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Proceedings of the 9th Electronic Computational Chemistry Conference. Part I.

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (30 November 2003) | Viewed by 42715

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Department of Chemistry, The Cooper Union for the Advancement of Science and Art, Cooper Square, New York, NY 10003-7120, USA
Interests: atomic and molecular nanoclusters; superheated gases; DNA damage; phase transitions; Monte Carlo and molecular dynamics calculations; path integrals; reaction rate theory; nonlinear dynamics
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Editorial

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117 KiB  
Editorial
Proceedings of the 9th Electronic Computational Chemistry Conference
by Robert Q. Topper and Olga Dmitrenko
Int. J. Mol. Sci. 2004, 5(2), 35-36; https://doi.org/10.3390/i5020035 - 28 Feb 2004
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Abstract
It is our privilege to introduce this special issue of the International Journal of Molecular Sciences, which presents the Proceedings of the 9th Electronic Computational Chemistry Conference (ECCC9).[...] Full article

Research

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201 KiB  
Article
Scalar Relativistic Study of the Structure of Rhodium Acetate
by Stephen D. Williams and Emily E. Edwards
Int. J. Mol. Sci. 2004, 5(2), 67-74; https://doi.org/10.3390/i5020067 - 30 Jan 2004
Cited by 9 | Viewed by 9126
Abstract
Rhodium acetate, related rhodium carboxylates, and rhodium amide complexes are powerful catalysts for carbene chemistry. They readily promote the decomposition of diazo compounds and transfer the resulting carbene to a variety of substrates. There have been several quantum chemistry studies of these compounds, [...] Read more.
Rhodium acetate, related rhodium carboxylates, and rhodium amide complexes are powerful catalysts for carbene chemistry. They readily promote the decomposition of diazo compounds and transfer the resulting carbene to a variety of substrates. There have been several quantum chemistry studies of these compounds, particularly of the acetate. These have all used non-relativistic methods, and all have shown optimized Rh-Rh bond lengths significantly longer than the experimental value. In this study we have surveyed several scalar relativistic DFT methods using Gaussian, Slater, and numerical basis functions (in DGAUSS, ADF, and DMOL3). Several combinations of exchange-correlation functionals with relativistic and non-relativistic effective core potentials (ECP) were investigated, as were non-relativistic and all electron scalar relativistic methods. The combination of the PW91 exchange and PW91 correlation functional with the Christiansen-Ermler ECP gave the best results: 2.3918 Å compared to the experimental value of 2.3855±0.0005 Å. Full article
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200 KiB  
Article
QSAR Study of Skin Sensitization Using Local Lymph Node Assay Data
by Adam Fedorowicz, Lingyi Zheng, Harshinder Singh and Eugene Demchuk
Int. J. Mol. Sci. 2004, 5(2), 56-66; https://doi.org/10.3390/i5020056 - 30 Jan 2004
Cited by 40 | Viewed by 10024
Abstract
Allergic Contact Dermatitis (ACD) is a common work-related skin disease that often develops as a result of repetitive skin exposures to a sensitizing chemical agent. A variety of experimental tests have been suggested to assess the skin sensitization potential. We applied a method [...] Read more.
Allergic Contact Dermatitis (ACD) is a common work-related skin disease that often develops as a result of repetitive skin exposures to a sensitizing chemical agent. A variety of experimental tests have been suggested to assess the skin sensitization potential. We applied a method of Quantitative Structure-Activity Relationship (QSAR) to relate measured and calculated physical-chemical properties of chemical compounds to their sensitization potential. Using statistical methods, each of these properties, called molecular descriptors, was tested for its propensity to predict the sensitization potential. A few of the most informative descriptors were subsequently selected to build a model of skin sensitization. In this work sensitization data for the murine Local Lymph Node Assay (LLNA) were used. In principle, LLNA provides a standardized continuous scale suitable for quantitative assessment of skin sensitization. However, at present many LLNA results are still reported on a dichotomous scale, which is consistent with the scale of guinea pig tests, which were widely used in past years. Therefore, in this study only a dichotomous version of the LLNA data was used. To the statistical end, we relied on the logistic regression approach. This approach provides a statistical tool for investigating and predicting skin sensitization that is expressed only in categorical terms of activity and nonactivity. Based on the data of compounds used in this study, our results suggest a QSAR model of ACD that is based on the following descriptors: nDB (number of double bonds), C-003 (number of CHR3 molecular subfragments), GATS6M (autocorrelation coefficient) and HATS6m (GETAWAY descriptor), although the relevance of the identified descriptors to the continuous ACD QSAR has yet to be shown. The proposed QSAR model gives a percentage of positively predicted responses of 83% on the training set of compounds, and in cross validation it correctly identifies 79% of responses. Full article
223 KiB  
Article
Exploring QSAR of Non-Nucleoside Reverse Transcriptase Inhibitors by Neural Networks: TIBO Derivatives
by Latifa Douali, Didier Villemin and Driss Cherqaoui
Int. J. Mol. Sci. 2004, 5(2), 48-55; https://doi.org/10.3390/i5020048 - 30 Jan 2004
Cited by 26 | Viewed by 10023
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) reverse transcriptase is an important target for chemotherapeutic agents against the AIDS disease. 4,5,6,7-Tetrahydro-5-methylimidazo[4,5,1-jk][1,4]benzodiazepin-2(1H)-ones (TIBO) derivatives are potent non-nucleoside reverse transcriptase inhibitors (NNRTIs). In the present work, quantitative structure-activity relationship (QSAR) analysis for a set of 82 [...] Read more.
Human Immunodeficiency Virus type 1 (HIV-1) reverse transcriptase is an important target for chemotherapeutic agents against the AIDS disease. 4,5,6,7-Tetrahydro-5-methylimidazo[4,5,1-jk][1,4]benzodiazepin-2(1H)-ones (TIBO) derivatives are potent non-nucleoside reverse transcriptase inhibitors (NNRTIs). In the present work, quantitative structure-activity relationship (QSAR) analysis for a set of 82 TIBO derivatives has been investigated by means of a three-layered neural network (NN). It has been shown that NN can be a potential tool in the investigation of QSAR analysis compared with the models given in the literature. NN gave good statistical results both in fitting and prediction processes (0.861 ≤ r² ≤ 0.928, 0.839 ≤q² ≤ 0.845). The relevant factors controlling the anti-HIV-1 activity of TIBO derivatives have been identified. The results are along the same lines as those of our previous studies on HEPT derivatives and indicate the importance of the hydrophobic parameter in modeling the QSAR for TIBO derivatives. Full article
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863 KiB  
Article
Molecular Similarity of MDR Inhibitors
by Mire Zloh and Simon Gibbons
Int. J. Mol. Sci. 2004, 5(2), 37-47; https://doi.org/10.3390/i5020037 - 30 Jan 2004
Cited by 12 | Viewed by 6953
Abstract
The molecular similarity of multidrug resistance (MDR) inhibitors was evaluated using the point centred atom charge approach in an attempt to find some common features of structurally unrelated inhibitors. A series of inhibitors of bacterial MDR were studied and there is a high [...] Read more.
The molecular similarity of multidrug resistance (MDR) inhibitors was evaluated using the point centred atom charge approach in an attempt to find some common features of structurally unrelated inhibitors. A series of inhibitors of bacterial MDR were studied and there is a high similarity between these in terms of their shape, presence and orientation of aromatic ring moieties. A comparison of the lipophilic properties of these molecules has also been conducted suggesting that this factor is important in MDR inhibition. Full article
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