Explanation of Theoretical Mechanism of Isomerization of L-Alanine Conformation for Experimental Results

B3LYP/6-31＋＋G＊＊ method was applied to investigate the mechanism of alanine isomerization.12 minima and 22 transition states were obtained after optimization and several paths of isomerization were found.It is found that intramolecular single-bond rotation and proton transfer might lead to isomerization.The energy barrier of C–N bond rotation was lower than 2.52 kcal·mol 1,while the energy barrier ranges of the rotation of C–C and C–O were separately 0.43~ 7.01 and 4.69~12.19 kcal·mol 1,and the minimum energy barrier of proton transfer was 30.76 kcal·mol 1.The most probable isomerization path and mechanism for the two most stable conformations was discussed to find that the highest energy barrier to be crossed in this path was 11.87 kcal·mol 1.In order to understand the microscopic nature why only 4 conformations were detected in the experiment,thermodynamic properties of all conformations at the experimental temperature of 391 K was calculated.It is found that conformations XII,XI,X and IX can only unidirectionally convert into conformations rapidly with low energy and vanish immediately.The other conformations were distributed according to Maxwell-Boltzman＇s law,and the distribution probabilities of conformations I,II,III,IV,V,VI,VII and VIII were respectively 27.2%,26.5%,25.8%,6.4%,5.2%,4.8%,2.5% and 1.6%.Conformations I,II and III with bigger probability and stronger absorption peak were easy to detect in the experiment.Conformation IV had a relatively smaller probability（6.4%） and weak absorption peak which,however,could also be identified.The other conformations had too small probability to identify in the spectrum.     

Theoretical Studies on the Hydrogen Bond Transfer and Proton Transfer between Anamorphoses of the Dihydrated Glycine Complex

The conversion between anamorphoses of the dihydrated glycine complex was studied by means of B3LYP/6-31++G**. It was found that proton transfer was accompanied by hydrogen bond transfer in the process of conversion between different kinds of anamorphoses. With proton transfer, the electrostatic action was notably increased and the hydrogen-bonding action was evidently strengthened when the dihydrated neutral glycine complex converts into dihydrated zwitterionic glycine complex. The activation energy required for hydrogen bond transfer between dihydrated neutral glycine complexes is very low (6.32 kJ·mol-1); however, the hydrogen bond transfer between dihydrated zwitterionic glycine complexes is rather difficult with the required activation energy of 13.52 kJ·mol-1 due to the relatively strong electrostatic action. The activation energy required by proton transfer is at least 27.33 kJ·mol-1, higher than that needed for hydrogen bond transfer. The activation energy for either hydrogen bond transfer or proton transfer is in the bond-energy scope of medium-strong hydrogen bond, so the four kinds of anamorphoses of the dihydrated glycine complex could convert mutually.     

Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Nitroamine Dimers

Ab initio self-consistent field(SCF) and Mφller-Plesset correlation correction methods employing 6-31G^** basis set have been applied to the optimizations of nitroamine dimers.The binding energies have been corrected for the basis set superposition error (BSSE) and the zero-point energy.Theree optimized dimers have been obtained.The BSSE corrected binding energy of the most stable dimer is predicted to be -31.85kJ/mol at the MP4/6-31G^**//MP2/6-31G^** level.The energy barriers of the Walden conversion for -NH2 group are 19.7kJ/mol and 18.3kJ/mol for monomer and the most stable dimer,respectively.The molecular interaction makes the internal rotation around N1-N2 even more difficult.The thermodynamic properties of nitroamine and its dimers at different temperatures have been calculated on the basis of vibrational analyses.The change of the Gibbs free energy for the aggregation from monomer to the most stable dimer at standard pressure and 298.2 K is predicted to be 14.05kJ/mol.     

The open-close mechanism of M2 channel protein in influenza A virus:A computational study on the hydrogen bonds and cation-π interactions among His37 and Trp41

The M2 protein from influenza A virus is a tetrameric ion channel. It was reported that the permeation of the ion channel is correlated with the hydrogen bond network among His37 residues and the cation-π interactions between His37 and Trp41. In the present study,the hydrogen bonding network of 4-methyl-imidazoles was built to mimic the hydrogen bonds between His37 residues,and the cation-π interactions between 4-methyl-imidazolium and indole systems were selected to represent the interac-tions between His37 and Trp41. Then,quantum chemistry calculations at the MP2/6-311G level were carried out to explore the properties of the hydrogen bonds and the cation-π interactions. The calcula-tion results indicate that the binding strength of the N-H···N hydrogen bond between imidazole rings is up to -6.22 kcal·mol-1,and the binding strength of the strongest cation-π interaction is up to -18.8 kcal·mol-1(T-shaped interaction) or -12.3 kcal·mol-1(parallel stacking interaction). Thus,the calcu-lated binding energies indicate that it is possible to control the permeation of the M2 ion channel through the hydrogen bond network and the cation-π interactions by altering the pH values.     

