A theoretical study of the CSH4 and CPH5 hypersurfaces. Geometries, tautomerization, and dissociation of sulfonium and phosphonium ylides

Calculations have been performed at four basis set levels (STO-3G, STO-3G*, 4-31G, 4-31G*) on the model ylides methylenesulfurane (CH2SH2) and methylenephosphorane (CH2PH3), their stable tautomers (CH3SH and CH3PH2), their dissociation products (SH2, PH3 and CH2), and the protonated species CH3SH2+ and CH3PH3+. At each basis set level all geometries have been optimized fully, using the FORCE method. The conformational behaviour of the ylides as a function of C—X bond-stretching, C—X torsion, and CH2 (or SH2) bending has been examined in some detail. The experimental properties (i.e., geometries, relative stabilities, proton affinities, rotation–inversion behaviour) of sulfonium and phosphonium ylides are reproduced well by the model calculations with the 4-31G* basis set, which contains d-type functions on both carbon and sulfur (or phosphorus). All other basis sets are deficient in different ways and for different reasons, which are discussed in detail. The principal result of this work is the conclusion that d-type functions are essential for a proper description of the hypervalent species CH2SH2 and CH2PH3, but not for the normal-valent species SH2, PH3, CH3SH, and CH3PH2. The conclusion concerning hypervalent species reverses our earlier views. The role of the d-type functions is to concentrate charge into the C—X region of the ylides, and thus to stabilize the system. Evidence for this effect has been obtained from quantitative perturbational molecular orbital (PMO) analyses of interactions associated with the carbon lone pair, as well as comparisons of electron density plots with and without the d AO's. A second conclusion is that the imposition of various geometrical constraints such as assumed C—X, C—H, or X—H bond lengths, and HCH or XHn bond angles, as was necessary for computational reasons in all previous work on such systems, has major and previously unrecognized consequences. For example, the assumption that the CH2 moiety is planar in CH2SH2 leads to very similar geometries with and without d AO's, although only in the latter case does such a geometry at carbon correspond to the true energy minimum; in the absence of d AO's the C—S bond length is maintained by a symmetry-enforced barrier to dissociation. These and other consequences of geometrical constraints at carbon, sulfur, or phosphorus are analyzed in detail.

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Theoretical Study of Solvent Effects on the Electronic and Thermodynamic Properties of Tetrathiafulvalene (TTF) Molecule Based on DFT

Asian Journal of Research and Reviews in Physics ◽

10.9734/ajr2p/2021/v5i230162 ◽

2021 ◽

pp. 42-54

Author(s):

Rabiu Nuhu Muhammad ◽

N. M. Mahraz ◽

A. S Gidado ◽

A. Musa

Keyword(s):

Thermodynamic Properties ◽

Bond Length ◽

Density Functional ◽

Theoretical Study ◽

Energy Gap ◽

Basis Set ◽

Basis Sets ◽

Frontier Molecular Orbital ◽

Orbital Energy ◽

Chemical Hardness

Tetrathiafulvalene () is an organosulfur compound used in the production of molecular devices such as switches, sensors, nonlinear optical devices and rectifiers. In this work, a theoretical study on the effects of solvent on TTF molecule was investigated and reported based on Density Functional Theory (DFT) as implemented in Gaussian 03 package using B3LYP/6-31++G(d,p) basis set. Different solvents were introduced as a bridge to investigate their effects on the electronic structure. The HUMO, LUMO, energy gap, global chemical index, thermodynamic properties, NLO and DOS analysis of the TTF molecule in order to determine the reactivity and stability of the molecule were obtained. The results obtained showed that the solvents have effects on the electronic and non-linear-optical properties of the molecule. The optimized bond length revealed that the molecule has strong bond in gas phase with smallest bond length of about 1.0834Å than in the rest of the solvents. It was observed that the molecule is more stable in acetonitrile with HOMO-LUMO gap and chemical hardness of 3.6373eV and 1.8187eV respectively. This indicates that the energy gap and chemical hardness of TTF molecule increases with the increase in polarity and dielectric constant of the solvents. The computed results agreed with the results in the literature. The thermodynamics and NLO properties calculation also indicated that TTF molecule has highest value of specific heat capacity (Cv), total dipole moment () and first order hyperpolarizability () in acetonitrile, while acetone has the highest value of entropy and toluene has a slightly higher value of zero point vibrational energy (ZPVE) than the rest of the solvents. The results show that careful selection of the solvents and basis sets can tune the frontier molecular orbital energy gap of the molecule and can be used for molecular device applications.

