Electronic structure and stability of C86 fullerene Isolated‐Pentagon‐Rule isomers

All 19 Isolated‐Pentagon‐Rule isomers of fullerene C₈₆ were investigated by Density Functional Theory (DFT) methods with B3LYP functional at 6‐31G, 6‐31G*, and 6‐31+G* levels. Preliminary distribution of single, double, and delocalized pi‐bonds in molecules of these isomers of fullerene C₈₆ is fulfilled. Obtained results are perfectly supported by DFT quantum–chemical calculations of electronic and geometrical structures of these isomers. The main reason of instability of isomers 1, 3–15, 18, and 19 are phenalenyl‐radical substructures. Thus, there is a possibility to obtain them only as endohedral metallofullerenes or exohedral derivatives. Isomer 2 (C₂) is unstable due to higher local molecular strain. It is shown that empty C₈₆ may be produced and extracted only as isomers 16 (C_s) and 17 (C₂). © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Electronic structure and stability of fullerene C82 isolated-pentagon-rule isomers

All nine isolated-pentagon-rule isomers of fullerene C(82) were investigated by the DFT method with the B3LYP functional at the 6-31G, 6-31G*, and 6-31+G* levels. The distribution of single, double, and delocalized π-bonds in the molecules of these isomers is shown for the first time. The obtained results are fully supported by DFT quantum-chemical calculations of electronic and geometrical structures of these isomers. The molecules of isomers 7 (C(3v)), 8 (C(3v)), and 9 (C(2v)) contain some radical substructures (such as the phenalenyl-radical substructure), which indicates that they are unstable and cannot be obtained as empty molecules. Thus, there is a possibility of obtaining them only as endohedral metallofullerenes or exohedral derivatives. Isomers 1 (C(2)), 2 (C(s)), 4 (C(s)), 5 (C(2)), and 6 (C(s)) with closed electronic shell are supposed to be stable, resembling isomer 3 (C(2)), which has just been extracted experimentally as an empty fullerene. We assume they can be produced as empty molecules.     

Investigation on Structure and Bonding of As_4S_4 Isomers

Mineral medicine, especially those containing heavy metals, is one of the characteristics of traditional Chinese medicine. A famous mineral medicine, realgar, containing heavy metal arsenic with a chemical formula of As_4S_4, has the function of detoxification, killing bacteria and viruses, and eliminating dampness and phlegm. Different As_4S_4 isomers are likely to have different drug effects and pharmacological actions. Therefore, it is of great scientific significance to find more stable As_4S_4 isomers. In view of this, ab initio molecular orbital theory and density functional theory(DFT) have been used to study ten isomers of As_4S_4 at the B3LYP/6-31 G*, B3LYP/6-311+G*, B3LYP/6-311+G(3 df, 2 p) and MP2/(6-311+G*, LanL2 MB) levels of theory. In addition to the two isomers having been studied previously, eight new isomers were investigated in the present paper. All the ten As_4S_4 isomers were proved to be true local minima on their potential energy surfaces. The calculated NICS values and molecular orbital analyses showed that, the D_(2d) symmetric As_4S_4, isomer 1, may be s-aromatic. The study proves that ten As_4S_4 isomers are stable thermodynamically, and are highly desirable for the future theoretical study of realgar.     

Effects of different basis sets and donor‐acceptor groups on linear and second‐order nonlinear optical properties and molecular frontier orbital energies

