Theoretical study of the reaction mechanism of proton transfer in glycinamide

To investigate the tautomerism of glycinamide that is induced by proton transfer, we present detailed theoretical studies on the reaction mechanism of both the isolated gas phase and H₂O‐assisted proton transfer process of glycinamide, using density functional theory calculations by means of the B3LYP hybrid functional. Twenty‐six geometries, including 10 significant transition states, were optimized, and these geometrical parameters are discussed in detail. The relative order of the activation energy for hydrogen atom transfer of all the conformers has been systematically explored in this essay. For the amido hydrogen atom transfer process, the relative order of the activation energy is: IV < II < III < I, while in the carbonic hydrogen atom transfer process, the relative order is IV > II > III > I. Meanwhile, the most favorable structure for both the amido hydrogen atom transfer and the carbonic hydrogen atom transfer has been found. The involvement of the water molecule not only can stabilize the transition states and the ground states, but can also reduce the activation energy greatly. The superior catalytic effect of H₂O has been discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

The mechanism of double proton transfer in dimers of uracil and 2-thiouracil--the reaction force perspective

The intermolecular double proton transfer in dimers of uracil and 2-thiouracil is studied through density functional theory calculations. The reaction force framework provides the basis for characterizing the mechanism that in all cases has been associated to a dynamic balance between polarization and charge transfer effects. It has been found that the barriers for proton transfer depend upon the nature of the acceptor atoms and its position within the seminal monomer. Actually, the change in the nature of the hydrogen bonds connecting the two monomers along the reaction coordinate may favor or disfavor the double-proton transfer.     

Theoretical analysis on the hydrogen bonding and reactivity that associated with the proton transfer reaction of carboxylic acid dimers and their monosulfur derivatives

Carboxylic acid dimers and their monosulfur derivatives are investigated by density functional theory calculations. Basis set superposition error (BSSE) counterpoise correction is included to compare the influence of BSSE on the interaction energies as well as on the geometries. The nature of hydrogen bond is determined on the basis of atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Good correlations have been established between H‐bond length versus AIM topological parameter, orbital interaction, and barrier height for proton transfer. The reactivity behavior along the reaction path of the double proton transfer reaction has also been studied. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

黄嘌呤异构体质子转移异构化反应机理的理论研究

采用量子化学密度泛函B3LYP/6-31G(d,p)和M06-2X/6-311++G(d,p)方法对黄嘌呤两种酮式异构体X(1,3,7)与X(1,3,9)间质子转移引起的互变异构反应机理进行了计算研究,获得了异构化反应过程的反应焓﹑活化吉布斯自由能和质子转移反应的速率常数等参数。水相计算采用极化连续(PCM)模型。结果表明,由于可能的氢迁移顺序差异,分子内由X(1,3,7)向X(1,3,9)异构化可能共有16条反应通道,涉及11个中间体和20个过渡态,其主反应通道速控步骤的活化吉布斯自由能为183.10k J/mol,速率常数为5.17×10-20s-1,其余各通道速控步骤活化吉布斯自由能均较高,而且整体水溶剂效应不利于质子转移的发生。     

5-氟胞嘧啶气相及水助质子转移异构化的理论研究

采用密度泛函B3LYP/6-311G**方法,对6种5-氟胞嘧啶异构体孤立分子的稳定性及质子转移引起的酮式-烯醇式、氨基式-亚胺式互变异构反应机理进行了计算研究,获得了零点能、吉布斯自由能及质子转移过程的反应焓、活化能、活化吉布斯自由能和速率常数等参数.计算结果表明,气相中烯醇-氨基式FC4是最稳定的异构体.分子内质子转移设计了FC1→FC2和FC1→FC6两条通道,分别标记为P(1)和P(2),各通道速控步骤的活化能和速率常数分别为155.9 kJ·mol-1,4.70×10-15 s-1和173.1 kJ·mol-1,1.41×10-18 s-1.水助催化时,相应通道P(3) 和P(4) 速控步骤的活化能和速率常数分别为51.0 kJ·mol-1,1.41×103 s-1和88.2 kJ·mol-1,4.53×10-3 s-1.可见,水分子的加入极大地降低了质子转移的活化能垒.另外发现,水分子参与形成协同的双质子转移机理比水助单质子转移机理更利于降低活化能垒.     

