2-氨基-2-咪唑啉异构化和质子迁移溶剂效应的密度泛函计算和Monte Carlo模拟

采用密度泛函理论和MonteCarlo模拟方法研究了2-氨基-2-咪唑啉在气相和水中的异构现象和质子迁移反应.考虑了直接迁移和水助催化迁移等两种质子迁移途径.气相中稳定点的几何结构和热力学性质是在B3LYP/6-311+G^**理论水平上计算得到的.溶剂效应的研究结果表明,水作为溶剂可降低直接迁移途径的速率,有利于水助催化反应途径的进行.     

2-羟基咪唑在气相和水中的异构平衡和质子迁移的从头算计算和Monte Carlo模拟

采用从头算方法在MP2/6-31＋G^*水平上研究了2-羟基咪唑分子在孤立分子和一水合物的异构体的相对稳定性和可能的质子迁移反应, 分析了一个水分子的参与对2-羟基咪唑分子异构体的相对稳定性和质子迁移速率的影响, 采用Monte Carlo模拟方法研究了反应体系在水溶液中反应的溶剂化效应. 结果表明: 2-羟基咪唑分子的孤立分子和一水合物的最稳定异构体相同, 都为酮式. 直接质子迁移反应在水溶液中活化能垒有轻微增加, 但产物能量得到降低; 水助催化质子迁移反应在水溶液中的活化能垒和产物能量都得到明显降低. 综合气相和水相的计算结果, 2-羟基咪唑水助催化的质子迁移反应较易进行, 且在水溶液中进行容易, 可以很容易被实验观察到.     

Reaction mechanism and tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution: a combined Monte Carlo and quantum mechanics study

A combined Monte Carlo and quantum mechanical study was carried out to analyze the tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution. Second- and fourth-order M?ller-Plesset perturbation theory calculations indicate that in the gas phase thiol (Pym-SH) is more stable than the thione (Pym-NH) by ca. 8 kcal/mol. In aqueous solution, thermodynamic perturbation theory implemented on a Monte Carlo NpT simulation indicates that both the differential enthalpy and Gibbs free energy favor the thione form. The calculated differential enthalpy is DeltaH(SH)(-->)(NH)(solv) = -1.7 kcal/mol and the differential Gibbs free energy is DeltaG(SH)(-->)(NH)(solv) = -1.9 kcal/mol. Analysis is made of the contribution of the solute-solvent hydrogen bonds and it is noted that the SH group in the thiol and NH group in the thione tautomers act exclusively as a hydrogen bond donor in aqueous solution. The proton transfer reaction between the tautomeric forms was also investigated in the gas phase and in aqueous solution. Two distinct mechanisms were considered: a direct intramolecular transfer and a water-assisted mechanism. In the gas phase, the intramolecular transfer leads to a large energy barrier of 34.4 kcal/mol, passing through a three-center transition state. The proton transfer with the assistance of one water molecule decreases the energy barrier to 17.2 kcal/mol. In solution, these calculated activation barriers are, respectively, 32.0 and 14.8 kcal/mol. The solvent effect is found to be sizable but it is considerably more important as a participant in the water-assisted mechanism than the solvent field of the solute-solvent interaction. Finally, the calculated total Gibbs free energy is used to estimate the equilibrium constant.     

Application of DFT and MP2 calculations on structural and water-assisted proton transfer in 3-amino-4-nitrofurazan

Density functional theory (DFT) and MP2 calculations have been employed to study of 3-amino-4-nitrofurazan molecule using the standard 6-311++G(d,p) basis set. The chemical properties of the 3-amino-4-nitrofurazan have been extensively studied. The geometries of molecules in the gas phase were optimized and compared with the crystallography of this substance. The results suggest that A form is the most stable form in the gas phase and it is the predominant tautomer in solution according to the DFT and MP2 calculations, respectively. In addition, variation of dipole moments in the gas phase, the specific solvent effects with addition of one molecule of water near the electrophilic centers of tautomers, the transition state of proton transfer assisted by a water molecule, the NBO charges of atoms and the potential energy surface were investigated. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are presented.     

