Theoretical Study of Inversion and Topomerization Processes of Substituted Cyclohexanes: The Relevance of the Energy 3D Hypersurface

High-Pressure-Limit and Pressure-Dependent Rate Rules for Unimolecular Reactions Related to Hydroperoxy Alkyl Radicals in Normal-Alkyl Cyclohexane Combustion. 2. Cyclization Reaction Class

The hydroperoxy alkyl radicals are important intermediates in the low-temperature combustion for normal-alkyl cycloalkanes, and the cyclization reactions of hydroperoxy alkyl radicals to form cyclic ethers are responsible for a major fraction of the OH formation, which has the potential to promote ignition. In most of the previous modeling studies for normal-alkyl cycloalkane combustion, the kinetic data of the cyclization reactions in the detailed combustion mechanism were mainly taken from the analogous reactions in cyclohexane, methyl cyclohexane, and alkanes in published literature studies. In this work, the kinetics of the cyclization reaction class of hydroperoxy alkyl radicals in normal-alkyl cycloalkanes is studied, where the reaction class is divided into subclasses depending upon the ring size of the transition states, the types of the carbons on which the -OOH site is located and the types of the carbons on which the radical site is located, and the positions of the cyclization (on the alkyl side chain, on the cycle, or between the alkyl side chain and the cycle). Energy barriers and high-pressure-limit site rate constants and pressure-dependent rates for reactions in all subclasses are calculated, and rate rules for all subclasses are developed. The high-pressure-limit rate constants are determined from CBS-QB3 electronic structure calculations combined with canonical transition-state theory calculations, and pressure-dependent rate constants are calculated by using the Rice-Ramsberger-Kassel-Marcus/Master Equation theory at pressures varying from 0.01 to 100 atm. Comparisons of the rate constants for cyclization reactions of hydroperoxy alkyl cyclohexylperoxy radicals calculated in this work with the values of the corresponding reactions in some of the popular combustion mechanisms show that it is unreasonable to use the kinetic data of analogous reactions in alkanes, cyclohexanes, or smaller normal-alkyl cyclohexanes. Therefore, the accurate kinetic calculations and the construction of rate rules for normal-alkyl cycloalkanes are necessary and significant for the reliable modeling of the low-temperature combustion of normal-alkyl cyclohexanes.

High-Pressure-Limit and Pressure-Dependent Rate Rules for Unimolecular Reactions Related to Hydroperoxy Alkyl Radicals in Normal Alkyl Cyclohexane Combustion. 1. Concerted HO2 Elimination Reaction Class and β-Scission Reaction Class

The reactions of the concerted HO₂ elimination from alkyl peroxy radicals and the β-scission of the C-OOH bond from hydroperoxy alkyl radicals, which lead to the formation of olefins and HO₂ radicals, are two important reaction classes that compete with the second O₂ addition step of hydroperoxy alkyl radicals, which are responsible for the chain branching in the low-temperature oxidation of normal alkyl cycloalkanes. These two reaction classes are also believed to be responsible for the negative temperature coefficient behavior due to the formation of the relatively unreactive HO₂ radical, which has the potential to inhibit ignition of normal alkyl cycloalkanes. In this work, the kinetics of the above two reaction classes in normal alkyl cycloalkanes are studied, where reactions in the concerted elimination class are divided into subclasses depending upon the types of carbons from which the H atom is eliminated and the positions of the reaction center (on the alkyl side chain or on the cycle), and the reactions in the β-scission reaction class are divided into subclasses depending upon the types of the carbons on which the radical is located and the positions of the reaction center. Energy barriers by using quantum chemical methods at the CBS-QB3 level, high-pressure-limit rate constants by using canonical transition state theory, and pressure-dependent rate constants at pressures from 0.01 to 100 atm by using Rice-Ramsberger-Kassel-Marcus/Master Equation theory are calculated for a representative set of reactions from methyl cyclohexane to n-butyl cyclohexane in each subclass, from which high-pressure-limit rate rules and pressure-dependent rate rules for each subclass are derived from the average rate constants of reactions within each subclass. A comparison of the rate constants for the reactions in the two reaction classes calculated in this work is made with the rate constants of the same reactions from available mechanisms published in the literature, where most of the rate constants are approximately estimated from analogous reactions in alkanes or small alkyl cyclohexanes, and it is found that a large difference may exist between them, indicating that the present work, which provides more accurate kinetic parameters and reasonable rate rules for these reaction classes, can be helpful to construct higher-accuracy mechanism models for normal alkyl cyclohexane combustion.