Proton Transfer Isomerization of Pyrazole in the Ground State:σν sπ Mechanism and Water Assisting Effect

The proton transfer isomerization of pyrazole and the water assisting effect by looping 1 to 4 water molecules on the singlet state potential energy surface have been investigated by using hybrid density functional theory method (B3PW91) with a 6-311++G** basis set. Two mechanisms were proposed to explain the mono- and multi-water assisting effects, respectively. The reactants and products of all groups have been characterized on their potential energy surfaces. For the isomerization of monomolecule pyrazole, the isomerization energy barrier is 46.4 kcal·mol-1. For the monohydration assisting mechanism, the reactant complex is connected to the product complex via two saddle points. The corresponding isomerization barriers are 46.7and 23.0 kcal(mol-1, respectively. As to the multihydration assisting mechanism, the isomerization barriers are 12.0, 10.9 and 13.14 kcal(mol-1 accordingly, when the number of water molecules is 2, 3 and 4, respectively. The multihydration assisting isomerization can occur in water-dominated environments, for example, in the organism, and thereby is crucial to energy transference. The deproton and dehydrogen energies of monomolecule pyrazole and various hydrated pyrazoles were calculated and then found much bigger than the isomerization barriers of their relative complexes, suggesting the impossibility of deprotonation or dehydrogenation. The isomerization of pyrazole is a proton-coupling-electron-migration process, but two different mechanisms are noticed, viz.σ- and π-type mechanisms. The π-bond of pyrazole participates in isomerization in the π-type mechanism, whereas only σelectron takes part in isomerization in the σ-type mechanism.     

Proton Transfer Isomerization of Pyrazole in the Ground State： σ vs π Mechanism and Water Assisting Effect

The proton transfer isomerization of pyrazole and the water assisting effect by looping 1 to 4 water molecules on the singlet state potential energy surface have been investigated by using hybrid density functional theory method （B3PW91） with a 6-311＋＋G^＊＊ basis set. Two mechanisms were proposed to explain the mono- and multi-water assisting effects, respectively. The reactants and products of all groups have been characterized on their potential energy surfaces. For the isomerizafion of monomolecule pyrazole, the isomeriz＇ation energy barrier is 46.4 kcal·mol^-1. For the monohydration assisting mechanism, the reactant complex is connected to the product complex via two saddle points. The corresponding isomerization barriers are 46.7and 23.0 kcal·mol^-1, respectively. As to the multihydration assisting mechanism, the isomerization barriers are 12.0, 10.9 and 13.14 kcal·mol^-1 accordingly, when the number of water molecules is 2, 3 and 4, respectively. The multihydration assisting isomerization can occur in water-dominated environments, for example, in the organism, and thereby is crucial to energy transference. The deproton and dehydrogen energies of monomolecule pyrazole and various hydrated pyrazoles were calculated and then found much bigger than the isomerization barriers of their relative complexes, suggesting the impossibility of deprotonation or dehydrogenation. The isomerization of pyrazole is a proton-coupling-electron-migration process, but two different mechanisms are noticed, viz. σ- and π-type mechanisms. The π-bond of pyrazole participates in isomerization in the π-type mechanism, whereas only o-electron takes part in isomerization in the σ-type mechanism.     

Semi-Empirical and DFT Studies on Structures and Spectra for C78（CH2）2

Eighteen possible isomers of C78（CH2）2 weTe investigated by the INDO method. It was indicated that the most stable isomer was 42,43,62,63-C78（CH2）2, where the -CH2 groups were added to the 6/6 bonds located at the same hexagon passed by the longest axis of C78 （C2v）, to form cyclopropane structures. Based on the most stable four geometries of C78（CH2）2 optimized at B3LYP/3-21G level, the first absorptions in the electronic spectra calculated with the INDO/CIS method and the IR frequencies of the C-C bonds on the carbon cage computed using the AM1 method were blue-shifted compared with those of C78 （C2v） because of the bigger LUMO-HOMO energy gap and the less conjugated carbon cage after the addition. The chemical shifts of ^13C NMR for the carbon atoms on the added bonds calculated at B3LYP/3-21G level were moved upfield thanks to the conversion from sp^2-C to sp^3-C.     

