Crystal and geometry-optimized structure of an anthracene-based Diels–Alder adduct

2020 ◽  
Vol 76 (7) ◽  
pp. 639-646
Author(s):  
Zachary E. Hillman ◽  
Joseph M. Tanski ◽  
Andrea Roberts
Keyword(s):  
Crystal Structure ◽  
Gas Phase ◽  
Density Functional ◽  
Population Analysis ◽  
Computational Cost ◽  
Diels Alder ◽  
Basis Set ◽  
Hybrid Functional ◽  
Computational Calculations ◽  
Alder Adduct

Computational calculations of an anthracene-based Diels–Alder adduct, namely, 17-ethyl-1-hydroxymethyl-17-azapentacyclo[6.6.5.02,7.09,14.015,19]nonadeca-2,4,6,9,11,13-hexaene-16,18-dione, C21H19NO3, predicting density functional theory (DFT) optimized geometries in the gas phase are compared in terms of accuracy relative to the solid-state crystal structure and computational cost. Crystal structure determination and Hirshfeld surface analysis of the racemic product reveal that the molecules are linked by O—H...O=C hydrogen bonds between the hydroxy and carbonyl groups, accounting for 9.5% of the intermolecular contacts, while H...H contacts represent 56.9% of the total. Boltzmann population analysis of computed relative rotamer abundances in the gas phase are based on lower-level geometry optimization and thermochemical corrections coupled with higher-level electronic energy calculations using the B2PLYP double-hybrid functional. As expected, the choice of density functional has a greater effect than the basis set on accuracy for all levels of theory. For any given functional, increasing the basis set size did not always correlate with increasingly accurate structures. The hybrid functional B3LYP without dispersion correction routinely gave the closest approximations to the crystal structure where the B3LYP/aug-cc-pVDZ combination afforded the best structure (r.m.s. deviation = 0.1314 Å). However, the B3LYP/6-31+G(d,p) level of theory represents the best compromise between accuracy (r.m.s. deviation = 0.1388 Å) and cost as it yielded appreciably accurate results in a fraction of the time compared to other method combinations.

scholarly journals DFT Study for the Spectroscopic and Structural Analysis of p-Dimethylaminoazobenzene

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Majid Ali ◽  
Asim Mansha ◽  
Sadia Asim ◽  
Muhammad Zahid ◽  
Muhammad Usman ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Gas Phase ◽  
Title Compound ◽  
Density Functional ◽  
Electronic Absorption Spectra ◽  
Population Analysis ◽  
Basis Set ◽  
Potential Energy Distribution ◽  
B3lyp Level ◽  
Computational Calculations

The study under consideration represents the computational calculations of Azo-based direct dye named p-(dimethylamino)azobenzene (DMAB) under the effect of solvents with different relative permittivities. A density functional theory (DFT) method at the B3LYP level with 6-311G++ was applied for the spectroscopic and structural analysis of the title compound. Calculations of geometric parameters (bond orders, bond lengths, and dihedral angles), electron densities, thermodynamic parameters, and orbital energies were performed for the title compound. Mulliken population analysis (MPA) as well as natural population analysis (NPA) was also performed at the B3LYP level with different solvents for finding solvent effects. In order to predict the reactivity of DMAB, molecular electrostatic potential (MESP) calculations were carried out for it. For vibrational analysis, the infrared (IR) spectra were computed for the title compound at the B3LYP/6-311G++ level in the gas phase and in different solvents with good agreement to the experimental FT-IR spectrum. The different modes of vibrations were assigned using potential energy distribution (PED). The computed Raman spectra also showed appreciable agreement with the experimental recorded Raman spectrum. The electronic absorption spectra of the title compound have been computed employing DFT/B3LYP with the 6-311G++ basis set in the gas phase and in four different solvents, that is, DMSO, ethanol, acetonitrile, and water which were compared with the experimental spectra with appreciable agreement. NBO analysis was carried out for understanding the intramolecular and intermolecular bonding of the compound and the density transfer from completely filled to unfilled orbital was found. The HOMO-LUMO energies were determined for analyzing the mechanism of intramolecular charge transfer.

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 Modeling organic aerosols in a megacity: comparison of simple and complex representations of the volatility basis set approach

2010 ◽  
Vol 10 (12) ◽  
pp. 30205-30277 ◽  
Author(s):  
M. Shrivastava ◽  
J. Fast ◽  
R. Easter ◽  
W. I. Gustafson ◽  
R. A. Zaveri ◽  
...  
Keyword(s):  
Gas Phase ◽  
Secondary Organic Aerosol ◽  
Computational Cost ◽  
Organic Aerosols ◽  
Field Measurements ◽  
Organic Aerosol ◽  
Basis Set ◽  
Aerosol Formation ◽  
Secondary Organic Aerosol Formation ◽  
The City