The calculation of molecular hyperpolarizability, molecular frontier orbital energies of some donor‐acceptor oxadiazoles ( 5a – f , 8a – f , and 9a – f ) have been investigated using ab initio methods and different basis sets. Ab initio optimizations were performed at the Hartree–Fock (HF) and density functional (Beckee‐3–Lee–Yang–Parr; B3LYP) levels of theory with 6‐31G basis set. The polarizability (<α>), anisotropy of polarizability (Δα), and ground‐state dipole moment (μ), first hyperpolarizability (β), and molecular frontier orbital (HOMO, highest occupied molecular orbital and LUMO, lowest unoccupied molecular orbital) energies of 5a – f , 8a – f , and 9a – f have been calculated at the HF and B3LYP methods with 6‐31G, 6‐31G(d), 6‐31+G(d), 6‐31++G(d,p), 6‐311G, 6‐311G(d), 6‐311+G(d), and 6‐311++G(d,p) basis sets. Also, the molecular hardness (η) and electronegativity (χ) parameters have been obtained using molecular frontier orbital energies. The <α>, Δα, μ, β, HOMO, LUMO energies, η and χ parameters have been investigated as dependence on the choice of method and basis set. The variation graphics of <α>, Δα, μ, β, η, and χ parameters using HF and B3LYP methods with different basis sets are presented. We have examined the frontier molecular orbital pictures of 5a – f , 8a – f , and 9a – f using B3LYP/6‐31++G(d,p) level. The 5a – f , 8a – f , and 9a – f display significant linear, second‐order molecular nonlinearity, and molecular parameters and provide the basis for future design of efficient nonlinear optical materials having the 1,3,4‐oxadiazole core. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Calculated structures and relative stabilities of furoxan,some 1,2-dinitrosoethylenes and other isomers

The structures and relative stabilities of furoxan and some of its isomers, e.g., the 1,2-dinitrosoethylenes, have been determined by means of ab initio Hartee–Fock and Møller–Plesset calculations. Geometries were optimized at the HF/3-21G, HF/6-31G* and MP2/6-31G* levels, and subsequently used for computing MP2/6-31G*, MP3/6-31G*, and MP4/6-31G* energies. The results are markedly affected by the inclusion of electronic correlation, which renders three of the isomers unstable. It also emphasizes the importance of a zwitterionic contribution to the structure of furoxan, which promotes ring-opening through a cis 1,2-dinitrosoethylene intermediate/transition state that has an MP4/6-31G*//MP2/6-31G* energy that is 31.6 kcal/mol above furoxan.     

Theoretical studies on the S-N interactions in sulfoximine

The potential energy surface of sulfoximines has been searched using ab initio MO and Density Functional Calculations. The electronic structures of the isomers of sulfoximine have been studied using HF/6-31+G*, MP2(full)/6-31+G* and B3LYP/6-31+G* levels. Final energies of these molecules have been calculated at the high accuracy G2 and CBS-Q levels. Though a formal SN double bond is generally considered between sulfur and nitrogen in these systems, theoretical studies do not show any π interaction between them. S-N rotational barriers, bond dissociation energies, atomic charge analysis, and NBO analysis all indicate only a single bond across S-N with a very strong ionic interaction.     

A quantum mechanical approach to the kinetics of the hydrogen abstraction reaction H2O2 + •OH → HO2 + H2O

The kinetics of the hydrogen abstraction from H₂O₂ by ^?OH has been modeled with MP2/6‐31G*//MP2/6‐31G*, MP2‐SAC//MP2/6‐31G*, MP2/6‐31+G**//MP2/6‐31+G**, MP2‐SAC// MP2/6‐31+G**, MP4(SDTQ)/6‐311G**//MP2/6‐31G*, CCSD(T)/6‐31G*//CCSD(T)/6‐31G*, CCSD(T)/6‐31G**//CCSD(T)/6‐31G**, CCSD(T)/6‐311++G**//MP2/6‐31G* in the gas phase. MD simulations have been used to generate initial geometries for the stationary points along the potential energy surface for hydrogen abstraction from H₂O₂. The effective fragment potential (EFP) has been used to optimize the relevant structures in solution. Furthermore, the IEFPCM model has been used for the supermolecules generated via MD calculations. IEFPCM/MP2/6‐31G* and IEFPCM/CCSD(T)/6‐31G* calculations have also been performed for structures without explicit water molecules. Experimentally, the rate constant for hydrogen abstraction by ^?OH drops from 1.75 × 10^?12 cm³ molecule^?1 s^?1 in the gas phase to 4.48 × 10^?14 cm³ molecule^?1 s^?1 in solution. The same trend has been reproduced best with MP4 (SDTQ)/6‐311G**//MP2/6‐31G* in the gas phase (0.415 × 10^?12 cm³ molecule^?1 s^?1) and with EFP (UHF/6‐31G*) in solution (3.23 × 10^?14 cm³ molecule^?1 s^?1). © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 502–514, 2005     

