Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

We have calculated redox potentials of the two metal clusters in Mo-nitrogenase with quantum mechanical (QM) calculations. We employ an approach calibrated for iron–sulfur clusters with 1–4 Fe ions, involving QM-cluster calculations in continuum solvent and large QM systems (400–500 atoms), based on structures from combined QM and molecular mechanics (QM/MM) geometry optimisations. Calculations on the P-cluster show that we can reproduce the experimental redox potentials within 0.33 V. This is similar to the accuracy obtained for the smaller clusters, although two of the redox reactions involve also proton transfer. The calculated P¹⁺/P^N redox potential is nearly the same independently of whether P¹⁺ is protonated or deprotonated, explaining why redox titrations do not show any pH dependence. For the FeMo cluster, the calculations clearly show that the formal oxidation state of the cluster in the resting E₀ state is MoIIIFe3IIFe4III , in agreement with previous experimental studies and QM calculations. Moreover, the redox potentials of the first five E₀–E₄ states are nearly constant, as is expected if the electrons are delivered by the same site (the P-cluster). However, the redox potentials are insensitive to the formal oxidation states of the Fe ion (i.e., whether the added protons bind to sulfide or Fe ions). Finally, we show that the later (E₄–E₈) states of the reaction mechanism have redox potential that are more positive (i.e., more exothermic) than that of the E₀/E₁ couple.     

Targeting the Rich Conformational Landscape of N-Allylmethylamine Using Rotational Spectroscopy and Quantum Mechanical Calculations

The highly variable conformational landscape of N-allylmethylamine (AMA) was investigated using Fourier transform microwave spectroscopy aided by high-level theoretical calculations to understand the energy relationship governing the interconversion between nine stable conformers. Spectroscopically, transitions belonging to four low energy conformers were identified and their hyperfine patterns owing to the ¹⁴N quadrupolar nucleus were unambiguously resolved. The rotational spectrum of the global minimum geometry, conformer I, shows an additional splitting associated with a tunneling motion through an energy barrier interconnecting its enantiomeric forms. A two-step tunneling trajectory is proposed by finding transition state structures corresponding to the allyl torsion and NH inversion. Natural bond orbital and non-covalent interaction analyses reveal that an interplay between steric and hyperconjugative effects rules the conformational preferences of AMA.     

Reaction of Nitrosonium Tetrafluoroborate with Nitroxyl Radicals

It was established by means of multinuclear magnetic resonance method (¹H, ^{1 3}C, ^{1 9}F and ^{1 4}N) that reaction of 2,2,6,6-tetramethyl-4-R-piperidin-1-oxyl radicals (R = H, OH, OMe, OCOPh, NHCOMe) with nitrosonium tetrafluoroborate gave rise to the corresponding 2,2,6,6-tetramethyl-1-oxo-4-R-piperidinium tetrafluoroborates. Linear correlations were found between the chemical shifts of atoms H⁴, C⁴ of cations and respectively ₁-constants of substituents R and chemical shifts of C⁴ atom calculated from increments of substitution. The conformational features of the generated nitrosonium cations are considered on the grounds of vicinal coupling constants J _{H H} and quantum-chemical calculations by AM1 method.     

Antioxidant Activties of Stable Nitroxyl Radicals in Oil

The nitroxides belong to stable free radicals which are widely used for spin labeling in ESR technique. Recently studies showed that nitroxide stable radicals demonstrate effective antioxidative activity in various biological systems ranging from molecular, cellular and laboratory animal level^[l]. But up to now there isn't reported about antioxidant activities on oil of nitroxides. Because antioxidants on oil play a very important role in the food industry^[2], therefore we want to utilize nitroxides as more effective antioxidants in the food industry.     

氮氧自由基催化有机物的分子氧氧化研究进展

各类有机物的氧化一直受到国内外工业的广泛关注,尤其是烷基芳烃、大环烷烃、醇类、氮杂环化合物等有机物的氧化具有巨大的工业应用前景.传统的工业规模的有机物氧化反应条件苛刻,存在诸多缺陷:或高温高压导致的高耗能,或使用卤化物导致对反应容器的腐蚀,或使用硝酸作氧化剂产生大量具有温室效应的气体一氧化二氮,以及反应的选择性不高带来大量的副产物等等.     