Vapor-Phase Raman Spectra and the Barrier to Planarity of Cyclohexane

The vapor-phase Raman spectra of an atmosphere of cyclohexane vapor heated to 90 and 110 °C collected over a large period of time and utilizing a high laser power of 4 W show hot band series starting at 380.8 cm^-1 and corresponding to the v₆(A_1g) ring-inversion vibration. Fitting this data with a one-dimensional potential energy function allows the barrier to planarity of 8600 cm^-1 (24.6 kcal/mol) to be calculated. Ab initio calculations (MP2/cc-pVTZ) predict a value of 10 377 cm^-1 (29.7 kcal/mol), while DFT (B3LYP/cc-pVTZ) calculations predict 8804 cm^-1 (25.2 kcal/mol).

Quantum chemical study of the equatorial/axial exchange of different substituents in nitrogen and phosphorous-containing 6-membered rings: Role of charge transfer interactions

Understanding the nature of equatorial/axial conversion in six-membered rings is important because of involvement of these motifs in some biological systems. In this work we have studied the equatorial/axial exchange of nitrogen and phosphorous bearing six-membered rings with different representative substituents by using quantum chemistry methods. Three possible routes, i.e. heteroatom inversion and two ring flipping modes were considered. The feasibility of equatorial/axial conversion (based on ΔE#) for the substituted piperidine rings with substituents was in the following order; H > CH 3> Cl ~ OH ~ F , whereas for the phosphorous bearing six-membered rings it was H ~ F > OH > Cl ~ CH 3. In the piperidine system hydrogen and methyl substituents preferred the atom inversion route while the other substituents ( Cl , F , OH ) favored C4 site ring flipping in equatorial/axial conversion. For the phosphorous bearing rings, however, phosphorous retards the atom inversion mechanism and heteroatom site ring flipping is the preferred route for all substituents. We demonstrate that charge transfer effect is one of the key factors that determines the favored route in the presence of various substituents. We show how wave function analysis by natural bond orbital (NBO) method can be used as a straightforward technique to explain the most favored route in the equatorial/axial conversion of substituted 6-membered rings.

Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design

Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications.

Diastereoselective hydrogen-transfer reactions: an experimental and DFT study

Radical reductions of halogenated precursors bearing a heterocycle exo (α) to the carbon-centered radical proceed with enhanced anti-selectivity, a phenomenon that we termed "exocyclic effect". New experimental data and DFT calculations at the BHandHLYP/TZVP level demonstrate that the origin of the exocyclic effect is linked to the strain energy required for a radical intermediate to reach its reactive conformation at the transition state (ΔE(≠)(strain)). Furthermore, radical reductions of constrained THP systems indicate that high 2,3-anti inductions are reached only when the radical chain occupies an equatorial orientation. Hydride deliveries to different acyclic substrates and calculations also suggest that the higher anti-selectivities obtained with borinate intermediates are not related to the formation of a complex mimicking an exocycle. From a broader standpoint, this study reveals important conformational factors for reactions taking place at a center vicinal to a heterocycle or an α-alkoxy group.

Interconversion study in 1,4-substituted six-membered cyclohexane-type rings. Structure and dynamics of trans-1,4-dibromo-1,4-dicyanocyclohexane

Cyclohexane is an extremely flexible molecule that oscillates, at room temperature, between two clearly distinct and extreme conformations that cannot be distinguished at room temperature; so much so that the NMR spectrum is a single line that includes all 12 protons be they axial or equatorial. This raises the interesting question as to what happens when there are equal substituents at the 1 and 4 carbon atoms of the ring. Therefore substitution in the 1,4-positions in the cyclohexane ring has been the subject of considerable interest because some form of interconversion between extreme conformations could lead to the existence of a rather unusual behavior. To study this problem, the interconversion in (di- or tetra-1,4)-substituted six-membered cyclohexane-type rings, trans-1,4-dibromo-1,4-dicyanocyclohexane, was found to be a particularly suitable candidate. Although X-ray diffraction studies on the crystalline solid found the molecule to be centrosymmetric, it still shows a significant dipole moment μ in solution, as determined with a procedure that leads to the vapor phase values of μ. Furthermore, the low magnetic field proton NMR spectrum at ambient temperature appears as a single line, a situation that changes with increasing field intensity and different solvents. Both these effects are attributed to dynamics, because small distortions can easily disrupt the exact cancellation of the individual dipoles (which are quite strong) associated with each end of the molecule. The molecule can exist in two forms, with both the bromines in an axial geometry or both in an equatorial position. Interconversion between these forms is observed, as in the parent cyclohexane. The single NMR line observed at low magnetic fields is due to fast exchange and requires that the two forms have roughly equal populations. Spectra obtained at low temperature confirm this, and variable-temperature studies allow measurement of the rates, leading to an enthalpy of activation of 62 kJ mol(-1). More details of the interconversion are provided by some new calculation methods. Even for a relatively small molecule like this, calculation of a full potential energy surface is prohibitive. However, methods are now available to follow the molecule along the reaction coordinate in quite an efficient way. The results of these calculations lead to an extremely detailed picture of chair-chair interconversion in a di- and tetrasubstituted six-membered ring of the cyclohexane family.