Abstract. The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is modified to include a volatility basis set (VBS) treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS) is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25%, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC) precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15% oxygen mass per generation of oxidation; however, all modeling cases still under-predict these ratios downwind as compared to measurements, suggesting a need to further improve chemistry parameterizations of secondary organic aerosol formation.

scholarly journals Accuracy and Reliability in the Simulation of Vibrational Spectra: A Comprehensive Benchmark of Energies and Intensities Issuing From Generalized Vibrational Perturbation Theory to Second Order (GVPT2)

2021 ◽  
Vol 8 ◽  
Author(s):  
Qin Yang ◽  
Marco Mendolicchio ◽  
Vincenzo Barone ◽  
Julien Bloino
Keyword(s):  
Perturbation Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Computational Cost ◽  
Theoretical Data ◽  
Infrared Region ◽  
Second Order ◽  
Basis Set ◽  
Molecular Systems ◽  
The Impact

Vibrational spectroscopy represents an active frontier for the identification and characterization of molecular species in the context of astrochemistry and astrobiology. As new missions will provide more data over broader ranges and at higher resolution, especially in the infrared region, which could be complemented with new spectrometers in the future, support from laboratory experiments and theory is crucial. In particular, computational spectroscopy is playing an increasing role in deepening our understanding of the origin and nature of the observed bands in extreme conditions characterizing the interstellar medium or some planetary atmospheres, not easily reproducible on Earth. In this connection, the best compromise between reliability, feasibility and ease of interpretation is still a matter of concern due to the interplay of several factors in determining the final spectral outcome, with larger molecular systems and non-covalent complexes further exacerbating the dichotomy between accuracy and computational cost. In this context, second-order vibrational perturbation theory (VPT2) together with density functional theory (DFT) has become particularly appealing. The well-known problem of the reliability of exchange-correlation functionals, coupled with the treatment of resonances in VPT2, represents a challenge for the determination of standardized or “black-box” protocols, despite successful examples in the literature. With the aim of getting a clear picture of the achievable accuracy and reliability of DFT-based VPT2 calculations, a multi-step study will be carried out here. Beyond the definition of the functional, the impact of the basis set and the influence of the resonance treatment in VPT2 will be analyzed. For a better understanding of the computational aspects and the results, a short summary of vibrational perturbation theory and the overall treatment of resonances for both energies and intensities will be given. The first part of the benchmark will focus on small molecules, for which very accurate experimental and theoretical data are available, to investigate electronic structure calculation methods. Beyond the reliability of energies, widely used for such systems, the issue of intensities will also be investigated in detail. The best performing electronic structure methods will then be used to treat larger molecular systems, with more complex topologies and resonance patterns.

The Syntheses and Crystal-Structures of Decahydro-5,14:6,13:7,12-Trimethanopentacene and Decahydro-5,14-7,12-Dimethanopentacene: Two Useful Molecules for Investigating Laticyclic Hyperconjugation

1986 ◽  
Vol 39 (10) ◽  
pp. 1587 ◽  
Author(s):  
DC Craig ◽  
MN Paddonrow ◽  
HK Patney
Keyword(s):  
Crystal Structure ◽  
Ab Initio Calculations ◽  
Crystal Structures ◽  
Reductive Dechlorination ◽  
Photoelectron Spectrum ◽  
Alder Reaction ◽  
Diels Alder ◽  
Basis Set ◽  
Orbital Interactions ◽  
Diels Alder Reaction

The syntheses of decahydro-5,14:6,13:7,12-trimethanopentacene and decahydro-5,14:7,12-dimethanopentacene are described (see Schemes 1 and 2 respectively). Diels -Alder reaction of diene (10) with two equivalents of tetrachlorothiophen 1,1-dioxide (11) gave the adduct (12), which was aromatized to (13) through treatment with base. Reductive dechlorination (Na/ PriOH ) of (13) gave (6). A similar set of reactions performed on (17), itself prepared from cyclohexa-1,4-diene and two equivalents of hexachlorocyclopentadiene (15), gave (7). The crystal structures of (6) and (7) were determined. An interesting feature of the structure of (7) is the slight endo pyramidalization (by c. 3°) of the trigonal carbon atoms C 4a, C 7a, C 11a and C 14a. Model ab initio calculations (STO-3G basis set) on complexes (27) and (28), whose geometries were culled from the crystal structure of (6), indicate that significant laticyclic hyperconjugative interactions (c. 0.3 eV ) are mainly responsible for causing the observed splitting between the πs+πs and πs-πs levels in the photoelectron spectrum of (6). Orbital interactions through the pair of six connecting sigma bonds (OIT-6-B) in (6) have a negligible effect (c. 0.08 eV ) on these levels. In agreement with prediction, laticyclic hyperconjugation does not affect the πa+πa and πa-πa levels.