Features of Radical Polymerization of Vinyl Chloride in the Presence of Nitroxyl Radicals

Radical polymerization of vinyl chloride in the presence of C-phenyl-N-tert-butylnitrone, 2-meth- yl-2-nitrosopropane, and 1-tert-butyl-3-phenyl-1-oxytriazene as potential sources of free radicals was studied.     

A Kinetic Evidence for the Nitroxyl Radicals Recycling Mechanism in the Photostabilizing Process of HALS

The photoinduced bulk polymerization of a reactive-hindered amine fight stabilizers(r-HALS), 4-acryloyl-2, 2, 6, 6-tetramethylpiperidinyl (ATMP), was performed at 80℃ by using a DPC technique. An unique periodic exponential attenuation-type oscillating curve was found when the polymerization was carried out in air, but this phenomenon was not found in nitrogen.It is supposed that this unique kinetic performance may be attributed to nitroxyl radicals that are produced in situ from the oxidation of ATMP. ATMP polymer with narrow polydispersity (d =1.03) can be obtained by photoinduced solution polymerization of ATMP. The signal detected in ESR may be assigned to the nitroxyl radicals in the matrix of ATMP polymer. Since this kind of recycling of nitroxyl radicals is well documented for the photostabilizing mechanism of HALS, the present results may serve as a kinetic evidence for this mechanism.     

Mutual Effect of Functional Groups and the Radical Center on the Reactivity of Nitroxyl Radicals

This review considers the correlation between the reactivity of nitroxyl radicals (piperidine, pyrroline, pyrrolidine, imidazoline, dihydroquinoline, tetrahydroquinoline, diphenyl nitroxide, etc.) and their chemical structure in terms of the rate constants of reactions between these radicals and hydrazobenzene. 4,4′-Di(tert-butyl)diphenyl nitroxyl has the highest reactivity, and the nitroxyl radical of benzoindolopyrrolidine is the least reactive (the difference is a factor of ∼10⁴). The effects of the metal atom in stable organometallic nitroxyl radicals and of the halogen atom in halogenated nitroxyl radicals on the reactivity of the nitroxyl center are considered. Data on the effect of the nitroxyl center on the reactivity of functional groups in the piperidine nitroxyl radical are generalized. Nitroxyl radicals with an activated double bond are shown by quantum chemical calculations to form cyclic transition complexes with amines, involving both the paramagnetic center and a double bond. This explains why the activated double bond in nitroxyl radicals is more reactive in nucleophilic additions of amines than the same bond in their diamagnetic analogues. The rate constants of nitroxyl reduction with hydrazobenzene and of nitroxyl oxidation with tetranitromethane are related to the σ_ESR constant derived from isotropic hyperfine coupling constants HFC_(aN), and their correlation with Hammett constants is demonstrated. The role of solvents in the reduction and oxidation of the nitroxyl radicals is considered. The influence of hydroxyl radical-polar solvent complexes and hydroxylamine-polar solvent H complexes on the course of reactions is considered for hydrogen atom transfer in systems of a sterically hindered nitroxyl radical and hydroxylamine.__________Translated from Kinetika i Kataliz, Vol. 46, No. 4, 2005, pp. 506–528.Original Russian Text Copyright © 2005 by Malievskii, Shapiro.     

Quantum Mechanical Calculations for Biomass Valorization over Metal-Organic Frameworks (MOFs)

Metal-organic framework (MOF) in biomass valorization is a promising technology developed in recent decades. By tailoring both the metal nodes and organic ligands, MOFs exhibit multiple functionalities, which not only extend their applicability in biomass conversion but also increase the complexity of material designs. To address this issue, quantum mechanical simulations have been used to provide mechanistic insights into the catalysis of biomass-derived molecules, which could potentially facilitate the development of novel MOF-based materials for biomass valorization. The aim of this review is to survey recent quantum mechanical simulations on biomass reactions occurring in MOF catalysts, with the emphasis on the studies of the catalytic activity of active sites and the effects of organic ligand and porous structures on the kinetics. Moreover, different model systems and computational methods used for MOF simulations are also surveyed and discussed in this review.     

Theoretical Modeling of Redox Potentials of Biomolecules

The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.     

