3-卤代吡唑质子转移过程的理论研究

采用密度泛函B3LYP/6-311G**方法,对3-卤(-F、-Cl、-Br)代吡唑几何构型进行了全自由度优化,获得了它们的几何结构和电子结构。计算结果显示,N1-H型的稳定性大于N2-H型。计算并考察了3-卤代吡唑进行结构互变的质子转移过程的四种可能途径:(a)分子内质子转移;(b)水助质子转移;(c)同种二聚体双质子转移;(d)异种二聚体双质子转移。计算结果表明(以3-氟代吡唑为例),途径d所需要的活化能最小(54.89 kJ/mol),而途径a所需要的活化能最大(198.83kJ/mol),途径b和c的活化能居中间分别为(104.05 kJ/mol和69.05 kJ/mol)。研究还表明氢键在降低活化能方面起着重要的作用,卤素(-F、-Cl、-Br)对活化能的影响不大。     

The effect of proton disorder on the structure of ice-Ih: a theoretical study

A precise and accurate measurement of the crystal structure of ice-Ih is hindered by its disordered H-bond network. In this work, we carried out first-principle calculations to study the effects of H-bond topology on the structure of ice-Ih with emphasis on the molecular geometry of water and the distortion in oxygen lattice. An analytic algorithm based on group and graph theory is employed to enumerate all possible configurations in a given unit cell and to select a set of structures for detailed examinations. In total we have studied more than 60 ice-Ih structures in a hexagonal unit cell of 48 water molecules by quantum-chemical methods and found a significant amount of static distortion in the oxygen positions from their crystallographic positions which is in good agreements with highly significant higher-order terms obtained from both x-ray and neutron-diffraction data. Much debated structural information such as H-O-H angle and O-H bond length is found to be 106.34+/-0.36 degrees and 0.9997+/-0.0008 A, compared to experimental value of 106.6+/-1.5 degrees and 0.986+/-0.005 A. Detailed benchmarking calculations were carried out to gauge the influence of using different exchange and correlation functionals, pseudopotentials, and unit-cell sizes. Our results have proven that first-principle methods are useful complementary tools to experiments, especially for cases in which experimental accuracy is limited by intrinsic orientational disorder.     

Hydrogen bond vs proton transfer in HZSM5 zeolite. A theoretical study

The interaction of a large set of bases covering a wide range of the basicity scale with HZSM5 medium-size zeolites has been investigated through the use of two model clusters, namely 5T and 7T:63T. The 5T cluster has been treated fully ab initio at the B3LYP level, whereas the 63T cluster has been treated with the ONIOM2 scheme using the B3LYP:MNDO combination for geometry optimizations and B3LYP:HF/3-21G for adsorption energies. The optimized geometries of the different hydrogen bond (HB) and ion pair (IP) complexes obtained with both models are rather similar. However, there are significant dissimilarities as far as the adsorption energies are concerned, in particular when dealing with IP clusters whose intrinsic stability is largely underestimated when the simpler 5T model is used. 5T clusters could be used to obtain reasonable estimates of adsorption energies provided these are scaled by a factor of 1.1 for HB complexes and 1.4 for IP complexes. The zeolite cavity favors the proton transfer process, similarly to that found by third polar partners in gas-phase HB trimers. The intrinsic basicity of the base and its adsorption energy within the zeolite are correlated. From this correlation, is possible to conclude that, in general, bases with proton affinities (PA) larger than 200 kcal mol(-1) should lead to the formation of IPs, whereas bases with PA smaller than this value should form HB complexes.     

Compression effect on structure and proton transfer in crystalline benzoic acid

Geometry optimizations for an isolated dimer and a crystal of benzoic acid were performed in order to evaluate the equilibrium geometries and the energy difference between the dimers in isolated and crystalline states using model potentials. The optimization in the crystal field results in a shortening of the O⋯O distance in comparison with that in an isolated dimer. The magnitude of the shortening agrees well with the difference between the observed values of the O⋯O distance in the gaseous (2.703 Å) and crystalline (2.64 Å) states. The energy increase due to this shortening is estimated to be about 0.24–0.40 kcal mol⁻¹ and is found to be one of the causes of the discrepancy between the barrier height of 1–2 kcal mol⁻¹ measured by NMR for crystalline carboxylic acids and that of 7.1–9.1 kcal mol⁻¹ calculated by the ab initio method for the isolated dimer.     

A theoretical study on the detection of proton transfer pathways in some mutants of human carbonic anhydrase II

Structural and kinetic studies of mutants can give much insight into the function of an enzyme. We report the detection of possible proton transfer pathways into the active site of a number of mutants of the enzyme human carbonic anhydrase II (HCA II). Using a recently developed method of path search in the protein conformational space, we identify hydrogen-bonded networks (or proton paths) that can dynamically connect the protein surface to the active site through fluctuations in protein structure and hydration. The feasibility of establishing such dynamical connectivities is assessed by computing the change in free energy of conformational fluctuations and compared to those identified earlier in the wild type enzyme. It is found that the point mutation facilitates or suppresses one or more of the alternative pathways. Our results allow the use of a generic set of pathways to correlate qualitatively the residual activity in the mutants to the molecular mechanism of proton transfer in the absence of His at position 64. We also demonstrate how the detected pathways may be used to compare the efficiencies of the mutants His-64-Ala/Asn-62-His and His-64-Ala/Asn-67-His using the empirical valence bond theory.     

