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Int. J. Mol. Sci., Volume 2, Issue 2 (June 2001), Pages 40-132

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Research

Open AccessArticle Structural And Energetic Changes of Si (100) Surface With Fluorine in Presence of Water – A Density Functional Study
Int. J. Mol. Sci. 2001, 2(2), 40-56; doi:10.3390/i2020040
Received: 16 November 2000 / Accepted: 28 January 2001 / Published: 1 May 2001
Cited by 1 | PDF Full-text (396 KB) | HTML Full-text | XML Full-text
Abstract
We report density functional electronic structure calculations to monitor the change in the surface characteristics of the Si (100)-2x1 surface after fluorination followed by interaction with water. Embedded finite silicon clusters are used to model an extended Si (100)-2x1 surface. Two high [...] Read more.
We report density functional electronic structure calculations to monitor the change in the surface characteristics of the Si (100)-2x1 surface after fluorination followed by interaction with water. Embedded finite silicon clusters are used to model an extended Si (100)-2x1 surface. Two high symmetry pathways and subsequent adsorption sites were examined: (i) adsorption of an fluorine atom directing onto a silicon dangling bond to form a monocoordinated fluorine atom (ii) adsorption of a fluorine atom directing on top of silicon dimer to form a bridging dicoordinated fluorine atom. However, in the later case we find that no barrier exists for the bridging fluorine atom to slide towards silicon dimer dangling bond to form more stable mono coordinated Si-F bond. We calculated activation barriers and equilibrium surface configuration as a function of fluorine coverage upto 2.0 ML. We compared the stability of the fluorinated surface. The results were compared with existing experimental and theoretical results. The reaction of water with HF treated Si surface is monitored. It produces, as a first step, the exchange of Si-F with water to form Si-OH groups reducing the concentration of the fluorine on the surface, followed by a rapture of Si-Si bonds and finally the Si-O-Si bridge formation in the lattice. Full article
Open AccessArticle Improved Molecular Descriptors Based on the Optimization of Correlation Weights of Local Graph Invariants
Int. J. Mol. Sci. 2001, 2(2), 57-65; doi:10.3390/i2020057
Received: 29 November 2000 / Accepted: 20 March 2001 / Published: 7 May 2001
Cited by 14 | PDF Full-text (56 KB) | HTML Full-text | XML Full-text
Abstract
We report the calculation of boiling points for several alkyl alcohols through the use of improved molecular descriptors based on the optimization of correlation weights of local invariants of graphs. As local invariants we have used the presence of different chemical elements [...] Read more.
We report the calculation of boiling points for several alkyl alcohols through the use of improved molecular descriptors based on the optimization of correlation weights of local invariants of graphs. As local invariants we have used the presence of different chemical elements (i.e. C, H, and O) and the existence of different vertex degree values (i.e. 1, 2, 3 and 4). The inherent flexibility of the chosen molecular descriptor seems to be rather suitable to obtain satisfactory enough predictions of the property under study. Comparison with other similar approximation reveals a very good behavior of the present method. The use of higher order polynomials do not seem to be necessary to improve results regarding the simple linear fitting equations. Some possible future extensions are pointed out in order to achieve a more definitive conclusion about this approximation. Full article
Open AccessArticle A Quantum Theory of Thermodynamic Relaxation
Int. J. Mol. Sci. 2001, 2(2), 66-71; doi:10.3390/i2020066
Received: 19 March 2001 / Accepted: 16 May 2001 / Published: 23 May 2001
Cited by 6 | PDF Full-text (32 KB) | HTML Full-text | XML Full-text
Abstract
A new approach to quantum Markov processes is developed and the corresponding Fokker-Planck-like equation is derived. The latter was examined to reproduce known results from classical and quantum physics. It was also applied to the phase-space description of a mechanical system thus [...] Read more.
A new approach to quantum Markov processes is developed and the corresponding Fokker-Planck-like equation is derived. The latter was examined to reproduce known results from classical and quantum physics. It was also applied to the phase-space description of a mechanical system thus leading to a new treatment of this problem different from the Wigner presentation. The equilibrium probability density obtained in the mixed coordinate-momentum space is a reasonable extension of the Gibbs canonical distribution. Full article
Open AccessArticle Characterizing Cavities in Model Inclusion Fullerenes: A Comparative Study
Int. J. Mol. Sci. 2001, 2(2), 72-88; doi:10.3390/i2020072
Received: 16 November 2000 / Accepted: 3 April 2001 / Published: 2 June 2001
Cited by 2 | PDF Full-text (160 KB) | HTML Full-text | XML Full-text
Abstract
The fullerene-82 cavity is selected as a model system in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecular surface, spherical tessellation of the [...] Read more.
The fullerene-82 cavity is selected as a model system in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecular surface, spherical tessellation of the molecular surface, numerical integration of the atomic volumes and surfaces, triangular tessellation of the molecular surface, and cubic lattice approach to the molecular volume. Accurate measures of the molecular volume and surface area have been performed with the pseudorandom Monte Carlo (MCVS) and uniform Monte Carlo (UMCVS) methods. These calculations serve as a reference for the rest of the methods. The SURMO2 method does not recognize the cavity and may not be convenient for intercalation compounds. The programs that detect the cavities never exceed 1% deviation relative to the reference value for molecular volume and 5% for surface area. The GEPOL algorithm, alone or combined with TOPO, shows results in good agreement with those of the UMCVS reference. The uniform random number generator provides the fastest convergence for UMCVS and a correct estimate of the standard deviations. The effect of the internal cavity on the solvent-accessible surfaces has been calculated. Fullerene-82 is compared with fullerene-60 and -70. Full article
