Intramolecular hydrogen bond in 3‐imino‐propenylamine isomers: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3‐imino‐propenyl‐amine were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (ρ), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3‐imino‐propenyl‐amin in water solution were also carried out at B3LYP/6‐311++G** and MP2/6‐311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine–amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA‐1 as global minimum. This stability is mainly due to the formation of a strong N? H···N intramolecular hydrogen bond, which is assisted by π‐electrons resonance, and this π‐electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3‐imino‐propenyl‐amine were obtained from the related rotamers methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Effect of methyl groups substitution on the strength of intramolecular hydrogen bonding of naphthazarin: DFT and NBO studies

A density functional theory (DFT) study-based method B3LYP/6-311++G** was carried out to investigate the methyl groups substitution effect on the structure and the strength of intramolecular hydrogen bonding in naphthazarin (NZ) (5,8-dihydroxy-1,4-naphthoquinone). The full geometry optimization of molecular structures, the difference between the energies of hydrogen-bonded and non-hydrogen-bonded rotamers, and the proton chemical shift of the hydroxyl groups in NZ and its methyl substituents obtained at the B3LYP/6-311++G** level. The vibrational frequencies of all samples and their deuterated analogues were calculated at the same theoretical level. The ¹H chemical shifts for NZ and its methyl substituents were computed at the B3LYP/6-311++G** level using the gauge-including atomic orbital method. Furthermore, in order to investigate the changes in bond order, electron density, electron delocalization, and steric effects caused by methyl substituents, natural bond orbital analysis were carried out at the B3LYP/6-311++G** level. After comparing these effective parameters in methyl substituents with those of their parent, NZ, we concluded that, in general, intramolecular hydrogen bonding strength increases by substituting methyl groups in the different positions of NZ.     

Intramolecular hydrogen bonding in structural conformers of 2‐amino methylene malonaldehyde: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energies of 44 conformers of 2‐Amino methylene malonaldehyde were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set and AIM and NBO analysis. The calculated geometrical parameters and conformational analysis in gas phase show that the closed ring via intramolecular hydrogen bonded conformers of this compound are more stable than the other ones. Hydrogen bond energies for H‐bonded conformers were obtained from the related rotamers method (RRM) and Schuster method, and also the nature of H‐bonding of them has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. Delocalization effects can be identified from the presence of off diagonal elements of the Fock matrix in the NBO basis. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要.在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型,B3LYP方法得到了三种构型(复合物Ⅰ,Ⅱ和Ⅲ),而MP2方法只能得到一种构犁(复合物Ⅱ).在复合物Ⅰ和Ⅲ中,HSO单元中的1H原子作为质子供体.与O3分子中的端基O原子作为质子受体相互作用,形成红移氢键复合物;而在复合物Ⅱ中,虽与复合物Ⅰ和Ⅲ中具有相间的质子供体和质子受体,却形成了蓝移氢键复合物.B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重甍误差(BSSE)和零点振动能(ZPVE)校正,其值在-3.37到-4.55 kJ·mol-1之间.采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要. 在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型, B3LYP方法得到了三种构型(复合物I, II和III), 而MP2方法只能得到一种构型(复合物II). 在复合物I和III中, HSO单元中的1H原子作为质子供体, 与O3分子中的端基O原子作为质子受体相互作用, 形成红移氢键复合物; 而在复合物II中, 虽与复合物I和III中具有相同的质子供体和质子受体, 却形成了蓝移氢键复合物. B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-3.37到-4.55 kJ·mol-1之间. 采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

