Relative Stability Of Intermediates Research Articles

A DFT investigation of the mechanisms of CO2 and CO methanation on Fe (111)

Insight into the detailed mechanism of the Sabatier reaction on iron is essential for the design of cheap, environmentally benign, efficient and selective catalytic surfaces for CO2 reduction. Earlier attempts to unravel the mechanism of CO2 reduction on pure metals including inexpensive metals focused on Ni and Cu; however, the detailed mechanism of CO2 reduction on iron is not yet known. We have, thus, explored with spin-polarized density functional theory calculations the relative stabilities of intermediates and kinetic barriers associated with methanation of CO2 via the CO and non-CO pathways on the Fe (111) surface. Through the non-CO (formate) pathway, a dihydride CO2 species (H2CO2), which decomposes to aldehyde (CHO), is further hydrogenated into methoxy, methanol and then methane. Through the CO pathway, it is observed that the CO species formed from dihydroxycarbene is not favorably decomposed into carbide (both thermodynamically and kinetically challenging) but CO undergoes associative hydrogenation to form CH2OH which decomposes into CH2, leading to methane formation. Our results show that the transformation of CO2 to methane proceeds via the CO pathway, since the barriers leading to alkoxy transformation into methane are high via the non-CO pathway. Methanol formation is more favored via the non-CO pathway. Iron (111) shows selectivity towards CO methanation over CO2 methanation due to differences in the rate-determining steps, i.e., 91.6 kJ mol−1 and 146.2 kJ mol−1, respectively.

ChemInform Abstract: Electrode Reactions and Electroanalysis of Organomercury Compounds

AbstractReview: 396 refs.

Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism.

The stereospecific cytochrome P450-catalyzed hydroxylation of the C(5)-H((5-exo)) bond in camphor has been studied theoretically by a combined quantum mechanical/molecular mechanical (QM/MM) approach. Density functional theory is employed to treat the electronic structure of the active site (40-100 atoms), while the protein and solvent environment (ca. 24,000 atoms) is described by the CHARMM force field. The calculated energy profile of the hydrogen-abstraction oxygen-rebound mechanism indicates that the reaction takes place in two spin states (doublet and quartet), as has been suggested earlier on the basis of calculations on simpler models ("two-state reactivity"). While the reaction on the doublet potential energy surface is nonsynchronous, yet effectively concerted, the quartet pathway is truly stepwise, including formation of a distinct intermediate substrate radical and a hydroxo-iron complex. Comparative calculations in the gas phase demonstrate the effect of the protein environment on the geometry and relative stability of intermediates (in terms of spin states and redox electromers) through steric constraints and electronic polarization.

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions.

The thermodynamic and kinetic aspects of molecular recognition for the methotrexate (MTX)-dihydrofolate reductase (DHFR) ligand-protein system are investigated by the binding energy landscape approach. The impact of 'hot' and 'cold' errors in ligand mutations on the thermodynamic stability of the native MTX-DHFR complex is analyzed, and relationships between the molecular recognition mechanism and the degree of ligand optimization are discussed. The nature and relative stability of intermediates and thermodynamic phases on the ligand-protein association pathway are studied, providing new insights into connections between protein folding and molecular recognition mechanisms, and cooperativity of ligand-protein binding. The results of kinetic docking simulations are rationalized based on the thermodynamic properties determined from equilibrium simulations and the shape of the underlying binding energy landscape. We show how evolutionary ligand selection for a receptor active site can produce well-optimized ligand-protein systems such as MTX-DHFR complex with the thermodynamically stable native structure and a direct transition mechanism of binding from unbound conformations to the unique native structure.

Metabolism and relative carcinogenic potency of chloroethylenes: A quantum chemical structure-activity study

Properties of six chloroethylenes which could serve as indicators of their relative metabolic behavior and carcinogenic activity have been calculated using Modified Neglect of Diatomic Overlap (MNDO), a semiempirical, all valence electron, molecular orbital method. Possible pathways of transformation of parent compounds to acylchlorides, chloroaldehydes and epoxides — their putative ultimate carcinogens — were considered, and heats of formation and relative stabilities of intermediates were calculated. Our results indicate that carbonyl compounds could be formed with and without the intermediacy of epoxides, suggesting the possibility of more than one pathway in activation of parent compounds. Electronic properties of carbonyl products and epoxide carbocations, putative ultimate carcinogens which could serve as indicators of their relative electrophilicities, were also calculated. The results obtained indicated that the relative extent of metabolism to carbonyl products, rather than their electrophilicity, is a determinant of the relative carcinogenic activity of the parent compound. Of the various thermodynamic criteria investigated, four were found to be indicators of both relative metabolic behavior and carcinogenic activity.