Inverse hydrogen bonds between XeH2 and hydride and fluoride derivatives of Li, Be, Na and Mg

A theoretical study of the inverse hydrogen bonds complexes formed by the XeH₂ molecule and hydride and fluoride derivatives of Li, Be, Na and Mg has been carried out by means of DFT (B3LYP/DGDZVP) and ab initio [MP2/DGDZVP and MP2/LJ18/6-311++G(2d,2p)] calculations. The complexes obtained present interaction energies up to ?81 kJ/mol. The analysis of the electron density shows electron transfer from the XeH₂ to the electron acceptor molecules. The calculated absolute chemical shieldings show the high sensitivity of the xenon atom upon complexation.     

N2O…HOCl复合物结构和性质的理论研究

分别在DFT-B3LYP和MP2/6-311++G**水平上求得HOCl + N2O复合物势能面上的六种(S1, S2, S3, S4, S5和S6)和四种(S1, S2, S4和S5)构型. 频率分析表明,其中的S1和S3为过渡态,其它为稳定构型. 在复合物S3, S5 和S6中,HOCl 单体的σ*(5O-6H)作为质子供体,与N2O单体中作为质子受体的3O原子相互作用,形成氢键结构,而在氢键复合物S2中, 质子受体为N2O单体中的端1N原子;复合物S1中,HOCl分子的σ*(5O-4Cl)作为质子供体与N2O分子中的端1N原子(质子受体)相互作用,形成卤键结构,而复合物S4中的卤键结构的质子受体为N2O分子中的端3O原子. 经B3LYP/6-311++G**水平上的计算,考虑了基组重叠误差(BSSE)校正的单体间相互作用能在-1.56 ~ -8.73 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.     

QM/MM study of the interaction between zigzag SnC nanotube and small toxic gas molecules

Adsorptions of small toxic molecules such as CO, N₂, HCN, SO₂, H₂CO, and NH₃ on a single‐walled (6,0) SnC nanotube (SnCNT) are investigated using Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The calculations are carried out at the B3LYP/6‐311++G(d,p)//LANL2DZ:UFF level of theory. The high layer of the model consists of a pyrene‐type ring on the nanotube surface as the adsorption site, where one gas molecule is allowed to interact. Conversely, for the adsorption of the two molecules, a larger site like a coronene ring is used for the high layer. Adsorption energy, Gibbs free energy change, Mulliken charge transfer, and total electron‐density maps are computed in each case. The adsorption strength of the gas molecule on the SnCNT surface is also analyzed from the density of states projected to different atoms (PDOS) of the nanotube–adsorbate complexes. The adsorptions of CO and N₂ on the (6,0) SnCNT surface require to cross potential barriers, and the corresponding transition structures are identified by ONIOM‐IRC calculations. For the remaining four molecules, the processes of adsorption are predicted to be barrier‐less. The calculations for the adsorption of H₂CO on (5,0) and (7,0) SnCNT surfaces are extended to study the effect of the size of the nanotube. Results for the adsorption of a single molecule on (6,0) SnCNT using B3LYP functional are compared with those obtained from a dispersion corrected functional such as M06‐2X. © 2015 Wiley Periodicals, Inc.     

Quantum chemical and experimental studies on the structure and vibrational spectra of substituted 2-pyranones

A systematic study on the structural characteristics of the 2-pyranone ring containing molecules with bromine, nitrile, and amide substituents at the C-3 position in the ring is conducted in the electronic ground (S ₀) state by DFT calculations using the B3LYP/6-311++G** method. The geometrical structure of the bromine substituted compound, which shows potent hepatoprotective activity, is studied both in the ground (S ₀) and first excited singlet (S ₁) states using RHF/6-311++G** and CIS/6-311++G** methods respectively. The molecules are found to exist in two isomeric forms gauche and trans that have the enthalpy difference of less than 3.32 kcal/mol; the latter is the preferred orientation in the gaseous phase. The S ₁ state is a ¹(π,π*) state that arises π-electron transfer from the region of a double bond in the pyranone ring to the region of the internuclear bond connecting the 2-pyranone and benzene rings. A complete vibrational analysis is conducted for the 3-bromo-6-(4-chlorophenyl)-4-thiomethyl-2H-pyran-2-one molecule based on the experimental infrared spectra in the 50–4000 cm⁻¹ region and DFT/6- 311++G** computations of vibrational frequencies for the gauche and trans isomeric forms. Spectral assignments based on the potential energy distribution along the internal coordinates confirm the nonplanar structure of the molecule.     

