Catalytic reaction mechanism of L-lactate dehydrogenase: an ab initio study

Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion H_r transfer, and the transfers of the hydride ionH _r and protonH _r are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between theH _r transfer process and the hydrogen bonding with lower barrier indicates that the H_r transfer process occurs by means of an unusual manner. In addition, in the transition state the electrostatic interaction between the substrate and the active site of LDH is quite strong and the polarization of the carbonyl in the substrate is gradually enhanced accompanying the formation of the transition state. These calculated results are well in accord with the previous experimental studies, and indicate that the charge on the hydride ion H_r is only +0.13e in the transition state, which is in agreement with the reported semiempirical quantum chemical calculations.     

Catalytic reaction mechanism of L-lactate dehydrogenase: anab initio study

Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion H_r transfer, and the transfers of the hydride ionH _r and protonH _r are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between theH _r transfer process and the hydrogen bonding with lower barrier indicates that the H_r transfer process occurs by means of an unusual manner. In addition, in the transition state the electrostatic interaction between the substrate and the active site of LDH is quite strong and the polarization of the carbonyl in the substrate is gradually enhanced accompanying the formation of the transition state. These calculated results are well in accord with the previous experimental studies, and indicate that the charge on the hydride ion H_r is only +0.13e in the transition state, which is in agreement with the reported semiempirical quantum chemical calculations.     

HMB体系分子内质子传递的量子化学计算研究

首次利用量子化学半经验AM1方法和从头算HF/6-31G方法对一种新型的苝醌类光? 艏?PQP)-菌生素(HMB)的结构及其分子内质子传递(IPT)进行了理论计算研究，并? 捎弥鸩皆黾硬嗔吹姆椒ㄉ杓屏艘幌盗心Ｐ突衔镆钥悸歉鞑嗔炊訦MBIPT的影响，? 峁推p醌(PQ)的IPT作了对比。同于HMB只有一个分子内氢键，此项研究对解释PQP的光敏活性有十分重要的意义。本研究主要结论：(1)基态时HMB的IPT势垒只有10.0180kJ/mol(反式)和37.9819kJ/mol(顺式)，分子中存在着快速的IPT。(2)侧链对HMB的IPT势垒影响较小，IPT主要受它的大共轭结构和共振模式的影响。(3)过渡态时质子的电荷增加，质子传递势垒与它的电荷变化成线性关系，此关系可推广到其它质子传递体系。(4)HMB的IPT势垒和IPT过程中羟基氧氢键以及氢键的键长变化均成较好的线性关系。(5)虽然只有一个IPT模式，HMB的IPT以及共振模式仍然和PQ十分相似，这是HMB保持光敏活性的基础。     

Freezing a single distal motion in dihydrofolate reductase

Constraining a single motion between distal residues separated by approximately 28 A in hybrid quantum/classical molecular dynamics simulations is found to increase the free energy barrier for hydride transfer in dihydrofolate reductase by approximately 3 kcal/mol. Our analysis indicates that a single distal constraint alters equilibrium motions throughout the enzyme on a wide range of time scales. This alteration of the conformational sampling of the entire system is sufficient to significantly increase the free energy barrier and decrease the rate of hydride transfer. Despite the changes in conformational sampling introduced by the constraint, the system assumes a similar transition state conformation with a donor-acceptor distance of approximately 2.72 A to enable the hydride transfer reaction. The modified thermal sampling leads to a substantial increase in the average donor-acceptor distance for the reactant state, however, thereby decreasing the probability of sampling the transition state conformations with the shorter distances required for hydride transfer. These simulations indicate that fast thermal fluctuations of the enzyme, substrate, and cofactor lead to conformational sampling of configurations that facilitate hydride transfer. The fast thermal motions are in equilibrium as the reaction progresses along the collective reaction coordinate, and the overall average equilibrium conformational changes occur on the slower time scale measured experimentally. Recent single molecule experiments suggest that at least some of these thermally averaged equilibrium conformational changes occur on the millisecond time scale of the hydride transfer reaction. Thus, introducing a constraint that modifies the conformational sampling of an enzyme could significantly impact its catalytic activity.     

Can hydridic-to-protonic hydrogen bonds catalyze hydride transfers in biological systems?