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An Assessment of Computational Methods for Calculating Accurate Structures and Energies of Bio-Relevant Polysulfur/Selenium-Containing Compounds

Molecules ◽

10.3390/molecules23123323 ◽

2018 ◽

Vol 23 (12) ◽

pp. 3323 ◽

Cited By ~ 3

Author(s):

Sahar Nikoo ◽

Paul Meister ◽

John Hayward ◽

James Gauld

Keyword(s):

Inorganic Chemistry ◽

Bond Length ◽

Gas Phase ◽

Electron Correlation ◽

Negative Charge ◽

Basis Set ◽

Proton Affinities ◽

Selenium Compounds ◽

Gas Phase Basicities

The heavier chalcogens sulfur and selenium are important in organic and inorganic chemistry, and the role of such chalcogens in biological systems has recently gained more attention. Sulfur and, to a lesser extent selenium, are involved in diverse reactions from redox signaling to antioxidant activity and are considered essential nutrients. We investigated the ability of the DFT functionals (B3LYP, B3PW91, ωB97XD, M06-2X, and M08-HX) relative to electron correlation methods MP2 and QCISD to produce reliable and accurate structures as well as thermochemical data for sulfur/selenium-containing systems. Bond lengths, proton affinities (PA), gas phase basicities (GPB), chalcogen–chalcogen bond dissociation enthalpies (BDE), and the hydrogen affinities (HA) of thiyl/selenyl radicals were evaluated for a range of small polysulfur/selenium compounds and cysteine per/polysulfide. The S–S bond length was found to be the most sensitive to basis set choice, while the geometry of selenium-containing compounds was less sensitive to basis set. In mixed chalcogens species of sulfur and selenium, the location of the sulfur atom affects the S–Se bond length as it can hold more negative charge. PA, GPB, BDE, and HA of selenium systems were all lower, indicating more acidity and more stability of radicals. Extending the sulfur chain in cysteine results in a decrease of BDE and HA, but these plateau at a certain point (199 kJ mol−1 and 295 kJ mol−1), and PA and GPB are also decreased relative to the thiol, indicating that the polysulfur species exist as thiolates in a biological system. In general, it was found that ωB97XD/6-311G(2d,p) gave the most reasonable structures and thermochemistry relative to benchmark calculations. However, nuances in performance are observed and discussed.

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A G2(MP2) theoretical study of substituent effects on H3BNHnCl3−n (n= 3-0) donor-acceptor complexes

Open Chemistry ◽

10.2478/s11532-008-0029-0 ◽

2008 ◽

Vol 6 (3) ◽

pp. 400-403 ◽

Cited By ~ 5

Author(s):

Hafid Anane ◽

Soufiane Houssame ◽

Abdelali Guerraze ◽

Abdeladim Guermoune ◽

Abderrahim Boutalib ◽

...

Keyword(s):

Theoretical Study ◽

Substituent Effects ◽

Lone Pair ◽

Proton Affinities ◽

Lone Pair Orbital ◽

Chlorine Substitution ◽

Donor Acceptor ◽

Nitrogen Lone Pair ◽

The Stability ◽

N Compounds

AbstractThe complexation energies of H3BNHnCl3−n (n= 3-0) complexes and the proton affinities of NHnCl3−n compounds have been computed at the G2(MP2) level of theory. G2(MP2) results show that the successive chlorine substitution on the ammonia decreases both the basicity of the NHnCl3−n ligands and the stability of H3BNHnCl3−n complexes. The findings are interpreted in terms of the rehybridisation of the nitrogen lone-pair orbital. The NBO partitioning scheme shows that the variation of the N-H and N-Cl bond lengths, upon complexation, is due to variation of “s” character in these bonds.

