Excitation energy transfer pathways in light-harvesting proteins: Modeling with PyFREC.

Excitation energy transfer (EET) determines the fate of sunlight energy absorbed by light-harvesting proteins in natural photosynthetic systems and photovoltaic cells. As previously reported (D. Kosenkov, J.

Ab initio study of molecular interactions in cellulose Iα.

Biomass recalcitrance, the resistance of cellulosic biomass to degradation, is due in part to the stability of the hydrogen bond network and stacking forces between the polysaccharide chains in cellulose microfibers. The fragment molecular orbital (FMO) method at the correlated Møller-Plesset second order perturbation level of theory was used on a model of the crystalline cellulose Iα core with a total of 144 glucose units. These computations show that the intersheet chain interactions are stronger than the intrasheet chain interactions for the crystalline structure, while they are more similar to each other for a relaxed structure.

Evaluation of the dependence of aqueous solubility of nitro compounds on temperature and salinity: a COSMO-RS simulation.

The solubility in pure and saline water at various temperatures was calculated for selected nitro compounds (nitrobenzene, 1,3,5-trinitrobenzene, 2-nitrotoluene, 3-nitrotoluene, 4-nitrotoluene, 2,4-dinitrotoluene, 2,6-dinitrotoluene, 2,3-dinitrotoluene, 3,4-dinitrotoluene, 2,4,6-trinitrotoluene) using the Conductor-like Screening model for Real Solvents (COSMO-RS). The results obtained were compared with experimental values. The COSMO-RS predictions have shown high accuracy in reproducing the trends of aqueous solubilities for both temperature and salinity.

Application of quantum chemical approximations to environmental problems: prediction of water solubility for nitro compounds.

Water solubility values for 27 nitro compounds with experimentally measured values were computed using the conductor-like screening model for real solvent (COSMO-RS) based on the density functional theory and COSMO technique. We have found that the accuracy of the COSMO-RS approach for prediction of water solubility of liquid nitro compounds is impressively high (the errors are lower than 0.1 LU).

Effect of a pH change on the conformational stability of the modified nucleotide queuosine monophosphate.

The naturally occurring modified nucleotide queuosine 5'-monophosphate (QMP) related to biochemical regulatory pathways in the cell was investigated using quantum chemical approaches. The relative stability of biologically relevant conformations of QMP in solvent under a pH change was predicted at the BVP86/TZVP and MP2/TZVP levels of theory. Hydrogen bonding in QMP was studied using Bader's approach.

Predicting water solubility of congeners: chloronaphthalenes--a case study.

Since the important physicochemical data for chloronaphtalenes (PCNs) are still scarce, we have predicted water solubility (logS) of all 75 congeners with the Quantitative Structure-Property Relationship (QSPR) scheme. The values of logS, predicted by the most efficient model, varied from 0.01 to 1660 microg dm(-3) (2.

Ab initio kinetic simulation of gas-phase experiments: tautomerization of cytosine and guanine.

A novel kinetic approach based on ab initio calculated rate constants has been developed and implemented in the kTSim program. The proposed approach allows prediction of the distribution of reactant and product concentrations over time, based exclusively on computationally obtained rate constants. The newly developed methodology was used to simulate the process of evaporation and tautomerization of guanine and cytosine under thermal (T = 490 K, cytosine; T = 620 K, guanine) and laser (T = 1000 K, 24 ns laser pulse) desorption conditions.

CL-20 photodecomposition: ab initio foundations for identification of products.

1,5-Dihydrodiimidazo[4,5-b:4'5'e]pyrazine, 1H-imidazo[4,5-b]pyrazine, and 1H-imidazole were considered as possible products of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) photodecomposition. Since we took as a reference the product obtained after CL-20 irradiation in methanol solution, the nature of intermolecular bonds between heterocycles under study and methanol molecules was analyzed in detail. Existing hydrogen bonds were found to be quite strong, so dependence of calculations results on an influence of solvent was taken into account using both the polarizable continuum model (PCM) and the supermolecular approach.

Application of quantum-chemical approximations to environmental problems: Prediction of physical and chemical properties of TNT and related species.

This paper presents accurate predictions of ecologically important properties of nitroaromatic compounds and their derivatives, including vapor pressure, Henry's law constants, water solubility, octanol/water partition coefficients, heats of formation and ionization potentials. The proposed technique of calculations was based on quantum-chemical methods. The relationship between the chemical structure and mentioned physico-chemical parameters of such widespread military produced contaminants as trinitrotoluene and its derivatives was considered.

The mechanism of unimolecular decomposition of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane. A computational DFT study.

By using the B3LYP level of density functional theory, possible decomposition reaction pathways of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) in the gas phase have been investigated. We have found several types of reactions for this process: homolytic cleavage of an N-N bond to form the NO2* group; HONO elimination; C-C and C-N bonds breaking leading to ring opening; and H-migration. On the basis of the results of computation scanning of the potential energy surface, the most favorite pathway of CL-20 unimolecular decomposition that results in the formation of the stable aromatic compound 1,5-dihydrodiimidazo[4,5-b:4',5'-e]pyrazine has been proposed.