Catalysis of hydride transfer by hydridic-to-protonic hydrogen (HHH) bonding in α-hydroxy carbonyl isomerization reactions was examined computationally in the lithium salts of 7-substituted endo-3-hydroxybicyclo[2.2.1]hept-5-en-2-ones. The barrier for intramolecular hydride transfer in the parent system was calculated to be 17.2 kcal/mol. Traditional proton donors, such as OH and NH(3)(+), stabilized the metal cation-bridged transition state by 1.4 and 3.3 kcal/mol, respectively. Moreover, among the conformers of the OH systems, the one in which the proton donor is able to interact with the migrating hydride (H(m)) has an activation barrier lower by 1.3 and 1.7 kcal/mol than the other possible OH conformers. By contrast, the presence of an electronegative group such as F, which disfavors the migration electronically by opposing development of hydridic charge, destabilizes the hydride migration by 1.5 kcal/mol relative to the epimeric exo system. In both ground and transition states the H(m)···H distance decreased with increasing acidity of the proton donor, reaching a minimum of 1.58 ? at the transition state for NH(3)(+). Both Mulliken and NPA charges show enhancement of negative character of the migrating hydride in the cases in which HHH bonding is possible.     

Kinetics of intramolecular charge transfer with N-phenylpyrrole in alkyl cyanides

For the electron acceptor/donor molecule N-phenylpyrrole (PP), the fast intramolecular charge transfer (ICT) reaction accompanied by dual fluorescence from a locally excited (LE) and an ICT state is investigated in alkyl cyanide solvents as a function of temperature. After a comparison of the X-ray crystal structure of PP with calculations from the literature, absorption and fluorescence spectra of PP in a series of solvents over a wide polarity range are discussed. ICT with PP strongly depends on solvent polarity and starts to appear in solvents more polar than diethyl ether. From an analysis of the ICT/LE fluorescence quantum yield ratio Phi'(ICT)/Phi(LE), approximate data for the change in enthalpy -DeltaH of the ICT reaction of PP are obtained, ranging from 9 kJ/mol in acetonitrile (MeCN) to 4 kJ/mol in n-butyl cyanide (BuCN). From ICT and LE fluorescence decays of PP measured as a function of temperature, the forward (Ea = 9 kJ/mol in ethyl cyanide (EtCN) and 6 kJ/mol in MeCN) and backward (Ed = 16 kJ/mol in EtCN and MeCN) ICT reaction barriers are determined. From these data, -Delta H (7 kJ/mol (EtCN); 10 kJ/mol (MeCN)) is calculated, in good agreement with the results coming from Phi'(ICT)/Phi(LE). The data for Ea show that the forward ICT barrier becomes smaller with increasing solvent polarity, whereas the absence of change for Ed comes from the compensating increase of -DeltaH. Both observations are indicative of a late transition state for the LE --> ICT reaction. For PP in EtCN and MeCN, the ICT radiative rate constant k'(f)(ICT) increases with temperature. This is caused by the ICT low transition dipole moment and hence does not contain information on the molecular structure (twisted or planar) of the ICT state. The fast ICT observed with PP supports our previous conclusion, based on a comparison of PP with its planarized derivative fluorazene, that the pyrrole and phenyl moieties in the ICT state of PP are coplanar and possess substantial electronic coupling.     

Development of predictive models of π-facial selectivity; a critical study of nucleophilic addition to sterically unbiased ketones

Quantum chemical calculations at B3LYP/6-31G* and semiempirical levels have been performed on a series of sterically unbiased ketones, where facial differentiation during nucleophilic additions is electronically induced through distal functional groups. The face selectivity data for fifty-four substrates representing nine different skeleta were computed and compared with the available experimental data on thirty-eight of them. The predictive abilities of various computational methods such as, charge model, hydride model, LiH transition state model, Cieplak hyperconjugation effect estimated by NBO analysis and the cation complexation model have been evaluated. A comparison of the computed and experimental face-selectivity data indicates that the hydride model and the LiH transition state model at the semiempirical levels are the best choices to predict diastereoselectivity. Unexpectedly, the performance of charge, hydride and LiH transition state models are inferior at the B3LYP level compared to the semiempirical methods in predicting the facial selectivities. On the other hand, the Cieplak type hyperconjugation evaluated using the NBO analysis, and cation complexation model are less reliable despite the fact that these two involve higher (B3LYP/6-31G*) level calculations. The inadequate performance of the charge model, NBO and the cation complexation models were traced to their emphasis on only one or two factors which are responsible for stereodifferentiation and undermining of the other subtle aspects involving a combination of orbital and electrostatic effects. On the other hand, the hydride and LiH transition state models, at semiempirical levels, provide reliable results to model the face-selectivities.     

