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.     

Impact of Water Molecules on the Isomerization of CH3S（OH）CH2 to CH3S（O）CH3： A Computational Investigation

The isomerization of CH3S（OH）CH2 to CH3S（O）CH3 in the absence and presence of water has been investigated at the G3XMP2//B3LYP/6-311 ＋ G（2df, p） level. The naked isomerization, the reaction without water, gives the high barrier height （21.56 kcal.mol^-1）. Three models are constructed to describe the water influence on the isomerization, that is, water molecules are the catalyst and the microsolvation, and water molecules act as the catalyst and microsolvation simultaneously. Our results show that the isomerization barrier heights of CH3S（OH）CH2 to CH3S（O）CH3 are reduced by 12.32, 11.04, and 7.80 kcal.mol^-1, respectively, when one, two, and three water molecules are performed as catalyst, in contrast to the naked isomerization. Moreover, the rate constants of the isomerization are calculated using the transition state theory with the Wigner tunneling correction over the temperature range of 240-425 K. We find that the rate constant of a single water molecule as the catalyst is 1.58 times larger than the naked isomerization at 325 K, whereas it is slower by 6 orders of magnitude when water molecule serves as the microsolvation at 325 K, compared to naked reaction. So the water-catalyzed isomerization of CH3S（OH）CH2 to CH3S（O）CH3 is predicted to be the key role in lowering the activation energy. The isomerization involving water molecules acting as mierosolvation is unfavorable under atmospheric conditions.     

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.     

Effect and Mechanism Analysis of Solvent on the Electron Transition of Fluoroquinolones Based on Quantum Chemical Calculation

Ciprofloxacin(CIP), moxifoxacin(MOX) and enrofloxacin(ENR) were selected as typical fluoroquinolones(FQs) to analyze the excitation-enhancing effect and mechanism of solvents on FQs' electron transition based on quantum chemical calculations. The UV spectra of three FQs in gas and five different solvents(water, cyclohexane, dimethylsulfoxide, methanol, acetone) were calculated using Gaussian 09 software. The transition mechanisms of FQs' main electron transitions were analyzed by natural bond orbital(NBO) theory, and the solvent effect on each electron transition was assessed qualitatively and quantitatively by sensitivity analysis and an established index system. The excitation enhancing mechanism of solvent on electron transitions of FQs was analyzed from the view of photo-induced reactions between solvent and FQs molecules. The results show that there are two main transitions located in the spectrum ranges of 300~380 and 240~300 nm for each FQ in any medium, which are assigned as n →π* and π→π* electron transitions, respectively. By comparison, the n →π* transition is more sensitive to solvent because of the energy transfer between solvent molecules and FQs, but the solvent effect on the π→π* transition is stronger than on the n →π* transition. The sequence of affected extent of solvent effect on electron transition was CIP MOX ENR, and the sequence of solvent effect was water DMSO methanol acetone cyclohexane(stronger solvent effect with increasing the dielectric constant of solvent). From the view of photo-induced reactions, the reaction between FQs*T1 and solvent*T1 has the decisive regulatory effect on the n →π* transition of FQs in solvent, and the reaction between FQsS0 and solvent*TI has an enhancing effect on the π→π* transition.     

Analysis of Potential Energy Surface for Butanone Isomerization

The potential energy surfaces for butanone isomerization have been investigated by density function theory calculation. Six main reaction pathways are confirmed using the intrinsic reaction coordinate method, and the corresponding isomerization products are 1-buten-2-ol, 2-buten-2-ol, butanal or 1-buten-l-ol, methyl 1-propenyl ether, methyl allyl ether, and ethyl vinyl ether, respectively. Among them, there are three pathways through butylene oxide, indicating butylene oxide is an important intermediate product during butanone isomer ization. The calculated vertical ionization energies of the reactant and its products are in a good agreement with the experimental values available. From the consideration for the relative energies Of transition states and the number of high-energy barriers we infer that the reaction pathway butanone-＊l-buten-2-ol---2-buten-2-oi is the most competitive. The obtained results are informative for future studies on isomerization of ketone molecules.     