Ab initio Molecular Orbital Study of Dithiopyrrolopyrrole and Its Structural Isomers

Abstract

Ab initio molecular orbital calculations at HF/6-31G*, HF/6-311+G**, and B3LYP/6-311+G** levels of theory for geometry optimization are reported for 1,4-dithiopyrrolo[3,4-c]pyrrole (DtPP, 1) and its twelve structural isomers (2–13). Compounds 1–3 include 2 C─CH and 2 NH─CS structural units. Structural isomers 4–7 include 2 C–CH units, together with 2 NH and 2 C–S groups. Isomers 8–13 possess 2 CH, 2 C, 2 NH, and 2 C─S fragments. According to these calculations, isomers 2, 4, and 8, are more stable than 1.     

DFT conformational studies of the HI‐6 molecule

A systematic study of the oxime HI‐6 [1‐(2‐hydroxyiminomethyl‐1‐pyridinium)‐1‐(4‐carboxy‐aminopyridinium)dimethyl ether] hydrochloride, which is one of the most promising antidotes against soman intoxication, was carried out using density functional theory with the B3LYP (Becke, Lee, Yang, and Parr) method and the 6‐31+G*, 6‐31+G*, and 6‐31+G** basis sets. Rotational barriers, equilibrium geometries, and charge distributions were calculated in order to investigate the role of the side chain for the larger oximes used as antidotes in the treatment of neurotoxic organophosphate poisoning. Also reported is the comparison between HI‐6 and pralidoxime (2‐PAM), a smaller oxime previously studied in our research group. It is shown that conformation minima for the protonated E isomer do not depend on the size of the side chain; on the other hand, this effect has a pronounced influence on the protonated Z isomer. For the unprotonated isomers, other effects, such as electrostatic interactions and resonance, should be taken into account in their conformational analysis. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Conformational analysis of carbonic anhydrase inhibitors using ab initio molecular orbital methods. 1. Rotational isomerism in methane sulfonamide anion, CH3-SO2-NH−

Ab initio calculations have been performed on methane sulfonamide anion. Geometries have been optimized using Hartree-Fock basis sets up to 6-31+G*, and single-point calculations employing those Hartree-Fock geometries have been performed at levels up to MP2/6-311++G**. In addition, geometry optimizations for the 0°, 90°, 150°, and 180° conformers have been carried out at the MP2/6-31G*, MP2/6-31+G*, and MP2/6-311++G** levels. Vibrational frequencies have been calculated using the HF/4-31G*, MP2/6-31G*, and MP2/6-31+G* geometries. All calculations at or above the 4-31G* level agree that H—N—S—C ˜90° is the global minimum. The H—N—S—C = 180° conformer is clearly higher in energy although the relative energy of this conformer varies from 0.36 to 1.03 kcal/mol for the post-HF calculations depending on basis set. The H—N—S—C = 180° conformer appears to be a very shallow local minimum. However, the potential energy surface is quite flat in this region, and the highest-level calculations, including MP2 optimizations and vibrational frequency analysis, are ambiguous on this point. The conformer with an H—N—S—C torsion of 0° is a transition state with a relative energy ˜8 kcal/mol. Received: 3 December 1996 / Accepted: 2 January 1997     

Proton affinities of molecules containing nitrogen and oxygen: comparing ab initio and semiempirical results to experiments

We report a comparison of theoretical and experimental proton affinities at nitrogen and oxygen sites within a series of small molecules. The calculated proton affinities are determined using the semiempirical methods AM 1, MNDO , and PM 3; the ab initio Hartree–Fock method at the following basis levels: 3-21G //3-21G , 3-21+G //3-21G , 6-31G *//6-31G *, and 6-31+G (d, p)//6-31G *; and Møller–Plesset perturbation calculations: MP 2/6-31G *//6-31G *, MP 3/6-31G *//6-31G *, MP 2/6-31G +(d, p)//6-31G *, MP 3/6-31G +(d, p)//6-31G *, and MP 4(SDTQ )/6-31G +G (d, p)//6-31G *. The semiempirical methods have more nonsystematic scatter from the experimental values, compared to even the minimal 3-21G level ab initio calculations. The thermodynamically corrected 6-31G *//6-31G * proton affinities provide acceptable results compared to experiment, and we see no significant improvement over 6-31G *//6-31G * in the proton affinities with any of the higher-level calculations. © 1992 John Wiley & Sons, Inc.     

