QSPR Prediction of Lipophilicity for Organic Compounds Using Random Forest Technique on the Basis of Simplex Representation of Molecular Structure.

The relationship between the octanol-water partition coefficient for more than twelve thousand organic compounds and their structures was investigated using a QSPR approach based on Simplex Representation of Molecular Structure (SiRMS). The dataset used in our study included 10973 compounds with experimental values of lipophilicity (LogKow ) for different chemical compounds. Random Forest (RF) method was used for statistical modeling at the 2D level of representation of molecular structure.

Could hydrolysis of arsenic substituted DNA be prevented? Protection arises from stacking interactions.

Investigation of the hydrolysis of dinucleoside-arsenate-deoxyguanylyl-3',5'-deoxyguanosine (dGAsdG(-)) reveals that base-stacking in DNA increases the resistance of As-DNA towards hydrolysis. Base-stacking raises the activation energy of hydrolysis. Hydrolysis of As-DNA is found to be endothermic.

Structural and electronic property responses to the arsenic/phosphorus exchange in GC-related DNA of the B-form.

The suggestion that phosphorus/arsenic replacement in DNA can play a role in living things has generated great controversy (Wolfe-Simon et al., Science 2011, 332, 1163). Examined here theoretically are substitution effects on Watson-Crick base pairing and base stacking patterns in realistic DNA subunits.

Room temperature synthesis of PbSe quantum dots in aqueous solution: stabilization by interactions with ligands.

An aqueous route of synthesis is described for rapid synthesis of lead selenide quantum dots (PbSe QDs) at room temperature in an attempt to produce water-soluble and stable nanocrystals. Several thiol-ligands, including thioglycolic acid (TGA), thioglycerol (TGC), 3-mercaptopropionic acid (MPA), 2-mercaptoethylamine hydrochloride (MEA), 6-mercaptohexanoic acid (MHA), and l-cysteine (l-cys), were used for capping/stabilization of PbSe QDs. The effects of the ligands on the stability of PbSe QDs were evaluated for a period of two months at room temperature under normal light conditions and at 4 °C in the dark.

Molecular simulations of adsorption of RDX and TATP on IRMOF-1(Be).

The influence of different sorption sites of isoreticular metal-organic frameworks (IRMOFs) on interactions with explosive molecules is investigated. Different connector effects are taken into account by choosing IRMOF-1(Be) (IRMOF-1 with Zn replaced by Be), and two high explosive molecules: 1,3,5-trinitro-s-triazine (RDX) and triacetone triperoxide (TATP). The key interaction features (structural, electronic and energetic) of selected contaminants were analyzed by means of density functional calculations.

Electron attachment to the cytosine-centered DNA single strands: does base stacking matter?

Electron attachment to the trimer of nucleotide, dGpdCpdG, has been investigated by a quantum mechanical approach at a reliable level of theory. The study of the electron attached dGpdCpdG species demonstrates that cytosine contained DNA single strands have a strong tendency to capture low-energy electrons and to form electronically stable cytosine-centered radical anions. The comparative study of the model molecules pdCpdG and dGpdCp reveals that base stacking has little contribution to the adiabatic electron affinity (AEA) of cytosine in DNA single strands.

Use of quantitative structure-enantioselective retention relationship for the liquid chromatography chiral separation prediction of the series of pyrrolidin-2-one compounds.

In this work, the enantioseparation of 15 structurally similar chiral solutes is studied, and analysis of the retention factors is performed using a genetic algorithm and multiple linear regression analysis technique. The present quantitative structure-enantioselective retention relationship model generated for retention factors' data has confirmed the importance of a number of descriptors altering the retention behavior and enantioselectivity of the studied compounds. Thus, fragment-based descriptor PSA, which encodes polar surface area, has confirmed the crucial role of heteroatoms in the retention behavior exhibited by pyrroliddin-2-ones.

Low energy electron attachment to the adenosine site of DNA.

