Conformers and intramolecular hydrogen bonding of the oxalic acid monomer and its anions

Density functional theory, B3LYP/6‐31G** and B3LYP/6‐311+G(2d,p), and ab initio MP2/6‐31G** calculations have been carried out to investigate the conformers, transition states, and energy barriers of the conformational processes of oxalic acid and its anions. QCISD/6‐31G** geometrical optimization is also performed in the stable forms. Its calculated energy differences between the two most stable conformers are very near to the related observed value at 7.0 kJ/mol. It is found that the structures and relative energies of oxalic acid conformers predicted by these methods show similar results, and that the conformer L1 (C_2h) with the double‐interfunctional‐groups hydrogen bonds is the most stable conformer. The magnitude of hydrogen bond energies depends on the energy differences of various optimized structures. The hydrogen bond energies will be about 32 kJ/mol for interfunctional groups, 17 kJ/mol for weak interfunctional groups, 24 kJ/mol for intra‐COOH in (COOH)₂, and 60 kJ/mol for interfunctional groups in (COOH)COO⁻¹ ion if calculated using the B3LYP/6‐311+G(2d,p) method. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 541–551, 2000     

Combined experimental and computational modeling studies on 3,5‐dimethyl‐pyrazole‐1‐carbodithioic acid benzyl ester

The title compound, 3,5‐Dimethyl‐pyrazole‐1‐carbodithioic acid benzyl ester, has been synthesized and structurally characterized by X‐ray single crystal diffraction, elemental analysis, IR spectra, and UV‐Vis spectrum. The crystal belongs to orthorhombic, space group P212121, with a = 5.3829(15), b = 11.193(3), c = 21.824(6) Å, V = 1315.0(6) ų, and Z = 4. The molecules are connected via intermolecular C–H···N hydrogen bonds into 1D infinite chains. The crystal structure is consolidated by the intramolecular C–H···S hydrogen bonds. Furthermore, Density functional theory (DFT) calculations of the structure, stabilities, orbital energies, composition characteristics of some frontier molecular orbitals and Mulliken charge distributions of the title compound were performed by means of Gaussian 03W package and taking B3LYP/6‐31G(d) basis set. The time‐dependent DFT (TD‐DFT) calculations have been employed to calculate the electronic spectrum of the title compound, and the UV‐Vis spectra has been discussed on this basis. The results show that DFT method at B3LYP/6‐31G(d) level can well reproduce the structure of the title compound. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical Study on Gas—phase Pyrolytic Reactions of N—Ethyl,Isopropyl and N—t—Butyl Substituted 2—Aminopyrazine

Density functional theory (DFT) and ab initio methods were used to study gas‐phase pyrolytic reaction mechanisms of iV‐ethyl, N‐isopropyl and N‐t‐butyl substituted 2‐aminopyrazine at B3LYP/6–31G* and MP2/6–31G*, respectively. Single‐point energies of all optimized molecular geometries were calculated at B3LYP/6–311 + G(2d,p) level. Results show that the pyrolytic reactions were carried out through a unimolecular first‐order mechanism which were caused by the migration of atom H(17) via a six‐member ring transition state. The activation energies which were verified by vibrational analysis and correlated with zero‐point energies along the reaction channel at B3LYP/6–311 + G(2d,p) level were 252.02 kJ. mo^?1 (N‐ethyl substituted), 235.92 kJ‐mol^?1 (N‐t‐isopropyl substituted) and 234.27 kJ‐mol^?1 (N‐t‐butyl substituted), respectively. The results were in good agreement with available experimental data.     

A mechanism of the 1,3‐dipolar cycloaddition between the hydrogen nitryl HNO2 and acetylene HCCH: The electron localization function study on evolution of the chemical bonds

The reaction between the simplest nitro compound HNO₂ (hydrogen nitryl) and acetylene HCCH ‐ formally proceeding via 1,3‐dipolar cycloaddition ‐ has been studied by means of the B3LYP, MPW1K and MP2 methods. The energy barrier of 20.74 ÷ 32.91 kcal/mol is similar to ΔE_a of the NNO + HCCH process but is essentially larger than computed for the reactions of HCCH with fulminic acid (HCNO) and NNCH₂. Whole process is exothermic with the reaction energy: ?10.87 ÷ ?17.94 kcal/mol. An evolution of the chemical bonding has been analyzed by means of the Bonding Evolution Theory (BET) at the B3LYP/6‐31+G(d) and B3LYP/cc‐pVTZ levels. Two approximations of the reaction path have been considered, namely: the IRC and pseudo‐reaction paths. The reaction requires five steps and seven catastrophes of the fold and cusp type. A different effect of first fold catastrophe has been noticed. At the B3LYP/6‐31+G(d) level one of two nonbonding V_i=1,2(N) attractors is annihilated (F), meanwhile at B3LYP/cc‐pVTZ new V(N) attractor is created (F^?). The chemical bonds are not formed/broken in TS. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synthesis of Bis(phosphinoyl)amines and Phosphinoyl–Phosphorylamines by the N‐Phosphinoylation and N‐Phosphorylation of 1‐Alkylamino‐2,5‐dihydro‐1H‐phosphole 1‐Oxides