Theoretical Study on the Reaction of Thymine with Iodomehane in the Water Phase

The reaction mechanisms of carcinogenic methylating agent iodomethane (MeI) with keto and enol tautomers of thymine (K- and E-thymine) were studied by using the B3LYP/6-311+G (d, p) method in water phase. The solvent effects were examined using the polarizable continuum model (PCM). Specifically, PCM single-point calculations at the same level of theory were performed in acetone and CCl4 that represent a range in nonpolarity. The calculated results show that the reaction of K-thymine with MeI is a two-step mechanism, whereas that of E-thymine is a one-step mechanism. Our calculations reveal that K-thymine is appreciably more stable than the enol form in the water phase or in the two solvents. The K- and E-form reaction barriers are 135.6 and 222.1 kJ/mol, respectively in water phase. These findings indicate that the reactions mentioned above could not occur efficiently in biological media in the absence of catalyst. Our conclusions are in agreement with the previous studies on the reactions of guanine with methyl chloride and methyl bromide.     

A theoretical study on the water-mediated asynchronous addition between urea and formaldehyde

The reaction between urea and formaldehyde in water solution was theoretically investigated by using B3LYP and MP2 methods.It was found that the addition of the nitrogen atom in urea to the carbonyl group in formaldehyde precedes the proton transfer and the proton migration from water to the carbonyl group occurs before the proton abstraction from the nitrogen.With one or two water molecules involved in the TS.the activation energy barrier is lowered compared to the TS of the mechanism with no water participation.The energy change along the reaction coordinate clearly shows that a zwitterionic-like intermediate does not exist on the PES.The reaction between urea and formaldehyde occurs in a concerted mechanism but with asynchronous characters.This is different from the stepwise mechanism recently found for the amination reactions of formaldehyde.     

Proton Transfer Mechanism of Alanine Induced by Zn~（2＋）： a Theoretical Study

In this paper, proton transfer mechanism of alanine induced by Zn2+ was investiga- ted by the CCSD/6-31++G**//B3LYP/6-31++G** method. Six neutral complexes and one ampho- teric complex were optimized, among which the amphoteric complex was the most stable with binding energy of 201.92 kcal·mol-1. In addition, the rotation of intramolecular single bond leads to the neutral configuration conversion, in which the rotation energy barriers of C–C single bonds are lower than 10.51 kcal·mol-1, and those of C–O single bonds range among 9.53~17.50 kcal·mol-1. On the other hand, the proton transfers among the carboxylic oxygen atoms can also result in the neutral configuration conversion, whose energy barriers of forward/back reaction are 53.90 and 32.46 kcal·mol-1, respectively. In detail, the proton transfers from carboxylic group to amino lead to their configuration conversion from neutral to amphoteric. Furthermore, under the catalysis of Zn2+, there was no energy barrier in this reaction. The conversion route from the most stable neutral configuration Ⅱ to the most stable amphoteric configuration I was: Ⅱ→Ⅱ-Ⅲ→Ⅲ→Ⅲ-Ⅵ→Ⅵ→Ⅴ-Ⅵ→Ⅴ→Ⅰ-Ⅴ→Ⅰ,with the energy barrier to be 64.64 kcal·mol-1.     

水/TX-100/正已醇/正辛烷反相微乳液的物化性质

Water/TX-100/Hexanol/Octane reverse microemulsion system is studied by Microcalorimeter and FT-IR methods. The formation process of reverse microemulsions is an exothermic process and is a two step reaction. The first step is that hydrogen-bonds are formed between ether oxygen bonds of TX-100 monomers and water molecules, the second step is hydrogen-bond formation between ether oxygen bonds which are buried in aggregates and water molecules. Three types of water: bind water, trapped water, free water exist in this reverse microemulsion. This result is also proven by FT-IR. The stretch vibration peaks of hydroxyl of water are treated by curve-fitting method from 3035 cm-1 to 3700cm-1. The O-H stretch vibration frequency of trapped water, bind water and free water are 3550±20cm-1, 3400±20cm-1, 3220±20cm-1 respectively. Alkyl ether is prior to phenyl ether in acting with water because their polarity is different. Enthalpy contribution is the main driving force in the spontaneous formation...更多 of this reverse microemulsion.     

Theoretical study on the reaction of VS^＋（^3∑^-, 1^Г） with CO

Two possible reaction mechanisms of VS^＋（^3∑^-, 1^Г） with CO in the gas phase have been studied by using B3LYP/TZVP and CCSD（T）/6-311＋G （3df, 3pd） methods： the O/S exchange reaction （VS^＋＋CO→VO^＋＋CS） and the S-transfer reaction （VS^＋ ＋ CO → V^＋ ＋ COS）. The two reactions proceed via two-step and one-step mechanism, respectively. The barriers of the triplet and singlet PESs are 30.6 and 50.9 kcal/mol, respectively, for O/S exchange reaction and 7.3 and 50.2 kcal/mol, respectively, for the S-transfer reaction. The results indicate that the triplet ground state reaction is more favorable, and the S-transfer reaction is more favorable than the O/S exchange reaction, which is in good agreement with the experimental observation.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Localized molecular orbital studies of certain compounds with [A_3X_3] six-membered rings