To evaluate the role of adenosine in low energy electron (LEE) induced DNA strand breaks, theoretical investigations of the LEE attachment induced C-O σ bonds and N-glycosidic bond breaking of 2'-deoxyadenosine-3',5'-diphosphate (3',5'-dAMP) were performed at the B3LYP/DZP++ level of theory. The results indicate that, although adenine-rich oligonucleotides are capable of capturing the near 0 eV electron to form the electronically stable radical anions in the gas phase, it is unlikely to undergo either C-O σ bond cleavage or the glycosidic processes due to the low electron detachment energy (VDE) of 3',5'-dADP(-) unit (0.26 eV).

SMILES-based QSAR approaches for carcinogenicity and anticancer activity: comparison of correlation weights for identical SMILES attributes.

CORAL software (http://www.insilico.eu/coral/) has been used for modeling of carcinogenicity (logTD50) of 401 compounds, and anticancer activity (-logIC50) of 100 compounds, on the basis of quantitative structure activity relationships (QSAR).

Echocardiographic evaluation of aorto-iliac occlusive disease.

Several studies demonstrated feasibility of visual assessment of the common femoral artery Doppler waveform, in an indirect evaluation of aorto-iliac segment stenosis. Patients with cardiac diseases referred for echocardiography often have coexistent arterial pathology. Since many of them are potential candidates for endovascular procedures, we decided to study, whether echocardiography can be useful for detection of aorto-iliac occlusive disease.

Electronic structures and thermochemical properties of the small silicon-doped boron clusters B(n)Si (n=1-7) and their anions.

We perform a systematic investigation on small silicon-doped boron clusters B(n)Si (n=1-7) in both neutral and anionic states using density functional (DFT) and coupled-cluster (CCSD(T)) theories. The global minima of these B(n)Si(0/-) clusters are characterized together with their growth mechanisms. The planar structures are dominant for small B(n)Si clusters with n≤5.

Theoretical studies on interactions between low energy electrons and protein-DNA fragments: valence anions of AT-amino acids side chain complexes.

Electron attachment to trimeric complexes that mimic most frequent hydrogen bonding interactions between an amino acid side chain (AASC) and the Watson-Crick (WC) 9-methyladenine-1-methylthymine (MAMT) base pair has been studied at the B3LYP/6-31++G(d,p) level of theory. Although the neutral trimers will not occur in the gas phase due to unfavorable free energy of stabilization (G(stab)) they should form a protein-DNA complex where entropy changes related to formation of such a complex will more than balance its disadvantageous G(stab). The most stable neutrals possess an identical pattern of hydrogen bonds (HBs).

Hydrazine bisalane is a potential compound for chemical hydrogen storage. A theoretical study.

Electronic structure calculations suggest that hydrazine bisalane (AlH(3)NH(2)NH(2)AlH(3), alhyzal) is a promising compound for chemical hydrogen storage (CHS). Calculations are carried out using the coupled-cluster theory CCSD(T) with the aug-cc-pVTZ basis set. Potential energy surfaces are constructed to probe the formation of, and hydrogen release from, hydrazine bisalane which is initially formed from the reaction of hydrazine with dialane.

Evaluation of natural and nitramine binding energies to 3-D models of the S1S2 domains in the N-methyl-D-aspartate receptor.

Overactivation of the N-methyl-D-aspartate receptor (NMDAR) in postsynaptic neurons leads to glutamate-related excitotoxicity in the central nervous system of mammals. We have built 3-D models of each domain for the universal screening of potential toxicants and their binding mechanisms. Our docking results show that the calculated pK (i) values of glycine and L: -glutamate significantly increase (>1) when the NR1 and NR2A S1S2 domains are closing, respectively.

Aromaticity in heterocyclic analogues of benzene: comprehensive analysis of structural aspects, electron delocalization and magnetic characteristics.

The degree of aromaticity of six-membered monoheterocycles with IV-VI group heteroatoms (C(6)H(5)X, where X = SiH, GeH, N, P, As, O(+), S(+), Se(+)) was analyzed using the results of ab initio calculations at the MP2/cc-pvtz level. Values of common aromaticity indices including those based on electronic delocalization properties, structural-dynamic features and magnetic properties all indicate high aromaticity of all considered heterocycles. A decrease in aromaticity is observed with increasing atomic number of the heteroatom, except in the case of the pyrylium cation.

