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Int. J. Mol. Sci., Volume 5, Issue 11 (November-December 2004), Pages 265-346

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Research

Open AccessArticle State Selective Electron Capture in the Collision of S3+ Ions in Atomic Hydrogen and Helium
Int. J. Mol. Sci. 2004, 5(11), 265-275; doi:10.3390/i5110265
Received: 8 September 2004 / Revised: 9 November 2004 / Accepted: 9 November 2004 / Published: 30 November 2004
Cited by 8 | PDF Full-text (455 KB) | HTML Full-text | XML Full-text
Abstract
A full theoretical treatment including an ab-initio molecular calculation of the potential energy curves and couplings followed by a semi-classical collision dynamics has been performed for the one-electron capture by S3+ ions in collision with atomic hydrogen. The present paper completes [...] Read more.
A full theoretical treatment including an ab-initio molecular calculation of the potential energy curves and couplings followed by a semi-classical collision dynamics has been performed for the one-electron capture by S3+ ions in collision with atomic hydrogen. The present paper completes a previous letter [9] and displays the full results concerning this process in order to provide a detailed understanding of the mechanism. These calculations show evidence of the predominance of the S2+(3s23p3d)3F° capture level, already pointed out by translational energy spectroscopy experiments and confirms experimental measurements. A compared study of the behaviour of the S3+ projectile colliding both hydrogen and helium targets is also presented. Full article
Open AccessArticle Nucleic Acid Quadratic Indices of the “Macromolecular Graph’s Nucleotides Adjacency Matrix”. Modeling of Footprints after the Interaction of Paromomycin with the HIV-1 Ψ-RNA Packaging Region
Int. J. Mol. Sci. 2004, 5(11), 276-293; doi:10.3390/i5110276
Received: 28 January 2004 / Revised: 9 November 2004 / Accepted: 10 November 2004 / Published: 30 November 2004
Cited by 32 | PDF Full-text (347 KB) | HTML Full-text | XML Full-text
Abstract
This report describes a new set of macromolecular descriptors of relevance to nucleic acid QSAR/QSPR studies, nucleic acids’ quadratic indices. These descriptors are calculated from the macromolecular graph’s nucleotide adjacency matrix. A study of the interaction of the antibiotic Paromomycin with the packaging region of the RNA present in type-1 HIV illustrates this approach. A linear discriminant function gave rise to excellent discrimination between 90.10% (91/101) and 81.82% (9/11) of interacting/noninteracting sites of nucleotides in training and test set, respectively. The LOO crossvalidation procedure was used to assess the stability and predictability of the model. Using this approach, the classification model has shown a LOO global good classification of 91.09%. In addition, the model’s overall predictability oscillates from 89.11% until 87.13%, when n varies from 2 to 3 in leave-n-out jackknife method. This value stabilizes around 88.12% when n was > 3. On the other hand, a linear regression model predicted the local binding affinity constants [log K (10-4M-1)] between a specific nucleotide and the aforementioned antibiotic. The linear model explains almost 92% of the variance of the experimental log K (R = 0.96 and s = 0.07) and LOO press statistics evidenced its predictive ability (q2 = 0.85 and scv = 0.09). These models also permit the interpretation of the driving forces of the interaction process. In this sense, developed equations involve short-reaching (k < 3), middle-reaching (4 < k < 9) and far-reaching (k = 10 or greater) nucleotide’s quadratic indices. This situation points to electronic and topologic nucleotide’s backbone interactions control of the stability profile of Paromomycin-RNA complexes. Consequently, the present approach represents a novel and rather promising way to chem & bioinformatics research. Full article
Open AccessArticle Enol and Enethiol Occurrence for Some Ketones and Thioketones. Mass Spectrometry and Theoretical Calculations
Int. J. Mol. Sci. 2004, 5(11), 294-300; doi:10.3390/i5110294
Received: 31 January 2004 / Revised: 9 October 2004 / Accepted: 5 November 2004 / Published: 30 November 2004
Cited by 12 | PDF Full-text (154 KB) | HTML Full-text | XML Full-text
Abstract
The mass spectra of ketones can provide valuable information with regards to keto-enol equilibria occurring in the gas phase. Mass spectra of selected ketones and thioketones have been analysed and specific fragmentation assignments have been done to characterised and weigh co-existing keto [...] Read more.
The mass spectra of ketones can provide valuable information with regards to keto-enol equilibria occurring in the gas phase. Mass spectra of selected ketones and thioketones have been analysed and specific fragmentation assignments have been done to characterised and weigh co-existing keto and enol tautomers. Thioketones are of particular interest due to their tendency to shift the tautomeric equilibrium towards the enethiol form. The predictive value of this methodology is not only supported by the influence of these compound’s nature and size of the substituent on these equilibria but also by the good correlation found between the selected fragments abundances ratio and semi-empirical calculation (AM1) of the corresponding heats of tautomerization. Full article
Open AccessArticle Vertical Ionization Energies of α-L-Amino Acids as a Function of Their Conformation: an Ab Initio Study
Int. J. Mol. Sci. 2004, 5(11), 301-332; doi:10.3390/i5110301
Received: 24 September 2004 / Accepted: 9 November 2004 / Published: 30 November 2004
Cited by 48 | PDF Full-text (318 KB) | HTML Full-text | XML Full-text
Abstract
Vertical ionization energies (IE) as a function of the conformation are determined at the quantum chemistry level for eighteen α-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT) framework using the hybrid method B3LYP and the [...] Read more.
Vertical ionization energies (IE) as a function of the conformation are determined at the quantum chemistry level for eighteen α-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT) framework using the hybrid method B3LYP and the 6-31G**(5d) basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF) method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO) can change a lot as a function of the nuclear structure. Full article
Open AccessArticle Calculated Electronic Behavior and Spectrum of Mg+@C60 Using a Simple Jellium-shell Model
Int. J. Mol. Sci. 2004, 5(11), 333-346; doi:10.3390/i5110333
Received: 13 July 2004 / Accepted: 15 November 2004 / Published: 30 November 2004
Cited by 1 | PDF Full-text (267 KB) | HTML Full-text | XML Full-text
Abstract
We present a method for calculating the energy levels and wave functions of any atom or ion with a single valence electron encapsulated in a Fullerene cage using a jelluim-shell model. The valence electron-core interaction is represented by a one-body pseudo-potential obtained [...] Read more.
We present a method for calculating the energy levels and wave functions of any atom or ion with a single valence electron encapsulated in a Fullerene cage using a jelluim-shell model. The valence electron-core interaction is represented by a one-body pseudo-potential obtained through density functional theory with strikingly accurate parameters for Mg+ and which reduces to a purely Coulombic interaction in the case of H. We find that most energy states are affected little by encapsulation. However, when either the electron in the non-encapsulated species has a high probability of being near the jellium cage, or when the cage induces a maximum electron probability density within it, the energy levels shift considerably. Mg+ shows behavior similar to that of H, but since its wave functions are broader, the changes in its energy levels from encapsulation are slightly more pronounced. Agreement with other computational work as well as experiment is excellent and the method presented here is generalizable to any encapsulated species where a one-body electronic pseudo-potential for the free atom (or ion) is available. Results are also presented for off-center hydrogen, where a ground state energy minimum of -14.01 eV is found at a nuclear displacement of around 0.1 Å. Full article

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