols and the strength of the OH … N hydrogen bond. The effect of hydrogen bonding on spectral and structural parameters and their inter relation are discussed. The natural bond orbital (NBO) analysis (occupation of σ* orbitals, hyperconjugative energies and atomic charges) is also carried out to elucidate the reason behind the spectral and structural changes due to hydrogen bond formation. Several correlations between hydrogen bond strength and bond properties are discussed.

scholarly journals Benchmarking on H2S and SO2 molecules using the software ORCA

2020 ◽  
Author(s):  
Maurício Gustavo Rodrigues ◽  
Leonardo Talavera Campos ◽  
Gabriel Soares Campos
Keyword(s):  
High School ◽  
Basis Function ◽  
Dft Method ◽  
Basis Set ◽  
Basis Sets ◽  
Quantum Calculation ◽  
Dft Methods ◽  
Quantum Method ◽  
Computational Costs ◽  
Brazilian Students

Choosing the best quantum method and basis function is sometimes difficult. It is necessary to take into account the computational costs in the same time of accuracy of the combination of quantum method and basis function. DFT methods and Pople basis set are the most common choices on molecular quantum calculation. This study makes a benchmark of DFT methods and different combinations of Pople basis sets on H2S and SO2 molecules. This choice aims decide this combination to explain better the formation on acid rain in environment, specially to high school Brazilian students. After the analysis of the better combinations of DFT method and Pople basis set, some IRC and TS calculations are going to be done to understand better inorganic reaction with sulfur.

Geometry, vibrational frequency, and isomerization of neutral and cation Cu–CN complex

2015 ◽  
Vol 14 (05) ◽  
pp. 1550032 ◽  
Author(s):  
Boli Nie ◽  
Shihai Yan ◽  
Lixiang Sun
Keyword(s):  
Potential Energy ◽  
Vibrational Frequency ◽  
Global Minimum ◽  
Energy Surface ◽  
Basis Set ◽  
Intrinsic Reaction Coordinate ◽  
Vibrational Modes ◽  
Biological Macromolecule ◽  
Dft Methods ◽  
Dissociation Mechanisms

The geometry structure, vibrational frequency, and the isomerization of neutral and cation copper cyanide systems ( CuCN and CuCN +) were investigated by employing three DFT methods (B3LYP, B3P86 and B3PW91) and MP2 functional with 6-311+G* basis set. The cyanides CuCN (1Σ+) is the most stable one among the isomers of CuCN , and CuNC +(2Σ+) isocyanides is the global minimum on its potential energy surface (PES). The vibrational modes of these isomers were assigned. Two dissociation mechanisms were designed for each species. The complex ( CuCN and CuCN +) tends to dissociate through neutral mechanism into CN cluster. The useful information is brought forward about the synthesis of material and biological macromolecule. The state–state isomerization pathways were established using the intrinsic reaction coordinate (IRC).

SPECTROSCOPIC STUDY, NLO PROPERTIES AND HOMO–LUMO ANALYSIS ON DIFFERENT DONOR AND ACCEPTOR SUBSTITUENTS OF THIAZOLYLAZOPYRIMIDINE CHROMOPHORES

2013 ◽  
Vol 12 (05) ◽  
pp. 1350039 ◽  
Author(s):  
ÖMER TAMER ◽  
DAVUT AVCI ◽  
YUSUF ATALAY
Keyword(s):  
Molecular Orbital ◽  
Density Functional ◽  
Atomic Orbital ◽  
Geometry Optimization ◽  
Vibrational Frequencies ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Potential Energy Distribution ◽  
Donor And Acceptor ◽  
The Mean

The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C chemical shift values of thiazolylazopyrimidine chromophores have been investigated by using density functional theories (DFT/B3LYP, PBE1PBE and BHand-HLYP) and Hartree–Fock (HF) methods with 6–31++G(d,p) basis set. The computed IR and NMR spectra are used to determine the types of the experimental bands observed. Also, the vibrational frequencies are supported on the basis of the potential energy distribution (PED) analysis calculated by using PBE1PBE method. The UV-vis spectrum has been obtained by TD-DFT and TD-HF methods. Total static dipole moment (μ), the mean polarizability (〈α〉), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability (〈β〉), highest occupied molecular orbital (HOMO), and lowest occupied molecular orbital (LUMO) energies of thiazolylazopyrimidine chromophores also have been investigated with quantum chemical calculations. Obtained nonlinear optical (NLO) parameters are compared with experimental ones. Additionally, the molecular hardness (η) and electronegativity (χ) parameters have been obtained by using the frontier molecular orbital energies. Obtained data from thiazolylazopyrimidine chromophores are important for associating the experimental and theoretical spectra with molecular structure and their properties.