Computational studies of the structure and cation-anion interactions in 1-ethyl-3-methylimidazolium lactate ionic liquid

Quantum chemical calculations of the structures and cation-anion interaction of 1-ethyl-3-methylimidazolium lactate ([Emim][LAC]) ion pair at the B3LYP/6-31++G** theoretical level were performed. The relevant geometrical characteristics, energy properties, intermolecular H-bonds (H-bonds), and calculated IR vibrations with respect to isolated ions were systematically discussed. The natural bond orbital (NBO) and atoms in molecule (AIM) analyses were also employed to understand the nature of the interactions between cation and anion. The five most stable geometries were verified by analyzing the relative energies and interaction energies. It was found that the most of the C-H···O intermolecular H-bonds interactions in five stable conformers have some covalent character in nature. The elongation and red shift in IR spectrum of C-H bonds which involve in H-bonds is proved by electron transfers from the lone pairs of the carbonyl O atom of [LAC] to the C-H antibonding orbital of the [Emim]+. The interaction modes are more favorable when the carbonyl O atoms of [LAC] interact with the C2-H of the imidazolium ring and the C-H of the ethyl group through the formation of triple H-bonds.     

Theoretical Study of Pnicogen Bonding Interactions between ECl_3(P,As) and Different Electron Donors

The pnicogen bond interaction between different electron donors(anion, π-electron, heteroatom) and ECl_3(E = As, P) was calculated by the method of MP_2/aug-cc-p VTZ. It has been indicated that the pnicogen bonds of complex formed by the anion and ECl_3 are more stable than that by the neutral electron donor, in which the pnicogen bonds of complex formed by NH_3 and ECl_3 are the most stable, and that by H_2S and ECl_3 is the least stable. The nature of pnicogen bond interaction is the closed shell interaction by AIM analysis, and BCP electron density is positively correlated to the complex interaction energy. RDG and DDF graphical analyses are performed to visualize the nature of pnicogen bond interaction from different donors, the position and strength of the pnicogen bond interaction, as well as the rearrangement of electron density after the formation of pnicogen bond system.     

Kinetics of the Oxidative Dehydrogenation of Propane over a VMgO Catalyst

The reaction kinetics of the oxidative dehydrogenation of propane was studied at 475-550℃ over a VMgO catalyst. Vanadium-magnesium-oxides are among the most selective and active catalysts for the dehydrogenation of propane to propylene. Selectivity to propylene up to about 60% was obtained at 10% conversion, but the selectivity decreased with increasing conversion. No oxygenates were detected, the only by-products were CO and CO2. The reaction rate of propane was found to be first order in propane and close to zero order in oxygen, which is in agreement with a Mars van Krevelen mechanism with the activation of the hydrocarbon as the rate determining step. The activation energy of the conversion of propane was found to be 122±6 kJ/mol.     

Theoretical Studies on the Proton Transfer Mechanism in Four-water Hydrated Glycine Complexes

The mp2/6-31++g**//b3lyp/6-31++g** method has been employed to study the proton transfer mechanism in 4H2O-glycine complexes(4W-G).Compared with bare glycine the four-water hydrated neutral glycine complexes(4W-GN) can turn into the corresponding zwitterionic glycine(4W-GZ) through proton transfer.The most stable conformation of 4W-GZ has a "double water-chain" structure and is more stable than its corresponding precursor 4W-GN by 0.97 KJ/mol though it is less stable than the most stable 4W-GN by 7.80 KJ/mol.It is a spontaneous reaction to form the most stable conformation of 4W-GZ,and the potential barrier is only 1.97 KJ/mol,so the probability of this reaction is very high and the most stable 4W-GZ may be detected in experiment or in the early stage of experiment.     

Theoretical Study on the Electronic Structures of Small TinNm （n ＋ m = 5, 6） Clusters

45 isomers of TinNm （n ＋ m = 5, 6） clusters, including linear, some planar and some stero configurations, have been predicted by density functional theory method. For five-atom clusters Ti3N2 and Ti2N3, the most stable structures are trigonal bipyramid in D3h symmetry, and for TiaN cluster, the isomer with one nitrogen atom occupying the center of quasi-tetrahedron is the most stable. In the isomers of Ti4N2 and Ti3N3, the planar networks are more stable, but for Ti2N4, the six-membered ring configuration is the most favorable. Most linear structures can form weak-strong bonds alternately with higher energy. As regards to planar structures, the more Ti-N bonds are formed, the more stable they will be; for stero closed polyhedral isomers, their energies are lower.     