Structures and Electronic Properties of HOCl···HCOCl Complexes

B3LYP/6-311++G** and MP2/6-311++G** calculations were used to analyze the interaction between hypochlorous acid (HOCl) and formyl chloride (HCOCl). The results showed that there were four equilibrium geometries (S1, S2, S3, and S4) optimized at B3LYP/6-311++G** level, and all the equilibrium geometries were confirmed to be in stable states by analytical frequency calculations. Complexes S1 and S3 use the 5H atom of HOCl as proton donor and the terminal 1O atom of HCOCl as acceptor to form red shift hydrogen bond systems. However, the blue-shifted hydrogen bond (2C-3H···6O) coexists with 4Cl···5O interaction in structures S2. As for S4, it uses the 7Cl atom of HOCl as proton donor and the terminal 1O atom of HCOCl as acceptor to form red shift halogen bond system. Interaction energies between monomers in the four complexes corrected with basis set superposition error (BSSE) and zero-point vibrational energy (ZPVE) lie in the range from −5.05 to −14.76 kJ·mol⁻¹ at MP2/6-311++G** level. The natural bond orbital (NBO) and atoms in molecules (AIM) theories have also been applied to explain the structures and the properties of the complexes.     

Kinetic Study and NBO Analysis of the Dehydrogenation Mechanism of Five‐membered Ring Heterocyclic 2,5‐Dihydro‐[furan,thiophene, selenophene

The theoretical study of the dehydrogenation of 2,5‐dihydro‐[furan ( 1 ), thiophene ( 2 ), and selenophene ( 3 )] was carried out using ab initio molecular orbital (MO) and density functional theory (DFT) methods at the B3LYP/6‐311G**//B3LYP/6‐311G** and MP2/6‐311G**//B3LYP/6‐311G** levels of theory. Among the used methods in this study, the obtained results show that B3LYP/6‐311G** method is in good agreement with the available experimental values. Based on the optimized ground state geometries using B3LYP/6‐311G** method, the natural bond orbital (NBO) analysis of donor‐acceptor (bond‐antibond) interactions revealed that the stabilization energies associated with the electronic delocalization from non‐bonding lone‐pair orbitals [LP(e)_X3] to δ*_{C(1)  H(2)} antibonding orbital, decrease from compounds 1 to 3 . The LP(e)_X3→δ*_{C(1)  H(2)} resonance energies for compounds 1 – 3 are 23.37, 16.05 and 12.46 kJ/mol, respectively. Also, the LP(e)_X3→δ*_{C(1)  H(2)} delocalizations could fairly explain the decrease of occupancies of LP(e)_X3 non‐bonding orbitals in ring of compounds 1 – 3 ( 3 > 2 > 1 ). The electronic delocalization from LP(e)_X3 non‐bonding orbitals to δ*_{C(1)  H(2)} antibonding orbital increases the ground state structure stability, Therefore, the decrease of LP(e)_X3→δ*_{C(1)  H(2)} delocalizations could fairly explain the kinetic of the dehydrogenation reactions of compounds 1 – 3 (k ₁ >k ₂ >k ₃ ). Also, the donor‐acceptor interactions, as obtained from NBO analysis, revealed that the (_C(4)C(7)→δ*_{C(1)  H(2)} resonance energies decrease from compounds 1 to 3 . Further, the results showed that the energy gaps between (_C(4)C(7) bonding and δ*_{C(1)  H(2)} antibonding orbitals decrease from compounds 1 to 3 . The results suggest also that in compounds 1 – 3 , the hydrogen eliminations are controlled by LP(e)→δ* resonance energies. Analysis of bond order, natural bond orbital charges, bond indexes, synchronicity parameters, and IRC calculations indicate that these reactions are occurring through a concerted and synchronous six‐membered cyclic transition state type of mechanism.     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1, S2, S3和S4). 其中, 在复合物S1和S3中, HOCl单体的5H原子作为质子供体, 与HCOCl单体中作为质子受体的1O原子相互作用, 形成红移氢键复合物; 在复合物S4中, HOCl单体的7Cl原子作为质子供体, 与HCOCl单体中作为质子受体的1O原子相互作用, 形成红移卤键复合物; 而在复合物S2中, 同时存在2C—3H…6O蓝移氢键和4Cl…5O相互作用. 在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-5.05与-14.76 kJ·mol-1之间. 采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

Intramolecular hydrogen bonding in 3‐imino‐propenylamine: Theoretical investigations

