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

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

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

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

<p>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 as well as 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 as well as reaction enthalpies and enthalpies of formation for each species were calculated using Pople basis sets and the (aug)-cc-pVnZ Dunning sets, with n=2-6. For the calculation of enthalpies of formation, atomization as well as 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 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 derived theoretically up to present. Different sources of error in the calculations are discussed in detail.</p

Atmospheric reactivity of HC≡CCH2OH (2-propyn-1-ol) toward OH radical: Experimental determination and theoretical comparison with its alkyne analogue

The rate coefficient for the reaction of propargyl alcohol (2-propyn-1-ol, 2P1OL) with OH radicals has been determined using gas chromatography with a flame ionization detector (GC/FID) at 298 K and atmospheric pressure. The experimental value obtained by the relative method using methyl methacrylate and butyl acrylate as references was (2.05 ± 0.30) × 10−11 cm3 per molecule per s. The present value was compared with previous determinations and a theoretical study of the reaction was performed in order to explain the differences in reactivity of the alcohol with that of the corresponding alkyne (propyne, P). A full discussion of the addition and abstraction mechanisms was developed for 2P1OL at the density functional and ab initio composite model levels. It was found that addition is much faster than abstraction for propyne but occurs at approximately the same rate for 2P1OL. In this last case, however, abstraction of hydrogen from the C1 carbon leads to a complex which can react further to yield addition products. Thermodynamic and kinetic data calculated for these reactions suggest that the products would be the 1,2- and 1,3-propanediol radicals. These products would react further with O2, in the case where it is present in the reaction mixture.Fil: Gibilisco, Rodrigo Gastón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Kieninger, Martina. Universidad de la República; UruguayFil: Teruel, Mariano Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Ventura, Oscar. Universidad de la República; Urugua

A Reinvestigation of the Deceptively Simple Reaction of Toluene with ●OH, and the Fate of the Benzyl Radical. I. a Combined Thermodynamic and Kinetic Study on the Competition Between ●OH Addition and Hydrogen Abstraction Reactions.

This work reports density functional and composite model chemistry calculations performed on the reactions of toluene with the hydroxyl radical. Both experimentally observed H-abstraction from the methyl group and possible additions to the phenyl ring were investigated. Reaction enthalpies and heights of the barriers 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. This is somehow contradictory 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 begs for an explanation. In this first part of our work we give the evidences that support the preference of hydrogen abstraction over ●OH addition and suggest an alternative mechanism which shows that cresols can actually arise also from the former reaction and not only from the latter

SVECV-f12: benchmark of a composite scheme for accurate and cost effective evaluation of reaction barriers.

A simple composite scheme is presented, based on a combination of density functional geometry and frequencies evaluation, valence energies obtained using the CCSD(T)-f12 method extrapolated to the complete basis set limit, and core-valence correlation corrections employing the MP2 method. The procedure was applied to the 38 reactions in Truhlar’s HTBH38/08 and NHTBH38/08 databases and the errors in the barriers with respect to their best values are presented. Mean unsigned deviation (MUD) for the complete set of 68 independent barriers is 0.40 kcal mol-1 , compared to 1.31 kcal/mol for G4 and 1.62 kcal/mol for the dispersion-corrected M06- 2X method. The accuracy of the procedure is also better that that of other calculations using composite methods of similar cost. The MUD of the new scheme on the barriers in the DBH24/08 subset (12 out of the 38 reactions in the other two sets) is 0.27 kcal mol-1 , better than that obtained at the expensive CCSD(T,full)/aug-cc-pCV(T+d)Z level (0.46 kcal mol-1 ) and comparable to the 2 most exact (and costly) Wn calculations (MUD=0.14 kcal mol-1 ). The maximum unsigned deviation (MaxUD) for all the reactions studied is 0.99 kcal/mol. G4 and M06-2X, on the other side, exhibit MaxUDs of 6.7 and 8.0 kcal/mol respectively. The method was further tested against a subset of the reactions in the databases, for which the geometry and energies of all species were determined at the much more demanding CCSD(T)-F12//pVQZ-F12 level. These results showed that Truhlar’s calculations in this subset are off the best values by a considerable amount, with an rmse of 0.56 kcal/mol. As a consequence, a new dataset of barrier heights, SV20, is presented. The SVECV-F12 procedure on this SV20 database results in rmse and MUD values of only 0.21 and 0.16 kcal/mol. The possible residual errors introduced by the approximations used for each component of the method are tested against more sophisticated calculations and shown to be accurate enough to obtain barriers well under the chemical precision limit at a reasonable cost for molecules of interest in atmospheric chemistry