Open AccessArticle Extended Coupled Cluster Approach for Molecular Properties: Study of H2O and HF Complexes
Int. J. Mol. Sci. 2001, 2(2), 89-102; doi:10.3390/i2020089
Received: 9 April 2001 / Accepted: 15 June 2001 / Published: 16 June 2001
Cited by 11 | PDF Full-text (174 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, we study stationary variant of extended coupled-cluster response approach for properties. This has been studied at the singles and doubles approximation using cubic-truncated functional. This approximation has been studied earlier around equilibrium for small molecules. In this paper, efficacy [...] Read more.
In this paper, we study stationary variant of extended coupled-cluster response approach for properties. This has been studied at the singles and doubles approximation using cubic-truncated functional. This approximation has been studied earlier around equilibrium for small molecules. In this paper, efficacy of this approximation has been shown using perturbative arguments. Further we have calculated dipole moments and polarizabilities of weakly interacting dimers of HF, H2O and H2O - HF complex. Results of HF and H2O monomers have been presented at the same level for comparison. The results have been compared with experimental results, wherever available and other theoretical results. Full article
Open AccessArticle Variational Perturbation Theory of the Confined Hydrogen Atom
Int. J. Mol. Sci. 2001, 2(2), 103-108; doi:10.3390/i2020103
Received: 28 March 2001 / Accepted: 15 June 2001 / Published: 16 June 2001
Cited by 6 | PDF Full-text (38 KB) | HTML Full-text | XML Full-text
Abstract
Variational perturbation theory was used to solve the Schrödinger equation for a hydrogen atom confined at the center of an impenetrable cavity. Ground state and excited state energies and expectation values calculated from the perturbation wavefunction are comparable in accuracy to results [...] Read more.
Variational perturbation theory was used to solve the Schrödinger equation for a hydrogen atom confined at the center of an impenetrable cavity. Ground state and excited state energies and expectation values calculated from the perturbation wavefunction are comparable in accuracy to results from direct numerical solution. Full article
Open AccessArticle Glycerol-Induced Aggregation of the Oligomeric L-Asparaginase II from E. coli Monitored with ATR-FTIR
Int. J. Mol. Sci. 2001, 2(2), 109-120; doi:10.3390/i2020109
Received: 9 April 2001 / Accepted: 15 June 2001 / Published: 28 June 2001
Cited by 5 | PDF Full-text (415 KB) | HTML Full-text | XML Full-text
Abstract
In this paper attenuated total reflectance Fourier transform infrared spectroscopy has been employed for the study of the structural composition of aggregates of the oligomeric L-asparaginase II from E.coli formed in the presence of glycerol after the induction of refolding of the [...] Read more.
In this paper attenuated total reflectance Fourier transform infrared spectroscopy has been employed for the study of the structural composition of aggregates of the oligomeric L-asparaginase II from E.coli formed in the presence of glycerol after the induction of refolding of the protein. Apart from the perfect coincidence of the secondary structure composition of EcA2 as determined by FTIR and crystallography [1], it has also been shown that secondary structure of protein in asparaginase deposits is similar to that of the native conformation: 20.7% extended, 22.3% disordered, 31.4% helix and 25.6% turn/bend/β sheet. Certain structural similarities in the range of experimental error was observed for all three protein deposits presented in this paper, indicating a common structural basis for the composition of this types of aggregates. It is concluded that in the constitution of such precipitates, a partially folded (molten globule like) state(s) is involved, and its stabilisation is a key factor leading to the aggregation. The results presented in this paper might serve to be a good explanation and an excellent basis for the fundamental theory of protein (oligomers) precipitation by osmotic substances. Full article
Open AccessArticle Maximum Topological Distances Based Indices as Molecular Descriptors for QSPR. 4. Modeling the Enthalpy of Formation of Hydrocarbons from Elements
Int. J. Mol. Sci. 2001, 2(2), 121-132; doi:10.3390/i2020121
Received: 9 April 2001 / Accepted: 15 June 2001 / Published: 28 June 2001
Cited by 12 | PDF Full-text (196 KB) | HTML Full-text | XML Full-text
Abstract
The enthalpy of formation of a set of 60 hydroarbons is calculated on the basis of topological descriptors defined from the distance and detour matrices within the realm of the QSAR/QSPR theory. Linear and non-linear polynomials fittings are made and results show [...] Read more.
The enthalpy of formation of a set of 60 hydroarbons is calculated on the basis of topological descriptors defined from the distance and detour matrices within the realm of the QSAR/QSPR theory. Linear and non-linear polynomials fittings are made and results show the need to resort to higher-order regression equations in order to get better concordances between theoretical results and experimental available data. Besides, topological indices computed from maximum order distances seems to yield rather satisfactory predictions of heats of formation for hydrocarbons. Full article

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