scholarly journals Regularized machine learning on molecular graph model explains systematic error in DFT enthalpies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Himaghna Bhattacharjee ◽  
Nikolaos Anesiadis ◽  
Dionisios G. Vlachos
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Statistical Tests ◽  
Molecular Graph ◽  
Chemical Species ◽  
Graph Model ◽  
Basis Set ◽  
Gaseous Species ◽  
Elementary Reactions ◽  
Gas Phase Molecules

AbstractA major goal of materials research is the discovery of novel and efficient heterogeneous catalysts for various chemical processes. In such studies, the candidate catalyst material is modeled using tens to thousands of chemical species and elementary reactions. Density Functional Theory (DFT) is widely used to calculate the thermochemistry of these species which might be surface species or gas-phase molecules. The use of an approximate exchange correlation functional in the DFT framework introduces an important source of error in such models. This is especially true in the calculation of gas phase molecules whose thermochemistry is calculated using the same planewave basis set as the rest of the surface mechanism. Unfortunately, the nature and magnitude of these errors is unknown for most practical molecules. Here, we investigate the error in the enthalpy of formation for 1676 gaseous species using two different DFT levels of theory and the ‘ground truth values’ obtained from the NIST database. We featurize molecules using graph theory. We use a regularized algorithm to discover a sparse model of the error and identify important molecular fragments that drive this error. The model is robust to rigorous statistical tests and is used to correct DFT thermochemistry, achieving more than an order of magnitude improvement.

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 Protonated heterocyclic derivatives of cyclopropane and cyclopropanone: classical species, alternate sites, and ring fragmentation

2015 ◽  
Vol 93 (7) ◽  
pp. 708-714 ◽  
Author(s):  
Margarida S. Miranda ◽  
Darío J.R. Duarte ◽  
Joaquim C.G. Esteves da Silva ◽  
Joel F. Liebman
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Proton Affinities ◽  
Functional Theory ◽  
Heterocyclic Derivatives ◽  
Gas Phase Basicities ◽  
Derivatives Of

A computational study has been performed for protonated oxygen- or nitrogen-containing heterocyclic derivatives of cyclopropane and cyclopropanone. We have searched for the most stable conformations of the protonated species using density functional theory with the B3LYP functional and the 6-31G(2df,p) basis set. More accurate enthalpy values were obtained from G4 calculations. Proton affinities and gas-phase basicities were accordingly derived.

Charge transfer complexes between 2-, 3- and 4-aminopyridines and some π-acceptors in the gas phase and in chloroform: DFT calculations

2016 ◽  
Vol 15 (04) ◽  
pp. 1650029 ◽  
Author(s):  
Nuha Ahmed Wazzan
Keyword(s):  
Charge Transfer ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Molecular Structures ◽  
Basis Set ◽  
Charge Transfer Complexes ◽  
Good Correspondence ◽  
Electronic Distribution ◽  
Picryl Chloride

This work reports density functional theory (DFT) calculations on the molecular structures, electronic distribution, and UV-Vis and IR spectroscopy analysis of charge transfer complexes between aminopyridines (APYs), namely 2-APY, 3-APY and 4-APY, as electron-donors and some [Formula: see text]-electron-acceptors, namely chloranil (CHL), tetracyanoethylene (TCNE) and picryl chloride (PC), formed in the gas phase at the B3LYP/6-31[Formula: see text]G(d,p) method/basis set, and in chloroform at the same method/basis set using PCM as solvation model. Good correspondence was generally obtained between the calculated parameters and the experimental ones.

scholarly journals Potential Energy Surface (PES) Scan of Gas-Phase L-Proline

2014 ◽  
Vol 38 ◽  
pp. 26-34
Author(s):  
Anouar el Guerdaoui ◽  
Yassine el Kahoui ◽  
Malika Bourjila ◽  
Rachida Tijar ◽  
Abderrahman el Gridani
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Density Functional ◽  
Energy Surface ◽  
Conformational Stability ◽  
Geometry Optimization ◽  
Basis Set ◽  
Absolute Minimum ◽  
Pes Scan

We performed here a systematic ab initio calculations on neutral gas-phase L-proline. A total of 8 local minima were located by geometry optimization of the trial structures using density functional theory (DFT) with B3LYP three parameter hybrid potential coupled with the 6-31G)d( basis set. The absolute minimum obtained will be subject to a rigid potential energy surface (PES) scan by rotating its carboxylic group using the same method with more accurate basis set B3LYP/6-311++G(d,p), to get a deeper idea about its conformational stability. The main aim of the present work was the study of the rigidity of the L-proline structure and the puckering of its pyrrolidine ring.

scholarly journals Contribution of gaseous and particulate species to droplet solute composition at the Puy de Dôme, France

2003 ◽  
Vol 3 (5) ◽  
pp. 1509-1522 ◽  
Author(s):  
K. Sellegri ◽  
P. Laj ◽  
A. Marinoni ◽  
R. Dupuy ◽  
M. Legrand ◽  
...  
Keyword(s):  
Liquid Phase ◽  
Gas Phase ◽  
Removal Rate ◽  
Chemical Species ◽  
Solute Concentration ◽  
Complex Nature ◽  
Gaseous Species ◽  
Phase Partitioning ◽  
Gas Phases ◽  
Set Up

