Conformational effects on the pro-S hydrogen abstraction reaction in cyclooxygenase-1: an integrated QM/MM and MD study

A key step in the cyclooxygenase reaction cycle of cyclooxygenase 1 (COX-1) is abstraction of the pro-S hydrogen atom of the arachidonic acid by a radical that is formed at the protein residue Tyr-385. Here we investigate this reaction step by a quantum-mechanics/molecular-mechanics approach in combination with molecular-dynamics simulations. The simulations identify the hydrogen abstraction angle as a crucial geometric determinant of the reaction, thus revealing the importance of the cyclooxygenase active site for calculating the potential energy surface of the reaction

Modeling of Hydrogen Storage Materials: A Reactive Force Field for NaH

Parameterization of a reactive force field for NaH is done using ab initio derived data. The parameterized force field(ReaxFFNaH) is used to study the dynamics governing hydrogen desorption in NaH. During the abstraction process of surface molecular hydrogen charge transfer is found to be well described by the parameterized force field. To gain more insight into the mechanism governing structural transformation of NaH during thermal decomposition a heating run in a molecular dynamics simulation is done. The result shows that a clear signature of hydrogen desorption is the fall in potential energy surface during heating

Parametrization of a reactive force field for aluminum hydride

A reactive force field, REAXFF, for aluminum hydride has been developed based on density functional theory (DFT) derived data. REAXFF_(AlH_3) is used to study the dynamics governing hydrogen desorption in AlH_3. During the abstraction process of surface molecular hydrogen charge transfer is found to be well described by REAXFF_(AlH_3). Results on heat of desorption versus cluster size show that there is a strong dependence of the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. In the gas phase, it was observed that small alane clusters agglomerated into a bigger cluster. After agglomeration molecular hydrogen was desorbed from the structure. This thermodynamically driven spontaneous agglomeration followed by desorption of molecular hydrogen provides a mechanism on how mobile alane clusters can facilitate the mass transport of aluminum atoms during the thermal decomposition of NaAlH_4

Modeling the sorption dynamics of NaH using a reactive force field

We have parametrized a reactive force field for NaH, ReaxFFNaH, against a training set of ab initio derived data. To ascertain that ReaxFFNaH is properly parametrized, a comparison between ab initio heats of formation of small representative NaH clusters with ReaxFFNaH was done. The results and trend of ReaxFFNaH are found to be consistent with ab initio values. Further validation includes comparing the equations of state of condensed phases of Na and NaH as calculated from ab initio and ReaxFFNaH. There is a good match between the two results, showing that ReaxFFNaH is correctly parametrized by the ab initio training set. ReaxFFNaH has been used to study the dynamics of hydrogen desorption in NaH particles. We find that ReaxFFNaH properly describes the surface molecular hydrogen charge transfer during the abstraction process. Results on heat of desorption versus cluster size shows that there is a strong dependence on the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. To gain more insight into the structural transformations of NaH during thermal decomposition, we performed a heating run in a molecular dynamics simulation. These runs exhibit a series of drops in potential energy, associated with cluster fragmentation and desorption of molecular hydrogen. This is consistent with experimental evidence that NaH dissociates at its melting point into smaller fragments

Gas-phase C-F bond cleavage in perfluorohexane using W-, Si-, P-, Br-, and I-containing ions: comparisons with reactions at fluorocarbon surfaces

Gas-phase reactions of W-, Si-, P-, Br-, and I-containing ions with the target molecule perfluorohexane at low collision energies (<15 eV) parallel known ion/surface reactions of the same projectile ions at fluorinated self-assembled monolayer surfaces. Charge exchange, dissociative charge exchange, and fluorine atom abstraction are observed and the majority of the projectile ions also undergo reactive charge exchange to produce specific fluorocarbon fragment ions of the target molecule in distinctive relative abundances. Abstraction of up to five fluorine atoms is observed upon collision of W+ with gaseous perfluorohexane, while similar experiments with CI+, SiCl+, and PCl+· show abstraction of one or two fluorine atoms. Other projectiles, including Si+·, PCl2+, Br+, CBr+, and I+, abstract only a single fluorine atom. These patterns of fluorine atom abstraction are similar to those observed in ion/surface collisions. Also paralleling the ion/surface reactions, halogen exchange (Cl-for-F) reactions occur between the Cl-containing projectile ions and perfluorohexane to produce C6F12Cl+, a product of chemical modification of the target. Collisions of PCl+. and PCl2+ also result in production of C6F12+·, indicating that the corresponding surface modification reaction involving molecular defluorination should be sought. Implications for previously proposed mechanisms, new ion/surface reactions, and for the use of gas-phase studies to guide investigations of the ion/surface reactions are discussed