2-巯基苯并咪唑及其类似物互变异构的理论研究

采用B3LYP/6-311G**方法, 计算了2-巯基苯并咪唑及其类似物(2-巯基苯并噁唑、2-巯基苯并噻唑、2-羟基苯并咪唑、2-羟基苯并噁唑、2-羟基苯并噻唑以及2-巯基咪唑、2-巯基噁唑、2-巯基噻唑、2-羟基咪唑、2-羟基噁唑、2-羟基噻唑)的(硫)醇式与(硫)酮式结构进行质子迁移的3种可能途径: (a)分子内质子迁移; (b)水助质子迁移; (c)甲醇助质子迁移．结果表明, 途经b和c所需要的活化能较小, 氢键在降低反应活化能方面起重要作用．采用PCM方法研究了反应体系的溶剂化效应．结果表明孤立分子、一水合物和一甲醇合物的最稳定异构体相同, 都为(硫)酮式, 与气相结论一致．溶剂化效应对异构化能垒的影响较小.     

3-氨基-2-吡啶酮互变异构的密度泛函理论计算

采用密度泛函理论,在B3LYP/6-3 l1G**基组水平上,计算并考察了3-氨基-2-吡啶酮分子酮式和烯醇式结构进行结构互变的质子迁移过程中的2种可能途径:(a)分子内质子迁移,(b)水助质子迁移.计算结果表明,途经b所需要的活化能较小,氢键在降低反应活化能方面起着重要作用.     

DFT investigation on the intramolecular and intermolecular proton transfer processes in 2-aminobenzothiazole (ABT) in the gas phase and in different solvents

DFT at the B3LYP/6-311++G(d,p) level of theory was performed to geometrically, thermodynamically, and kinetically investigate the tautomerism process of 2-aminobenzothiazole (ABT) with n water molecules (n = 1–3) and without water in the gas phase and in different solvents with a gradual increase in their dielectric constants. The geometries of the envisaged tautomers were optimized in the gas phase and in solution with the polarized continuum model (PCM). Equilibrium and rate constants for the forward and reverse intra-/intermolecular isolated and water-assisted tautomerism reactions were also calculated. The results suggest that the activation energy of the transition state of direct proton transfer in the isolated reaction is very high and that the rate constant is very slow (~ 10^?24 s), reflecting that the reaction is thermodynamically unfavored, whereas the barrier differences between the transition states of the tautomers decrease gradually as the number of water molecules increases from one to three. Moreover, the rate constants of the proposed reactions are ~ 10²³–10²⁵ faster than those of the isolated reaction, and the water-assisted tautomerism paths can be performed quickly, especially with the assistance of two molecules of water.

     

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: water-assisted mechanism and cluster-continuum model

The hydrolysis reaction of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine (DMPFA), a model compound of the antivirus drug amidine-3TC (3TC = 2', 3'-dideoxy-3'-thiacytidine), is investigated by the hybrid density functional theory B3LYP/6-31+G (d,p) method. The hydrolysis reaction of the title compound is predicted to undergo via two pathways, each of which is a stepwise process. Path A is the addition of H2O to the C=N double bond in the amidine group to form a tetrahedral structure in its first step, and then the transfer of the H atom of hydroxyl leads to the corresponding products via four possible channels. Path B simultaneously involves the nucleophilic attack of H2O to the C atom of the C=N bond and the proton transfer to the N atom of amino group leading to the cleavage of the C-N single bond in the amidine group. The results indicate that path A is more favorable than path B in the gas phase. Moreover, to simulate the title reaction in aqueous solution, water-assisted mechanism and the cluster-continuum model, based on the SCRF/CPCM model, are taken into account in our work. The results indicate that it is rational for two water molecules served as a bridge to assist in the first step of path A and that cytosine rather than the cytosine-substituted formamide should be released from the tetrahedral intermediate via s six-membered cycle transition state (channel 2). Our calculations exhibit that the process toward the tetrahedral intermediate is the rate-determining step both in the gas phase and in aqueous solution.     

