Calculation of the Geometries and Infrared Spectra of the Stacked Cofactor Flavin Adenine Dinucleotide (FAD) as the Prerequisite for Studies of Light-Triggered Proton and Electron Transfer

Kieninger M, Ventura ON, Kottke T. Calculation of the Geometries and Infrared Spectra of the Stacked Cofactor Flavin Adenine Dinucleotide (FAD) as the Prerequisite for Studies of Light-Triggered Proton and Electron Transfer. Biomolecules. 2020;10(4): 573.Flavin cofactors, like flavin adenine dinucleotide (FAD), are important electron shuttles in living systems. They catalyze a wide range of one- or two-electron redox reactions. Experimental investigations include UV-vis as well as infrared spectroscopy. FAD in aqueous solution exhibits a significantly shorter excited state lifetime than its analog, the flavin mononucleotide. This finding is explained by the presence of a “stacked” FAD conformation, in which isoalloxazine and adenine moieties form a π-complex. Stacking of the isoalloxazine and adenine rings should have an influence on the frequency of the vibrational modes. Density functional theory (DFT) studies of the closed form of FAD in microsolvation (explicit water) were used to reproduce the experimental infrared spectra, substantiating the prevalence of the stacked geometry of FAD in aqueous surroundings. It could be shown that the existence of the closed structure in FAD can be narrowed down to the presence of only a single water molecule between the third hydroxyl group (of the ribityl chain) and the N7 in the adenine ring of FAD

Electronic and structural distortions in graphene induced by carbon vacancies and boron doping

We present an ab initio study on the structural and electronic distortions of modified graphene by creation of vacancies, inclusion of boron atoms, and the coexistence of both, by means of thermodynamics and band structure calculations. In the case of coexistence of boron atoms and vacancy, the modified graphene presents spin polarization only when B atoms locate far from vacancy. Thus, when a boron atom fills single- and di-vacancies, it suppresses the spin polarization of the charge density. In particular when B atoms fill a di-vacancy a new type of rearrangement occurs, where a stable BC4 unit is formed inducing important out of plane distortions to graphene. All these findings suggest that new chemical modifications to graphene and new type of vacancies can be used for interesting applications such as sensor and chemical labeling.Comment: 22 pages, 9 figures and 3 table

Kinetics and thermodynamics of the hydroxylation products in the photodegradation of the herbicide Metolachlor

Electronic structure calculations have been performed to determine the thermochemistry and kinetics of the reaction between OH and the radicals of the S enantiomer of the herbicide Metolachlor, 2-chloro-N-(2-methyl-6-ethylphenyl)-N(2-methoxy-1-methylethyl) acetamide (MC), produced by photoinduced breaking of the C–Cl bond. Both density functional and ab initio composite methods were employed to calculate the structure of reactants, intermediates, transition states and products, in gas phase and in aqueous solution. The expected relative abundance of each product was calculated and compared to the experimentally observed concentrations. It is shown that a combination of thermodynamic and kinetic characteristics interplay to produce the expected theoretical abundances, which turn out to be in agreement with the experimentally observed distribution of products

A reinvestigation of the deceptively simple reaction of toluene with OH, and the fate of the benzyl radical : a combined thermodynamic and kinetic study on the competition between OH-addition and H-abstraction reactions

This work reports density functional and composite model chemistry calculations performed on the reactions of toluene with the hydroxyl radical. Both the experimentally observed H-abstraction from the methyl group and possible OH additions to the phenyl ring were investigated. Reaction enthalpies and barrier heights suggest that H-abstraction is more favorable than OH-addition to the ring. The calculated reaction rates at room temperature and the radical intermediate product fractions support this view. At first sight, this might seem to disagree with the fact that, under most experimental conditions, cresols are observed in a larger concentration than benzaldehyde. Since the accepted mechanism for benzaldehyde formation involves H-abstraction, a contradiction arises that calls for a more elaborate explanation. In this first exploratory study, we provide evidence that support the preference of H-abstraction over OH addition and present an alternative mechanism which shows that cresols can be actually produced also through H-abstraction and not only from OH-addition, thus justifying the larger proportion of cresols than benzaldehyde among the products

MAGIC and H.E.S.S. detect VHE gamma rays from the blazar OT081 for the first time: a deep multiwavelength study

https://pos.sissa.it/395/815/pdfPublished versio

Basis Set Effects in the Description of the Cl-O Bond in ClO and XClO/ClOX Isomers (X = H, O, and Cl) Using DFT and CCSD(T) Methods

The performance of a group of density functional methods of progressive complexity for the description of the ClO bond in a series of chlorine oxides was investigated. The simplest ClO radical species and the two isomeric structures XClO/ClOX for each X = H, Cl, and O were studied using the PW91, TPSS, B3LYP, PBE0, M06, M06-2X, BMK, and B2PLYP functionals. Geometry optimizations and reaction enthalpies and enthalpies of formation for each species were calculated using Pople basis sets and the (aug)-cc-pVnZ Dunning sets, with n = D, T, Q, 5, and 6. For the calculation of enthalpies of formation, atomization and isodesmic reactions were employed. Both the precision of the methods with respect to the increase of the basis sets, as well as their accuracy, were gauged by comparing the results with the more accurate CCSD(T) calculations, performed using the same basis sets as for the DFT methods. The results obtained employing composite chemical methods (G4, CBS-QB3, and W1BD) were also used for the comparisons, as well as the experimental results when they are available. The results obtained show that error compensation is the key for successful description of molecular properties (geometries and energies) by carefully selecting the method and basis sets. In general, expansion of the one-electron basis set to the limit of completeness does not improve results at the DFT level, but just the opposite. The enthalpies of formation calculated at the CCSD(T)/aug-cc-pV6Z for the species considered are generally in agreement with experimental determinations and the most accurate theoretical values. Different sources of error in the calculations are discussed in detail

Unraveling the role of additional OH-radicals in the H–Abstraction from Dimethyl sulfide using quantum chemical computations

Dimethyl sulfide (DMS) is the main organosulfur compound in the atmosphere. Oxidation by OH radicals to form the methyl thiomethyl species (MTMr) has been studied under normal atmospheric conditions and in reaction chambers at different O2 partial pressure, including complete absence of oxygen. Scarce attention has been devoted however to the possibility of further reaction of OH with MTMr. We present here a computational study using DFT, CCSD(T) and composite methods, on the properties of two stable intermediates never fully investigated before, methanesulfenyl methanol (MSMOH) and S-methyl-methanesulfenic acid (SMMSA), arising from addition of a second OH radical to MTMr

An AM1 semiempirical study of the mechanism of sintering for ZnO in the presence of water and carbon dioxide

AM1 calculations were performed for the absorption of H2O and CO2 molecules on the surface of model ZnO crystals. The absorption of isolated molecules of each species and the co-absorption of both compounds simultaneously were considered. It was found that the absorption of H2O near a site where CO; is already absorbed favors the process of sintering, in agreement with the experimental findings. This is explained by the formation of Zn(OH)CO3H bound to the surface, a more mobile species than the ZnO unit itself. The roundening of the grains observed in atmospheres containing dry CO2 but suppressed when H2O is present, is also explained by these calculations. After absorption of CO2, the rupture of one bond - so that diffusion of the ZnCO3 species on the surface is allowed - requires much less energy than the breaking of two bonds, necessary for ZnO migration. These facts explain why the speed of surface transport does not decrease in CO2 atmospheres while sintering is indeed slowed down. © 1994