A DFT study of methane activation on graphite surfaces with vacancy defects

The activation of methane on graphite surfaces with monovacancies and 5-8-5 vacancies have been investigated using density functional theory. Sixteen different initial adsorption configurations were investigated to identify the most favorable activation site.It is found that methane tends to be activated on the defective graphite surfaces,and the most stable configuration is that methane activation happened in the center hole of the monovacancy site,with a reaction energy of 1.13 eV.Electron transfer and weaker electrostatic potential of the vacancy region indicate that carbon atom of methane tends to fill the vacancy and makes the system more stable.     

Three-dimensional supramolecular architecture based on 4,4’-methylene-bis(benzenamine) and aromatic carboxylic acid guests:Synthons cooperation,robust motifs and structural diversity

The two-component solid forms involving 4,4’-methylene-bis(benzenamine) included both salts and co-crystals,while 4,4’methylene-bis(benzenamine) crystallized exclusively as a salt,in agreement with the differences in the pK a values.Many of the crystal structures displayed either the neutral or the ionic form of the carboxylic acid-amino heterosynthon,and the similarity in crystal structures between the neutral and the ionized molecules makes the visual distinction between a salt and co-crystal dependent on the experimental location of the acidic proton.A variety of supramolecular hydrogen bonded motifs involving interactions between the aza molecules and carboxylic acid groups are observed rather than just the O-H···N/O-H···O motif.The motifs are identical in all the two compounds analyzed showing the robustness of these supramolecular synthons.In all adducts,recognition between the constituents is established through either N-H···O and/or O-H···O/O-H···N pairwise hydrogen bonds.In all adducts,COOH functional groups available on 1 and 2 interact with the N-donor compounds.The COOH moieties in 1 forms only single N-H···O hydrogen bonds,whereas in 2,it forms pairwise O-H···N/N-H···O hydrogen bonds.The supramolecular architectures are elegant and simple,with stacking of networks in 2,but a rather complex network with a threefold interpenetration pattern was found in 1.Thermal stability of these compounds has been investigated by thermogravimetric analysis(TGA) of mass loss.     

A DFT Study on the Stable Structures and Dissociation Mechanism of C3O6 Cluster

Using geometrical optimization and DFT method at the B3LYP/6-31G (d) level, nineteen equilibrium geometries were identified, and three transition states of dissociation reaction of C3O6 clusters were also found. The vibrational frequencies and intrinsic reaction coordinate (IRC) verification at the same level were computed to verify the transitions. And then we calculated the dissociation energies and analyzed the dissociation channels. The computational results show that the dissociation energies of C3O6 isomers relative to three CO2 are between 1.509 × 103 and 10.61 × 103 kJ·kg-1, and the energy barriers of the reactions are 92.857, 131.138 and 185.793 kJ·mol-1. Both the high dissociation energies and high energy barriers show that C3O6 clusters studied in this paper are stable enough to be used as high-energy-density materials.     

3-单酰胺喹唑啉酮衍生物的表征及密度泛函理论研究

Several 3-aminoquinazolin-4-(3H)-one derivatives were synthesized and characterized.Using proton nuclear magnetic resonance (NMR) spectra,we have investigated the barriers to rotation around the N ― N bond as a function of temperature.Changes in the NMR spectra at high temperatures are explained in terms of hindered rotations of the N ― N bond.Free energies of activation for the rate determining stereochemical process were calculated to be as high as 67-75 kJ · mol-1.Ground state molecular geometries and vibrational frequencies were calculated using the HF/6-31G and B3LYP/6-31G level of theories.The optimized bond lengths and bond angles are in good agreement with experimental values at both theoretical levels.     