Theoretical studies on tautomerism of imidazole-2-selenone

The tautomerism of all possible forms of imidazole selenone (ISe1–ISe6), induced by proton transfer was studied theoretically in different environments including gas phase, continuum solvent, and microhydrated environment with one explicit water molecule. The calculations were performed at the MP2 and CAM-B3LYP levels of theory, separately. It was found that the imidazole selenone, in the form of ISe3, is the most stable isomer in both gas phase and solvent. The activation energy for conversion of ISe3 to imidazole selenol (ISe6), as the second stable form, is 41.72 and 43.0 kcal/mol in the gas phase and water, respectively. The infrared spectral frequencies as well as the vibrational frequency shifts were reported and assigned to their corresponding vibrational modes. In addition, the variation of dipole moments and charges on the atoms with change of solvent was studied. The energies of HOMO, LUMO, and HOMO–LUMO gap were calculated in both gas phase and solvent. Specific solvent effects with addition of water molecule near the electrophilic centers of tautomers and the transition states of proton transfer, assisted by water molecule, were investigated. It was found that the water molecule can form different hydrogen bonds with the molecule. Aggregation of the isomers with water molecule does not change the order of stability of isomers, but proton transfer reaction assisted by a water molecule needs less energy than when the proton shifts through the intramolecular process.     

Theoretical Study of Molecular Structure, Tautomerism, and Geometrical Isomerism of N-Methyl- and N-Phenyl-Substituted Cyclic Imidazolines, Oxazolines, and Thiazolines

The geometries of various tautomers and isomers of 2-methylamino-2-imidazoline, 2-methylamino-2-oxazoline, 2-methylamino-2-thiazoline, 2-phenylamino-2-imidazoline, 2-phenylamino-2-oxazoline, and 2-phenylamino-2-thiazoline have been studied using the Becke3LYP/6–31+G(d,p) DFT, ONIOM(Becke3LYP/6–31+G(d,p):HF/3–21G^*) and ONIOM(Becke3LYP/6–31+G(d,p):AM1) methods. The optimized geometries indicate that these molecules show a distinctly nonplanar configuration of the cyclic moieties. In the gas phase, the amino tautomers (with exception of 2-phenylamino-2-imidazoline) are computed to be more stable than the imino tautomers. Of the two possible (E and Z) isomers of methyl and phenyl derivatives of imino-oxazolidine and imino-thiazolidine species, the (Z) isomers have the lowest energy. The iminozation free energies in the gas phase were found to be 5 – 15 kJ/mol. Absolute values of K _T depend strongly on the accuracy of the method used for calculation of free energy. Solvation (using the MD simulations) causes, in most cases, a shift in tautomeric preference toward the imino species.     

A Theoretical Study on the Photochromic Mechanism of 1-Phenyl-3-methyl-4-（6-hydro-4-amino-5-sulfo-2,3-pyrazine）-pyrazole-5-one

The photochromic mechanism of 1-phenyl-3-methyl-4-（6-hydro-4-amino-5-sulfo-2,3- pyrazine）-pyrazole-5-one has been investigated using the density functional theory（DFT）. The solvent effect is simulated using the polarizable continuum model（PCM） of the self-consistent reaction field theory. According to the crystal structure of the title compound, an intramolecular proton transfer mechanism from enol to keto form was proposed to interpret its photochromism. Bader＇s atom-in-molecule（AIM） theory is used to investigate the nature of hydrogen bonds and ring structures. Time-dependent density functional theory（TDDFT） calculation results show that the photochromic process from enol to keto form is reasonable. The conformation and molecular orbital analysis of enol and keto forms explain why only intramolecular proton transfer is possible. The results from analyzing the energy and dipole moments of enol form, transition state and keto form in the gas phase and in different solvents have been used to assess the stability of the title compound.     