On Transition Structures for Hydride Transfer Step in Enzyme Catalysis. A Comparative Study on Models of Glutathione Reductase Derived from Semiempirical, HF, and DFT Methods

As a model of the chemical reactions that take place in the active site of gluthatione reductase, the nature of the molecular mechanism for the hydride transfer step has been characterized by means of accurate quantum chemical characterizations of transition structures. The calculations have been carried out with analytical gradients at AM1 and PM3 semiempirical procedures, ab initio at HF level with 3-21G, 4-31G, 6-31G, and 6-31G basis sets and BP86 and BLYP as density functional methods. The results of this study suggest that the endo relative orientation on the substrate imposed by the active site is optimal in polarizing the C4-Ht bond and situating the system in the neighborhood of the quadratic region of the transition structure associated to the hydride transfer step on potential energy surface. The endo arrangement of the transition structure results in optimal frontier HOMO orbital interaction between NADH and FAD partners. The geometries of the transition structures and the corresponding transition vectors, that contain the fundamental information relating reactive fluctuation patterns, are model independent and weakly dependent on the level of theory used to determine them. A comparison between simple and complex molecular models shows that there is a minimal set of coordinates describing the essentials of hydride transfer step. The analysis of transition vector components suggests that the primary and secondary kinetic isotope effects can be strongly coupled, and this prompted the calculation of deuterium and tritium primary, secondary, and primary and secondary kinetic isotope effects. The results obtained agree well with experimental data and demonstrate this coupling.     

锰配合物催化CO2加氢生成甲酸的理论研究

采用密度泛函理论(DFT)对锰配合物催化二氧化碳加氢生成甲酸的反应进行了理论研究. 整个催化循环主要包括氢气活化和二氧化碳氢化2个阶段. 计算结果表明, 甲酸的参与明显降低了氢气活化的反应能垒; 二氧化碳的氢化过程遵循外层机理并且氢转移是分步进行的, 决速步骤为氢负离子的转移过程, 自由能垒为21.0 kJ/mol. 对配合物中硫原子上的取代基R进行了调变, 研究结果表明, 当R为吸电子基团时能降低氢气裂解和二氧化碳氢化过程中质子转移的能垒, 而当R为推电子基团时有利于氢负离子的转移,当R=CF₃时整个反应的能量跨度(80.4 kJ/mol)最小.     

Role of the direct reaction H2S + SO2 in the homogeneous Claus reaction

Quantum chemical methods at the Gaussian-2 and -3 levels of theory have been used to investigate the reactions between H(2)S, SO(2), and S(2)O such as might occur in the front-end furnace of the Claus process. The direct reaction between H(2)S and SO(2) occurs via a 5-centered transition state with an initial barrier of approximately 135 kJ mol(-1) and an overall barrier of approximately 153 kJ mol(-1) to produce S(2)O and H(2)O. We indicate approximate values here because there are a number of isomers in the reaction pathway that have barriers slightly different from those quoted. The presence of a water molecule lowers this by approximately 60 kJ mol(-1), but the van der Waals complex required for catalysis by water is thermodynamically unfavorable under the conditions in the Claus reactor. The direct reaction between H(2)S and S(2)O can occur via two possible pathways; the analogous reaction to H(2)S + SO(2) has an initial barrier of approximately 117 kJ mol(-1) and an overall barrier of approximately 126 kJ mol(-1) producing S(3) and H(2)O, and a pathway with a 6-centred transition state has a barrier of approximately 111 kJ mol(-1), producing HSSSOH. Rate constants, including a QRRK analysis of intermediate stabilization, are reported for the kinetic scheme proposed here.     

(H_2O)_n(n=0～2)催化HS和HOCl反应机理的理论研究

在CCSD(T)/6-311+G(3df,2p)//M06-2X/6-311+G(3df,2p)水平上研究了(H_2O)n(n=0~2)催化HS和HOCl的反应机理.结果表明,HS与HOCl反应中HS夺取HOCl上的H原子形成产物H_2S和ClO.在无水催化时,该反应存在2种不同的路径(分别经过过渡态TS1和TS2,二者互为顺反结构),对应的能垒分别为100.28和100.91kJ/mol,到达产物(H_2S+ClO)需吸收18.99kJ/mol能量,反应不易发生;在单个水分子参与时,水分子可通过形成弱相互作用或者作为H原子转移桥梁影响反应机理,获得了4种水催化路径,能垒(间于53.97~92.39kJ/mol之间)均低于无水催化过程.同时发现,在反应到达产物前,水分子可以与产物形成中间体IM,IM相对能仅为0.46kJ/mol,有利于产物形成;有2个水分子参与反应时,找到了3条催化路径,最优反应路径过渡态TS7的能垒为45.05kJ/mol,低于无水催化过程,相比单个水分子最优路径能垒(53.97kJ/mol)并无显著降低.     

