Resonance (chemistry)

Summary

In chemistry, resonance, also called mesomerism, is a way of describing bonding in certain molecules or polyatomic ions by the combination of several contributing structures (or forms, also variously known as resonance structures or canonical structures) into a resonance hybrid (or hybrid structure) in valence bond theory. It has particular value for analyzing delocalized electrons where the bonding cannot be expressed by one single Lewis structure. Overview Under the framework of valence bond theory, resonance is an extension of the idea that the bonding in a chemical species can be described by a Lewis structure. For many chemical species, a single Lewis structure, consisting of atoms obeying the octet rule, possibly bearing formal charges, and connected by bonds of positive integer order, is sufficient for describing the chemical bonding and rationalizing experimentally determined molecular properties like bond lengths, angles, and dipole moment. However, in some case

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Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation

Matteo Dal Peraro

The protein farnesyltransferase (FTase) is a Zn2+-metalloenzyme that catalyzes the farnesylation reaction, i.e., the transfer of the 15-carbon atom farnesyl group from farnesyl diphosphate (FPP) to a specific cysteine of protein substrates. Oncogenic Ras proteins, which are among the FTase substrates, are observed in about 20−30% of human cancer cells. Thus, FTase represents a target for anticancer drug design. Herein, we present a classical force-field-based and quantum mechanics/molecular mechanics (QM/MM) computational study of the FTase reaction mechanism. Our findings offer a detailed picture of the FTase catalytic pathway, describing structural features and the energetics of its saddle points. A moderate dissociation of the diphosphate group from the FPP is observed during the nucleophilic attack of the zinc-bound thiolate. At the transition state, a resonance structure is observed, which indicates the formation of a metastable carbocation. However, no stable intermediate is found along the reaction pathway. Thus, the reaction occurs via an associative mechanism with dissociative character, in agreement with the mechanism proposed by Fierke et al. ( Biochemistry 2000, 39, 2593−2602 and Biochemistry 2003, 42, 9741−9748 ). Moreover, a fluorine-substituted FPP analogue (CF3-FPP) is used to investigate the inhibitory effect of fluorine, which in turn provides additional agreement with experimental data.

2009

Proteins and even small peptides play crucial role in almost any biological. Biological activity and functionality of these building blocks of life are determined not only by their primary structure, but also by their 3D orientation â secondary, tertiary and quaternary structural motifs. This structure-function relationship is one of the most important paradigms in structural biology and makes characterization of the geometry of biological molecules an extremely important task. In contrast to experimental techniques in condensed phase Cold Ion Spectroscopy studies biomolecular ions isolated in the gas phase and provides vibrational fingerprints specific for each conformer, allowing a direct comparison with high-level calculations. The method, widely known as âdouble-resonanceâ spectroscopy, has several fundamental and practical limitations and is applicable only for peptides smaller then 10 - 15 amino acids, necessarily containing at least one of aromatic amino acids and having vibrationally resolved electronic spectrum. The main goal of this thesis is development and demonstration of a novel conformer-selective spectroscopic technique, IR-IR-(D)UV hole-burning spectroscopy. This multi-laser experiment has an important advantage over the double-resonance approach, as it does not depend on the shape or resolution of the electronic spectrum of peptide, and allows extending the application of Cold Ion Spectroscopy to peptides with any amino acid composition. The first part of this work describes application of this technique for recording the conformer selective vibrational spectra of protonated aromatic amino acids tryptophan and histidine, for which the double-resonance cold ion spectroscopy was precluded due to their unstructured electronic spectra. Combined with high-level anharmonic calculations, conformer specific vibrational spectra allowed solving structures of gas-phase conformers of these biomolecular ions. The second part describes the use of peptide bond as an alternative natural chromophore, present in any peptide. The electronic spectra of peptide bonds in cold protonated peptides in the gas-phase as well as the influence of an IR pre-excitation are explored in details. The use of peptide bonds allows recording high-quality linear vibrational spectra of peptides even without aromatic amino acids, for which only IRMPD and tagging spectroscopies were available until recently. This feature makes IR-IR-DUV hole-burning spectroscopy the most universal conformer-selective spectroscopic tool. The third part of this thesis is dedicated to the relationship of gas-phase and native structures of biomolecular ions. The lack of solvent in the gas-phase mimics to some extent hydrophobic media of cell membranes or receptors, where intramolecular hydrogen bonds rather than interaction with the solvent largely determine the structure of peptides. In such cases general structural motifs can survive the transfer to the gas phase. Experimental data and theoretical calculations for stereoisomers of an opioid peptide drug leucine enkephalin and an intrinsically disordered peptide neurokinin A are the first steps towards testing this hypothesis. Finally, the presence of more than one conformer at cryogenic temperatures for almost all of the peptides suggests that collisional cooling is a fast, non-adiabatic process. In the last part we explore the efficiency of the energy transfer during the collisional cooling of ions in a buffer gas.

EPFL2017

Isolation and characterization of diazoolefins

Zhaowen Dong, Farzaneh Fadaei Tirani, Rosario Scopelliti, Kay Severin, Paul Varava

Diazoolefins tend to be highly reactive compounds that rapidly lose dinitrogen. So far, most experimental evidence for diazoolefins is indirect, via trapping experiments. Here we show that diazoolefins are observed to form in reactions of N-heterocyclic olefins with nitrous oxide. The products benefit from resonance stabilization, which enables isolation on a preparative scale, and comprehensive characterization, which includes crystallographic analyses. N-heterocyclic diazoolefins show a strong ylidic character, with a high charge density at the carbon atom next to the diazo group. Despite the presence of terminal N2 groups, N-heterocyclic diazoolefins display a good thermal stability, which surpasses that observed for most diazoalkanes. N-heterocyclic diazoolefins can bind transition and main group metal complexes without the liberation of dinitrogen, and spectroscopic data show that they are strong electron donors. They can also undergo reactions that involve the N2 group, as evidenced by cycloaddition reactions.

2021

EPFL2017