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     

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。     

Excited state intramolecular proton transfer in 5-hydroxy flavone: A DFT study

Potential energy surfaces (PES) for the ground and excited state intramolecular proton transfer (ESIPT) processes in 5-hydroxy-flavone (5HF) were studied using DFT-B3LYP/6-31G(d) and TD-DFT/6-31G(d) level of theory, respectively. Our calculations suggest the non-viability of ground state intramolecular proton transfer (GSIPT) in 5HF. Excited states PES calculations support the existence of ESIPT process in 5HF. ESIPT in 5HF has been explained in terms of HOMO, LUMO electron density of the enol and keto tautomer of 5HF. PES scan by phenyl group rotation suggests that the twisted form, i.e., phenyl group rotated by 18.7° out of benzo-γ-pyrone ring plane is the most stable conformer of 5HF.     

The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study

This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg²⁺, Zn²⁺, and Hg²⁺. Our results point out that this reaction corresponds to a two‐stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.     

Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-glycine complex have been investigated employing the B3LYP/6-311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and -1.83 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H-bonded glycinamide-glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H-bond.     

尿嘧啶水助质子转移反应机理的研究

用密度泛函理论,在B3LYP/6-311++G**计算水平下分别对尿嘧啶所有的气相、液相、过渡态和质子转移异构体的结构进行全优化,获得它们在气相和水相中的几何结构和电子结构,PGM反应场溶剂模型用于水相计算.结果显示:在气相和水相中,水参与反应降低了互变异构质子迁移的反应活化能,对互变异构质子迁移的反应起到催化作用,但...     

Catalytic and bulk solvent effects on proton transfer: Formamide as a case study

Structural, thermodynamic, and kinetic aspects of the tautomerization of formamide through direct and solvent-assisted proton transfer have been investigated. Both specific and bulk effects of the solvent play a role in determining the overall result so that only a mixed discrete-continuum model is sufficiently reliable. Structural modifications induced by the solvent are significant, but have only a slight effect on thermodynamic and kinetic quantities. The same remarks apply to the vibrational shifts induced by the solvent. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1993–2000, 1997     

A QM/MM simulation study of transamination reaction at the active site of aspartate aminotransferase: Free energy landscape and proton transfer pathways

Transaminase is a key enzyme for amino acid metabolism, which reversibly catalyzes the transamination reaction with the help of PLP (pyridoxal 5^' -phosphate) as its cofactor. Here we have investigated the mechanism and free energy landscape of the transamination reaction involving the aspartate transaminase (AspTase) enzyme and aspartate-PLP (Asp-PLP) complex using QM/MM simulation and metadynamics methods. The reaction is found to follow a stepwise mechanism where the active site residue Lys258 acts as a base to shuttle a proton from α -carbon (CA) to imine carbon (C4A) of the PLP-Asp Schiff base. In the first step, the Lys258 abstracts the CA proton of the substrate leading to the formation of a carbanionic intermediate which is followed by the reprotonation of the Asp-PLP Schiff base at C4A atom by Lys258. It is found that the free energy barrier for the proton abstraction by Lys258 and that for the reprotonation are 17.85 and 3.57 kcal/mol, respectively. The carbanionic intermediate is 7.14 kcal/mol higher in energy than the reactant. Hence, the first step acts as the rate limiting step. The present calculations also show that the Lys258 residue undergoes a conformational change after the first step of transamination reaction and becomes proximal to C4A atom of the Asp-PLP Schiff base to favor the second step. The active site residues Tyr70* and Gly38 anchor the Lys258 in proper position and orientation during the first step of the reaction and stabilize the positive charge over Lys258 generated at the intermediate step.     

氢键链质子接受能力对质子转移反应影响的理论研究

采用密度泛函B3LYP方法,6-311+g(d,p)基组,对甲酸与质子性溶剂分子形成的HCOOH-S_1-S_2(S_1和S_2分别为H_2O和NHF2)复合物在气相时发生的基态三质子转移反应过程进行了理论研究.4个甲酸复合物HCOOH-H_2O-H_2O,HCOOH-NHF2-NHF2,HCOOH-H_2O-NHF2及HCOOH-NHF2-H_2O中发生的三质子转移反应都是以异步协同质子迁移方式进行的.甲酸复合物中的氢键链组成和连接方式对基态三质子转移反应能垒有显著影响.HCOOH-S_1-S_2复合物中氢键链的质子接受能力可以表示为a×β1+b×β2(a+b=1).当a=0.45,b=0.55时,HCOOH-S_1-S_2中氢键链的质子接受能力和HCOOH-S_1-S_2复合物中的质子转移反应能垒成线性关系.氢键链的质子接收能力越强,反应能垒越低.     