Density Functional Theory and ab initio Hartree-Fock Calculations of Molecular Structure and Vibrational Spectra of Anilinium Nitrate

2008 ◽  
Vol 63 (10-11) ◽  
pp. 712-720 ◽  
Author(s):  
Davut Avcı ◽  
Adil Başoğlu ◽  
Yusuf Atalay
Keyword(s):  
Molecular Structure ◽  
Density Functional Theory ◽  
Density Functional ◽  
Molecular Geometry ◽  
Vibrational Frequencies ◽  
Basis Set ◽  
Dft Methods ◽  
Functional Theory ◽  
Hartree Fock ◽  
Infrared Intensities

The molecular geometry, vibrational frequencies, infrared intensities, Raman scattering activities and several thermodynamic parameters of anilinium nitrate in the ground state have been calculated by both Hartree-Fock (HF) and three density functional theory (DFT) methods (B3LYP, BLYP and B3PW91) using the 6-31G(d) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray structure. The optimized geometric bond lengths are described very well by the HF method while bond angles are reproduced more accurately by the DFT methods. Comparison between the observed fundamental vibrational frequencies of anilinium nitrate and the results of DFT and HF methods indicates that B3LYP is superior to the scaled HF, BLYP and B3PW91 approaches for molecular vibrational problems. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. In addition, calculated results are related to the linear correlation plot of computed data versus experimental geometric parameters and IR data.

scholarly journals Computational Studies of Vibration Spectra and Thermodynamic Properties of Metformin Using HF, DFT Methods

2011 ◽  
Vol 8 (1) ◽  
pp. 165-172
Author(s):  
S. Srinivasan ◽  
V. Renganayaki
Keyword(s):  
Fourier Transform ◽  
Thermodynamic Properties ◽  
Vibrational Energy ◽  
Solid Phase ◽  
Optimization Procedure ◽  
Vibrational Frequencies ◽  
Basis Set ◽  
Dependent Diabetes Mellitus ◽  
Dft Methods ◽  
Experimental Values

The molecular vibrations of metformin, one of the important anti-diabetic drugs to treat Non Insulin Dependent Diabetes Mellitus (NIDDM) have been investigated at room temperature by Fourier transform infrared (FTIR) and Fourier transform Raman (FTR) spectroscopies. The solid phase FTIR and FT-Raman spectra of the title compound have been recorded in the regions 4000-400 and 3500-250 cm-1. A satisfactory band assignment has been made on the fundamental modes of vibration. Employing the ab - initio Hatree –Fock (HF) and Density Function Theory (DFT) methods, the theoretical vibrational frequencies and geometry parameters like bond lengths, bond angles etc have been calculated and compared with the experimental values. HF and DFT calculations were performed using the standard B3LYP/6-31G** method and basis set combination. Optimized geometries were obtained using the global optimization procedure. Theoretical investigations of harmonic vibrational frequencies and thermodynamic properties viz. the zero point vibrational energy (ZPVE), entropy, heat capacity have been carried out. It has been found that both methods gave consistent data for geometric parameters, but DFT yielded vibrational frequencies much closer to the experimental values.

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

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

scholarly journals Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Christoph A. Bauer ◽  
Gisbert Schneider ◽  
Andreas H. Göller
Keyword(s):  
Machine Learning ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Training Data ◽  
Free Energies ◽  
Hydrogen Bond Donor ◽  
Chemical Application ◽  
Hydrogen Bond Acceptor ◽  
Donor And Acceptor ◽  
Target Values

Abstract We present machine learning (ML) models for hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD) strengths. Quantum chemical (QC) free energies in solution for 1:1 hydrogen-bonded complex formation to the reference molecules 4-fluorophenol and acetone serve as our target values. Our acceptor and donor databases are the largest on record with 4426 and 1036 data points, respectively. After scanning over radial atomic descriptors and ML methods, our final trained HBA and HBD ML models achieve RMSEs of 3.8 kJ mol−1 (acceptors), and 2.3 kJ mol−1 (donors) on experimental test sets, respectively. This performance is comparable with previous models that are trained on experimental hydrogen bonding free energies, indicating that molecular QC data can serve as substitute for experiment. The potential ramifications thereof could lead to a full replacement of wetlab chemistry for HBA/HBD strength determination by QC. As a possible chemical application of our ML models, we highlight our predicted HBA and HBD strengths as possible descriptors in two case studies on trends in intramolecular hydrogen bonding.

scholarly journals Unknown Knowns: Case Studies in Uncertainties in the Computation of Thermochemical Parameters

2020 ◽  
Author(s):  
John Simmie
Keyword(s):  
Heat Capacity ◽  
Gas Phase ◽  
Basis Set ◽  
Statistical Thermodynamic ◽  
Vibrational Modes ◽  
Heavy Atoms ◽  
New Methods ◽  
Formation Enthalpies ◽  
Thermochemical Parameters

<div>Both the computation of, and the uncertainties associated, with gas-phase molar formation enthalpies are now quite well established for systems comprised of tens of ‘heavy’ atoms chosen from the commonest elements. The same cannot be said for derived thermochemical quantities such as entropy, heat capacity and an enthalpy function. Whilst the application of well known statistical thermodynamic relations is mostly understood, the determination of the uncertainty with which such values can be obtained has been little studied — apart, that is, for a general protocol devised by Goldsmith et al. [J. Phys. Chem. A, 2012, 116, 9033–9057]. Specific examples from that work are explored here and it is shown that their estimates are overly pessimistic. It is also evident that for some species the calculated thermochemical parameters show very little variation with either the level of theory, or basis set, or treatment of vibrational modes — this renders the inclusion of such species in databases designed to validate new methods of limited value.<br></div>

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