Structure and singly occupied molecular orbital analysis of anionic tautomers of guanine

Recently we reported the discovery of adiabatically bound anions of guanine which might be involved in the processes of DNA damage by low-energy electrons and in charge transfer through DNA. These anions correspond to some tautomers that have been ignored thus far. They were identified using a hybrid quantum mechanical-combinatorial approach in which an energy-based screening was performed on the library of 499 tautomers with their relative energies calculated with quantum chemistry methods. In the current study we analyze the adiabatically bound anions of guanine in two aspects: 1) the geometries and excess electron distributions are analyzed and compared with anions of the most stable neutrals to identify the sources of stability; 2) the chemical space of guanine tautomers is explored to verify if these new tautomers are contained in a particular subspace of the tautomeric space. The first task involves the development of novel approaches – the quantum chemical data like electron density, orbital and information on its bonding/antibonding character are coded into holograms and analyzed using chemoinformatics techniques. The second task is completed using substructure analysis and clustering techniques performed on molecules represented by 2D fingerprints. The major conclusion is that the high stability of adiabatically bound anions originates from the bonding character of the pi orbital occupied by the excess electron. This compensates for the antibonding character that usually causes significant buckling of the ring. Also the excess electron is more homogenously distributed over both rings than in the case of anions of the most stable neutral species. In terms of 2D substructure, the most stable anionic tautomers generally have additional hydrogen atoms at C8 and/or C2 and they don’t have hydrogen atoms attached to C4, C5 and C6. They also form an “island of stability” in the tautomeric space of guanine

Percolation transition of hydration water at hydrophilic surfaces

An analysis of water clustering is used to study the quasi-2D percolation transition of water adsorbed at planar hydrophilic surfaces. Above the critical temperature of the layering transition (quasi-2D liquid-vapor phase transition of adsorbed molecules) a percolation transition occurs at some threshold surface coverage, which increases with increasing temperature. The location of the percolation line is consistent with the existence of a percolation transition at the critical point. The percolation threshold at a planar surface is weakly sensitive to the size of the system when its lateral dimension increases from 80 to 150 A. The size distribution of the largest water cluster shows a specific two-peaks structure in a wide range of surface coverage : the lower- and higher-size peaks represent contributions from non-spanning and spanning clusters, respectively. The ratio of the average sizes of spanning and non-spanning largest clusters is about 1.8 for all studied planes. The two-peak structure becomes more pronounced with decreasing size of the planar surface and strongly enhances at spherical surfaces.Comment: 17 pages, 11 figure

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

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

Precise 3D track reconstruction algorithm for the ICARUS T600 liquid argon time projection chamber detector

Liquid Argon Time Projection Chamber (LAr TPC) detectors offer charged particle imaging capability with remarkable spatial resolution. Precise event reconstruction procedures are critical in order to fully exploit the potential of this technology. In this paper we present a new, general approach of three-dimensional reconstruction for the LAr TPC with a practical application to track reconstruction. The efficiency of the method is evaluated on a sample of simulated tracks. We present also the application of the method to the analysis of real data tracks collected during the ICARUS T600 detector operation with the CNGS neutrino beam.Comment: Submitted to Advances in High Energy Physic

A search for the analogue to Cherenkov radiation by high energy neutrinos at superluminal speeds in ICARUS

The OPERA collaboration has claimed evidence of superluminal {\nu}{_\mu} propagation between CERN and the LNGS. Cohen and Glashow argued that such neutrinos should lose energy by producing photons and e+e- pairs, through Z0 mediated processes analogous to Cherenkov radiation. In terms of the parameter delta=(v^2_nu-v^2_c)/v^2_c, the OPERA result implies delta = 5 x 10^-5. For this value of \delta a very significant deformation of the neutrino energy spectrum and an abundant production of photons and e+e- pairs should be observed at LNGS. We present an analysis based on the 2010 and part of the 2011 data sets from the ICARUS experiment, located at Gran Sasso National Laboratory and using the same neutrino beam from CERN. We find that the rates and deposited energy distributions of neutrino events in ICARUS agree with the expectations for an unperturbed spectrum of the CERN neutrino beam. Our results therefore refute a superluminal interpretation of the OPERA result according to the Cohen and Glashow prediction for a weak current analog to Cherenkov radiation. In particular no superluminal Cherenkov like e+e- pair or gamma emission event has been directly observed inside the fiducial volume of the "bubble chamber like" ICARUS TPC-LAr detector, setting the much stricter limit of delta < 2.5 10^-8 at the 90% confidence level, comparable with the one due to the observations from the SN1987A.Comment: 17 pages, 6 figure

Search for anomalies in the {\nu}e appearance from a {\nu}{\mu} beam

We report an updated result from the ICARUS experiment on the search for {\nu}{\mu} ->{\nu}e anomalies with the CNGS beam, produced at CERN with an average energy of 20 GeV and travelling 730 km to the Gran Sasso Laboratory. The present analysis is based on a total sample of 1995 events of CNGS neutrino interactions, which corresponds to an almost doubled sample with respect to the previously published result. Four clear {\nu}e events have been visually identified over the full sample, compared with an expectation of 6.4 +- 0.9 events from conventional sources. The result is compatible with the absence of additional anomalous contributions. At 90% and 99% confidence levels the limits to possible oscillated events are 3.7 and 8.3 respectively. The corresponding limit to oscillation probability becomes consequently 3.4 x 10-3 and 7.6 x 10-3 respectively. The present result confirms, with an improved sensitivity, the early result already published by the ICARUS collaboration