An Ab Initio Molecular Orbital Study of Isophosphinines

Ab initio molecular orbital calculation at HF/6-31G*, HF/6-31G**, HF/6-311G**, HF/6-311++G**, RMP2-FC/6-31G*, and B3LYP/6-31G* levels of theory for geometry optimization and MP4(SDQ)/6-31G* for a single-point total energy calculation are reported for phosphinine and 13 isophosphinines 7-19 . Isomers 7-11 with an allenic system are calculated to be 8-18 kcal mol m 1 more stable than structures 12-17 with an acetylenic moiety. The calculated energy difference (66.19 kcal mol m 1 ) between phosphinine and the most stable isophosphinine (1-phospha-1,2,4-cyclohexatriene, 10 ) is smaller than the difference (78.96 kcal mol m 1 ) between benzene and the most stable isobenzene (cyclohexa-1,2,4-triene, 2 ). The isophosphinines 18 and 19 , with a butatriene moiety, are calculated to be the least stable isomers.     

Unusual pentagon and hexagon geometry of three isomers (no 1, 20, and 23) of fullerene C84

Three isomers 23 (D_2d), 1 (D₂), and 20 (T_d) of fullerene C₈₄ have been investigated by PM3, HF/6‐31G*, and DFT methods with B3LYP functional at the 6‐31G and 6‐31G* levels. In this article we reveal for the first time that some distortion of hexagon (pentagon), measured as its maximal dihedral angles, caused by local molecular strains may serve as a new criterion of stability of fullerenes with closed shell. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

UV-, VIS- and IR-light-induced isomerization of HSNO in a low-temperature matrix

An infrared spectroscopic investigation has been performed on the trans and cis isomers of thionitrous acid (HSNO) and their D- and ¹⁵NO-isotopic modifications in argon matrices at 12 K. The substances were prepared photolytically from thionylimide (HNSO) isotopes in the matrix. With UV (250 nm), VIS (585 nm), and IR irradiation the cis → trans or the trans → cis isomerization of HSNO was induced, allowing an unequivocal distinction between the closely resembling IR spectra of the trans and cis isomers. Complete sets of fundamental frequencies of both rotamers were obtained and assigned by normal coordinate analysis using the transferable valence force field (TVFF) approach. Parallel to this analysis ab initio calculations on the SCF- and CI-levels were performed to predict energy, geometry, and barrier of internal rotation for the two HSNO rotamers.     

A Quantum Chemical Study of N14 Cluster

Ab initio molecular orbital theory and density functional theory have been employed to study N₁₄ cluster with low spin at the HF/6-31G*, B3LYP/6-31G*, B3PW91/6-31G*, BP86/6-31G*, and BHLYP/6-31G* levels of theory. Twelve isomers were studied, including one previously investigated cage molecule. The most stable isomer of N₁₄ is a C _2h -symmetric molecule that contains two separated five-membered nitrogen rings connected by a —N=N—N=N— bridge. The second, third, and fifth most stable isomers each have one five-membered nitrogen ring. The theoretical results suggest that the five-membered nitrogen ring gives rise to a particularly stable structural unit, and the more side chains that the five-membered nitrogen ring links with, the less stable the structure will become.     

An Ab Initio Molecular Orbital Study of Valence Bond Isomers of Silabenzene and Phosphabenzene

Ab initio molecular orbital calculation at HF/6-31G*, HF/6-31G**, HF/6-311G**, HF/6-311++G**, RMP2-FC/6-31G*, and B3LYP/6-31G* levels of theory for geometry optimization and MP4(SDQ)/6-31G* for a single point total energy calculation are reported for silabenzene ( 7 ), phosphabenzene ( 8 ) and 16 valence bond isomers of silabenzene and phosphabenzene ( 9-24 ). The calculated energy difference (19.78 kcal mol m 1 ) between silabenzene and the most stable valence bond isomer of silabenzene (1-silabenzvalene, 9 ) is much smaller than the difference (73.60 kcal mol m 1 ) between benzene and benzvalene ( 2 ). The energy difference between phosphabenzene and the most stable valence bond isomer of phosphabenzene (1-phosphabenzvalene, 17 ) is calculated to be 43.29 kcal mol m 1 .     