Integrating Molecular Modeling with Semiempirical Quantum Mechanical Calculations into the Upper-Level Inorganic Chemistry Course

The analysis of chemical bonding and reactivity from the perspective of molecular orbital theory is challenging for students at the undergraduate level. In an attempt to improve the instruction of this material in my upper-level inorganic chemistry course I developed a series of computational experiments using a molecular modeling program that can perform semiempirical quantum mechanical calculations. These exercises explore the chemistry of molecular systems through an analysis of the variation in the attractive and repulsive forces in the system as a function of structure or composition. The exercises challenge the analysis skills of the students by requiring them to consider how two or more factors contribute to the properties of the system. Examples of exercises that demonstrate different types of computational experiments are given. These sample exercises examine the structure of simple molecules, the reactivity of Lewis acids, and the bonding in transition metal complexes.     

Mechanistic Insights into a Stibene Cleavage Oxygenase NOV1 from Quantum Mechanical/Molecular Mechanical Calculations

NOV1, a stilbene cleavage oxygenase, catalyzes the cleavage of the central double bond of stilbenes to two phenolic aldehydes, using a 4-His Fe(II) center and dioxygen. Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the reaction mechanism of the central double bond cleavage of phytoalexin resveratrol by NOV1. Our results showed that the oxygen molecule prefers to bind to the iron center in a side-on fashion, as suggested from the experiment. The quintet Fe−O₂ complex with the side-on superoxo antiferromagnetic coupled to the resveratrol radical is identified as the reactive oxygen species. The QM/MM results support the dioxygenase mechanism involving a dioxetane intermediate with a rate-limiting barrier of 10.0 kcal mol⁻¹. The alternative pathway through an epoxide intermediate is ruled out due to a larger rate-limiting barrier (26.8 kcal mol⁻¹). These findings provide important insight into the catalytic mechanism of carotenoid cleavage oxygenases and also the dioxygen activation of non-heme enzymes.     

稳定氮氧自由基TMPO和TMPRO的合成与应用

本文评述了近年来4-氧-2,2,6,6-四甲基哌啶-1-氧自由基(TMPO)和2,2,5,5-四甲基吡咯啉-1-氧自由基(TMPRO)及其衍生物在合成和应用方面的进展,着重讨论了这些氮氧自由基的合成方法和作为自旋标记试剂的应用。     

Redox Potentials of Samarium and Europium in Molten Cesium Chloride

The method of direct potentiometry was applied to measure redox potentials of Sm^{3 +}/Sm^{2 +} and Eu^{3 +}/Eu^{2 +} in molten cesium chloride relative to chlorine reference electrode in the temperature range 973-1173 K. Changes in the Gibbs energy of the redox reaction LnCl₂(l) + 1/2Cl₂(g) LnCl₃(l) were calculated.     

Conformational Analysis of C-Disaccharides using Molecular Mechanics Calculations

ABSTRACT

Relaxed-residue energy maps based on the MM3 force field were computed for the methyl glycosides of eight C-linked D-glucosyl disaccharides: the two-bond axial-equatorial linked disaccharides β-kojibioside [(1→2)α–], β-nigeroside [(1→3)α–] and β-maltose [(1→4)α–], the two-bond equatorial-equatorial linked disaccharides β-sophoroside [(1→2)β–], β–laminarabioside [(1→3)β-], β–cellobioside [(1→4)β–] and the three-bond-linked (1→6) disacharides C-isomaltoside and C-gentiobioside. Optimized structures were calculated on a 20° grid spacing of the torsional angles about the C-glycosidic bonds and the final isoenergy surfaces were based on 11664 conformations, for the two-bond-linked disaccharides and 69984 conformations for the three-bond-linked disaccharides. Boltzmann-weighted ³J coupling constants were calculated and compared to the experimental values. They are satisfactory except for maltose where hydrogen bonds cause an over-estimation of the energy differences between the conformers. The energy maps are similar to maps of the corresponding O-disaccharides, but there are differences in the locations and the relative energies of the minima. The preferred conformations of the C-glycosidic bonds are as if they were conforming to the exo-anomeric effect but are closer to staggered conformations than shown by the MM3 results for the O-linkages.     

Polymerization of Styrene in the Presence of Nitroxyl Radicals Generated Directly in the Course of the Polymer Synthesis (in situ)

The features of radical polymerization of styrene in the presence of nitroxyl radicals generated directly in the course of the polymer synthesis (in situ) by irreversible reaction of stable organic compounds 2-methyl-2-nitrosopropane, C-phenyl-N-tert-butylnitrone, and nitrosodurene with propagating polymer radicals were studied.