A DFT study of proton transfers for the reaction of phenol and hydroxyl radical leading to dihydroxybenzene and H2O in the water cluster

Reactions of phenol and hydroxyl radical were studied under the aqueous environment to investigate the antioxidant characters of phenolic compounds. M06‐2X/6‐311 + G(d,p) calculations were carried out, where proton transfers via water molecules were examined carefully. Stepwise paths from phenol + OH^• + (H₂O)_n (n = 3, 7, and 12) to the phenoxyl radical (Ph O^•) via dihydroxycyclohexadienyl radicals (ipso, ortho, meta, and para OH‐adducts) were obtained. In those paths, the water dimer was computed to participate in the bond interchange along hydrogen bonds. The concerted path corresponding to the hydrogen atom transfer (HAT, apparently Ph OH + OH^• → Ph O^• + H₂O) was found. In the path, the hydroxyl radical located on the ipso carbon undergoes the charge transfer to prompt the proton (not hydrogen) transfer. While the present new mechanism is similar to the sequential proton loss electron transfer (SPLET) one, the former is of the concerted character. Tautomerization reactions of ortho or para (OH)C₆H₅=O + (H₂O)_n → C₆H₄(OH)₂(H₂O)_n were traced with n = 2, 3, 4, and 14. The n = 3 (and n = 14) model of ortho and para was calculated to be most likely by the strain‐less hydrogen‐bond circuit.     

Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed     

Theoretical study of intermolecular proton transfer reaction in isolated 5-hydroxyisoxazole–water complexes

A systematic investigation in isolated 5-hydroxyisoxazole–water complexes (5-HIO · (H₂O)_nn = 1–3) is performed at the DFT level, employing B3LYP/6-31G(d, p) basis set. Single-point energy calculations are also performed at the MP2 level using B3LYP/6-31G(d, p) optimized geometries and the 6-311++G(d, p) basis set. The computational results show that the keto tautomer K₂ is the most stable isomer in the gas phase, and the tautomer K₁ to be the next most stable tautomer. Hydrogen bonding between HIO and the water molecule(s) will dramatically lower the barrier by a concerted multiple proton transfer mechanism. The proton transfer process of 3WE_cis ↔ 3WK₁ and 2WE_trans ↔ 2WK₂ is found to be more efficient in two tautomerization, and the barrier heights are 7.03 and 14.15 kcal/mol at B3LYP/6-31G(d, p) level, respectively. However, the proton transfer reaction between E_cis and K₁ cannot happen without solvent-assisted.     

Photo-excited intramolecular charge transfer and excited state intramolecular proton transfer behaviors for HPIBT system: A theoretical investigation

Given facile synthetic route and excellent photo stability, excited state intramolecular proton transfer (ESIPT)-active luminous materials have gained more and more attention. Here, we focus on photo-induced excitation process and the ESIPT reaction process for the novel 5-benzothiazol-2-yl-6-hydroxy-2-methyl-isoindole-1,3-dione (HPIBT) molecule. On the level of chemical geometries and infrared spectra, we verify that O─H⋯N of HPIBT should be enhanced. We find that a proton is likely to be attracted by enhanced electronic densities around N, that is, charge transfer impetus ESIPT trend. Combing potential energy curves and searching for transition state, we clarify the ultrafast ESIPT mechanism of HPIBT due to a low barrier, which legitimately explains previous experimental characteristics.     

DFT and MP2 study of isomery scheme in Formazan and intermolecular and intramolecular proton transfer between its tautomers

DFT and Moller Plesset (MP2) calculations were applied to study of isomery scheme in formazan. Formazan that can be presented by three tautomers and eight isomers has various applications in dyes, complexes, and biochemistry. The structures of its isomers and related transition states were optimized, and important molecular parameters, IR frequencies, and energetic results were extracted. The relative stabilities of formazan isomers in the gas phase were found to be as 1EZ >1ZZ >1EE >1ZE >2EE > 3 >2EZ >2ZZ >TS1 >TS3 >TS2. Thermodynamic data confirms that tautomer 1 is major tautomer, and all possible tautomerism interconversions have small rates at room temperature. Then, relative stabilities were calculated in different solvents (chloroform, tetrahydrofuran, acetone, and water). The relative stabilities and thermodynamic data in solvents are nearly similar to those in the gas phase, but the rate constants are slightly more than that in the gas phase. Moreover, relative stabilities of formazan isomers and intermolecular proton transfer in presence of one to three molecules of water have been studied. The results showed that activation barriers in water‐assisted tautomerisms are in general lower than those in the gas phase, but the relative energies of isomers do not change importantly by water clusters. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012