Theoretical studies of a hydrogen abstraction tool for nanotechnology

In the design of a nanoscale, site-specific hydrogen abstraction tool, the authors suggest the use of an alkynyl radical tip. Using ab initio quantum-chemistry techniques including electron correlation they model the abstraction of hydrogen from dihydrogen, methane, acetylene, benzene and isobutane by the acetylene radical. By conservative estimates, the abstraction barrier is small (less than 7.7 kcal mol^-1) in all cases except for acetylene and zero in the case of isobutane. Thermal vibrations at room temperature should be sufficient to supply the small activation energy. Several methods of creating the radical in a controlled vacuum setting should be feasible. The authors show how nanofabrication processes can be accurately and inexpensively designed in a computational framework

A gyökfogó dokozahexaénsav mint agyvédő = Docosahexaenoic acid (DHA) as a free radical scavenger brain protector

Telítetlen zsírsavak (PUFA) fontos szerepet játszanak mint antioxidánsok az emberi testben, különös tekintettel az agyban. Lipidek szisztematikus számítási vizsgálatait az OTKA támogatás előtt már elkezdtük. A támogatás alatt 4 fő tématerületen értünk el eredményeket: Téma 1: Molekuláris konformció változások termodinamikai alapjai Egyszerű szerves molekulák, mint különböző szénhidrogén származékok, peptidek, folytonos termodinamikai fügvényeit állítottuk elő konformációs mozgások mentén. Téma 2: Zsirsavak konformációs információ Igazoltuk a PUFA-k flexibilátásbeli hasonlóságát a peptidekhez a potenciál felületek hasonlóságával. DHA a legfontosabb képviselője a PUFA családnak. Téma 3: Foszfolipidek konformációs információi Az első két téma eredmnyeinek felhasználásával egyszerű foszfolipid modelleket konstruáltunk. A két zsirsavlánc relativ helyzte, kölcsönhatásai, membránszerű elrendeződés esetén állt vizsgálataink homlokterében. Téma4 Szabadgyökök reakciói PUFA és PUFA modellekkel Szabadgyökök és reakcióik PUFA-val lipidek kettősrétegeiben biológiailag nagyon fontos folyamatok. Az E vitamin az egyik leghatékonyabb gyökfogó membránokban. A PUFA-kban mindig megtalálható allil-C-H kötések és különböző típusú gyökök reakcióinak kiterjedt vizsgálata folyt. | Polyunsaturated fatty acids (PUFA) play an important role as an antioxidant in the whole human body but more specifically in the brain. The overall project had 4 Topics: Topic 1 Fundamental Thermodynamics of Molecular Conformational Changes: Simple organic molecules were investigated in computing continues thermodynamic functions along conformational changes. These included a variety of compounds from hydrocarbons to peptides. Topic 2 Conformational information of fatty acid: Interestingly enough their felxibility was similar to that of peptides as could be judged from the similarity of their conformational potential energy surfaces. Topic 3 Conformational information of phospholipids: The results and experience obtained from the first two topics were used to construct simple phospholipids. The relative orientations of the two fatty acids in a phospholipid had to be studied to see if the nearly parallel arrangement within the lipid bilayer is enforced by nearest neighbour interaction or if such a geometry is an intrinsically stable structure. Topic 4 Free radical reactions with PUFA and PUFA models: Free radicals and their reactions with PUFA within the lipid bilayer are a biologically very important reactions. The generation of free radicals and their transformation as well as their reactions with allylic C-H bonds, which are always present is PUFA, has been studied in details

Grain Surface Models and Data for Astrochemistry

AbstractThe cross-disciplinary field of astrochemistry exists to understand the formation, destruction, and survival of molecules in astrophysical environments. Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. A broad consensus has been reached in the astrochemistry community on how to suitably treat gas-phase processes in models, and also on how to present the necessary reaction data in databases; however, no such consensus has yet been reached for grain-surface processes. A team of ∼25 experts covering observational, laboratory and theoretical (astro)chemistry met in summer of 2014 at the Lorentz Center in Leiden with the aim to provide solutions for this problem and to review the current state-of-the-art of grain surface models, both in terms of technical implementation into models as well as the most up-to-date information available from experiments and chemical computations. This review builds on the results of this workshop and gives an outlook for future directions