Influence of the water molecules (n?=?1–6) on the interaction between Li+, Na+, K+ cations and indole molecule as tryptophan amino acid residue

Influence of the addition of water molecules (n = 1–6) on the interaction energy between Li⁺, Na⁺, K⁺ cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation–π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation–π interaction indicates that there is a correlation between the electron density (ρ(r)) in the cage critical points generated upon complexation and the distance between metal cation and centroid of phenyl ring in indole molecule.     

A comparative spectroscopic,electronic structure and chemical shift investigations of o-Chloronitrobenzene,p-Chloronitrobenzene and m-Chloronitrobenzene

The structural characteristics and substituent effects of o-Chloronitrobenzene, m-Chloronitrobenzene and p-Chloronitrobenzene have been analysed by experimental FTIR, FT-Raman and FT-NMR spectroscopic studies. A detailed quantum chemical calculations have been performed using DFT/B3LYP method with 6-311++G^**, 6-31G^** and cc-pVTZ basis sets. Complete vibrational analyses of the compounds were performed. The temperature dependence of thermodynamic properties has been analysed. The atomic charges and charge delocalisation of the molecule have been performed by natural bond orbital (NBO) analysis. Molecular electrostatic surface potential (MESP), total electron density distribution and frontier molecular orbitals (FMOs) are constructed at B3LYP/6-311++G^** level to understand the electronic properties. The charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESPs). The electronic properties, HOMO and LUMO energies were measured by time-dependent TD-DFT approach. ¹H and ¹³C NMR spectra were recorded and ¹H and ¹³C nuclear magnetic resonance chemical shifts of the molecule were calculated. The ¹H and ¹³C nuclear magnetic resonance (NMR) chemical shifts of the molecules in chloroform solvent were calculated by using the Gauge-Independent Atomic Orbital (GIAO) method and are found to be in good agreement with experimental values.     

Mechanism for the gas‐phase hydrogen fluoride‐mediated decomposition of peroxyacetyl nitrate (PAN) studied by DFT method

Density functional theory has been used to study the mechanism of the decomposition of peroxyacetyl nitrate (CH₃C(O)OONO₂) in hydrogen fluoride clusters containing one to three hydrogen fluoride molecules at the B3LYP/6‐311++G(d,p) and B3LYP/6‐311+G(3df,3pd) levels. The calculations clarify some of the uncertainties in the mechanism of PAN decomposition in the gas phase. The energy barrier decreases from 30.5 kcal mol^?1 (single hydrogen fluoride) to essentially 18.5 kcal mol^?1 when catalyzed by three hydrogen fluoride molecules. As the size of the hydrogen fluoride cluster is increased, PAN shows increasing ionization along the O? N bond, consistent with the proposed predissociation in which the electrophilicity of the nitrogen atom is enhanced. This reaction is found to proceed through an attack of a fluorine to the PAN nitrogen in concert with a proton transfer to a PAN oxygen. On the basis of our calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

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 investigations on nonlinear optical and spectroscopic properties of 6-(3,3,4,4,4-pentafluoro-2-hydroxy-1-butenyl)-2,4-pyrimidinedione: An efficient NLO material