Intramolecular H‐bonds existing for derivatives of 3‐imino‐propenylamine have been studied using the B3LYP/6‐311++G** level of theory. The nature of these interactions, known as resonance‐assisted hydrogen bonds, has been discussed. Vibrational frequencies for α‐derivatives were calculated at the same level of theory. The topological properties of the electron density distributions for N? H···N intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Calculation for 3‐imino‐propenylamine derivatives in water solution were also carried out at B3LYP/6‐311++G** level of theory. Finally, the analysis of hydrogen bond in this molecule and their derivatives by quantum theory of natural bond orbital methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations

Ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2‐methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets. The 6‐31G* and 6‐311++G** basis sets make up the B3LYP/6‐31G* and B3LYP/6‐311++G** procedures. Internal coordinates were fully relaxed, and structures were gradient optimized at both levels of theory. Ten conformations were studied at the B3LYP/6‐31G* level, and five of these were continued with full gradient optimization at the B3LYP/6‐311++G** level of theory. The details of the ab initio optimized geometries are presented here, with particular attention given to the positions of the atoms around the anomeric center and the effect of the particular anomer and hydrogen bonding pattern on the maltose ring structures and relative conformational energies. The size and complexity of the hydrogen‐bonding network prevented a rigorous search of conformational space by ab initio calculations. However, using empirical force fields, low‐energy conformers of maltose were found that were subsequently gradient optimized at the two ab initio levels of theory. Three classes of conformations were studied, as defined by the clockwise or counterclockwise direction of the hydroxyl groups, or a flipped conformer in which the ψ‐dihedral is rotated by ∼180°. Different combinations of ω side‐chain rotations gave energy differences of more than 6 kcal/mol above the lowest energy structure found. The lowest energy structures bear remarkably close resemblance to the neutron and X‐ray diffraction crystal structures. © 2000 John Wiley & Sons, Inc. * J Comput Chem 21: 1204–1219, 2000     

Theoretical Study on Hydrogen Interaction between 5-Fluorouracil and Glycine

The geometries,electronic structure,IR spectrum and other properties of hydrogen interaction between 5-fluorouracil and glycine were studied at the B3LYP/6-31+G* level.Single point energy calculations were executed at the B3LYP/6-311++G** and B3LYP/aug-cc-pvdz levels,and natural bond orbital (NBO) analysis was carried out at the B3LYP/6-31+G* level.Finally,the hydrogen bonds were discussed via AIM electronic density topology analysis.     

Theoretical Studies on Intermolecular Hydrogen-bond Interactions between Hexamethylenetetramine and Nitric Acid

The structures of the complexes generated by hexamethylenetetramine and nitric acid have been fully optimized by B3LYP method at the 6-311++G** and aug-cc-pVTZ levels. The intermolecular hydrogen-bonding interactions have been calculated by the B3LYP/6-311++G**, B3LYP/aug-cc-pVTZ, MP2(full)/6-311++G** and CCSD(T)/6-311++G** methods, respectively. The NBO (nature bond orbital), AIM (atom in molecule), temperature effect and solvation effect have been analyzed to reveal the origin of the interactions. The results indicate that the stable hydrogen-bonded complexes could be generated by hexamethylenetetramine and nitric acid. The interactions follow the order of (a)>>(e)>(b)>(c)>(d)>(f)>(g). The C-N bonds which are adjacent to the methylene involving the hydrogen bonds tend to break in the chemical reaction. Due to the exothermic process, low temperature is conducive to the formation of the composition, which tallies with the experimental result.     

