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1.
J. Andras V. Moliner J. Krechl E. Silla 《International journal of quantum chemistry》1993,45(5):433-444
The carbon dioxide (CO2) to methylamine (CH3NH2) addition reaction is investigated using an ab initio MO method with the aim of obtaining an insight into the relation between transition-state structure and reactivity. The complete potential energy hypersurface was explored and the stationary points representing reactants, transition state, and product were localized. To establish the relevance of different basis sets, calculations were carried out at different levels of theory: STO -3G , 3-21G , 4-21G , 4-31G , 6-31G , 6-311G , 6-31G *, and MP 2/6-31G *//HF /6-31G *. A reaction analysis done by correlation of bond-order indices using the More O'Ferrall-Jencks diagram reveals the reaction mechanism as an asynchronous process. The transition state can be described as a four-membered ring. The lone nitrogen electron pair of the amine appears as the driving force of the reaction, where a positive hydrogen rather than a radical is more likely to be transferred. © 1993 John Wiley & Sons, Inc. 相似文献
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Arturo Arnau Estanislao Silla Iaki Tun 《International journal of quantum chemistry》1993,46(2):231-238
By means of ab initio calculations, the rotational constants and dipole moments of HnC3N (n = 1, 3, 5, 7, and 9) species have been calculated at the HF / 6-31G * level of theory. Selected cases have been also calculated at the MP 2/6-31G * level and the influence of calculation level on rotational constant values is briefly discussed. Some of these species were discovered in the interstellar medium, while others have still not been detected there, although their existence is very probable. The results given here could help in their detection. © 1993 John Wiley & Sons, Inc. 相似文献
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Martí S Andrés J Moliner V Silla E Tuñón I Bertrán J 《Chemistry (Weinheim an der Bergstrasse, Germany)》2003,9(4):984-991
In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that presenting a structure similar to the transition state of the reaction to be catalyzed--with shorter distances between the carbon atoms to be bonded and more diaxial character. With respect to the reorganization effect, an energy decomposition analysis of the potential energies of the reactive reactant and of the reaction transition state in aqueous solution and in the enzyme shows that the enzyme structure is better adapted to the transition structure. This means not only a more negative electrostatic interaction energy with the transition state but also a low enzyme deformation contribution to the energy barrier. Our calculations reveal that the structure of the enzyme is responsible for stabilizing the transition state structure of the reaction, with concomitant selection of the reactive form of the reactants. This is, the same enzymatic pattern that stabilizes the transition structure also promotes those reactant structures closer to the transition structure (i.e., the reactive reactants). In fact, both reorganization and preorganization effects have to be considered as the two faces of the same coin, having a common origin in the effect of the enzyme structure on the energy surface of the substrate. 相似文献
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The Lagrangian smoothed particle hydrodynamics (SPH) method is used to simulate shock waves in inviscid, supersonic (compressible) flow. It is shown for the first time that the fully Lagrangian SPH particle method, without auxiliary grid, can be used to simulate shock waves in compressible flow. The wall boundary condition is treated with ghost particles combined with a suitable repulsive potential function, whilst corners are treated by a novel ‘angle sweep’ technique. The method gives accurate predictions of the flow field and of the shock angle as compared with the analytical solution. The study shows that SPH is a good potential candidate to solve complex aerodynamic problems, including those involving rarefied flows, such as atmospheric re‐entry. Copyright © 2016 John Wiley & Sons, Ltd. 相似文献
6.
Silla JM Cormanich RA Duarte CJ Freitas MP Ramalho TC Barbosa TM Santos FP Tormena CF Rittner R 《The journal of physical chemistry. A》2011,115(35):10122-10127
Suitable (3)J(H,H) coupling constants and theoretical calculations were used to define the conformational preferences of trans-2-bromoalkoxycyclohexanes (alkoxy = OMe, OEt, O(i)Pr, and O(t)Bu) for the isolated molecule and as a function of the medium. The diaxial conformer was preponderant, or at least similarly populated to the diequatorial form, for the tert-butoxy derivative only, while the diequatorial conformer was prevalent for the remaining alkoxy derivatives (except for the OMe derivative in CCl(4) solution). The conformational behavior of these compounds was analyzed on the basis of classical steric effects and attractive electron delocalizations, by means of natural bond orbital analysis. 相似文献
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Josué M. Silla Laize A.F. Andrade Matheus P. Freitas 《Magnetic resonance in chemistry : MRC》2019,57(7):373-379
The Perlin effect and its analog for fluorinated compounds (the fluorine Perlin-like effect) manifest on one-bond C─H (C─F for the fluorine Perlin-like effect) spin–spin coupling constants (SSCCs) in six-membered rings. These effects can be useful to probe the stereochemistry (axial or equatorial) of the C─H and C─F bonds, respectively. The origin of these effects has been debatable in the literature as being due to hyperconjugative interactions, dipolar effects, and induced current density. Accordingly, a variety of model compounds has been used to probe such effects since the cyclohexanone carbonyl group and the endocyclic heteroatom lone pairs play different roles on the above-mentioned effects. Thus, the 1JC─F SSCC in fluorinated lactams and lactones were theoretically studied to gain further insight on the nature of the fluorine Perlin-like effect. In addition, because the intramolecular α-effect has recently gained attention for its importance in the reactivity and stereoelectronic interactions in peroxide compounds, some fluorinated 1,2-dioxanes and 1,2-dithianes were studied to evaluate the role of the α-effect on the behavior of 1JC─F SSCCs. Differently from fluorinated ketones and ethers, the fluorine Perlin-like effect in the amides and esters cannot be explained by hyperconjugative or dipolar interactions alone, because the resonance in these groups affect the 1JC─F values. The O─O and S─S-containing systems exhibit a strong fluorine Perlin-like effect, but unlike the α-effect, this behavior cannot be explained neither by hyperconjugation nor by dipolar interactions alone; the spatial proximity of the C─F and O─O/S─S bonds is proposed to affect the magnitude of the 1JC─F SSCC. 相似文献
9.
Martí S Andrés J Moliner V Silla E Tuñón I Bertrán J 《Chemistry (Weinheim an der Bergstrasse, Germany)》2008,14(2):596-602
The Diels-Alder reaction is one of the most important and versatile transformations available to organic chemists for the construction of complex natural products, therapeutics agents, and synthetic materials. Given the lack of efficient enzymes capable of catalyzing this kind of reaction, it is of interest to ask whether a biological catalyst could be designed from an antibody-combining site. In the present work, a theoretical study of the different behavior of a germline catalytic antibody (CA) and its matured form, 39 A-11, that catalyze a Diels-Alder reaction has been carried out. A free-energy perturbation technique based on a hybrid quantum-mechanics/molecular-mechanics scheme, together with internal energy minimizations, has allowed free-energy profiles to be obtained for both CAs. The profiles show a smaller barrier for the matured form, which is in agreement with the experimental observation. Free-energy profiles were obtained with this methodology, thereby avoiding the much more demanding two-dimensional calculations of the energy surfaces that are normally required to study this kind of reaction. Structural analysis and energy evaluations of substrate-protein interactions have been performed from averaged structures, which allows understanding of how the single mutations carried out during the maturation process can be responsible for the observed fourfold enhancement of the catalytic rate constant. The conclusion is that the mutation effect in this studied germline CA produces a complex indirect effect through coupled movements of the backbone of the protein and the substrate. 相似文献
10.
Martí S Andrés J Moliner V Silla E Tuñón I Bertrán J 《The journal of physical chemistry. A》2006,110(2):726-730
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. 相似文献