Theoretical studies on the hydrolysis mechanism of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide

Density functional theory (B3LYP) and ab initio (MP2) methods with the 6-31G(d,p) basis set are used to study the mechanisms for the hydrolysis of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide (PFA) in the gas phase. The direct and the water-assisted hydrolysis processes are considered, involving one and two water molecules, respectively. Three different pathways are explored in each case. In the first pathway, the O atom of water first attacks at the C atom of amide while one H atom of water transfers toward the oxygen of amide, leading to an intermediate of tetrahedral coordinated carbon with two OH groups. In the subsequent step, the hydroxyl H atom transfers to the N atom of pyrimidine ring and the C-N covalent bond of amide dissociates simultaneously. In the second path, the O and one H of water attack at the C of amide and the N of pyrimidine ring, respectively, while the C-N bond of amide dissociates. In the third path, three processes occur simultaneously: the O of water attacks at the C of amide, one H atom attacks at the N of amide, and the C-N bond of amide is broken. It is shown that the second pathway is favored for the direct hydrolysis while the first pathway is favored for the water-assisted hydrolysis. It is also shown that the water-assisted hydrolysis is slightly more favorable than the direct hydrolysis. Moreover, solvent effects on five pathways are evaluated with Monte Carlo simulation (MC) and free energy perturbation methods. It is shown that the solvent water slightly reduces the energy barrier in each pathway. The first pathway in the water-assisted hydrolysis remains the most favorable when the solvent effects of bulk water are taken into account.     

Theoretical studies on the chemical decomposition of 5-aza-2′-deoxycytidine: DFT study and Monte Carlo simulation

The decomposition mechanism of 5-Aza-2??-deoxycytidine has been studied by the use of computational techniques. Optimized structures for all of the stationary points in the gas phase were investigated at B3LYP/6-31+G(d,p) level of theory. Single-point energies were determined employing the ab initio MP2 method in conjunction with the 6-311++G(d,p) basis set. Five possible pathways, paths 1?C5, were evaluated. In each pathway, the direct (A-paths 1?C5) and water-assisted (B-paths 1?C5) processes were considered. Meanwhile, the local microhydration model with the direct participation of three water molecules around the reaction centers was adopted to mimic the system for the water-assisted decomposition mechanisms above, where one water molecule is the nucleophilic reactant and the other two are the auxiliary molecules located on each side of the nucleophilic water. The results in the gas phase exhibit that the energy barriers of the water-assisted pathways based on the local microhydration model decrease dramatically by about 15?C20?kcal/mol as compared with those of the direct pathways because of the contribution of the auxiliary water molecules. In addition, bulk solvent effects of water were determined by means of the self-consistent reaction field based on the conductor-like polarized continuum model and Monte Carlo simulation with free energy perturbation (MC-FEP) technique, respectively. Our computational results indicate that B-path 3 in the decomposition reaction of 5-azadC is the most favorable, where the calculated rate constant (1.68?×?10^?3?min^?1) using the MC-FEP method is within the range of the experimentally determined values [(5.89?±?0.54)?×?10^?3?min^?1 by UV and (1.46?±?0.08)?×?10^?3?min^?1 by NMR].     

Mechanism of the hydration of carbon dioxide: direct participation of H2O versus microsolvation