Theoretical study of the interaction mechanism of single-electron halogen bond complexes H3C⋯Br-Y (Y = H, CN, NC, CCH, C2H3)

The characteristics and structures of single-electron halogen bond complexes [H₃C?Br-Y (Y = H, CCH, CN, NC, C₂H₃)] have been investigated by theoretical calculation methods. The geometries were optimized and frequencies calculated at the B3LYP/6-311++G** level. The interaction energies were corrected for basis set superposition error (BSSE) and the wavefunctions obtained by the natural bond orbital (NBO) and atom in molecule (AIM) analyses at the MP2/6-311++G** level. For each H₃C?Br-Y complex, a single-electron Br bond is formed between the unpaired electron of the CH₃ (electron donor) radical and the Br atom of Br-Y (electron acceptor); this kind of single-electron bromine bond also possesses the character of a “three-electron bond”. Due to the formation of the single-electron Br bond, the C-H bonds of the CH₃ radical bend away from the Br-Y moiety and the Br-Y bond elongates, giving red-shifted single-electron Br bond complexes. The effects of substituents, hybridization of the carbon atom, and solvent on the properties of the complexes have been investigated. The strengths of single-electron hydrogen bonds, single-electron halogen bonds and single-electron lithium bonds have been compared. In addition, the single-electron halogen bond system is discussed in the light of the first three criteria for hydrogen bonding proposed by Popelier.     

β‐Aminoacrolein: An ab initio,AIM and NBO study

The molecular structure and the intramolecular hydrogen bonding of β‐aminoacrolein and its simple derivatives were investigated at the MP2 and B3LYP levels of theory using the standard 6‐311++G(d, p) basis set. The “atoms in molecules” or AIM theory of Bader which is based on topological properties of the electron density (ρ), was used. Additionally, an analysis of the critical points was performed to study the nature hydrogen bonding in these systems. Natural bond orbital (NBO) analysis was also carried out for to better comprehend the nature of the intramolecular interactions in β‐aminoacrolein and its derivatives. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical Studies on the Intermolecular Interactions of Aza-calix[2]arene[2]-triazines with RDX

Six fully optimized structures of the aza-calix[2]arene[2]-triazines/RDX supramo-lecular complexes have been obtained at the DFT-B3LYP/6-311++G** level,and the corresponding intermolecular interactions have been investigated using the B3LYP,mPWPW91 and MP2 methods at the 6-311++G** level,respectively.The natural bond orbital(NBO) and atoms in molecules(AIM) analyses have been performed to reveal the origin of interactions.To our interest,the result indicates that the strongest interaction is up to -22.34 kJ/mol after basis set superposition error(BSSE) and zero point energy(ZPE) correction at the MP2/6-311++G** level.Furthermore,the intermolecular interactions between aza-calix[2]arene[2]-triazines with the substituted amidos and RDX are stronger than those of other complexes.Thus,the complexes with amidos can be used as the candidates to increase the stability of explosive and eliminate the explosive wastewater.     

N, P, and As ylides and aza- and arsa-Wittig reactions from topological analyses of electron density

The nature of bonding between N, P, and As constituent atoms in ylide systems with the R(3)XYR' formula (X = N, P, As; Y = N, P, As; R = F, H; R' = H, CH(3)) has been characterized by ab initio (MP2/6-311++G**) and density functional theory (B3LYP/6-311++G**) calculations. Its electronic structure has been analyzed through electron density with the quantum theory of atoms in molecules and the electron localization function (ELF). The characteristics of the central bond are inspected with the calculated rotational barriers. The results show that N has a behavior different from that of the remaining pnicogen atoms (P, As), where the bond is much stronger. Fluorine substituents strengthen the X-Y bond, reduce the bond distance, and increase the electron density in the central bond so that the substituent pulls charge from the bond in the pnicogen X atom. For the N-pnicogen ylides, the results showed different bonding characters between F and X atoms; depending on the position of the F atom, the difference of the bond character is sensed by the basin synaptic order, as it is deduced from the analysis of the ELF basins. The energy profiles of the rotational barriers have been calculated at the MP2/6-311++G** level, indicating that the electronegativity of the substituents is a relevant factor that has consequences in the characteristics of the X-Y bond.     