尿酸质子转移反应的理论研究I——分子内质子转移研究

使用量子化学中的Hartree-Fock方法和密度泛函理论中的B3LYP方法，分别在3－21G^*和6－31G（d)水平上，计算了尿酸分子从三羰基异构体向三羟基异构体的转化。结果表明，转化过程经历了单羟基和双羟基异构体2种中间物和3种过渡态时的分子内质子转移（IPT），转移中的H原邻近的N，O和C原子形成了具有四元环结构的过渡态。随着IPT的进行，N－H键逐渐被削弱和断裂，O－H键则逐渐生成。3个反应的活化能分别为190.3kJ/mol,181.4kJ/mol和249.9kJ/mol(B3LYP/6-31G(d))。较高的活化能表明在室温下，无催化剂的IPT难以进行。     

Tunnel effect in proton transfer

Semiempirical computations were carried out to determine the tunneling rates in the case of coupled motion of two protons along the reaction coordinate. The following molecular systems were studied for medium intermolecular distances (A—B = 2.72 or 2.75 Å); ⁺AH—BH—A, where A was NH₃ or H₂O and BH was HF or H₂O. In the cases where the bridge was HF, solvation was modeled with just one water molecule attached to each side of the perpendicular axis through HF at 2.75 Å. Coupled motion of three protons was also included in the case of H₃O—H₂O—H₂O—H₂O.     

别嘌醇质子迁移过程的理论研究

别嘌醇(Allopurinol)是次黄嘌呤的位置异构体,是唯一在临床上应用的黄嘌呤氧化酶抑制剂.     

Excited state proton transfer in guanine in the gas phase and in water solution: a theoretical study

Theoretical investigations were performed to study the phenomena of ground and electronic excited state proton transfer in the isolated and monohydrated forms of guanine. Ground and transition state geometries were optimized at both the B3LYP/6-311++G(d,p) and HF/6-311G(d,p) levels. The geometries of tautomers including those of transition states corresponding to the proton transfer from the keto to the enol form of guanine were also optimized in the lowest singlet pipi* excited state using the configuration interaction singles (CIS) method and the 6-311G(d,p) basis set. The time-dependent density function theory method augmented with the B3LYP functional (TD-B3LYP) and the 6-311++G(d,p) basis set was used to compute vertical transition energies using the B3LYP/6-311++G(d,p) geometries. The TD-B3LYP/6-311++G(d,p) calculations were also performed using the CIS/6-311G(d,p) geometries to predict the adiabatic transition energies of different tautomers and the excited state proton transfer barrier heights of guanine tautomerization. The effect of the bulk aqueous environment was considered using the polarizable continuum model (PCM). The harmonic vibrational frequency calculations were performed to ascertain the nature of potential energy surfaces. The excited state geometries including that of transition states were found to be largely nonplanar. The nonplanar fragment was mostly localized in the six-membered ring. Geometries of the hydrated transition states in the ground and lowest singlet pipi* excited states were found to be zwitterionic in which the water molecule is in the form of hydronium cation (H3O(+)) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH(-)) and the guanine is in the cationic form. It was found that proton transfer is characterized by a high barrier height both in the gas phase and in the bulk water solution. The explicit inclusion of a water molecule in the proton transfer reaction path reduces the barrier height drastically. The excited state barrier height was generally found to be increased as compared to that in the ground state. On the basis of the current theoretical calculation it appears that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form.     

A theoretical study on the structure and hygroscopicity of ammonium dinitramide

Density functional theory (DFT) and the dispersion corrected DFT have been used to investigate the hygroscopicity of ammonium dinitramide (ADN). Calculation results show that the gaseous ADN has a strong hydrogen bond. But the ionic pair structure NH₄ ⁺ · N(NO₂)^? is stabilized upon the addition of water molecules. Natural bond orbital calculations suggest that the intra- and intermolecular orbital interactions LP(O) → σ*(N–H) or LP(O) → σ*(O–H) make the system stabilized as a whole. En energy decomposition analysis reveals that the interactions between ADN and H₂O are dominated by the electrostatic and orbital interactions. The formation reactions become more spontaneous with the increasing number of water molecules but can be weakened by the growing temperature from 200 to 400 K. Moreover, the molecular dynamic method is applied to explore a more realistic cluster model to study the interactions between ADN and H₂O.     