Thermochemical parameters of carbonic acid and the stationary points on the neutral hydration pathways of carbon dioxide, CO 2 + nH 2O --> H 2CO 3 + ( n - 1)H 2O, with n = 1, 2, 3, and 4, were calculated using geometries optimized at the MP2/aug-cc-pVTZ level. Coupled-cluster theory (CCSD(T)) energies were extrapolated to the complete basis set limit in most cases and then used to evaluate heats of formation. A high energy barrier of approximately 50 kcal/mol was predicted for the addition of one water molecule to CO 2 ( n = 1). This barrier is lowered in cyclic H-bonded systems of CO 2 with water dimer and water trimer in which preassociation complexes are formed with binding energies of approximately 7 and 15 kcal/mol, respectively. For n = 2, a trimeric six-member cyclic transition state has an energy barrier of approximately 33 (gas phase) and a free energy barrier of approximately 31 (in a continuum solvent model of water at 298 K) kcal/mol, relative to the precomplex. For n = 3, two reactive pathways are possible with the first having all three water molecules involved in hydrogen transfer via an eight-member cycle, and in the second, the third water molecule is not directly involved in the hydrogen transfer but solvates the n = 2 transition state. In the gas phase, the two transition states have comparable energies of approximately 15 kcal/mol relative to separated reactants. The first path is favored over in aqueous solution by approximately 5 kcal/mol in free energy due to the formation of a structure resembling a (HCO 3 (-)/H 3OH 2O (+)) ion pair. Bulk solvation reduces the free energy barrier of the first path by approximately 10 kcal/mol for a free energy barrier of approximately 22 kcal/mol for the (CO 2 + 3H 2O) aq reaction. For n = 4, the transition state, in which a three-water chain takes part in the hydrogen transfer while the fourth water microsolvates the cluster, is energetically more favored than transition states incorporating two or four active water molecules. An energy barrier of approximately 20 (gas phase) and a free energy barrier of approximately 19 (in water) kcal/mol were derived for the CO 2 + 4H 2O reaction, and again formation of an ion pair is important. The calculated results confirm the crucial role of direct participation of three water molecules ( n = 3) in the eight-member cyclic TS for the CO 2 hydration reaction. Carbonic acid and its water complexes are consistently higher in energy (by approximately 6-7 kcal/mol) than the corresponding CO 2 complexes and can undergo more facile water-assisted dehydration processes.     

DFT and MP2 Calculations on Tautomers and Water-Assisted Proton Transfer on 1,2,5-Oxadiazol-4,3-diamine

In this work a detailed quantum-chemical comparison of the relative stability of six tautomers of 1,2,5-oxadiazol-4,3-diamine studied in the gas phase and solution. Theoretical calculations are carried out by the density functional theory (DFT/B3LYP) and MP2 methods using the standard 311++G(d,p) basis set. The results indicate that A is the most stable form in the gas phase and also is the predominant tautomer in solution at the DFT and MP2 methods. The transition states of proton transfer reaction are calculated. The variation of dipole moments and charges on atoms are studied in various solvent. Specific solvent effects with addition of one water molecule near the electrophilic centers of tautomer investigated. Also the transition state of proton transfer assisted by a water molecule was investigated.     

Computational Investigation of the Substituent Effect on the Intramolecular Proton Transfer Reaction of 3-Hydroxytropolone

The effects of substituent type and position on the proton transfer reaction of 3-hydroxytropolone(3-OHTRN) have been investigated theoretically by using density functional theory at the level of B3LYP/ 6-31+G** method. The influence of solvent on the proton transfer reactions of substituted 3-OHTRN has been examined using the self-consistent isodensity polarized continuum model(SCI-PCM) in water. As a result, while the proton transfer reaction is kinetically the easiest by substitution on position 3 of-NH2 group in the gas phase, it is kinetically the easiest by substitution on position 5 of the same group in water. In addition, these reactions are either kinetically or thermodynamically easier in the gas phase than that in water, except the reaction of structure with-NH2 group at position 6.     

Theoretical studies on the chemical decomposition of 5-aza-2′-deoxycytidine: DFT study and Monte Carlo simulation

The decomposition mechanism of 5-Aza-2′-deoxycytidine has been studied by the use of computational techniques. Optimized structures for all of the stationary points in the gas phase were investigated at B3LYP/6-31+G(d,p) level of theory. Single-point energies were determined employing the ab initio MP2 method in conjunction with the 6-311++G(d,p) basis set. Five possible pathways, paths 1–5, were evaluated. In each pathway, the direct (A-paths 1–5) and water-assisted (B-paths 1–5) processes were considered. Meanwhile, the local microhydration model with the direct participation of three water molecules around the reaction centers was adopted to mimic the system for the water-assisted decomposition mechanisms above, where one water molecule is the nucleophilic reactant and the other two are the auxiliary molecules located on each side of the nucleophilic water. The results in the gas phase exhibit that the energy barriers of the water-assisted pathways based on the local microhydration model decrease dramatically by about 15–20 kcal/mol as compared with those of the direct pathways because of the contribution of the auxiliary water molecules. In addition, bulk solvent effects of water were determined by means of the self-consistent reaction field based on the conductor-like polarized continuum model and Monte Carlo simulation with free energy perturbation (MC-FEP) technique, respectively. Our computational results indicate that B-path 3 in the decomposition reaction of 5-azadC is the most favorable, where the calculated rate constant (1.68 × 10⁻³ min⁻¹) using the MC-FEP method is within the range of the experimentally determined values [(5.89 ± 0.54) × 10⁻³ min⁻¹ by UV and (1.46 ± 0.08) × 10⁻³ min⁻¹ by NMR].     

