Stereoselectivity behavior of the AZ28 antibody catalyzed oxy-Cope rearrangement

Catalytic antibodies are very interesting not only because of the rate enhancement of the reactions that they catalyze but also because of the selectivities they can achieve that are sometimes not present in natural enzyme processes. We have selected the study of the stereoselectivity of the matured AZ28 that catalyzes an oxy-Cope rearrangement. For this particular case, the presence of a chiral center in the substrate provokes the existence of two different enantiomers, R and S. Furthermore, it is also possible to locate two different orientations for the hydroxyl group in the central ring of the substrate in the transition state, equatorial and axial, rendering two different conformers. In this paper we present the free energy profiles obtained for different substrate isomers in the cavity created by the matured catalytic antibody. Our simulations have reproduced the stereoselectivity of the matured AZ28, differentiating between the axial or equatorial orientations and preferentially stabilizing the S forms, at a qualitative level. Finally, the inclusion of the substrate-CA interactions in a flexible molecular model has allowed us to observe the different pattern of interactions that are related to different interaction energies, which seem to be crucial in the stereoselectivity behavior of the catalytic antibody.     

单重态Cl2N＝B：重排反应的从头算研究

采用量子化学中的从头算方法,在HF／6－311G^**水平上研究了单重态Cl2N＝B：重排反应的机理。结果发现,该重排反应经过一个面外三元环过渡态,根据计算结果,详细研究了该反应的热力学及动力学函数。     

Antibody-catalyzed oxy-cope rearrangement: mechanism and origins of catalysis and stereoselectivity from DFT quantum mechanics and flexible docking

Density functional theory using B3LYP and flexible ligand docking methods were used to investigate the complete potential surface for the uncatalyzed and the AZ28 antibody-catalyzed oxy-Cope reaction of 2,5-diaryl-1,5-hexadien-3-ol derivatives. The reaction mechanism is stepwise, involving a cyclohexane diyl intermediate. Theoretical deuterium isotope effects match well with those from experiment. Gas-phase transition structures show mixed preferences for the axial vs equatorial hydroxyl group, while solvation favors the axial isomer. Specific phenyl group conformations are shown to be critical to transition-state stabilization (by up to 15 kcal/mol), and the effective conformation is not that found in the hapten used to generate the germline and affinity-matured AZ28 catalytic antibodies. Docking studies support greater transition-state binding than reactant binding. Docking studies also predict the S stereoselectivity of mature AZ28 and suggest that binding modes quite different from those of the hapten might play a role in catalysis, with specific focus on ligand hydrogen bonding to Asp(H101).     

The neutral and ionic vinylidene—acetylene rearrangement

Transition state structures for the neutral, cationic and anionic vinylidene—acetylene rearrangement are calculated by ab initio methods. While the barriers for the neutral and cationic H-shift are found to be low or even zero involving a planar structure, rearrangement of the vinylidene anion proceeds with high activation energy possibly via a perpendicular transition state.     

单重态H_2N=B:→HNBH重排反应的理论研究

用量子化学中的从头算方法, 在MP2/6-311++G(d,p)水平上研究了单重态H_2N=B→HNBH重排反应的机理。结果表明, 该重排反应经过一个三元环过渡态。根据计算结果，初步讨论了该反应的热力学及动力学函数。     

A theoretical study of neighboring-group participation in thione-to-thiol rearrangement of xanthates. molecular orbital calculation using a conductor-like screening model (COSMO) approach.

The transition structures of the thione-to-thiol rearrangement of O-(2-dimethylaminoethyl and 2-methylthio-) S-methyl xanthates in several solvents were located by semiempirical molecular orbital method (PM3) using the conductor-like screening model (COSMO) approach. Each transition state transforms into the ion-pair intermediate with a three-membered ring structure (aziridinium or thiiranium), indicating that the rearrangement proceeds through an ionic intermediate with the anchimeric assistance of the neighboring group. The intermediary structures in gas phase are also analyzed by ab initio and density functional theory calculations.     

On the calculation of transition states

An algorithm has been developed to calculate transition state geometries directly in the framework of ab initio single-determinant molecular orbital theory. As an example, the procedure is applied to the rearrangement of ethenylidene to acetylene.     

