International Journal of Molecular Sciences

196 KiB

Open AccessArticle

Maximum Topological Distances Based Indices as Molecular Descriptors for QSPR. 4. Modeling the Enthalpy of Formation of Hydrocarbons from Elements

by Andrés Mercader, Eduardo A. Castro and Andrey A. Toropov

Int. J. Mol. Sci. 2001, 2(2), 121-132; https://doi.org/10.3390/i2020121 - 28 Jun 2001

Cited by 36 | Viewed by 8602

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 the [...] 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

415 KiB

Open AccessArticle

Glycerol-Induced Aggregation of the Oligomeric L-Asparaginase II from E. coli Monitored with ATR-FTIR

by Koba Adeishvili

Int. J. Mol. Sci. 2001, 2(2), 109-120; https://doi.org/10.3390/i2020109 - 28 Jun 2001

Cited by 9 | Viewed by 9162

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 protein. [...] 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

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Figure 1
Comparison of the amide I and II regions of the ATR-FTIR spectrum of L-asparaginase II from E.coli in its native state ( wide connected) , refolded and aggregated from 1M GuHCl (dashed), from 2M GuHCl ( connected) and from 3M GuHCl (dotted). FSD resolution enhancement of raw amide I spectra has not been performed. Full article ">Figure 2
The second derivative specra of the amide I region of the ATR-FTIR spectrum of L-asparaginase II from E.coli in its native state (wide connected) , refolded and aggregated from 1M GuHCl (dashed) ,from 2M GuHCl (connected) and from 3M GuHCl (dotted). FSD resolution enhancement of raw amide I spectra has been performed. The best coincidence between all aggregated forms is evident. Full article ">Figure 3
Presentation of curve-fit spectra of amide I region of the ATR-FTIR spectrum after FSD resolution enhancement. A: Native state, b: Refolded and aggregated from 1M GuHCl, c and d:from 2M GuHCl and from 3M GuHCl, respectively. Clear similarities in aggregated forms can aslo be seen. Notice that the peak positions are slightly shifted and a number of fitted peaks have also changed. Full article ">Figure 4
The spectra of the amide III region from the ATR-FTIR spectrum of L-asparaginase II in the native state (wide connected) , refolded and aggregated from 1M GuHCl (dashed) ,from 2M GuHCl (connected) and from 3M GuHCl (dotted). All three deposits of protein exhibit a nearly identical shape, suggesting a similar structural composition. Full article ">Figure 5
The second derivative of amide III region of FTIR spectra of L-asparaginase II in ist native state (wide connected) , refolded and aggregated from 1M GuHCl (dashed) ,from 2M GuHCl (connected) and from 3M GuHCl (dotted). A substantial difference from the native spectra of all protein aggregates can easily be noticed. Full article ">Figure 6
Kinetics of L-asparaginase refolding monitored with circular dichroism at 225 nm and 22°C in Tris/HCl buffer pH=8.0. The protein concentration was 2 mg/ml. The enzyme was unfolded in 3M GuHCl solution and refolding was inititated by diluting into refolding buffer. The upper bar indicates kinetic traces measured on stopped-flow device. The lower bar theoretical double-exponential curve fit the stopped flow data. The kinetic parameters are as follow: A1= -0.67 deg cm2 dmol-1 , A2= -2.09 deg cm2 dmol-1, Ainfinity= -1.89 deg cm2 dmol-1, k1=0.15, k2=0.0041. Full article ">

38 KiB

Open AccessArticle

Variational Perturbation Theory of the Confined Hydrogen Atom

by H. E. Montgomery, Jr.

Int. J. Mol. Sci. 2001, 2(2), 103-108; https://doi.org/10.3390/i2020103 - 16 Jun 2001

Cited by 11 | Viewed by 5516

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 from [...] 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

174 KiB

Open AccessArticle

Extended Coupled Cluster Approach for Molecular Properties: Study of H2O and HF Complexes

by Nayana Vaval, Aparna Basu Kumar and Sourav Pal

Int. J. Mol. Sci. 2001, 2(2), 89-102; https://doi.org/10.3390/i2020089 - 16 Jun 2001

Cited by 17 | Viewed by 7357

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 of [...] 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

160 KiB

Open AccessArticle

Characterizing Cavities in Model Inclusion Fullerenes: A Comparative Study

by Francisco Torrens

Int. J. Mol. Sci. 2001, 2(2), 72-88; https://doi.org/10.3390/i2020072 - 2 Jun 2001

Cited by 6 | Viewed by 8575

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 molecular [...] 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

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32 KiB

Open AccessArticle

A Quantum Theory of Thermodynamic Relaxation

by Roumen Tsekov

Int. J. Mol. Sci. 2001, 2(2), 66-71; https://doi.org/10.3390/i2020066 - 23 May 2001

Cited by 6 | Viewed by 8776

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 leading [...] 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

56 KiB

Open AccessArticle

Improved Molecular Descriptors Based on the Optimization of Correlation Weights of Local Graph Invariants

by Germán Krenkel, Eduardo A. Castro and Andrey A. Toropov

Int. J. Mol. Sci. 2001, 2(2), 57-65; https://doi.org/10.3390/i2020057 - 7 May 2001

Cited by 27 | Viewed by 11011

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 (i.e. [...] 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

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396 KiB

Open AccessArticle

Structural And Energetic Changes of Si (100) Surface With Fluorine in Presence of Water – A Density Functional Study

by Abhijit Chatterjee, Takashi Iwasaki and Takeo Ebina

Int. J. Mol. Sci. 2001, 2(2), 40-56; https://doi.org/10.3390/i2020040 - 1 May 2001

Cited by 4 | Viewed by 11698

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 symmetry [...] 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

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Int. J. Mol. Sci., Volume 2, Issue 2 (June 2001) – 8 articles , Pages 40-132

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