A theoretical study of the effect of basis sets on stationary structures for the addition of carbon dioxide to methylamine: A relation among geometries,energy status,and electronic structures

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.     

Ab initio rotational constants of interstellar species: Cyanoacetylene hydrogenated derivatives

By means of ab initio calculations, the rotational constants and dipole moments of H_nC₃N (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.     

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

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.     

SPH simulation of oblique shocks in compressible flows

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.     

Alkyl group effect on the conformational isomerism of trans-2-bromoalkoxycyclohexanes analyzed by nmr spectroscopy and theoretical calculations

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.     

Influence of stereoelectronic effects on the 1JC─F spin–spin coupling constant in fluorinated heterocyclic compounds

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 ¹J_C─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 ¹J_C─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 ¹J_C─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 ¹J_C─F SSCC.     

Theoretical study of catalytic efficiency of a Diels-Alderase catalytic antibody: an indirect effect produced during the maturation process

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.