The N‐phosphinoylation and N‐phosphorylation reaction of 1‐alkylamino‐2,5‐dihydro‐1H‐phosphole 1‐oxides with diphenylphosphinoyl chloride and diethylphosphoryl chloride/diphenylphosphoryl chloride afforded new families of compounds comprising bis(phosphinoyl)amines and phosphinoyl‐phosphorylamines, respectively, whose stereostructures were elucidated by B3LYP/6‐31G(d,p) and B3LYP/6‐31G++(d,p) calculations. The P analogues of the mixed imides may be valuable intermediates in syntheses.     

DFT studies of ESR parameters for N?O centered radicals,N‐alkoxyaminyl and aminoxyl radicals

Theoretical calculations of ESR parameters for aminoxyl radicals have been widely studied using the density functional theory (DFT) calculations. However, the isomer N‐alkoxyaminyl radicals have been limitedly studied. With the use of experimental data for 46 N‐alkoxyaminyl and 38 aminoxyl radicals, the isotropic ¹⁴N hyperfine coupling constants (a_N) and g‐factors have been theoretically estimated by several DFT calculations. The best calculation scheme of a_N for N‐alkoxyaminyl radicals was PCM/B3LYP/6‐31 + + G(d,p) (R² = 0.9519, MAE = 0.034 mT), and that for aminoxyl radicals was PCM/BHandHLYP/6‐31 + + G(3df,3pd) (R² = 0.9336, MAE = 0.057 mT). For aminoxyl radicals, the solvation models in calculations enhanced the accuracy of reproducibility. In contrast, for N‐alkoxyaminyl radicals the calculations with solvation models provided no improvement. The differences in the best functionals between two types of radicals were thought to come from the contribution ratios of neutral and dipolar canonical structures in resonance forms. The a_N for N‐alkoxyaminyl radicals that were stabilized by small contribution of dipolar canonical structures could be precisely reproduced by B3LYP with only 20% HF exact exchange. In contrast, the a_N for aminoxyl radicals stabilized by large contribution of dipolar canonical structures was well reproduced by BHandHLYP with 50% HF exchange. The best calculation scheme of g‐factors was IEFPCM/B3LYP/6‐31 + G(d,p) (R² = 0.9767, MAE = 0.0001) for not only aminoxyl but also N‐alkoxyaminyl radicals. Copyright © 2011 John Wiley & Sons, Ltd.     

Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction. The calculation results indicate that compared with MP2 results, B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ mol^?1 for both the terminal and central hydrogen bonds, whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds, but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol^?1 for the hydrogen bonds near the center. Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends. The weakest individual hydrogen bonding energy is about ?29.0 kJ mol^?1 found in the dimer, whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as ?62.5 kJ mol^?1 found in the N-methylacetamide decamer, showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains. The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H?O=C bond, corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital, and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.     

Mismatch base pairing of the mutagen 8‐oxoguanine and its derivatives with adenine: A theoretical search for possible antimutagenic agents

Molecular geometries of 8‐oxoguanine (8OG), those of its substituted derivatives with the substitutions CH₂, CF₂, CO, CNH, O, and S in place of the N7H7 group, adenine (A), and the base pairs of 8OG and its substituted derivatives with adenine were optimized using the RHF/6‐31+G* and B3LYP/6‐31+G* methods in gas phase. All the molecules and their hydrogen‐bonded complexes were solvated in aqueous media employing the polarized continuum model (PCM) of the self‐consistent reaction field (SCRF) theory using the RHF/6‐31+G* and B3LYP/6‐31+G* methods. The optimized geometrical parameters of the 8OG‐A base pair at the RHF/6‐31+G* and B3LYP/6‐31+G* levels of theory agree satisfactorily with those of an oligonucleotide containing the base pair found from X‐ray crystallography. The pattern of hydrogen bonding in the CF₂‐ and O‐substituted 8OG‐A base pair is of Watson–Crick type and that in the unsubstituted and CH₂‐, CNH‐, and S‐substituted base pairs is of Hoogsteen type. In the CO‐substituted base pair, the hydrogen bonding pattern is of neither Watson–Crick nor Hoogsteen type. The CF₂‐substitution appears to introduce steric hindrance for stacking of DNA bases. On the basis of these results, it appears that among all the substituted 8OG molecules considered here, the O‐substituted derivative may be useful as an antimutagenic drug. It is, however, subject to experimental verification. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Many‐body energy decomposition analysis of cooperativity in hydrogen fluoride clusters