Theoretical study of intramolecular proton transfer of perylenequinone

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Am1 and pm3 transition structure for the hydride transfer. A model of reaction catalyzed by dihydrofolate reductase

The transition state structure for the hydride transfer in dihydrofolate reductase, DHFR, enzyme has been calculated with analytical gradients at semiempirical levels: AM1 and PM3. The geometry, electronic structure and transition vector components are qualitatively semiempirical level independent. Comparing the transition structures for the hydride transfer step in models of liver alcohol dehydrogenase, formate dehydrogenase, lactate dehydrogenase, and glutathione reductase, the geometries of these stationary points are transferable and invariant. The topology of the transition structures in these enzymes resembles the one calculated in this paper.     

OH-initiated oxidation of toluene. 3. Low-energy routes to cresol and oxoheptadienal

The toluene-OH-O2 system implicated in the atmospheric degradation of toluene is studied further using quantum chemistry methods. Two new reaction mechanisms are explored as alternatives to the previously proposed mechanism. While the previous mechanism involves surmounting a 170 kJ/mol barrier, the new equivalent cresol formation route has a barrier above the asymptotic state calculated to be 12 kJ/mol at the B3LYP/6-311G(2df,2pd) level. The new oxoheptadienal formation route occurs via two successive reactions with OH, with the highest barrier lying 200 kJ/mol below the energy of the reactants. Neither of the newly proposed reaction mechanisms involves forming a toluene oxide intermediate.     

A quantum mechanical/molecular mechanical study on the catalysis of the pyridoxal 5'-phosphate-dependent enzyme L-serine dehydratase

The catalytic mechanism of a pyridoxal 5'-phosphate-dependent enzyme, l-serine dehydratase, has been investigated using ab initio quantum mechanical/molecular mechanical (QM/MM) methods. New insights into the chemical steps have been obtained, including the chemical role of the substrate carboxyl group in the Schiff base formation step and a proton-relaying mechanism involving the phosphate of the cofactor in the beta-hydroxyl-leaving step. The latter step is of no barrier and follows sequentially after the elimination of the alpha-proton, leading to a single but sequential alpha, beta-elimination step. The rate-limiting transition state is specifically stabilized by the enzyme environment. At this transition state, charges are localized on the substrate carboxyl group, as well as on the amino group of Lys41. Specific interactions of the enzyme environment with these groups are able to lower the activation barrier significantly. One major difficulty associated with studies of complicated enzymatic reactions using ab initio QM/MM models is the appropriate choices of reaction coordinates. In this study, we have made use of efficient semiempirical models and pathway optimization techniques to overcome this difficulty.     

含酮基团对煤焦异相还原NO的影响

基于量子化学密度泛函理论和过渡态理论研究了含酮基团对煤焦异相还原NO的影响及其产物发生氧脱附的微观反应机理。计算结果表明，NO更易于吸附在含酮基团煤焦表面。椅形含酮基团强化了煤焦异相还原NO；锯齿形含酮煤焦表面与NO异相反应决速步能垒值（495.45 kJ/mol）大于锯齿形纯碳基煤焦表面与NO决速步能垒值（331.32 kJ/mol），基于锯齿形含酮煤焦模型中的氧浓度不在利于NO还原的范围内而不易于NO的还原。中间产物P1在无CO存在情况下，较纯碳基煤焦表面更易于发生氧脱附而产生表面缺陷；在CO存在条件下，含酮煤焦表面为氧脱附过程提供自由活性位点，降低了过程能垒消耗。     

Rate-equilibrium relationships in hydride transfer reactions: the role of intrinsic barriers