A theoretical study of the structure of tricarbonatodioxouranate

The results of a study on the ground states of tricarbonato complexes of dioxouranate using multiconfigurational second-order perturbation theory (CASSCF/CASPT2) are presented. The equilibrium geometries of the complexes corresponding to uranium in the formal oxidation states VI and V, [UO(2)(CO(3))(3)](4)(-) and [UO(2)(CO(3))(3)],(5)(-) have been fully optimized in D(3)(h)() symmetry at second-order perturbation theory (MBPT2) level of theory in the presence of an aqueous environment modeled by a reaction field Hamiltonian with a spherical cavity. The uranyl fragment has also been optimized at CASSCF/CASPT2, to obtain an estimate of the MBPT2 error. Finally, the effect of distorting the D(3)(h)() symmetry to C(3) has been investigated. This study shows that only minor geometrical rearrangements occur in the one-electron reduction of [UO(2)(CO(3))(3)](4)(-) to [UO(2)(CO(3))(3)],(5)(-) confirming the reversibility of this reduction.     

A theoretical study of the structure of pentadienyllithium

Conclusions MNDO quantum-chemical calculations indicated a mechanism for the rapid rearrangement of PDL with migration of lithium along the hydrocarbon skeleton of the ligand.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2132–2134, September, 1986.     

A theoretical analysis of excited state proton transfer in 3-hydroxyflavone. Promoting effect of a low frequency bending mode

The dynamical properties of excited state intramolecular proton transfer in 3-hydroxyflavone have been analyzed on the basis of the time evolution of the quantum states of the two isomeric forms. Potential energy surfaces have been computed at the MNDO/AM1 level. The results shed light on the essential features of the proton transfer mechanism: in particular, the rapidity of the process is to be attributed to the promoting effect of a low frequency bending vibration, which shortens the distance between donor and acceptor atoms.     

A theoretical study of the ground and first excited singlet state proton transfer reaction in isolated 7-azaindole–water complexes

A systematic study of the proton transfer in the 7-azaindole–water clusters (7-AI(H₂O)_n; n=1–4) in both the ground and first excited singlet electronic states is undertaken. DFT(B3LYP) calculations for the ground electronic state shows that the more stable geometry of the initial normal tautomer presents a cyclic set of hydrogen bonds that links the two nitrogen atoms of the base across the waters. For the n=4 cluster the water molecules adopt a double ring structure so that two cycles of hydrogen bonds are found there. From this structure full tautomerization implies only one transition state so that a concerted but non-synchronous process is predicted by our theoretical calculations. This behavior is found both in the ground and the excited states where CIS geometry optimizations and TD(B3LYP) energy calculations are performed. The difference between both states is the height of the energy barrier that is much lower in the excited state. Another clear difference between both electronic states is that full tautomerization is an endergonic process in the ground state whereas it is clearly exergonic (then favorable) in the excited state. This is so because electronic excitation implies a charge transfer from the five-member cycle to the six-member one of 7-azaindole so that the proton transfer from the pyrrolic side to the pyridinic one is favored. These results clearly indicate that full tautomerization will not likely occur in the ground state but it will be quite easy (and fast) in the excited state. Reaction is already feasible in the S₁ 1:1 complex but it is faster in the 1:2 complex. However the reaction slows again for the 1:3 complex and, finally, reaches a new maximum for the largest cluster studied here, the n=4 case. These results, which are in agreement with experimental data, are explained in terms of the number of hydrogen bonds that are involved in the transfer. The proton transfer through a ring formed by the substrate and two water molecules is found to be the more efficient one, at least in this system.     

Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps

Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.     

S2BrH的构型及其异构化反应的理论研究

由于在合成化学、大气化学和环境保护中的重要性，过硫化物XSSX(X=H，CH3，F，Cl等)被广泛研究。本文采用量子化学的密度泛函方法(DFT)，对S2BrH可能存在的2种构型的几何结构、相对稳定性以及可能的分子内原子迁移过程进行研究，探讨分叉型异构体SSBrH存在的可能性。     

Methyl transfer in glycine N-methyltransferase. A theoretical study

Density functional theory calculations using the hybrid functional B3LYP have been performed to study the methyl transfer step in glycine N-methyltransferase (GNMT). This enzyme catalyzes the S-adenosyl-L-methionine (SAM)-dependent methylation of glycine to form sarcosine. The starting point for the calculations is the recent X-ray crystal structure of GNMT complexed with SAM and acetate. Several quantum chemical models with different sizes, employing up to 98 atoms, were used. The calculations demonstrate that the suggested mechanism, where the methyl group is transferred in a single S(N)2 step, is thermodynamically plausible. By adding or eliminating various groups at the active site, it was furthermore demonstrated that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to the carboxylate group raise the barrier.     

Substituent effect on the reaction mechanism of proton transfer in formamide

MP2 and B3LYP methods at 6‐311++G** basis set have been used to explore proton transfer in keto‐enol forms of formamide and to investigate the effect of substituent, i.e., H, F, Cl, OH, SH, and NH₂ on their transition states. Additionally, the vibrational frequencies of aforementioned compounds are calculated at the same levels of theory. It is proposed that the barrier heights values in kJ/mol for F, Cl, OH, and SH substituents are significantly greater than that of the bare tautomerization reaction, implying the importance of the substituents effect on the intramolecular proton transfer. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012