Theoretical study of the influence of para- and meta-substituents on X-pyridineHF hydrogen bonding

The effects of O⁻, N (CH₃)₂, NH (CH₃), NH₂, C₂H₅, CH₃, OH, F, Cl, OF, Br, NO₂ and substituents in para- and meta-positions on X-pyridineHF hydrogen bond has been studied by HF, B3LYP and MP2 methods using 6-311++G(d,p) basis set. The relationship between hydrogen bond formation energy ΔE and electron donating (or withdrawing) of substituents has been investigated. In this respect, population analysis has been performed by atoms in molecules (AIM) and natural bond orbital (NBO) theories. The results of AIM and NBO analyses are in good agreement with calculated energy values. The relationship between Hammett coefficient and complexation energy has been established and the ρ constant has been calculated for hydrogen bonding. There is a relationship between σ and ΔE with a correlation coefficient equal to 0.94.     

DFT computational studies on rotation barriers,tautomerism, intramolecular hydrogen bond,and solvent effects in 8‐hydroxyquinoline

Intramolecular hydrogen binding interactions in 8‐hydroxyquinoline, both in its zwitterionic tautomer and in the rotamer without the intramolecular hydrogen bond (IHB), have been computed using the B3LYP and MPW1K density functionals. The rotation of the O? H bond and intramolecular proton transfer reactions were studied theoretically. The following theory levels have been applied: B3LYP/6‐31G(d,p), B3LYP/6‐311++G(d,p), MPW1K/6‐311++G(d,p), and MPW1K/6‐311++G(2d,3p)//MPW1K/6‐311++G(d,p). Natural bond orbital (NBO) analysis has also been carried out. The effect of medium (benzene, chloroform, tetrahydrofuran, 1,2‐dichloroethane, acetone, water) was simulated using the self‐consistent reaction field (SCRF) method within the framework of the polarizable continuum model (PCM), at the MPW1K/6‐311++G(d,p) level. The evolution of geometry, relative energies, heights of rotation (around the O? H bond) and tautomerization barriers, IHB energies, and ΔG(solv) have been systematically investigated. The results obtained have shown the failure to neglect some changes of the above characteristics in polar media with respect to the gaseous phase. The series of stability of the forms under study in the gaseous phase remains the same in solution. Thus, in spite of the important role of the solvent electrostatic effects, the intrinsic stability of those species overcomes the solvent effects. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

The O···H intramolecular hydrogen bond in 4‐X‐2‐hydroxybenzaldehydes: The relationships between geometrical parameters,estimated binding energies,and NMR data

The relationships among geometrical parameters, estimated binding energies, and nuclear magnetic resonance data in –C?O···H? O? intramolecular H‐bond of some substituted 2‐hydroxybenzaldehyde have theoretically been studied by B3LYP and MP2 methods with 6‐311++G** and AUG‐cc‐PVTZ basis sets. All substituents increase estimated hydrogen bond energies E_HBs (with the exception of NO₂ and C₂H₅), which are in good correlation with geometrical parameters, topological properties of electron density calculated at O···H bond critical points and ring critical points by using atoms in molecules method, the results of natural bond orbital analysis, and calculated nuclear magnetic resonance data. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Complexes of 4‐substituted phenolates with HF and HCN: Energy decomposition and electronic structure analyses of hydrogen bonding

We have computationally studied para‐X‐substituted phenols and phenolates (X = NO, NO₂, CHO, COMe, COOH, CONH₂, Cl, F, H, Me, OMe, and OH) and their hydrogen‐bonded complexes with B^? and HB (B = F and CN), respectively, at B3LYP/6‐311++G** and BLYP‐D/QZ4P levels of theory. Our purpose is to explore the structures and stabilities of these complexes. Moreover, to understand the emerging trends, we have analyzed the bonding mechanisms using the natural bond orbital scheme as well as Kohn–Sham molecular orbital (MO) theory in combination with quantitative energy decomposition analyses [energy decomposition analysis (EDA), extended transition state‐natural orbitals for chemical valence (ETS‐NOCV)]. These quantitative analyses allow for the construction of a simple physical model that explains all computational observations. © 2012 Wiley Periodicals, Inc.