Biogenesis of sesquiterpene lactones pseudoguaianolides from germacranolides: theoretical study on the reaction mechanism of terminal biogenesis of 8-epiconfertin

The fundamental study of the biogenetic origin of natural products has always been limited from the experimental point of view because proposed reaction mechanisms have only been supported on the molecular structures of reagents and the reaction products. In a seminal contribution, Ortega and Maldonado (Ortega, A.; Maldonado, E. Heterocycles, 1989, 29, 635-638.) described an experiment relevant for the development of the biogenetic theory of sesquiterpene lactones. They were able to obtain the one-pot transformation of a pseudoguaianolide sesquiterpenic lactone from a germacranolide using bentonitic earth as the catalyst. This transformation involved two steps in the biogenesis of these compounds (germacranolide --> guaianolide --> pseudoguaianolide) and is significant because when Brönsted or Lewis acids are used, it is only possible to isolate the product of the next step of the biogenesis. The results presented here support the biogenetic theories by Hendrickson and Fischer and question the concerted nature of the Herz proposal. Some questions about the mechanisms still remain unanswered; mainly because it was only possible to isolate a few stable byproducts. Using the third generation functional mPWB95 developed by Truhlar, it was possible to study the mechanisms associated with the biogenesis of pseudoguaiananolides. Its application can explain the origin of all the byproducts obtained in the original experiment and establish the validity of the original biogenetic hypothesis. The performance of the above-mentioned functional was compared to B3LYP, B97-2, and B1B95 functionals and the MP2 method, finding that mPWB95 competes successfully with all the latter in both, the determination of the magnitude of the activation energies and the ability to map the potential energy surface. Therefore, the mPWB95 method can be considered good to deal with this type of study.

The Conformational Free Energy Landscape of β-d-Glucopyranose. Implications for Substrate Preactivation in β-Glucoside Hydrolases

Using ab initio metadynamics we have computed the conformational free energy landscape of beta-D-glucopyranose as a function of the puckering coordinates. We show that the correspondence between the free energy and the Stoddard's pseudorotational itinerary for the system is rather poor. The number of free energy minima (9) is smaller than the number of ideal structures (13). Moreover, only six minima correspond to a canonical conformation. The structural features, the electronic properties, and the relative stability of the predicted conformers permit the rationalization of the occurrence of distorted sugar conformations in all the available X-ray structures of beta-glucoside hydrolase Michaelis complexes. We show that these enzymes recognize the most stable distorted conformers of the isolated substrate and at the same time the ones better prepared for catalysis in terms of bond elongation/shrinking and charge distribution. This suggests that the factors governing the distortions present in these complexes are largely dictated by the intrinsic properties of a single glucose unit.

Computational study of 1,3-dithiane 1,1-dioxide (1,3-dithiane sulfone). Description of the inversion process and manifestation of stereoelectronic effects on 1JC-H coupling constants

A theoretical study on the conformational interconversions in 1,3-dithiane 1,1-dioxide (1,3-dithiane sulfone) has been carried out. Nineteen conformations have been considered. Four minima and five transition states have been identified. A description of the inversion-topomerization process of 1,3-dithiane sulfone is presented. Calculations show that two transition states are associated with inversion and three more with topomerization. IGLO calculations of the (1)J(C-H) one-bond coupling constants in 1,3-dithiane sulfone have also been carried out. These constants are compared with those obtained for 1,3-dithiane, thiane, and thiane sulfone and their magnitude is explained in terms of stereoelectronic interactions.

Substrate Distortion in the Michaelis Complex of Bacillus 1,3–1,4-β-Glucanase

The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3-1,4-beta-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the -1 subsite adopts a distorted 1S3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4C1 chair conformation, the 1S3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the beta region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the -1 sugar ring. It thus provides a powerful tool to model E.S complexes for which experimental information is not yet available.