Targeted Car-Parrinello molecular dynamics: elucidating double proton transfer in formic acid dimer

The targeted molecular dynamics method, making possible the study of rare events, has been assessed in the framework of Car-Parrinello ab initio molecular dynamics. As a test case, we have studied the staggered-eclipsed rotation of ethane. The technique has subsequently been applied to investigate the nature of double proton transfer in formic acid dimer. The latter is found to follow a concerted transfer mechanism involving an essentially planar transition state. A "funnel-like region" of the potential energy surface is identified, where floppy intermolecular modes stiffen upon approaching the transition state.     

Influence of the cluster dimensionality on the binding behavior of CO and O2 on Au13

We present an ab initio density functional theory study of the binding behavior of CO and O(2) molecules to two- and three-dimensional isomers of Au(13) in order to investigate the potential catalytic activity of this cluster towards low-temperature CO oxidation. First, we scanned the potential energy surface of Au(13) and studied the effect of spin-orbit coupling on the relative stabilities of the 21 isomers we identified. While spin-orbit coupling increases the stability of the three-dimensional more than the two-dimensional isomers, the ground state structure at 0 K remains planar. Second, we systematically studied the binding of CO and O(2) molecules onto the planar and three-dimensional structures lowest in energy. We find that the isomer dimensionality has little effect on the binding of CO to Au(13). O(2), on the other hand, binds significantly to the three-dimensional isomer only. The simultaneous binding of multiple CO molecules decreases the binding energy per molecule. Still, the CO binding remains stronger than the O(2) binding. We did not find a synergetic effect due to the co-adsorption of both molecular species. On the three-dimensional isomer, we find O(2) dissociation to be exothermic with an dissociation barrier of 1.44 eV.     

3-羟基丙烯醛单键旋转异构光反应机理的从头算研究

应用从头算分子轨道法分别在RHF/6-31G**和UHF/6-31G**水平上对3腔┤┓肿拥幕?S0)和三重激发态(T1)单键旋转异构反应机理进行了研究,优化出反应物和产物在S0态和T1态的4种平衡态和过渡态的几何构型,通过振动分析得到的虚频和计算的内禀反应坐标对过渡态进行了确认,并得到了零点能,根据基态和激发态反应途径分析了光反应机理。计算结果表明,基态和激发态的3腔┤┓肿拥ゼ旃狗从ξ焕萁系停嘏湃菀追⑸永砺凵涎橹ち斯夥从κ笛橹屑钢忠旃固宓拇嬖凇?     

Exploring potential energy surfaces for chemical reactions: an overview of some practical methods

Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described.     

Ab initio Study on Enantioselective Reduction of Ketones Catalyzed by Thiazolidino[3,4-c]oxazaborolidines

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Calculating geochemical reaction pathways--exploration of the inner-sphere water exchange mechanism in Al(H2O)6(3+)(aq) + nH2O with ab Initio calculations and molecular dynamics

We have simulated exchange of inner-sphere and bulk water molecules for different sizes of Al3+(aq) clusters, Al(H2O)63+ + nH2O for n = 0, 1, 6, or 12, with ab initio and molecular dynamics simulations, in order to understand how robust the ab initio method is for identifying hydrolytic reaction pathways of particular importance to geochemistry. In contrast to many interfacial reactions, this particular elementary reaction is particularly simple and well-constrained by experiment. Nevertheless, we find that a rich array of parallel reaction pathways depend sensitively on the details of the solvation sphere and structure and that larger clusters are not necessarily better. Inner-sphere water exchange in Al3+(aq) may occur through two Langford-Gray dissociative pathways, one in which the incoming and outgoing waters are cis, the other in which they are trans to one another. A large majority of exchanges in the molecular dynamics simulations occurred via the trans mechanism, in contrast to the predictions of the ab initio method. In Al(H2O)63+ + H2O, the cis mechanism has a transition state of 84.3 kJ/mol, which is in good agreement with previous experimental and ab initio results, while the trans mechanism has only a saddle point with two negative frequencies, not a transition state, at 89.7 kJ/mol. In addition to the exchange mechanisms, dissociation pathways could be identified that were considerably lower in energy than experiment and varied considerably between 60 and 100 kJ/mol, depending on the particular geometry and cluster size, with no clear relation between the two. Ab initio calculations using large clusters with full second coordination spheres (n = 12) were unable to find dissociation or exchange transition states because the network of hydrogen bonds in the second coordination sphere was too rigid to accommodate the outgoing inner-sphere water. Our results indicate that caution should surround ab initio simulation of complicated dynamic processes such as hydrolysis, ion exchange, and interfacial reactions that involve several steps. Dynamic methods of simulation need to accompany static methods such as ab initio calculation, and it is best to consider simulated pathways as hypotheses to be tested experimentally rather than definitive properties of the reaction.     