Reaching for two new stable ambiphilic quinoline‐derived N‐heterocyclic carbenes at DFT level

A detailed investigation on the thermodynamic and kinetic stability of four carbenic tautomers of quinoline 1 , including quinoline‐2‐ylidene 2 , quinoline‐3‐ylidene 3 , quinoline‐4‐ylidene 4 , and 3,4‐dihydroquinoline‐4‐ylidene 5 , reveals that singlet planar six‐membered ring N‐heterocyclic carbenes (NHCs) 2 and 4 have less stability than Arduengo type NHC but seems to have enough conceivably for reaching at B3LYP/aug‐cc‐pVTZ//B3LYP/6–31+G* and B3LYP/6–311++G**//B3LYP/6–31+G* levels. All these six‐membered NHCs are extremely ambiphilic with the more nucleophilic and electrophilic characters compared to the Arduengo type one. The aromaticity of singlet 2 and 4 is a significant contributor to their stability which is confirmed through their Nucleus‐independent chemical shift(1)_zz values. Finally, among 2–5 , the normal NHC 2 is thermodynamically preferred but the remote NHC 4 is kinetically proffered over the other isomeric carbenes. The effects of different N‐ or C‐substituted NHCs of 2 are studied using appropriate isodesmic reactions. The trimethylsilyl substituent exhibits slightly larger carbene stabilization in quinoline‐derived NHCs than the pyridine analogue. © 2014 Wiley Periodicals, Inc.     

Conformational study of the structure of 12-crown-4-alkali metal cation complexes

A conformational search was performed for the 12-crown-4 (12c4)-alkali metal cation complexes using two different methods, one of them is the CONFLEX method, whereby eight conformations were predicted. Computations were performed for the eight predicted conformations at the HF/6-31+G*, MP2/6-31+G*//HF/6-31+G*, B3LYP/6-31+G*, MP2/6-31+G*//B3LYP/6-31+G*, and MP2/6-31+G* levels. The calculated energies predict a C4 conformation for the 12c4-Na+, -K+, -Rb+, and -Cs+ complexes and a C(s) conformation for the 12c4-Li+ complex to be the lowest energy conformations. For most of the conformations considered, the relative energies, with respect to the C4 conformation, at the MP2/6-31+G*//B3LYP/6-31+G* are overestimated, compared to those at the MP2/6-31+G* level, the highest level of theory considerd in this report, by 0.2 kcal/mol. Larger relative energy differences are attributed to larger differences between the B3LYP and MP2 optimized geomtries. Binding enthalpies (BEs) were calculated at the above-mentioned levels for the eight conformations. The agreement between the calculated and experimental BEs is discussed.     

Importance of CH/π hydrogen bonds in recognition of the core motif in proline-recognition domains: an ab initio fragment molecular orbital study

We examined CH/π hydrogen bonds in protein/ligand complexes involving at least one proline residue using the ab initio fragment molecular orbital (FMO) method and the program CHPI. FMO calculations were carried out at the Hartree–Fock (HF)/6‐31G*, HF/6‐31G**, second‐order Møller–Plesset perturbation (MP2)/6‐31G*, and MP2/6‐31G** levels for three Src homology 3 (SH3) domains and five proline‐recognition domains (PRDs) complexed with their corresponding ligand peptides. PRDs use a conserved set of aromatic residues to recognize proline‐rich sequences of specific ligands. Many CH/π hydrogen bonds were identified in these complexes. CH/π hydrogen bonds occurred, in particular, in the central part of the proline‐rich motifs. Our results suggest that CH/π hydrogen bonds are important in the recognition of SH3 and PRDs by their ligand peptides and play a vital role in the signal transduction system. Combined use of the FMO method and CHPI analysis is a valuable tool for the study of protein/protein and protein/ligand interactions and may be useful in rational drug design. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011