The localized molecular orbitals (LMOs) of certain quasi-aromatic organic and inor-ganic molecules with six-membered rings have been calculated by virtue of the ab initio methodusing STO-3G and 4-31G basis sets as well as the CNDO/2 method. It is shown that there existsextensively-delocalized p-pπ bonding in these quasi-aromatic systems. The localized pictures ofthe π-type LMOs for the heterocyclic and homocyclic systems from the σ-π localization schemeare discussed. The Generator Orbital approach is utilized to account for the bonding patterns.     

Addition Mechanisms of Phenol toward Formaldehyde under Acidic Condition： a Theoretical Investigation

The reaction mechanisms of phenol with formaldehyde in the first and second addition at the ortho- and para-position in acid solution were theoretically investigated at the PW91/DNP level with solvent effects included. The reaction of phenol with protonated methanediol firstly forms an adduct intermediate, via a SN2 mechanism with a water molecule as the leaving group. From the adduct intermediate, there are two reaction channels involving a proton transfer to form the addition products. One is that a proton directly transfers via a four-membered ring transition state with a notable energy barrier (Four-member mechanism). Another mechanism involving a water molecule as catalyst to mediate the proton transfer (WCP mechanism), is a barrierless process, indicating that the formation of the adduct intermediate, the first reaction step, is rate-limiting. The reaction products are free hydroxymethyl phenols and/or hydroxybenzy carbocation (HOC6H4CH2+) which plays an important role in the following formation of methylene and methylene ether linkages. The second addition reactions between formaldehyde and hydroxymethyl phenol at all possible reaction sites of the phenol ring in acid solution were also investigated and discussed.     

How Effective Is the Single-point Energy Calculation in Investigating the Reaction Mechanisms？ New Decarboxylation Mechanism of Pyrrole-2-carboxylic Acid by Full Optimization with CPCM Solvation Model

The decarboxylation of pyrrole-2-carboxylic acid in acid solutions was elucidated by full optimization with the CPCM solvation model at the B3LYP/6-31 l＋＋G（d,p） level. Compared with the single-point energy calculation, CPCM full optimization is better to model solvent environments to gain reasonable reaction mechanisms. The π interactions play a significant role in the decarboxylation of pyrrole-2-carboxylic acid （R）. Firstly, the a hydrogen is protonated, but all of the carbonyl hydration pathways bear relatively higher energy barriers. The carbonyl group can rove over the pyrrole ring, but it does not lead to the speciation of pyrrole and protonated carbon dioxide for the latter is an energy-rich species. The decarboxylation mechanism proposed here is that, the protonated pyrrole-2-carboxylic acid （RH） decarboxylates via direct C-C bond cleavage with the aid of a water molecule to accommodate the proton on the carbonyl group.     

DFT Study of Hydrogen-Bonded 1,3,5-Triazine-Water Complexes

The 1,3,5-triazine-water hydrogen bonding interactions have been investigated using the density functional theory B3LYP method and 6-31 ＋＋G^＊＊ basis, obtaining one, two and seven energy minima of the ground states for the 1,3,5-triazine-water, 1,3,5-triazine-（water）2 and 1,3,5-triazine-（water）3 complexes respectively. The fully optimized geometries and binding energies were reported for the various stationary points. The global minima of 1,3,5-triazine-（water）2 and 1,3,5-triazine-（water）3 complexes have a hydrogen bond N…H-O and a chain of water molecules, terminated by a hydrogen bond O…H-C. The binding energies are 13.38, 39.52 and 67.79 kJ/mol for the most stable 1,3,5-triazine-water, 1,3,5-triazine-（water）2 and 1,3,5-triazine-（water）3 complexes respectively, after the basis set superposition error and zero point energy corrections. The H-O symmetric stretching modes of water in the complexes are red-shifted relative to those of the monomer water. In addition, the NBO analysis indicates that inter-molecule charge transfer is 0.02145 e, 0.02501 e and 0.02777 e for the most stable 1 ： 1, 1 ： 2 and 1 ： 3 complexes between 1,3,5-triazine and water, respectively.     

