Carlos A. Del Carpio

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

Ligand–protein interactions have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. Fragmented quantum molecular chemical studies are also a choice to study the enzyme–ligand system holistically, however there are still restrictions on the number of water molecules that can be included in a study of this nature. In this work we adopt a completely different approach to study ligand–protein interactions accounting explicitly for as many solvent molecules as possible and without the need for a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum chemical molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, which combined with the MD paradigm results in an ultra-accelerated QCMD method for protein–ligand interaction evaluations. We have applied our newly developed system to the dihydrofolate reductase (DHFR)–methotrexate (MTX) system. We show how the proposed method leads us to new insights into the main interactions that bind MTX to the enzyme, mainly the interaction between the amino group of MTX and Asp27 of DHFR, as well as MTX amino group with Thr113 of DHFR, which have been only elucidated experimentally to date.

Experimental and Molecular Dynamics Simulations of Tribochemical Reactions with ZDDP: Zinc Phosphate–Iron Oxide Reaction

Zinc phosphate glass is considered to be the main constituent of tribofilms generated under boundary lubrication with zinc dialkyldithiophosphate (ZDDP), a well-known antiwear additive. The reaction occurring during friction between zinc phosphate glasses and steel native iron oxide layer is investigated by both an experimental approach and by Molecular Dynamics simulations (MD). The importance of this “tribochemical” reaction in the general ZDDP antiwear process is discussed.

Tight-Binding Quantum Chemical Molecular Dynamics Study on First Proton Transfer Process of ORR Catalyzed by Cobalt-Porphyrin Complex

We investigated oxygen reduction reaction (ORR) dynamics catalyzed by cobalt-porphyrin using our original novel tight-binding quantum chemical molecular dynamics method. First, we determined parameters for tight-binding calculation based on first-principles parameterization. We have successfully simulated a first proton transfer process of the oxygen reduction reaction with the explicit consideration of surrounding water molecules. The transferred proton formed hydrogen bonding with a water molecule and conformational change of the OOH species was observed. It was proved that our tight-binding quantum chemical molecular dynamics method is effective for the investigation of oxygen reduction reaction dynamics in large complex system.

Effect of Surface Termination on Superlow Friction of Diamond Film: A Theoretical Study

We have applied molecular dynamics simulation and density functional theory calculations to analyze the effects of H and OH terminations on the frictional properties of diamond films at the atomistic and electronic levels. Molecular dynamics simulations were carried out for H-, OH-, and non-terminated diamond surfaces against an iron surface. Results of molecular dynamics simulations show that the frictional force is clearly decreased by the H or OH termination on the diamond surfaces. Moreover, results of density functional calculations show that a covalent bond is formed between Fe and C, while H- or OH-terminated diamond surfaces interact repulsively with an iron surface owing to antibonding interactions. We concluded that this interaction change between iron and diamond surfaces is the major contributing factor for achieving a low friction in H- or OH-terminated diamond.

Theoretical Study on Electronic and Electrical Properties of Nanostructural ZnO

The electronic and electrical properties of ZnO semiconductor single wall nanotube were investigated using periodic supercell approach within density functional theory combined with tight-binding quantum chemistry method. Armchair (10,10) and zigzag (10,0) nanotubes were considered. The lower strain energies required to roll up a ZnO graphitic sheet into a tube and the negative cohesive energies implied the possibility for the formation of ZnO single wall nanotubes. It was shown that the band gaps between the valence band maximum (VBM) and conduction band minimum (CBM) of nanotubes calculated by means of the two methods are similar and are larger than that of the bulk ZnO. It was found that the band gaps of ZnO nanotube are relatively insensitive to the chirality and diameter. According to the estimated electrical conductivities, the non-defect bulk and nanotube ZnO exhibited insulator properties, while they exhibited semiconductor properties when oxygen vacancies are introduced in the structures. The relative stability and band gap of fullerene-like ZnO clusters were also analyzed.

Theoretical investigation of the photophysical properties of black dye sensitizer [(H3-tctpy)M(NCS)3]-(M = Fe, Ru, Os) in dye sensitized solar cells

The electronic properties and optical absorption spectrum of the photovoltaic sensitizer [(H3-tctpy)M(NCS)3]- (M = Fe, Ru and Os) in ethanol solvent are investigated using density functional theory/time-dependent density functional theory. The calculated absorption spectrum is in agreement with experiment for ruthenium complex, thus allowing an assignment of UV–visible spectral features of the dye. Red shift in the absorption spectrum is observed moving down the group from iron to osmium. The observed red shift in ruthenium and osmium complexes appears to be related to the destabilization of the occupied orbitals with t2g-NCS π* character. In osmium complex, the increase in the orbital splitting energy d (t2g–eg) is found due to the destabilization of the eg orbitals. The weak d–d transitions are observed only in iron and ruthenium complexes.