In this study, quantum chemical calculations of geometric parameters, conformational, natural bond orbital (NBO) and nonlinear optical (NLO) properties, vibrational frequencies, ¹H and ¹³C NMR chemical shifts of the title molecule [C₉H₇F₅N₂O₃] in the ground state have been calculated with the help of Density Functional Theory (DFT-B3LYP/6-311++G(d,p)) and Hartree-Fock (HF/6-311++G(d,p)) methods. The optimized geometric parameters, vibrational frequencies, ¹H and ¹³C NMR chemical shifts values are compared with experimental values of the investigated molecules. Comparison between experimental and theoretical results showed that B3LYP/6-311++G(d,p) method is able to provide more satisfactory results. In order to understand this phenomenon in the context of molecular orbital picture, we examined the molecular frontier orbital energies (HOMO, HOMO-1, LUMO, and LUMO + 1), the energy difference (ΔE) between E _HOMO and E _LUMO, electronegativity (χ), hardness (η), softness (S) calculated by HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels. The molecular surfaces, Mulliken, NBO, and Atomic polar tensor (APT) charges of the investigated molecule have also been calculated by using the same methods.     

A theoretical study of the interaction between [HB≡CH]<Superscript>−</Superscript>, [H<Subscript>2</Subscript>B=CH<Subscript>2</Subscript>]<Superscript>−</Superscript>, and boratabenzene anions with alkali and alkaline earth metals: properties and structures

The nature of [HB≡CH]⁻, [H₂B=CH₂]⁻, and boratabenzene interactions with alkaline and alkaline earth metals are studied by ab initio calculations. The interaction energies are calculated at the B3LYP/6-311++G(d,p) level. The calculations suggest that the cation size and charge are two influential factors that affect the nature of the interaction. AIM and NBO analyses of the complexes indicate that the variation of densities and the extent of charge transfers upon complexation correlate well with the obtained interaction energies.     

Contemplation on Some Prismatic Polynitrogen Structures – A DFT Treatment

Polynitrogen compounds, are rare molecules having only nitrogen atoms. In recent years, they have been considered as promising candidates of clean (green) high energy density materials. They possess high energy content and their sole decomposition product is N₂. Presently some prismatic polynitrogen structures (N₆ – N₁₄) are considered within the limitations of density functional theory at the levels of B3LYP/6‐311++G(d,p) and B3LYP/cc‐PVTZ. The calculations reveal that they are all highly endothermic but stable. Certain quantum chemical properties, IR and UV/Vis spectra are reported. Homolytic bond cleavage of top rings are considered. Then, the transition state and activation energies, and also homolytic bond dissociation energies for the top rings have been calculated at the level of UB3LYP/6‐311++G(d,p). Also NICS(0) values have been calculated at the level of B3LYP/6‐311++G(d,p). The results indicate that N₆ and N₁₀ have aromatic and nonaromatic top (and also base) rings, respectively. All the rest of the structures have antiaromatic rings (all the structures have antiaromatic N₄ rings).     

FT-IR, FT-Raman vibrational spectra and molecular structure investigation of 2-chloro-4-methylaniline: A combined experimental and theoretical study

In this work, the experimental and theoretical vibrational spectra of 2-chloro-4-methylaniline (2Cl4MA, C₇H₈NCl) were studied. FT-IR and FT-Raman spectra of 2Cl4MA in the liquid phase have been recorded in the region 4000–400 cm⁻¹ and 3500–50 cm⁻¹, respectively. The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree-Fock (HF) and density functional method (B3LYP) with the 6-31G(d), 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p) and 6-311G(d), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p) basis sets. The vibrational frequencies have been calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The DFT-B3LYP/6-311++G(d,p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 2Cl4MA. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of aniline and p-methylaniline molecules.     