Donor Functionalized Perylene and Different π-Spacers Based Sensitizers for DSSC Applications - A Theoretical Approach

2021 ◽  
Author(s):  
D. Nicksonsebastin ◽  
P. Pounraj ◽  
Prasath M
Keyword(s):  
Density Functional Theory ◽  
Solar Cell ◽  
Gas Phase ◽  
Density Functional ◽  
Basis Set ◽  
Dye Sensitized Solar Cell ◽  
Functional Theory ◽  
Dye Sensitized ◽  
Td Dft ◽  
Organic Sensitizers

Abstract Perylene based novel organic sensitizers for the Dye sensitized solar cell applications are investigated by using Density functional theory (DFT) and time dependant density functional theory (TD-DFT).The designed sensitizers have perylene and dimethylamine (DM) and N-N-dimethylaniline(DMA) functionalized perylene for the dssc applications.π-spacers are thiophene andcyanovinyl groups and cyanoacrylic acid is chosen as the acceptor for the designed sensitizers. The studied sensitizers were fully optimized by density functional theory at B3LYP/6-311G basis set on gas phase and DMF phase. The electronic absorption of the sensitizers is analyzed by TD-DFT at B3LYP/6-311G basis set in both gas and DMF phase.

SOLVENT EFFECTS ON THE ELECTRONIC STRUCTURE AND NON-LINEAR OPTICAL PROPERTIES OF PYRENE AND SOME OF ITS DERIVATIVES BASED ON DENSITY FUNCTIONAL THEORY

2021 ◽  
Vol 4 (4) ◽  
pp. 236-251
Author(s):  
A. S. Gidado ◽  
L. S. Taura ◽  
A. Musa
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Energy Gap ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Lumo Energy ◽  
Functional Theory ◽  
Organic Optoelectronic ◽  
Homo Lumo

Pyrene (C16H10) is an organic semiconductor which has wide applications in the field of organic electronics suitable for the development of organic light emitting diodes (OLED) and organic photovoltaic cells (OPV). In this work, Density Functional Theory (DFT) using Becke’s three and Lee Yang Parr (B3LYP) functional with basis set 6-311++G(d, p) implemented in Gaussian 03 package was  used to compute total energy, bond parameters, HOMO-LUMO energy gap, electron affinity, ionization potential, chemical reactivity descriptors, dipole moment, isotropic polarizability (α), anisotropy of polarizability ( Δ∝) total first order hyper-polarizability () and second order hyperpolarizability (). The molecules used are pyrene, 1-chloropyrene and 4-chloropyrene  in gas phase and in five different solvents: benzene, chloroform, acetone, DMSO and water. The results obtained show that solvents and chlorination actually influenced the properties of the molecules. The isolated pyrene in acetone has the largest value of HOMO-LUMO energy gap of and is a bit closer to a previously reported experimental value of  and hence is the most stable. Thus, the pyrene molecule has more kinetic stability and can be described as low reactive molecule. The calculated dipole moments are in the order of 4-chloropyrene (1.7645 D) < 1-chloropyrene (1.9663 D) in gas phase. The anisotropy of polarizability ( for pyrene and its derivatives were found to increase with increasing polarity of the solvents.  In a nutshell, the molecules will be promising for organic optoelectronic devices based on their computed properties as reported by this work.

scholarly journals In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents

2020 ◽  
Vol 3 (4) ◽  
pp. 989-1000
Author(s):  
Mustapha Abdullahi ◽  
Shola Elijah Adeniji
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
In Silico ◽  
Density Functional ◽  
Docking Simulation ◽  
Basis Set ◽  
Hybrid Functional ◽  
Standard Drug

AbstractMolecular docking simulation of thirty-five (35) molecules of N-(2-phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamide (IPA) with Mycobacterium tuberculosis target (DNA gyrase) was carried out so as to evaluate their theoretical binding affinities. The chemical structure of the molecules was accurately drawn using ChemDraw Ultra software, then optimized at density functional theory (DFT) using Becke’s three-parameter Lee–Yang–Parr hybrid functional (B3LYP/6-311**) basis set in a vacuum of Spartan 14 software. Subsequently, the docking operation was carried out using PyRx virtual screening software. Molecule 35 (M35) with the highest binding affinity of − 7.2 kcal/mol was selected as the lead molecule for structural modification which led to the development of four (4) newly hypothetical molecules D1, D2, D3 and D4. In addition, the D4 molecule with the highest binding affinity value of − 9.4 kcal/mol formed more H-bond interactions signifying better orientation of the ligand in the binding site compared to M35 and isoniazid standard drug. In-silico ADME and drug-likeness prediction of the molecules showed good pharmacokinetic properties having high gastrointestinal absorption, orally bioavailable, and less toxic. The outcome of the present research strengthens the relevance of these compounds as promising lead candidates for the treatment of multidrug-resistant tuberculosis which could help the medicinal chemists and pharmaceutical professionals in further designing and synthesis of more potent drug candidates. Moreover, the research also encouraged the in vivo and in vitro evaluation study for the proposed designed compounds to validate the computational findings.

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.

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