Enantioselective ester hydrolysis catalyzed by imprinted polymers

Highly cross-linked network polymers prepared by molecular imprinting catalyzed enantioselectively the hydrolysis of N-tert-butoxycarbonyl phenylalanine-p-nitrophenyl ester (BOCPheONP). The templates were designed to allow incorporation of the key catalytic elements, found in the proteolytic enzyme chymotrypsin, into the polymer active sites. Three model systems were evaluated. These were constructed from a chiral phosphonate analogue of phenylalanine (series A, C) or L-phenylalanine (series B) attached by a labile ester linkage to an imidazole-containing vinyl monomer. Free radical copolymerization of the template with methacrylic acid (MAA) and ethylene glycol dimethacrylate (EDMA) gave a highly cross-linked network polymer. The templates could be liberated from the polymers by hydrolysis, giving catalytically active sites envisaged to contain an enantioselective binding site, a site complementary to a transition state like structure (series A, C), and a hydroxyl, imidazole, and carboxylic acid group at hydrogen bond distance. As predicted, the enantiomer of BOCPheONP complementary to the configuration of the template was preferentially hydrolyzed with D-selectivity for the series A polymers (kD/kL = 1.9) and L-selectivity for the series B polymers (kL/kD = 1.2). The maximum rate enhancement, when compared with a control polymer, prepared using a benzoyl-substituted imidazole monomer as template, was 2.5, and comparing with the imidazole monomer in solution, a maximum rate enhancement of 10 was observed. The catalytic activity was higher for polymers subjected to the nucleophilic treatment. This was explained by a higher site density and flexibility of the polymer matrix caused by this treatment. In a comparison of template rebinding to polymers imprinted with a template containing either a carboxylate (planar ground state structure) or a phosphonate (tetrahedral transition state like structure) functionality, it was observed that imprinted polymers are able to discriminate between a transition state like and a ground state structure for transesterification. However the influence of transition state stabilization on the observed rate enhancements remains obscure. Only at acidic pH's was catalysis observed, whereas at basic pH's the polymers inhibit the reaction. At a later stage, the catalytic activity of the polymers for nonactivated D- and L-phenylalanine ethyl esters was investigated. A rate enhancement of up to 3 was observed when compared to the blank. Most important, however, the polymers imprinted with a D template preferentially hydrolyzed the D-ethyl ester and exhibited saturation kinetics.     

Mechanism of the aminolysis of methyl benzoate: a computational study

Density functional and ab initio methods were applied in examining the possible mechanistic pathways for the reaction of methyl benzoate with ammonia. Transition state structures and energies were determined for concerted and neutral stepwise mechanisms. The theoretical results show that the two possible pathways have similar activation energies. The general base catalysis of the process was also examined. The predictions reveal that the catalytic process results in considerable energy savings and the most favorable pathway of the reaction is through a general-base-catalyzed neutral stepwise mechanism. The structure and transition vectors of the transition states indicate that the catalytic role of ammonia is realized by facilitating the proton-transfer processes. Comparison of the energetics of the aminolysis for methyl benzoate and methyl formate shows the more favorable process to be that for the aliphatic ester. The differing reactivity of the two esters is explained in terms of the electrostatic potential values at the atoms of the ester functionality.     