Substituent effect on intramolecular hydrogen bonding in 2‐hydroxybenzaldehyde

The effect of some substituents on intramolecular hydrogen bonding of 5‐X‐2‐hydroxybenzaldehyde (5‐X‐2‐HBA) has been studied by B3LYP and MP2 methods using 6‐311++G** and AUG‐cc‐PVTZ basis sets. The relationship between hydrogen bond energy E_HB and electron donation (or withdrawal) of substituents has been investigated. An approximately good linear relationship has been detected between Hammett coefficients and hydrogen bond formation energy (R² = 0.98). Herein, population analysis has been performed by atoms in molecules (AIM) and natural bond orbital (NBO) methods. The results of AIM and NBO analyses are in a good agreement with calculated energy values. Furthermore, correlation between ring aromaticity and hydrogen bonding has been investigated by nucleus‐independent chemical shift (NICS) at GIAO/B3LYP/6‐311++G** level of theory. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Calculation of dissociation constants and chemical hardness of some biologically important molecules: A theoretical study

The gas‐phase geometries of neutral, protonated, and deprotonated forms of some biologically important molecules, alanine (Ala), glycine (Gly), phenylalanine (Phe), and tyrosine (Tyr), were optimized using density functional theory at B3LYP/6‐311++G(d) and the ab initio HF/6‐311++G(d) level of theories. The neutral and different stable ionic states of Ala, Gly, Phe, and Tyr have also been solvated in aqueous medium using polarizable continuum model for the determination of solvation free energies in the aqueous solution. The gas‐phase acidity constants of above four molecules have been also calculated at both levels of theories and found that the values calculated at HF/6‐311++G(d) method are in good agreement with experimental results. A thermodynamic cycle was used to determine the solvation free energies for the proton dissociation process in aqueous solution and the corresponding pK_a values of these molecules. The pK_a values calculated at B3LYP/6‐311++G(d) method are well supported by the experimental data with a mean absolute deviation 0.12 pK_a units. Additionally, the chemical hardness and the ionization potential (IP) for these molecules have been also explored at both the level of theories. The Tyr has less value of chemical hardness and IP at both levels of theories compared with other three molecules, Ala, Gly, and Phe. The calculated values of chemical hardness and IP are decreasing gradually with the substitution of the various functional groups in the side chain of the amino acids. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Mechanism of atmospheric pressure chemical ionization of morphine,codeine, and thebaine in corona discharge–ion mobility spectrometry: Protonation,ammonium attachment,and carbocation formation

Atmospheric pressure chemical ionizations (APCIs) of morphine, codeine, and thebaine were studied in a corona discharge ion source using ion mobility spectrometry (IMS) at temperature range of 100°C–200°C. Density functional theory (DFT) at the B3LYP/6‐311++G(d,p) and M062X/6‐311++G(d,p) levels of theory were used to interpret the experimental data. It was found that in the presence of H₃O⁺ as reactant ion (RI), ionization of morphine and codeine proceeds via both the protonation and carbocation formation, whereas thebaine participates only in protonation. Carbocation formation (fragmentation) was diminished with decrease in the temperature. At lower temperatures, proton‐bound dimers of the compounds were also formed. Ammonia was used as a dopant to produce NH₄⁺ as an alternative RI. In the presence of NH₄⁺, proton transfer from ammonium ion to morphine, codeine, and thebaine was the dominant mechanism of ionization. However, small amount of ammonium attachment was also observed. The theoretical calculations showed that nitrogen atom of the molecules is the most favorable proton acceptor site while the oxygen atoms participate in ammonium attachment. Furthermore, formation of the carbocations is because of the water elimination from the protonated forms of morphine and codeine.     

Mechanism of Dissolution of a Lithium Salt in an Electrolytic Solvent in a Lithium Ion Secondary Battery: A Direct Ab Initio Molecular Dynamics (AIMD) Study