Theoretical Investigation on the Geometries and Properties of Guanine-BX3 （X = F, Cl） Complex

Geometries and binding energies were predicted at the B3LYP/6-311+G* level for the guanine-BX3 (X = F, Cl) systems and four isomers with no imaginary frequencies have been obtained for both guanine-BF3 and guanine-BCl3, respectively. Single energy calculations using much larger basis sets (6-311+G(2df,p) and aug-cc-pVDZ were carried out as well. It was found that the most stable isomer of guanine-BF3 is BF3 connected to N3 of guanine with the stabilization energy of –19.93 kcal/mol (BSSE corrected), while that of guanine-BCl3 is BCl3 connected to O10 of guanine having stabilization energy of –15.02 kcal/mol at the same level. The analyses for the combining interaction between BX3 and guanine with the atom-in-molecules theory (AIM) and natural bond orbital (NBO) methods have been performed. The results indicated that all the isomers are formed with σ-p type interactions between guanine and BX3, in which pyridine-type nitrogen or carbonyl oxygen or nitrogen atom of amino group offers its lone pair electrons to the empty p orbital of boron atom and the concomitance of charge transfer from guanine to BX3 has occurred. Still, one or two hydrogen bonds exist in some isomers of guanine-BX3 system and contribute to the stability of complex systems. Frequency analysis suggested that the stretching vibration of BX3 undergoes a red shift in complexes. Guanine-BF3 complex is more stable than guanine-BCl3 although the B–Y (Y=N, O) bond distance in the latter is shorter.     

Molecular Mechanism of High Energy Proton Radiation——Raman Spectroscopic Character of Microcosmic Damage in the Space Structure of DNA

High energy proton is an important type of the space radiation. The paper investigates the radiatione ffect of high energy proton (27.9 MeV) on DNA aqueous solution in the field of the molecular mechanism. The following information about the microcosmic damage to the space structure of DNA was obtained: (ⅰ) breakage of a part of interbase hydrogen bonds which maintained double helical structure of DNA; (ⅱ) damage on four bases, in which the damage on adenine ring was the most serious; (ⅲ) obvious change of deoxyribose; (ⅳ) serious damage on backbone phosphate ion (PO_2~-) and phosphate diester (PO_2) and the occurrence of scissions of double-stranded and single-stranded DNAs; (ⅴ) obvious decrease in the amount of B-form conformation.     

Stereoselective interactions of chiral dipeptides on amylose based chiral stationary phases

Dipeptides are stereo-specifically involved in several biological functions that are challenging to separate enantiomerically. Elution order of enantiomers is an important issue in chiral chromatography. Amylose tris-(3,5-dimethylphenylcarbamate) chiral stationary phase(CSP) is the best and most-widely-used CSP in chiral separations, but experimental data of enantiomeric separation of dipeptides on this CSP is lacking. Simulation studies were conducted to determine the order of elution and the chiral recognition mechanism of didpetides on this CSP. Results indicated that the docking energy of SR-enantiomers were higher than SS-antipodes. The range of docking energies for SR-enantiomers was -7.44 to -5.92 kcal/mol with CSP, but -7.15 to -5.87 kcal/mol for SS-stereoisomers. Therefore it is predicted that SS-enantiomer will elute first, followed by SR-antipode. Furthermore, hydrogen bondings, van der Waal’s interactions and electrostatic interactions were observed among SR- and SSenantiomers and chiral grooves of CSP. The number of hydrogen bonds was one in each enantiomer binding except S-Ala-R-Tyr, which contained two hydrogen bonds. No hydrogen bond was found in S-Ala-R-Trp, S-Leu-S-Trp, and S-Leu-S-Tyr dipeptides bindings. The chiral recognition mechanisms dictate different strengths of stereoselective bindings of the enantiomers on CSP.     

A Density Functional Theory Study of the Hydrates of 2NH_3:H_2SO_4 and Its Implications for the Formation of Atmosphere Particles

Density functional theory was used at the B3LYP/6-311++G(d,p) level of theory to study the hydrates of 2NH3:H2SO4:nH2O for n = 0～4. Neutrals of the most stable clusters, when n = 0 and 1, spontaneously formed and were determined to be hydrogen-bonded molecular complexes of monomeric species. Double ions (clusters containing a NH4+ cation and a HSO4- anion) or even ternary ions (clusters with two NH4+ cations and one SO42- anion) spontaneously formed in the most stable clusters of 2NH3:H2SO4:nH2O (n = 2, 3, 4). The energetics of binding and incremental association was also calculated. Double ions are not energetically favorable until 2NH3:H2SO4:2H2O because of the about equal free energies for forming the neutral (the most stable) and double ion (the second stable) isomers. The free energy of incremental association from free H2O and 2NH3:H2SO4:nH2O has a maximum at n = 2 at room temperature with ΔG ≈ -2 kcal/mol. The comparison of incremental association energies between 2NH3:H2SO4:nH2O, NH3:H2SO4:nH2O and H2SO4:nH2O clusters revealed that NH3 plays an important role in the atmospheric particle nucleation.