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Model calculations of chemical interactions. Part 3.—Rotational energy profiles in simple molecules: evaluation, additivity and role of bond–bond, bond–lone-pair and lone-pair–lone-pair interactions

Journal of the Chemical Society Faraday Transactions ◽

10.1039/ft9918700249 ◽

1991 ◽

Vol 87 (2) ◽

pp. 249-258 ◽

Cited By ~ 18

Author(s):

Augusto Rastelli ◽

Marina Cocchi

Keyword(s):

Lone Pair ◽

Rotational Energy ◽

Chemical Interactions ◽

Model Calculations ◽

Energy Profiles ◽

Simple Molecules ◽

Lone Pair Interactions ◽

Pair Interactions

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A theoretical study of silyl anions and radicals. Change of mechanism from vertex inversion to edge inversion with increasing substitution by halogens

Canadian Journal of Chemistry ◽

10.1139/v90-202 ◽

1990 ◽

Vol 68 (8) ◽

pp. 1309-1316 ◽

Cited By ~ 12

Author(s):

A. C. Hopkinson ◽

C. F. Rodriquez ◽

M. H. Lien

Keyword(s):

Theoretical Study ◽

Single Point ◽

Lone Pair ◽

Basis Set ◽

Transition Structure ◽

Silyl Radicals ◽

Inversion Mechanism

Structures for trivalent silyl anions [Formula: see text] and [Formula: see text], where n takes values from 0 to 3, have been optimized at the HF/6-31 + +G* level and single point calculations made at the MP2/6-31 + +G* level (core included). SiH3− and ions containing one halogen invert by the vertex mechanism in which the lone-pair has π-symmetry, and the monosubstituted ions have high barriers (SiH2F− 45.2 kcal/mol and SiH2Cl− 44.0 kcal/mol). Further substitution by halogens results in a change to the edge inversion mechanism involving a T-shaped transition structure with the lone-pair coplanar with the ligands. Barriers (kcal/mol) at the MP2/6-31 + +G* level including ZPE are lower than for the monosubstituted ions and are SiHF2− 35.0, SiF3− 35.9, SiHCl2− 28.4, and SiCl3−32.5. In SiLi3− edge inversion is preferred, but the surface is much flatter and the barrier is low (9.8 kcal/mol). Trivalent silyl radicals SiHnF(3−n), SiHnCl(3−n) and SiFnCl(3−n) (with n having values 0 to 3) have also been examined with the 6-31 + +G* basis set, with optimization at the UHF level and single point calculations at the UMP2 level. Radicals SiH3, SiH2F, SiH2Cl, and SiHCl2 all invert by the vertex mechanism. Increased halogenation results in a change of mechanism and SiF3, SiCl3, SiF2Cl, and SiFCl2 invert by the edge mechanism. For radical SiHF2 the calculated barriers for the two mechanisms are almost identical with the higher level of theory slightly favouring edge inversion. Keywords: inversion mechanism, halogenated silyl radicals and anions.

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Comparative experimental and theoretical study on the molecular structure and spectroscopic properties of sideroxol isolated from Sideritis stricta and its electronic properties

French-Ukrainian Journal of Chemistry ◽

10.17721/fujcv9i2p94-107 ◽

2021 ◽

Vol 9 (2) ◽

pp. 94-107

Author(s):

Akin Azizoglu ◽

◽

Zuleyha Ozer ◽

Carikci Sema ◽

Turgut Kilic ◽

...

Keyword(s):

Density Functional ◽

Theoretical Study ◽

Chemical Shifts ◽

Molecular Geometry ◽

Spectroscopic Properties ◽

Basis Set ◽

Basis Sets ◽

Polarization Functions ◽

Nmr Properties ◽

Theory And Experiments

Sideroxol, a kaurene diterpene, was obtained from the acetone extract of Sideritis stricta plant. The ground-state molecular geometry, vibrational frequencies, and NMR chemical shifts were also investigated by using various density functional theories and Pople basis sets. The computed geometries are in good conformity with the experimental data. The comparison between theory and experiments indicates that B3LYP and M06 methods with the 6-31G(d) basis set are able to provide satisfactory results for predicting vibrational and NMR properties. There seems to be no significant effect of addition of diffuse and polarization functions in the basis set used herein.