The mechanism of dissolution of the Li⁺ ion in an electrolytic solvent is investigated by the direct ab initio molecular dynamics (AIMD) method. Lithium fluoroborate (Li⁺BF₄^?) and ethylene carbonate (EC) are examined as the origin of the Li⁺ ion and the solvent molecule, respectively. This salt is widely utilized as the electrolyte in the lithium ion secondary battery. The binding of EC to the Li⁺ moiety of the Li⁺BF₄^? salt is exothermic, and the binding energies at the CAM–B3LYP/6‐311++G(d,p) level for n=1, 2, 3, and 4, where n is the number of EC molecules binding to the Li⁺ ion, (EC)_n(Li⁺BF₄^?), are calculated to be 91.5, 89.8, 87.2, and 84.0 kcal mol^?1 (per EC molecule), respectively. The intermolecular distances between Li⁺ and the F atom of BF₄^? are elongated: 1.773 Å (n=0), 1.820 Å (n=1), 1.974 Å (n=2), 1.942 Å (n=3), and 4.156 Å (n=4). The atomic bond populations between Li⁺ and the F atom for n=0, 1, 2, 3, and 4 are 0.202, 0.186, 0.150, 0.038, and 0.0, respectively. These results indicate that the interaction of Li⁺ with BF₄^? becomes weaker as the number of EC molecules is increased. The direct AIMD calculation for n=4 shows that EC reacts spontaneously with (EC)₃(Li⁺BF₄^?) and the Li⁺ ion is stripped from the salt. The following substitution reaction takes place: EC+(EC)₃(Li⁺BF₄^?)→(EC)₄Li⁺?(BF₄^?). The reaction mechanism is discussed on the basis of the theoretical results.     

A theoretical study of the neutral and the double-charged cation of cyclo[8]pyrrole and its interaction with inorganic anions

A theoretical study of the complexation of cyclo[8]pyrrole dication, 2, and the corresponding system in neutral form, 3, with six anionic molecules has been carried out up to the B3LYP/6–311++G(2d,2p) computational level. The effect of the water solvation has been taken into account by means of the PCM method. The gas phase results correspond to the very large interaction energies expected for the interaction of molecules of opposite charge. In all the complexes, the analysis of the electron density by means of the Atoms In Molecules (AIM) methodology shows the presence of eight intermolecular interactions between the individual molecules. The results, using the water solvent model, indicate that the 2:SO₄ ²⁻ complex is more stable than the 2:NO₃ ⁻, in agreement with experimental results.      

Molecular complexes between π‐excedent heterocycles (indoles and carbazole) and π‐deficient polynitrobenzenes

Five charge‐transfer complexes 1–5 derived from indoles (including a carbazole) and halogenopolynitrobenzenes (ClDNB, FDNB, ClTNB) as well as their individual components have been studied in the solid state by ¹³C CPMAS NMR. The stacking effects on the ¹³C chemical shifts have been rationalized by means of M05‐2X functional and GIAO/B3LYP/6‐311 ++G(d,p) calculations. The results, although only semiquantitative, are very promising for studying such structures. Copyright © 2009 John Wiley & Sons, Ltd.     

Relationship between calculated NMR data and intermolecular hydrogen bond properties in X-pyridine⋯HF

The effect of different substituents in para and metapositions on the NMR data of X-pyridine?HF complex has been studied at B3LYP/6-311++G(d,p) level of theory. The relationship between NMR data and electron donation of substituents has been investigated. The results of topological properties of electron charge density calculated using atoms in molecules (AIM) analysis can be used to predict some NMR data. The magnetism-based indices, nucleus independent chemical shift NICS(1) and its z component NICS(1)_ZZ, were used to investigate the ring aromaticity changes on complexation. A linear correlation between Hammett coefficients and some NMR data could be found with a good correlation coefficient.     

Strong effect of methyl group on the strength of ionic hydrogen bond between C2H2 and H3O+

The effect of methyl group on the strength of the ionic hydrogen bond between C₂H₂ and H₃O⁺ has been studied with quantum chemical calculations at the UMP2/6‐311++G(d,p) level. The presence of a methyl group in the proton acceptor results in an energetic increase of 6.02 kcal/mol, increased by about 39%, whereas that in the proton donor leads to an energetic decrease of 2.18 kcal/mol, decreased by 14%. The charge analyses indicate that the methyl group in the proton acceptor is electron‐donating and that in the proton donor is electron‐withdrawing. The former plays a positive contribution to the formation of ionic hydrogen bond and the latter plays a negative contribution to the formation of ionic hydrogen bond. The weakening effect of solvent on the role of methyl group in the ionic hydrogen bond has also been studied at the UB3LYP/6‐311++G(d,p) level. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009