Combinatorial–computational–chemoinformatics (C3) approach to finding and analyzing low-energy tautomers

Finding the most stable tautomer or a set of low-energy tautomers of molecules is critical in many aspects of molecular modelling or virtual screening experiments. Enumeration of low-energy tautomers of neutral molecules in the gas-phase or typical solvents can be performed by applying available organic chemistry knowledge. This kind of enumeration is implemented in a number of software packages and it is relatively reliable. However, in esoteric cases such as charged molecules in uncommon, non-aqueous solvents there is simply not enough available knowledge to make reliable predictions of low energy tautomers. Over the last few years we have been developing an approach to address the latter problem and we successfully applied it to discover the most stable anionic tautomers of nucleic acid bases that might be involved in the process of DNA damage by low-energy electrons and in charge transfer through DNA. The approach involves three steps: (1) combinatorial generation of a library of tautomers, (2) energy-based screening of the library using electronic structure methods, and (3) analysis of the information generated in step (2). In steps 1–3 we employ combinatorial, computational and chemoinformatics techniques, respectively. Therefore, this hybrid approach is named “Combinatorial*Computational*Chemoinformatics”, or just abbreviated as C3 (or C-cube) approach. This article summarizes our developments and most interesting methodological aspects of the C3 approach. It can serve as an example how to identify the most stable tautomers of molecular systems for which common chemical knowledge had not been sufficient to make definite predictions

Chemical Hieroglyphs: Abstract Depiction of Complex Void Space Topology of Nanoporous Materials

In general, most porous materials are so complex that structural information cannot be easily observed with 3D visualization tools. To address this problem, we have developed a special abstract 2D representation to depict all important topological features and geometrical parameters. Our approach involves reducing these structures based on symmetry and perceived building blocks to a compressed, graph representation that allows for quick structure analysis, classification, and comparison. © 2010 American Chemical Society

Mild hydration of didecyldimethylammonium chloride modified DNA by 1H-nuclear magnetic resonance and by sorption isotherm

The gaseous phase hydration of deoxyribonucleic acid and didecyldimethylammonium chloride (C19H42ClN) complexes (DNA-DDCA) was observed using hydration kinetics, sorption isotherm, and high power nuclear magnetic resonance. Three bound water fractions were distinguished: (i) a very tightly bound water not removed by incubation over silica gel, (ii) a tightly bound water saturating with the hydration time t(1)(h) (0.596 +/- 0.04) h, and a loosely bound water fraction, (iii) with the hydration time t(2)(h) (20.9 +/- 1.3) h. Proton free induction decay was decomposed into the signal associated with the solid matrix of DNA-DDCA complex (T-2S approximate to 30 mu s) and two liquid signal components coming from tightly bound (T-2L1 approximate to 100 mu s) and from loosely bound water fraction (T-2L2 approximate to 1000 mu s)

Fluorescence Efficiency and Visible Re-emission Spectrum of Tetraphenyl Butadiene Films at Extreme Ultraviolet Wavelengths

A large number of current and future experiments in neutrino and dark matter detection use the scintillation light from noble elements as a mechanism for measuring energy deposition. The scintillation light from these elements is produced in the extreme ultraviolet (EUV) range, from 60 - 200 nm. Currently, the most practical technique for observing light at these wavelengths is to surround the scintillation volume with a thin film of Tetraphenyl Butadiene (TPB) to act as a fluor. The TPB film absorbs EUV photons and reemits visible photons, detectable with a variety of commercial photosensors. Here we present a measurement of the re-emission spectrum of TPB films when illuminated with 128, 160, 175, and 250 nm light. We also measure the fluorescence efficiency as a function of incident wavelength from 120 to 250 nm.Comment: 15 pages, 9 figures, Submitted to Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipmen

Methane storage capabilities of diamond analogues

Methane can be an alternative fuel for vehicular usage provided that new porous materials are developed for its efficient adsorption-based storage. Herein, we search for materials for this application within the family of diamond analogues. We used density functional theory to investigate structures in which tetrahedral C atoms of diamond are separated by -CC- or -BN- groups, as well as ones involving substitution of tetrahedral C atoms with Si and Ge atoms. The adsorptive and diffusive properties of methane are studied using classical molecular simulations. Our results suggest that the all-carbon structure has the highest volumetric methane uptake of 280 VSTP/V at p = 35 bar and T = 298 K. However, it suffers from limited methane diffusion. Alternatively, the considered Si and Ge-containing analogies have fast diffusive properties but their adsorption is lower, ca. 172-179 VSTP/V, at the same conditions. © 2013 the Owner Societies