This article studies the cooperativity present in hydrogen fluoride clusters, (FH)_n, by means of a many‐body decomposition of the binding energy. With the aim of quantifying how the results depend on the calculation level, the partition was performed from dimer to hexamer at the RHF, MP2, and density functional (B3LYP) levels, and for the heptamer and octamer at the RHF and B3LYP levels, using a 6‐31++G(d, p) basis set in all cases. We obtain that, for a proper representation of the cooperative effects in hydrogen fluoride, at least the inclusion of the three‐body terms is fundamental. The contributions are found to be underestimated at the RHF level and overestimated at the B3LYP level, with respect to the MP2 results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Density functional theoretical study of pKa of RCOOH (RH,CH3, and C2H5) using the combination of the extended clusters‐continuum model

The accurate pK_a determinations for three carboxylic acids have been investigated using the combination of the extended clusters‐continuum model at B3LYP/6‐31+g(d,p) and B3LYP/6‐311++g(d,p) levels. To take into account of the effect of the water combined with carboxylic acids in different positions, eleven molecular clusters were considered. Among these clusters, the one involving the carboxylic acid wrapped up with water molecules and saturated with hydrogen bonds (four hydrogen bonds around ? COOH) leads to the best B3LYP pK_a results compared to the experimental data. For those clusters saturated with hydrogen bonds, when n = 3 (the number of water molecules), the average absolute errors between the calculated pK_a results and experimental data of these three carboxylic acids were 0.19 (0.23) and 0.12 (0.22) pK_a at B3LYP/6‐31+g(d,p)//PCM (IEFPCM) and B3LYP/6‐311++g(d,p)//PCM (IEFPCM) levels, respectively; when n = 4, they are 0.53 (1.23) and 1.09 (1.03) pK_a, respectively. On the basis of the above results, the molecular cluster saturated with four hydrogen bonds formed by three waters and one carboxylic acid molecule was the chief existence in the carboxylic acid solution. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical Studies on Energetic Property and Stability of Pyrazine and Pyridine Derivatives

Density functional calculations at the B3LYP level with 6‐311G** and aug‐cc‐pVDZ basis sets were performed to predict the heats of formation (HOFs) for two pyrazine derivatives and eight pyridine derivatives. In the isodesmic reactions designed for the computation of heats of formation (HOFs), pyrazine and pyridine were chosen as reference compounds. The N‐oxidations for the ring nitrogen of pyrazine and pyridine derivatives decrease the HOF values when N‐oxide oxygen is neighboring with amino groups, but increase when it neighbors with nitro groups. Thermal stability was evaluated via bond dissociation energies (BDE) at the UB3LYP/6‐311G** level. As a whole, the homolysis of C–NO₂ bonds is the main step for bond dissociation of the title compounds. The BDE values of title compounds are influenced by intramolecular hydrogen bonds. The hydrogen bond effects associated with the length of the H···O bonds were analyzed by the electron density at the critical points and natural bond orbital.     

Structural diversity in imidazolidinone organocatalysts: a synchrotron and computational study

(S)‐1‐(Methylaminocarbonyl)‐3‐phenylpropanaminium chloride (S2·HCl), C₁₀H₁₅N₂O⁺·Cl⁻, crystallizes in the orthorhombic space group P2₁2₁2₁ with a single formula unit per asymmetric unit. (5R/S)‐5‐Benzyl‐2,2,3‐trimethyl‐4‐oxoimidazolidin‐1‐ium chloride (R3 and S3), C₁₃H₁₉N₂O⁺·Cl⁻, crystallize in the same space group as S2·HCl but contain three symmetry‐independent formula units. (R/S)‐5‐Benzyl‐2,2,3‐trimethyl‐4‐oxoimidazolidin‐1‐ium chloride monohydrate (R4 and S4), C₁₃H₁₉N₂O⁺·Cl⁻·H₂O, crystallize in the space group P2₁ with a single formula unit per asymmetric unit. Calculations at the B3LYP/6–31G(d,p) and B3LYP/6–311G(d,p) levels of the conformational energies of the cation in R3, S3, R4 and S4 indicate that the ideal gas‐phase global energy minimum conformation is not observed in the solid state. Rather, the effects of hydrogen‐bonding and van der Waals interactions in the crystal structure cause the molecules to adopt higher‐energy conformations, which correspond to local minima in the molecular potential energy surface.     