Density functional study on the reaction mechanism of proton transfer in 2-pyridone: effect of hydration and self-association

The proton-transfer mechanism in the isolated, mono, dehydrated forms and dimers of 2-pyridone and the effect of hydration or self-assistance on the transition state structures corresponding to proton transfer from the keto form to the enol form have been investigated using B3LYP and BH-LYP hybrid density functional methods at the 6-311++G (2d, 2p) basis set level. The barrier heights for both H2O-assisted and self-assisted reactions are significantly lower than that of the bare tautomerization reaction from 2-pyridone to 2-hydroxypyridine, implying the importance of the superior catalytic effect of H2O and (H2O)2 and the important role of 2-pyridone itself for the intramolecular proton transfer. Long-range solvent effects have also been taken into account by using the continuum model (Onsager model and polarizable continuum model (PCM)) of water. The tautomerization energies and the potential energy barriers are increased both for the water-assisted and for the self-assisted reaction because of the bulk solvent, which imply that the tautomerization of PY becomes less favorable in the polar solvent.     

Reaction dynamics simulations of the identity S(N)2 reaction H(2)O + HOOH(2)(+)--> H(2)OOH(+)+ H(2)O. Requirements for reaction and competition with proton transfer

Despite the fact that the transition structure of the gas phase S(N)2 reaction H(2)O + HOOH(2)(+)--> HOOH(2)(+)+ H(2)O is well below the reactants in potential energy, the reaction has not yet been observed by experiment. Variational transition state RRKM theory reveals a strong preference for the competing proton transfer reaction H(2)O + HOOH(2)(+)--> H(3)O(+)+ HOOH due to entropy factors. Born-Oppenheimer reaction dynamics simulations confirm these results. However, by increasing the collision energy to around 7.5 eV the probability for nucleophilic substitution increases relative to proton transfer. These observations are explained by the presence of the key common intermediate HOO(H)[dot dot dot]H-OH(2)(+) which leads to effective proton transfer, but can be avoided with increasing collision energy. However, the S(N)2 probability remains below 0.2 since successful passage through the TS requires optimum initial orientation of the reactants, excitation of the relative translational motion and good phase correlation between the O-O vibration and the motion of the incoming water.     

A CASSCF-CASPT2 study of the excited-state intramolecular proton transfer reaction in 1-amino-3-propenal using different active spaces

In this work we analyze how the choice of the active space in the CASSCF (the complete-active-space multiconfiguration self-consistent-field method) and CASPT2 (the second-order perturbation theory based on the CASSCF reference wave function) calculations affects the computed potential energy curves (PECs) for the intramolecular proton transfer reaction in the ground state and the two lowest lying singlet excited states of 1-amino-3-propenal. As anticipated, the results revealed that, qualitatively, the proton transfer in the different states can be correctly described even by minimal active spaces, which include the orbitals involved in the electronic excitation of the considered state and the antibonding sigma orbital corresponding to the bond formed by the molecule with the migrating hydrogen atom. However, quantitatively, the relative energies of the two tautomers and the energy barriers computed at the CASSCF level change when the active space is increased, indicating importance of the dynamic electron correlation. Introducing the dynamic correlation effects via CASPT2 makes the calculated energy parameters more uniform among the different active spaces. The analysis suggested certain optimal active spaces for studying proton transfer reactions in systems similar to 1-amino-3-propenal. The PEC calculations for excited states showed that the results are sensitive to the molecular geometries used in the calculations, particularly near the transition point. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1422–1431 (1999)