A literature survey on the kinetics of hydride abstractions from CH-groups by carbocations reveals a general phenomenon: Variation of the hydride acceptor affects the rates of hydride transfer to a considerably greater extent than an equal change of the thermodynamic driving force caused by variation of the hydride donor. The origin of this relationship was investigated by quantum chemical calculations on various levels of ab initio and DFT theory for the transfer of an allylic hydrogen from 1-mono- and 1,1-disubstituted propenes (XYC=CH-CH(3)) to the 3-position of 1-mono- and 1,1-disubstituted allyl cations (XYC=CH-CH(2)(+)). The discussion is based on the results of the MP2/6-31+G(d,p)//RHF/6-31+G(d,p) calculations. Electron-releasing substituents X and Y in the hydride donors increase the exothermicity of the reaction, while electron-releasing substituents in the hydride acceptors decrease exothermicity. In line with Hammond's postulate, increasing exothermicity shifts the transition states on the reaction coordinate toward reactants, as revealed by the geometry parameters and the charge distribution in the activated complexes. Independent of the location of the transition state on the reaction coordinate, a value of 0.72 is found for Hammond-Leffler's alpha = deltaDeltaG/deltaDelta(r)G degrees when the hydride acceptor is varied, while alpha = 0.28 when the hydride donor is varied. The value of alpha thus cannot be related with the position of the transition state. Investigation of the degenerate reactions XYC=CH-CH(3) + XYC=CH-CH(2)(+) indicates that the migrating hydrogen carries a partial positive charge in the transition state and that the intrinsic barriers increase with increasing electron-releasing abilities of X and Y. Substituent variation in the donor thus influences reaction enthalpy and intrinsic barriers in the opposite sense, while substituent variation in the acceptor affects both terms in the same sense, in accord with the experimental findings. Marcus theory is employed to treat these effects quantitatively.     

Theoretical study of mechanism of cycloaddition reaction between dichloro‐germylene carbene (Cl2GeC:) and aldehyde

The mechanism of the cycloaddition reaction between singlet dichloro‐germylene carbene and aldehyde has been investigated with MP2/6‐31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by zero‐point energy and CCSD (T)//MP2/6‐31G* method. From the potential energy profile, it can be predicted that the reaction has two competitive dominant reaction pathways. The channel (A) consists of four steps: (1) the two reactants (R1, R2) first form an intermediate INT2 through a barrier‐free exothermic reaction of 142.4 kJ/mol; (2) INT2 then isomerizes to a four‐membered ring compound P2 via a transition state TS2 with energy barrier of 8.4 kJ/mol; (3) P2 further reacts with aldehyde (R2) to form an intermediate INT3, which is also a barrier‐free exothermic reaction of 9.2 kJ/mol; (4) INT3 isomerizes to a germanic bis‐heterocyclic product P3 via a transition state TS3 with energy barrier of 4.5 kJ/mol. The process of channel (B) is as follows: (1) the two reactants (R1, R2) first form an intermediate INT4 through a barrier‐free exothermic reaction of 251.5 kJ/mol; (2) INT4 further reacts with aldehyde (R2) to form an intermediate INT5, which is also a barrier‐free exothermic reaction of 173.5 kJ/mol; (3) INT5 then isomerizes to a germanic bis‐heterocyclic product P5 via a transition state TS5 with an energy barrier of 69.4 kJ/mol. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A theoretical approach to the complexation and decomplexation processes in the reaction C60 + He ⇌ (He@C60)

To theoretically investigate the complexation and decomplexation processes in the reaction C₆₀ + He ? (He@C₆₀), four possible reaction paths are assumed, so that while He approaches and penetrates the C₆₀ cage (a) a pentagon, (b) a hexagon, (c) a short bond, or (d) a long bond will be expanded on its original sphere or plane to form a window. The computation is performed by the quantum chemical method EHMO/ASED. The results show that the probability of completing this reaction in terms of the tunnel effect can be neglected and the reaction is completed by overcoming a potential barrier of the reaction. It is easily completed by opening a planar window than by opening a shperical window. The probability through reaction path (b) with a barrier of 1247.94 kJ/mol is larger than that through reaction path (a) with a barrier of 1438.26 kJ/mol. The probability through reaction path (d) is the largest with a barrier of 1076.78 kJ/mol, when the planar expansion forming a window of a 9-membered ring is at the optimized value of 0.40 å. When He deviates the center and approaches the C₆₀ cage, there will be a charge distribution on C₆₀ with changing in size and even in sign along the longitude corresponding to the symmetry axis, but the absolute value gradually decreases. This situation is similar to the charge transfer on carbons in sraight-chain polyene. © 1995 John Wiley & Sons, Inc.