Abstract. Chemical reactions of dissolved gases in the liquid phase play a key role in atmospheric processes both in the formation of secondary atmospheric compounds and their wet removal rate but also in the regulation of the oxidizing capacity of the troposphere. The behavior of gaseous species and their chemical transformation in clouds are difficult to observe experimentally given the complex nature of clouds. During a winter field campaign at the summit of the Puy de Dôme (central France, 1465 m a.s.l), we have deployed an experimental set-up to provide a quantification of phase partitioning of both organic (CH3COOH, HCOOH, H2C2O4) and inorganic (NH3, HNO3, SO2, HCl) species in clouds. We found that nitric and hydrochloric acids can be considered close to Henry's law equilibrium, within analytical uncertainty and instrumental errors. On another hand, for NH3 and carboxylic acids, dissolution of material from the gas phase is kinetically limited and never reaches the equilibrium predicted by thermodynamics, resulting in significant sub-saturation of the liquid phase. On the contrary, SIV is supersaturated in the liquid phase, in addition to the presence of significant aerosol-derived SVI transferred through nucleation scavenging. Upon droplet evaporation, a significant part of most species, including SIV, tends to efficiently return back into the gas phase. Overall, gas contribution to the droplet solute concentration ranges from at least 48.5 to 98% depending on the chemical species. This is particularly important considering that aerosol scavenging efficiencies are often calculated assuming a negligible gas-phase contribution to the solute concentration. Our study emphasizes the need to account for the in-cloud interaction between particles and gases to provide an adequate modeling of multiphase chemistry systems and its impact on the atmospheric aerosol and gas phases.

A computational study of the SNAr reaction of 2-ethoxy-3,5-dinitropyridine and 2-methoxy-3,5-dinitropyridine with piperidine

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Oluwakemi A. Oloba-Whenu ◽  
Idris O. Junaid ◽  
Chukwuemeka Isanbor
Keyword(s):  
Hydrogen Bonding ◽  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Density Functional Theory Method ◽  
Basis Set ◽  
Slow Step ◽  
Functional Theory ◽  
Snar Reaction ◽  
Hybrid Density Functional

AbstractA computational study of the chemical kinetics and thermodynamics study of the SNAr between 3,5-dinitroethoxypyridine 1a and 3,5-dinitromethoxypyridine 1b with piperidine 2 in the gas phase is reported using hybrid density functional theory method B3PW91 and 6–31G(d,p) basis set. The reaction was modeled via both the catalyzed and base-catalyzed pathways which proceeded with the initial attack of the nucleophile 2 on the substrates 1 to yield the Meisenheimer complex intermediate that is stabilized with hydrogen bonding. Calculations show that the reaction goes via the formation and decomposition of a Meisenheimer complex, which was observed to be stabilized by hydrogen bonding. Along the uncatalyzed pathway, the decomposition of the Meisenheimer complex was the slow step and requires about 28 kcal/mol. This barrier was reduced to about 14.8 kcal/mol with the intervention of the base catalyst, thus making the formation of the Meisenheimer complex rate determining. All reactions were calculated to be exothermic, about −6.5 kcal/mol and −0.6 kcal/mol, respectively, for the reaction of 1a and 1b with 2.

scholarly journals Vibrational spectra of aniline in gas phase: An ab-initio study

2010 ◽  
Vol 7 (2) ◽  
pp. 449-455
Author(s):  
S. D. S. Chauhan ◽  
A.K. Sharma ◽  
R. Kumar ◽  
D. Kulshreshtha ◽  
R. Gupta ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Basis Set ◽  
Basis Sets ◽  
Ab Initio Study ◽  
Functional Theory ◽  
Hartree Fock ◽  
Modes Of Vibration ◽  
Experimental Findings

Vibrational frequencies of aniline in gas phase have been calculated and each of their modes of vibration assigned properly at RHF and DFT with 6-31G(d) basis set. In the present study, it has been observed that the 6-31G(d) basis set at both RHF and DFT levels of calculations provides better agreement to the experimental findings as compared to other basis sets. Simultaneously, Density functional theory is found to be superior to its counterpart Hartree Fock method.

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.

BOREPIN, BORANORBORNADIENE AND BORANORCARADIENE: SUBSTITUENT EFFECTS ON INTERCONVERSIONS AT THEORETICAL LEVELS

2010 ◽  
Vol 09 (01) ◽  
pp. 379-392 ◽  
Author(s):  
M. Z. KASSAEE ◽  
S. M. MUSAVI ◽  
E. MOTAMEDI
Keyword(s):  
Gas Phase ◽  
Relative Stability ◽  
Density Functional ◽  
Substituent Effects ◽  
Basis Set ◽  
Electronic Effects ◽  
Bond Length Alternation ◽  
Ab Initio Hf ◽  
Rule Out ◽  
Hf Calculations

Density-functional B3LYP and ab initio HF calculations are used to study three isomeric systems including: borepin I, boranorbornadiene II, and boranorcaradiene III as well as their X-substituted analogues at two different positions ( X = F, Cl, Br, CH3, OCH3, CF3, CN , and NH2 ). Geometries, enthalpies, and energy barriers for two series of interconversions, IIIX → IX and IIIX → IIX, are calculated using 6-311G* basis set. The B3LYP calculated relative stability is in the order: I (0.00 kcal/mol) > II (23.33 kcal/mol) > III (39.07 kcal/mol). Except for NH2 , the electronic effects of the substituents are generally insignificant on the relative stability. At B3LYP, the gas-phase activation enthalpies for III → I and III → II interconversions are estimated to be very small (0.6 and 0.75 kcal/mol, respectively). The reverse conversions, I → III and II → III, have activation energies of 39.67 and 16.49 kcal/mol, respectively. These energies rule out the possibility of a rapid interconversion of the isomers in the gas phase. Again, none of the substituents, X, can change this situation. Two pathways are proposed for the possible [1, 3]-suprafacial sigmatropic shifts of IIIX → IIX. The partial aromatic characters of planar borepins are estimated using magnetic (NICS) and structural criteria (bond length alternation).

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