Blue‐shifted and red‐shifted hydrogen bonds: Theoretical study of the CH3CHO· · ·HNO complexes

The blue‐shifted and red‐shifted H‐bonds have been studied in complexes CH₃CHO…HNO. At the MP2/6‐31G(d), MP2/6‐31+G(d,p) MP2/6‐311++G(d,p), B3LYP/6‐31G(d), B3LYP/6‐31+G(d,p) and B3LYP/6‐311++G(d,p) levels, the geometric structures and vibrational frequencies of complexes CH₃CHO…HNO are calculated by both standard and CP‐corrected methods, respectively. Complex A exhibits simultaneously red‐shifted C? H…O and blue‐shifted N? H…O H‐bonds. Complex B possesses simultaneously two blue‐shifted H‐bonds: C? H…O and N? H…O. From NBO analysis, it becomes evident that the red‐shifted C? H…O H‐bond can be explained on the basis of the two opposite effects: hyperconjugation and rehybridization. The blue‐shifted C? H…O H‐bond is a result of conjunct C? H bond strengthening effects of the hyperconjugation and the rehybridization due to existence of the significant electron density redistribution effect. For the blue‐shifted N? H…O H‐bonds, the hyperconjugation is inhibited due to existence of the electron density redistribution effect. The large blue shift of the N? H stretching frequency is observed because the rehybridization dominates the hyperconjugation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Complexation of Phenol and Thiophenol by Amine N‐Oxides: Isothermal Titration Calorimetry and ab Initio Calculations

To develop a new solvent‐impregnated resin (SIR) system for removal of phenols from water, the complex formation of dimethyldodecylamine N‐oxide (DMDAO), trioctylamine N‐oxide (TOAO), and tris(2‐ethylhexyl)amine N‐oxide (TEHAO) with phenol (PhOH) and thiophenol (PhSH) is studied. To this end we use isothermal titration calorimetry (ITC) and quantum chemical modeling (on B3LYP/6‐311G(d,p)‐optimized geometries: B3LYP/6‐311+G(d,p), B3LYP/6‐311++G(2d,2p), MP2/6‐311+G(d,p), and spin component scaled (SCS) MP2/6‐311+G(d,p); M06‐2X/6‐311+G(d,p)//M06‐2X/6‐311G(d,p), MP2 with an extrapolation to the complete basis set limit (MP2/CBS), as well as CBS‐Q). The complexes are analyzed in terms of structural (e.g., bond lengths) and electronic elements (e.g., charges). Furthermore, complexation and solvent effects (in benzene, toluene, and mesitylene) are investigated by ITC measurements, yielding binding constants K, enthalpies ΔH⁰, Gibbs fre energies ΔG⁰, and entropies ΔS⁰ of complex formation, and stoichiometry N. The ITC measurements revealed strong 1:1 complex formation between both DMDAO–PhOH and TOAO–PhOH. The binding constant (K=1.7–5.7×10⁴ M ^?1) drops markedly when water‐saturated toluene was used (K=5.8×10³ M ^?1), and π–π interaction with the solvent is shown to be relevant. Quantum mechanical modeling confirms formation of stable 1:1 complexes with linear hydrogen bonds that weaken on attachment of electron‐withdrawing groups to the amine N‐oxide moiety. Modeling also showed that complexes with PhSH are much weaker than those with PhOH, and in fact too weak for ITC determination. CBS‐Q incorrectly predicts equal or even higher binding enthalpies for PhSH than for PhOH, which invalidates it as a benchmark for other calculations. Data from the straightforward SCS‐MP2 method without counterpoise correction show very good agreement with the MP2/CBS values.     