Large-scale electronic structure calculation on blue phosphor BaMgAl10O17:Eu2+ using tight-binding quantum chemistry method implemented for rare-earth elements

In this study, we carried out large-scale electronic structure calculations on blue phosphor BaMgAl10O17:Eu2+ (BAM) using an self-consistent charge (SCC) tight-binding quantum chemistry method with an improved convergence for the 4 f orbitals of rare-earth elements. Calculation results obtained by the present method are in good agreement with first-principles and experimental results. We first compared the thermodynamic stability and the electronic structures for three different Eu sites. A first-principles calculation showed that the Beevers–Ross site was the most stable site for the Eu atom. Large-scale electronic structure calculations by the improved SCC tight-binding quantum chemistry method suggested that the electronic structures of Eu 5d orbitals are dependent on the shape of Eu 5d orbitals and the positions of oxygen atoms around the Eu atom. We also investigated the effects of an oxygen vacancy (VO) on the luminescence properties of BAM. We found that energy levels of molecular orbitals (MOs) with main contributions from Eu 5d orbitals were shifted lower by the VO near the Eu atom, and thus our results suggested that the formation of the VO near the Eu atom leads to the red shift of the luminescence color.

Quantum chemical studies for oxidation of morpholine by Cytochrome P450

Since morpholine oxidation has recently been shown to involve Cytochrome P450, the study on its mechanism at molecular level using quantum chemical calculations for the model of cytochrome active site is reported here. The reaction pathway is investigated for two electronic states, the doublet and the quartet, by means of density functional theory. The results show that morpholine hydroxylation occurs through hydrogen atom abstraction and rebound mechanism. However, in the low spin state, the reaction is concerted and hydrogen atom abstraction yields directly ferric-hydroxy morpholine complex without a distinct rebound step while in quartet state the reaction is stepwise. The presence of nitrogen in a morpholine heterocycle is postulated to greatly facilitate hydrogen abstraction. The hydroxylated product undergoes intramolecular hydrogen atom transfer from hydroxy group to nitrogen, leading to the cleavage of the C-N bond and the formation of 2-(2-aminoethoxy) acetaldehyde. The cleavage of the C-N bond is indicated as the rate-determining step for the studied reaction. The assistance of explicit water molecule is shown to lower the energy barrier for the C-N bond cleavage in enzymatic environment whereas solvent effects mimicked by COSMO solvent model have minor influence on relative energies along the pathway.

Development of Multiscale Simulator for Dye-Sensitized TiO2 Nanoporous Electrode Based on Quantum Chemical Calculation

In this study, we have developed a novel multiscale simulator for a dye-sensitized TiO2 porous electrode. In the simulator, we can estimate the properties of the dye-sensitized TiO2 porous electrode using the three-dimensional mesoscopic structure model constructed on the basis of our original porous structure simulator. The microscopic physical properties of the materials were estimated by quantum chemistry calculation using a tight-binding quantum chemical molecular dynamics program. From the calculation results, we determined the absorption coefficient and the diffusion coefficient of excited carriers used in the macroscopic simulation for photoelectrode characteristics. By using this multiscale simulator, we will be able to determine the best electrode system efficiently.

Host emission from BaMgAl10O17 and SrMgAl10O17 phosphor: Effects of temperature and defect level

— Understanding the mechanism of blue-light emission in Eu-doped BAM phosphor as well as its sensitive degradation is required because this is a very important material in fluorescent lamps and plasma-display panels. In this study, both theoretical and experimental investigations on the host emissions in BaMgAl10O17 and SrMgAl10O17 were performed. Host emissions from BaMgAl10O17 and SrMgAl10O17 by photoluminescence and thermoluminescence spectra were observed. Photoluminescence spectra suggested that the host emission from SrMgAl10O17 was easily quenched by thermal vibrations. The thermoluminescence spectra showed the existence of shallow and deep defect levels in BaMgAl10O17 and SrMgAl10O17 phosphors. It was shown that SrMgAl10O17 and its conduction plane could undergo degradation during irradiation of vacuum-ultra-violet (VUV) lights based on the calculated energy of formation of an oxygen vacancy. Moreover, the structural defects, such as oxygen vacancies, would cause localizing levels in the upper level in the valence band and in theconduction band. The results suggest the contribution of the host emission to the energy transfer to the Eu atoms would not be significant and the oxygen vacancies would act as the traps for excited carriers.