QSAR analysis of the toxicity of nitroaromatics in Tetrahymena pyriformis: structural factors and possible modes of action.

The Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) was applied to 95 diverse nitroaromatic compounds (including some widely known explosives) tested for their toxicity (50% inhibition growth concentration, IGC₅₀) against the ciliate Tetrahymena pyriformis. The dataset was divided into subsets according to putative mechanisms of toxicity. The Classification and Regression Trees (CART) approach implemented within HiT QSAR has been used for prediction of mechanism of toxicity for new compounds.

CORAL: quantitative structure-activity relationship models for estimating toxicity of organic compounds in rats.

For six random splits, one-variable models of rat toxicity (minus decimal logarithm of the 50% lethal dose [pLD50], oral exposure) have been calculated with CORAL software (http://www.insilico.eu/coral/).

The electronic spectra of the sandwich stacked PFBT: a theoretical study.

Stacked models that include 9,9'-bis(6''-N,N,N-trimethylammonium)hexyl]fluorene-co-alt-4,7-(2,1,3-benzothiadiazole)dibromide (F(BT)F) monomer sandwiched between two stacked 2,1,3-benzothiadiazole (BT) units were explored using theoretical approaches. Molecular structures and the optical characteristics of the investigated species were investigated at the M06-2X/6-311G(d,p)//TD-M06-2X/6-311G(d,p) level of theory. In all models, the electronic excitation to the lowest singlet ππ* excited state (S1(ππ*)) is governed by the highest occupied molecular orbital to lowest unoccupied molecular orbital (HOMO → LUMO) transitions.

Toward robust computational electrochemical predicting the environmental fate of organic pollutants.

A number of density functionals was utilized for the calculation of electron attachment free energy for nitrocompounds, quinones and azacyclic compounds. Different solvation models have been tested on the calculation of difference in free energies of solvation of oxidized and reduced forms of nitrocompounds in aqueous solution, quinones in acetonitrile, and azacyclic compounds in dimethylformamide. Gas-phase free energies evaluated at the mPWB1K/tzvp level and solvation energies obtained using SMD model to compute solvation energies of neutral oxidized forms and PCM(Pauling) to compute solvation energies of anion-radical reduced forms provide reasonable accuracy of the prediction of electron attachment free energy, difference in free solvation energies of oxidized and reduced forms, and as consequence yield reduction potentials in good agreement with experimental data (mean absolute deviation is 0.

Activation of the cisplatin and transplatin complexes in solution with constant pH and concentration of chloride anions; quantum chemical study.

The thermodynamics of cisplatin and transplatin hydration is studied within the model of constant pH solution. Several implicit solvation models were chosen for the determination of pK(a) and pK constants of the hydration reactions. The polarizable dielectric model (DPCM), integral equation formalism polarizable model (IEFPCM), and polarizable conductor model (CPCM) were combined with the 'united atom model for Hartree-Fock' (UAHF) method for cavity construction and the B3LYP/6-31++G(2dp,2pd) level of calculations for the determination of electronic energies.

Theoretical study of the surface properties of poly(dimethylsiloxane) and poly(tetrafluoroethylene).

Molecular dynamics (MD) simulations of poly(dimethylsiloxane) (PDMS) and poly(tetrafluoroethylene) (PTFE) were carried out to determine their surface properties and energies. This study helps to gain better insight into the molecular modeling of PDMS and PTFE, in particular how different approaches affect calculations of surface energy. Current experimental and theoretical data were used to further understand the surface properties of PDMS and PTFE as well as to validate and verify results obtained from the combination of density functional theory (DFT) calculations (including periodic boundary conditions) and MD simulations.

QSAR modeling of acute toxicity on mammals caused by aromatic compounds: the case study using oral LD50 for rats.

The goal of the study was to predict toxicity in vivo caused by aromatic compounds structured with a single benzene ring and the presence or absence of different substituent groups such as hydroxyl-, nitro-, amino-, methyl-, methoxy-, etc., by using QSAR/QSPR tools. A Genetic Algorithm and multiple regression analysis were applied to select the descriptors and to generate the correlation models.