Chemical Reactivity of Oxo‐ and Aza‐γ‐lactam Rings

Different mechanisms for the alkaline hydrolysis of oxo and aza‐γ‐lactam rings have been studied by ab initio calculations at the MP2/6‐31+G*//MP2/6‐31+G* and B3LYP/6‐31+G*//B3LYP/6‐31+G* levels. The tetrahedral intermediate can undergo two different reactions, the cleavage of the C₂−N₂ bond (the classical mechanism) and the cleavage of the C₂−X₆ bond (X=O, N). Both compounds present similar energy barriers for the classical fragmentation, and show considerably lower barriers for the alternative mechanism. Because of this reactivity, the compounds studied are expected to be β‐lactamase inhibitors.     

Factors influencing the C?ON bond strength of the alkoxyamines in the styrene–acrylonitrile–TEMPO copolymerization system

Homolytic bond dissociation energy (BDE) of the (C? ON) bond for several N‐alkoxyamines derived from 2,2,6,6‐tetramethylpiperidine‐1‐oxyl (TEMPO) and the corresponding (C? H) bonds were determined from quantum‐mechanical calculations including the B3‐LYP6‐31G(d), B3‐LYP/6‐311++G(2df,p), UB3‐LYP/6‐311+G(3df,2p), and integrated IMOMO (G3:ROMP2/6‐31G(d)) method. The investigated N‐alkoxyamines were considered as models for dormant forms of propagating chains in the radical copolymerization process of styrene with acrylonitrile in the presence of TEMPO according to the terminal and penultimate model. The substituent effect on BDE was investigated. Radical stabilization energies (RSE) for radicals created from homolysis of the investigated N‐alkoxyamines were calculated according to Rüchardt's method. Polar, steric, and stabilization effects on C? ON alkoxyamine bond homolysis were studied. A dramatically weakened C? ON bond in the alkoxyamine‐containing two consecutive styrene units in the propagating chain was ascribed to geometric parameters characterizing energetically unfavorable conformation of the substituents. These phenomena can be regarded as the penultimate effect in the radical living/controlled copolymerization system of styrene with acrylonitrile. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1165–1177, 2008     

Theoretical Study of Ammonolysis of Monobactams: Kinetic Role of the N‐Sulfonate Group

The ammonolysis reaction of 3‐(formylamino)‐4‐methyl‐2‐oxoazetidine‐1‐sulfonate is investigated by quantum‐chemical methods (B3LYP/6‐31+G*) as a model system of the aminolysis reaction of monobactam antibiotics involved in the allergic reaction to these drugs. The influence of the N‐sulfonate group on the β‐lactam ring, reaction intermediates, and transition states is characterized in terms of the geometries and relative energies of the corresponding critical structures located on the B3LYP/6‐31+G* potential‐energy surface. It is shown that the N‐sulfonate group, which has only a moderate impact on the structure and charge distribution of the β‐lactam ring, reduces the rate‐determining ΔG barrier by ca. 20 kcal/mol with respect to a purely uncatalyzed ammonolysis of the unsubstituted system, azetidin‐2‐one. This intramolecular catalytic effect occurs through a −NH−SO↔[−N−SO₃H]⁻ isomerization process, which is involved in the proton relay from the attacking ammonia molecule to the β‐lactam N‐atom. Our theoretical results predict that, in aqueous solution, monobactams will show an intrinsic reactivity against amine nucleophiles more important than that of penicillins.     

DFT investigation of the mechanism of CH2CO + O(3P) reaction

A detailed theoretical survey of the potential energy surface (PES) for the CH₂CO + O(³P) reaction is carried out at the QCISD(T)/6‐311+G(3df,2p)//B3LYP/6‐311+G(d,p) level. The geometries, vibrational frequencies, and energies of all stationary points involved in the reaction are calculated at the B3LYP/6‐311+G(d,p) level. More accurate energy information is provided by single‐point calculations at the QCISD(T)/6‐311+G(3df,2p) level. Relationships of the reactants, transition states, intermediates, and products are confirmed by the intrinsic reaction coordinate (IRC) calculations. The results suggest that P1(CH₂+CO₂) is the most important product. This study presents highlights of the mechanism of the title reaction. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Streptidinium sulfate monohydrate

In streptidinium sulfate monohydrate {systematic name: 1,1′‐[(1S,3R,4S,6R)‐2,4,5,6‐tetrahydroxycyclohexane‐1,3‐diyl]diguanidinium sulfate monohydrate}, C₈H₂₀N₆O₄²⁺·SO₄²⁻·H₂O, at 100 (2) K, the components are arranged in double helices based on hydrogen bonds. One helix contains streptidinium cations and the other contains disordered sulfate anions and solvent water molecules. The helices are linked into a three‐dimensional hydrogen‐bonded network by O—H...O and N—H...O hydrogen bonds.