Competitive coupling of amide anion over menthyl propionate anion with aryl radical

A competitive coupling of amide anion over menthyl propionate anion with aryl radicalin photo-S_(RN) 1 mechanism was encountered. The rcaction afforded N-aryl propionic amide in excel-lent yield. In contrast, the expected nucleophilic photo-S_(RN) 1 substitution originating from the carb-anion was observed in the case of t-butyl propionate. According to the proposed mechanisms and MOcorrelation diagrams of the coupling step of nucleophiles with aryl radical, the interesting con-trast is reasonably attributed to the variation in energy gap between π~*c-o and π~*Ar of (ArNu)-Usually, the odd electron of (ArNu)- is weightly populated at π~*c-o, however, the diminished priv-ilege of π~*c-o in menthyl propionate promotes a dominant population of the odd electron at π~*Ar,which leads to the fragmentation of (ArNu)- into the starting carbanion and aryl radical.     

Theoretical study on the reaction of VS~ (~3∑~-,~1Γ)with CO

Two possible reaction mechanisms of VS~ (~3∑~-,~1Γ)with CO in the gas phase have been studied by using B3LYP/TZVP and CCSD(T)/6-311 G(3dr,3pd)methods:the O/S exchange reaction(VS~ CO→VO~ CS)and the S-transfer reaction (VS~ CO→V~ COS).The two reactions proceed via two-step and one-step mechanism,respectively.The barriers of the triplet and singlet PESs are 30.6 and 50.9 kcal/mol,respectively,for O/S exchange reaction and 7.3 and 50.2 kcal/mol,respectively, for the S-transfer reaction.The results indicate that the triplet ground state reaction is more favorable,and the S-transfer reaction is more favorable than the O/S exchange reaction,which is in good agreement with the experimental observation.     

Experimental Study of Hydrogen Isotope Kinetic Fractionation Between Ilvaite and Water——The Kinetics of D-H Exchange in Ilvaite-H_2O

Hydrogen isotope kinetic fractionation in the ilvaite and water system has been studied experimentally at 350-650℃. The result of study shows that the exchange mechanism of hydrogen isotope between ilvaite and water is dominated by hydrogen diffusion.The activation energy for hydrogen diffusion in ilvaite is 118.4 kJ/mol for cylinder model and 115.5 kJ/mol for plate model, respectively.The activation energy for hydrogen isotope exchange in ilvaite is 122.6 kJ/mol.The closure temperature for the cessation of hydrogen isotope exchange between ilvaite and water is much lower than its formation temperature.So, after ilvaite crystallizes, the hydrogen isotope exchange between ilvaite and late hydrothermal solution will continue to take place.     

Theoretical study on the reaction of NbS~+(~3∑~-,~1Γ) with CO

Two possible reactions ofNbS+ (<3∑-,1ΓF) with CO in the gas phase have been studied by using B3LYP and CCSD(T) methods:the O/S exchange reaction (NbS+?" CO→NbO+?"CS) and the S-transfer reaction (NbS+?"CO→Nb+?"COS). The two reactions have a one-step mechanism. The barriers of the O/S exchange reaction on the triplet and singlet surfaces are 51.2 and 52.4 kcal/mol,respectively, and the barriers of the S-transfer reaction are 58.3 and 78.0 kcal/mol, respectively. The results indicate that the S-transfer and the O/S exchange reaction of the 3∑- ground state of NbS+ are competing, but, for the S-transfer reaction, the 1Γ exited state is more reactive. The differences between the reactions of NbS+ (3∑-, 1F) and VS+ (3∑-, 1Γ) are discussed.     

DFT Study on the Effect of Hydrogen-bond Formation on the Adsorption of Aminotriazines on Graphene

DFT calculations have been performed to explore the aminotriazine adsorption on graphene surfaces.Relative energies,equilibrium geometries and electronic structures of monomer and dimer of aminotriazine molecules adsorbed at the surface were investigated and analyzed in details.It was found that the hydrogen atoms in the NH2 group of aminotriazine molecules are directed toward the graphene surface,and the adsorption energy increases as the NH2 group is added.The adsorbed aminotriazine molecules facilely form a dimer through the hydrogen bonding interactions,and the two aromatic rings of optimized structure of 2-amino-1,3,5-triazine(B) dimmer(denoted by B2) and melamine(D) dimmer(denoted by D2) are parallel to the graphene sheet.The large deviation of the averaged adsorption energy of B2 and D2 compared to monor adsorption may reflect the increase of π-π repulsion and the effect of hydrogen bond formation.The electronic structure analyses reveal that the formation of hydrogen bonds in melamine dimer has great influence on the adsorption mode at the graphene surface.