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Hartree-Fock Stability and Broken Symmetry Solutions of O2- and S2- Anions in External Confinement

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc20070197 ◽

2007 ◽

Vol 72 (2) ◽

pp. 197-222 ◽

Cited By ~ 8

Author(s):

Filip Holka ◽

Pavel Neogrády ◽

Miroslav Urban ◽

Josef Paldus

Keyword(s):

Model Systems ◽

Basis Set ◽

Broken Symmetry ◽

Basis Sets ◽

Gaussian Basis Sets ◽

Hartree Fock ◽

Harmonic Confinement ◽

Electron Correlation Effects ◽

Doubly Charged

We study the effect of a confining potential on systems that exhibit Hartree-Fock (HF) instabilities, and thus admit broken symmetry (BS) HF solutions, by relying on the O2- and S2- doubly-charged anions as model systems. We find that with the increasing strength of the external harmonic confinement potential, W(r) = 1/2(ωr)2 (with 0.0 ≤ ω < 0.2), the BS solutions are systematically eliminated. We use extended, diffuse, doubly-augmented Gaussian basis sets up to and including d-aug-cc-pV6Z, and find that the number and the character of BS solutions exhibit significant basis set effects. These basis sets were further extended by additional ghost basis functions, located away from the atomic center. The role of the electron correlation effects for the BS HF solutions was examined by the CCSD(T) method. In addition to modelling the confinement by the harmonic-like potential W(r), we also examined a more realistic "confinement", realized by a grid of point charges modelling the crystal structure of MgO. Again, we find that the HF instabilities and the implied BS solutions disappear with the increasing magnitude of the model charges simulating the crystal environment. At the same time, the O2- anion is energetically stabilized with respect to both the O- anion and the neutral oxygen atom.

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Effects of H/D substitution on thermal vibrations in piperazinium hexanoate-h11,d11

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768195011025 ◽

1996 ◽

Vol 52 (2) ◽

pp. 357-368 ◽

Cited By ~ 6

Author(s):

J. Luo ◽

J. R. Ruble ◽

B. M. Craven ◽

R. K. McMullan

Keyword(s):

Crystal Structures ◽

Basis Set ◽

Basis Sets ◽

Mean Square ◽

Bond Stretching ◽

Rigid Body Model ◽

Out Of Plane ◽

Average Factor ◽

Experimental Values ◽

Thermal Vibrations

The crystal structures of piperazinium hexanoate-h11, {{1}\over{2}}C4H12N2+ 2.C6H11O− 2, and piperazinium hexanoate-d11, {{1}\over{2}}C4H12N2+ 2.C6D11O− 2, have been determined from neutron diffraction data collected at 15 K. Nuclear anisotropic displacement parameters have been analyzed to obtain the internal molecular displacements of the H and D nuclei, given by 〈 u 2 obs〉 − 〈 u 2 ext〉 where 〈 u 2 ext〉 is the contribution assuming all H/D to be carried rigidly on the vibrating molecular framework consisting of the heavier nuclei. In both crystal structures the cation ring is well fitted by the rigid-body model and the anion chain by a model with two rigid segments. In the piperazinium cations the corresponding protons in the two structures have about the same internal vibrational directions and magnitudes except for the two N—H protons, perhaps owing to differences in N—H...O hydrogen bonding. The internal vibrations of corresponding H/D in the h11 and d11 anions have approximately the same vibrational directions. The internal mean-square displacements of the H nuclei are systematically greater than the values of the corresponding D nuclei by an average factor 1.7 (3). For both anions, normal-mode analyses have been carried out using the force fields derived from ab initio quantum-mechanical calculations with HF/3-21 G and HF/6-31G** basis sets. The values of the resultant H/D internal displacements for C—H(D) bond stretching and methylene out-of-plane vibrations are in good agreement with experiment. However, with either basis set, theory predicts methylene in-plane mean-square displacements significantly greater than the experimental values.

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