Binding site optimisation for artificial enzymes by diffusion NMR of small molecules

A binding site optimisation protocol for the design of artificial enzymes based on "small molecule-small molecule" binding studies by diffusion NMR is presented. Since the reaction chosen was the hydrolysis of ester 1 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phenethyl ester), an analogous phosphonate ester 2 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phosphonic phenethyl ester) was selected as a suitable transition state analogue (TSA). The key objective of the NMR studies was to find a unit with functional groups capable of binding to the acidic sites of the TSA. Nine dipeptides, mainly with basic and hydroxyl groups, were used and their affinity to the TSA was studied by measuring the change in the diffusion coefficient, D(pep), upon binding by pulse field gradient NMR. The value of D(pep) at 298 K in D(2)O at pD 5, 7 and 10 was measured both in free solution, and mixtures containing one dipeptide and the TSA. As both components are low molecular weight species with M < 500, a TSA-to-dipeptide ratio of 10:1 was used to detect significant changes in D(pep). The results revealed that dipeptides with basic residues show higher affinity to the TSA than those with hydroxyl or aliphatic side chains in aqueous solutions. The dipeptide showing the most significant relative change in D(pep) was H-Arg-Arg-OH, and the binding constant was estimated to be 86 L M(-1) by measuring D(pep) at varying concentrations of the TSA. In addition, binding of the TSA to a new water-soluble polymer with a polyallylamine backbone and randomly distributed Arg-Arg binding sites was examined, and the binding constant was estimated to be > or =1500 L M(-1). As confirmed by further catalytic activity tests, polymers containing Arg-Arg as a binding site are capable of significant rate accelerations in the hydrolysis of ester 1.     

羟氨(H2NOH)重排反应的理论研究

羟氨H_2NOH是人们所熟知的分子,但至今还没有确切的实验证据证实有氨氧化物H_2NO的存在,尽管其取代物R_3NO已被分离出。鉴于类羟氨R_2NOH和N-氧化物在生物学上的重要意义,研究H_2NOH和H_3NO的结构以及二者重排反应的动力学行为就成了一个重要课题。本文用内禀反应坐标方法对此反应进行了反应路径解析,并给出了沿反应途径上的振动频率相关。     

Predissociation via conformational change: photodissociation of N,N-dimethylnitrosamine in the S(1) state

We investigated the photodissociation mechanism of N,N-dimethylnitrosamine (CH(3))(2)NNO (DMN) by ab intio quantum chemical methods. Inspired by an earlier study we calculated two-dimensional potential energy surfaces of the S(1) state of DMN in its planar and pyramidal conformations. While the planar molecular geometry appears to possess no direct dissociation channel, the pyramidal configuration is dissociative yielding the products NO + (CH(3))(2)N. Using wave packet dynamics on the planar S(1) potential energy surface the experimental absorption spectrum was well reproduced which gives indirect but strong support for the nondissociative nature of this surface. The transition from the planar to the pyramidal conformation of DMN was then investigated by an ab initio molecular dynamics method which revealed the time evolution of the geometrical parameters of the molecule up to the dissociation of the N-N bond. This occurs about 90 fs after photon excitation. The calculated minimum energy path along the N-N coordinate and the structural changes of the molecule along this coordinate provided a detailed picture of this indirect dissociation or, more specific, predissociation process via conformational change.     

Crucial role of protein flexibility in formation of a stable reaction transition state in an α-amylase catalysis

Conformational flexibility of proteins provides enzymes with high catalytic activity. Although the conformational flexibility is known to be pivotal for the ligand binding and release, its role in the chemical reaction process of the reactive substrate remains unclear. We determined a transition state of an enzymatic reaction in a psychrophilic α-amylase by a hybrid molecular simulation that allows one to identify the optimal chemical state in an extensive conformational ensemble of protein. The molecular simulation uncovered that formation of the reaction transition state accompanies a large and slow movement of a loop adjacent to the catalytic site. Free energy calculations revealed that, although catalytic electrostatic potentials on the reactive moiety are formed by local and fast reorganization around the catalytic site, reorganization of the large and slow movement of the loop significantly contributes to reduction of the free energy barrier by stabilizing the local reorganization.