Molecular clusters of hydrogen, deuterium, and tritium: especially cationic species H3+(H2)m: m=2, 5 and 14

Presentado a la Conferencia "Nanotechnology: Power of Computation for Nanotechnology" celebrada en Gran Canaria (España) el 19 de mayo de 2003.Two recent experimental studies by Zweiback et al. and by Gobet et al. have motivated us to study the ground-state geometry and the consequent electronic structure of the singly-charged cationic hydrogen cluster H3+(H2)m for m=2,5 and 14, using at first the Hartree-Fock approximation. For the H+7 cluster the fully optimized ground-state geometry yeilds an isosceles triangle H3, with charge ~ 0.85(e), and sides 0.852 and 0.884 Å flanked by two H2 molecules lying parallel to each other, wiht bond lengths of 0.740 Å. In contrast, for the H+13 cluster, the central 'building block' is equilateral H3 with bond length 0.861 Å, and with charge ~0.815(e). This configuration of H3 is flanked by three almost-parallel H2 molecules with bond length 0.739 A. MP2 refinements of geometry, charge distribution and normal mode vibrational frequencies of the cationic tritium cluster T+7 and the corresponding deuterium cluster D+13 are also reported. Finally, Hartree-Fock and MP2 results are recorded for H+13.KVA thanks the University of Antwerp for financial support under grant GOA-BOF-UA nr 23. This work received financial support from MCyT of Spain Grants MAT2001-04499 and MAT2001-0946 and the EC-RTN program NANOPHASE (contract HPRN-CT-2000-00167), Basque Country University and Basque Hezkuntza Saila.Peer reviewe

Vibrational spectra and conformations of bis(N-ethyl)nitramine molecule

The Raman (50-3200 cm-1) and infrared (50-3200 cm-1) spectra of bis(N-ethyl)nitramine, (CH3CH2)2NNO2, in the liquid and crystal states have been recorded. Optimized geometries and conformational stabilities have been obtained from ab initio calculations utilizing the RHF/6-31G** level. This compound was shown to have two stable conformations with a planar nitramine fragment and the CH3 groups orthogonal to it and located either on the same or on the different sides of it. The computed energy difference between two conformers is 0.57 kcal/mol. (CH3CH2)2NNO2 exists as a mixture of the two conformations in the liquid state, while only the most stable one, with the CH3 groups located on the different sides of the nitramine fragment, remains in crystal state. The vibrational frequencies have been calculated using ab initio scaled force fields, and the vibrational spectra have been interpreted in detail

Trends in template/fragment-free protein structure prediction

Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward