ABSTRACT Advances in Mathematical Chemistry and Applications (eBook), Volume 2 Edited By Subhash ... more ABSTRACT Advances in Mathematical Chemistry and Applications (eBook), Volume 2 Edited By Subhash C. Basak, International Society of Mathematical Chemistry, and UMD-NRRI, Duluth MN, USA Guillermo Restrepo, Laboratorio de Química Teórica, Universidad de Pamplona, Colombia & José L. Villaveces, Universidad de los Andes, Bogotá, D. C., Colombia CONTENTS Foreword by Professor Lemont B. Kier page - i Preface by Subhash C. Basak, Guillermo Restrepo and José L. Villaveces Page - iii List of Contributors v CHAPTERS 1. Topological Efficiency Approach to Fullerene Stability – Case Study with C50, Ante Graovac, Ali Reza Ashrafi and Ottorino Ori 2. Similarity in Chemical Reaction Networks: Categories, Concepts and Closures, Andrés Bernal, Eugenio Llanos, Wilmer Leal and Guillermo Restrepo 3. Discrimination of Small Molecules Using Topological Molecular Descriptors, Chandan Raychaudhury and Debnath Pal 4. The Periodicity of Molecules Fanao Kong, Weiqiang Wu, Na Ji and C. L. Calson 5. The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences, Ashesh Nandy 6. Linear Regression, Model Averaging, and Bayesian Techniques for Predicting Chemical Activities from Structure, Jarad B. Niemi and Gerald J. Niemi 7. Marine Algal Toxicity Models with Dunaliella tertiolecta: In Vivo and In Silico, Melek T. Saçan, Marjana Novic, M. Doğa Ertürk and Nikola Minovski 8. Anti-Tubercular Drug Designing Using Structural Descriptors, Manish C. Bagchi and Payel Ghosh 9. Integrating Bioinformatics and Systems Biology for Exploring Novel Lipid Pathways in Infectious Diseases, Sonali Shinde, Vineetha Mandlik and Shailza Singh 10. Applications of Molecular Docking and Molecular Dynamics on the Inhibition of Quorum Sensing Systems, Santiago Medina, Susana Casas, Mariana Restrepo, Alejandro Alvarez, Adriana J. Bernal and Andrés F. González 11. Designing Models for Metalloenzymes, James F. Weston 12. The Multi-Factor Coupled Protein Folding: Insights from Molecular Dynamics Simulations, Xiaomin Wu, Gang Yang and Lijun Zhou 13. Generalized Topologies: Hypergraphs, Chemical Reactions, and Biological Evolution, Christoph lamm, Bärbel M. R. Stadler and Peter F. Stadler Subject Index List of Contributors: Alejandro Alvarez Mycology and plant disease Laboratory (LAMFU), Department of Biological Sciences, Universidad de los Andes Bogotá, Colombia Ali Reza Ashrafi Department of Pure Mathematics, Faculty of Mathematical Sciences, University of Kashan, Kashan 87317 – 51167, I. R., Iran Manish C. Bagchi School of Bioscience & Engineering, Jadavpur University, Kolkata 700032, India Adriana J. Bernal Mycology and plant disease Laboratory (LAMFU), Department of Biological Sciences, Universidad de los Andes Bogotá, Colombia Andrés Bernal Grupo de Química Teórica, Universidad Nacional de Colombia, Bogotá, Colombia C. L. Calson The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Susana Casas Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia M. Doğa Ertürk Boğaziçi University, Institute of Environmental Sciences, 34342, Hisar Campus, Bebek, Istanbul, Turkey Christoph Flamm Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A- 1090 Vienna, Austria Payel Ghosh Structural Biology Laboratory, Centre for DNA Fingerprinting and Diagnostics (Dept. of Biotechnology, Govt. of India), Nampally, Hyderabad 500001, India Andrés F. González Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia Ante Graovac Faculty of Science, University of Split, Nikole Tesle 12, HR-21000 Split, Croatia NA JI The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Fanao Kong The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Wilmer Leal Fundación Instituto de Inmunología de Colombia FIDIC, Bogotá, Colombia Eugenio Llanos Corporación Colombiana del Saber Científico SCIO, Bogotá, Colombia Vineetha Mandlik Computational and Systems Biology Laboratory, Lab 9, New Building, NCCS, Pune -411007, India Santiago Medina Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia Nikola Minovski National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia Ashesh Nandy Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India Gerald J. Niemi Natural Resources Research Institute and Department of Biology, University of Minnesota, 5013 Miller Trunk Highway, Duluth, MN 55811, USA Jarad B. Niemi Department of Statistics, Iowa State University, Ames, IA 50011, USA Marjana Novic National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia Ottorino Ori Actinium Chemical Research, Via Casilina 1626/A, 00133 Rome, Italy Debnath Pal Bioinformatics Centre, Indian Institute of Science, Bangalore 560012, India Chandan…
ABSTRACT Advances in Mathematical Chemistry and Applications (eBook), Volume 2 Edited By Subhash ... more ABSTRACT Advances in Mathematical Chemistry and Applications (eBook), Volume 2 Edited By Subhash C. Basak, International Society of Mathematical Chemistry, and UMD-NRRI, Duluth MN, USA Guillermo Restrepo, Laboratorio de Química Teórica, Universidad de Pamplona, Colombia & José L. Villaveces, Universidad de los Andes, Bogotá, D. C., Colombia CONTENTS Foreword by Professor Lemont B. Kier page - i Preface by Subhash C. Basak, Guillermo Restrepo and José L. Villaveces Page - iii List of Contributors v CHAPTERS 1. Topological Efficiency Approach to Fullerene Stability – Case Study with C50, Ante Graovac, Ali Reza Ashrafi and Ottorino Ori 2. Similarity in Chemical Reaction Networks: Categories, Concepts and Closures, Andrés Bernal, Eugenio Llanos, Wilmer Leal and Guillermo Restrepo 3. Discrimination of Small Molecules Using Topological Molecular Descriptors, Chandan Raychaudhury and Debnath Pal 4. The Periodicity of Molecules Fanao Kong, Weiqiang Wu, Na Ji and C. L. Calson 5. The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences, Ashesh Nandy 6. Linear Regression, Model Averaging, and Bayesian Techniques for Predicting Chemical Activities from Structure, Jarad B. Niemi and Gerald J. Niemi 7. Marine Algal Toxicity Models with Dunaliella tertiolecta: In Vivo and In Silico, Melek T. Saçan, Marjana Novic, M. Doğa Ertürk and Nikola Minovski 8. Anti-Tubercular Drug Designing Using Structural Descriptors, Manish C. Bagchi and Payel Ghosh 9. Integrating Bioinformatics and Systems Biology for Exploring Novel Lipid Pathways in Infectious Diseases, Sonali Shinde, Vineetha Mandlik and Shailza Singh 10. Applications of Molecular Docking and Molecular Dynamics on the Inhibition of Quorum Sensing Systems, Santiago Medina, Susana Casas, Mariana Restrepo, Alejandro Alvarez, Adriana J. Bernal and Andrés F. González 11. Designing Models for Metalloenzymes, James F. Weston 12. The Multi-Factor Coupled Protein Folding: Insights from Molecular Dynamics Simulations, Xiaomin Wu, Gang Yang and Lijun Zhou 13. Generalized Topologies: Hypergraphs, Chemical Reactions, and Biological Evolution, Christoph lamm, Bärbel M. R. Stadler and Peter F. Stadler Subject Index List of Contributors: Alejandro Alvarez Mycology and plant disease Laboratory (LAMFU), Department of Biological Sciences, Universidad de los Andes Bogotá, Colombia Ali Reza Ashrafi Department of Pure Mathematics, Faculty of Mathematical Sciences, University of Kashan, Kashan 87317 – 51167, I. R., Iran Manish C. Bagchi School of Bioscience & Engineering, Jadavpur University, Kolkata 700032, India Adriana J. Bernal Mycology and plant disease Laboratory (LAMFU), Department of Biological Sciences, Universidad de los Andes Bogotá, Colombia Andrés Bernal Grupo de Química Teórica, Universidad Nacional de Colombia, Bogotá, Colombia C. L. Calson The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Susana Casas Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia M. Doğa Ertürk Boğaziçi University, Institute of Environmental Sciences, 34342, Hisar Campus, Bebek, Istanbul, Turkey Christoph Flamm Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A- 1090 Vienna, Austria Payel Ghosh Structural Biology Laboratory, Centre for DNA Fingerprinting and Diagnostics (Dept. of Biotechnology, Govt. of India), Nampally, Hyderabad 500001, India Andrés F. González Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia Ante Graovac Faculty of Science, University of Split, Nikole Tesle 12, HR-21000 Split, Croatia NA JI The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Fanao Kong The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Wilmer Leal Fundación Instituto de Inmunología de Colombia FIDIC, Bogotá, Colombia Eugenio Llanos Corporación Colombiana del Saber Científico SCIO, Bogotá, Colombia Vineetha Mandlik Computational and Systems Biology Laboratory, Lab 9, New Building, NCCS, Pune -411007, India Santiago Medina Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia Nikola Minovski National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia Ashesh Nandy Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India Gerald J. Niemi Natural Resources Research Institute and Department of Biology, University of Minnesota, 5013 Miller Trunk Highway, Duluth, MN 55811, USA Jarad B. Niemi Department of Statistics, Iowa State University, Ames, IA 50011, USA Marjana Novic National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia Ottorino Ori Actinium Chemical Research, Via Casilina 1626/A, 00133 Rome, Italy Debnath Pal Bioinformatics Centre, Indian Institute of Science, Bangalore 560012, India Chandan…
Five hydrogen abstraction reactions, CH4 + R ? CH3 + HR have been studied usingab initio SCF and ... more Five hydrogen abstraction reactions, CH4 + R ? CH3 + HR have been studied usingab initio SCF and CI methods. R was successively chosen as H, CH3, NH2, OH and F. Geometries were fully optimized at SCF level and energies were computed at CI level for products, reactants and transition states. Quadratic hypersurfaces were fitted in the neighborhood of the
A study was performed on the HLA-DRbeta1*0401-collagen II peptide complex using the computation o... more A study was performed on the HLA-DRbeta1*0401-collagen II peptide complex using the computation of electronic multipolar variables proposed by us previously. Furthermore, these results were compared with those obtained for the HLA-DRbeta1*0101-haemaglutinin peptide complex studied by us with the same tools, confirming that Pocket 1 for this new complex is also the most important pocket for the interaction between the presenting molecule and the presented peptide. The pocket hierarchy established for HLA-DRbeta1*0401 allele was P1 > P9 approximately P7 > P6 > P4, whilst a P1 > P4 > P9 approximately P7>P6 pocket hierarchy was found for HLA-DRbeta1*0101, showing how the relative importance of the pockets distinguishes the two alleles. There are high correlation levels with experimental results (when possible), again confirming the validity of using calculated values for electronic multipolar variables as a useful tool for studying interactions between immune system molecules and peptides.
Calculations for C chemisorption on a finely divided nickel catalyst modeled by Ni5, Ni7 and Ni14... more Calculations for C chemisorption on a finely divided nickel catalyst modeled by Ni5, Ni7 and Ni14 clusters were carried out by using the MINDOSR semiempirical method. Vertical adsorption on several sites in the border and in the center of these clusters were evaluated. The adsorption energy depends not only on the type of site but also on the cluster size,
Page 1. Precise Determination of the Absorption Maxima in Wide Bands In analytical chemistry and ... more Page 1. Precise Determination of the Absorption Maxima in Wide Bands In analytical chemistry and spectroscopy, the analys~r of ~olutionr hy spectroscopic methods, one frequentlv m-counters compcmndn wh ~ rh have vrn. ...
ABSTRACT In this article we propose a new topology, based on the stable attractors of the gradien... more ABSTRACT In this article we propose a new topology, based on the stable attractors of the gradient field of the potential energy hypersurface, that may be used as a general definition of a stable chemical structure. We further construct two examples of particular realizations of this abstract topology. One of them is closely related to the catchment–region topology of Mezey and the other one to the molecular–graph model of Bader. A particularly interesting point is that both topologies lead to equivalent definitions of molecular structure; in particular, they permit us to differentiate between cis-trans isomers and rotational conformers, that had equivalent structures in the definition proposed by Bader.
Abstract We analyze the connections of Lavoisier system of nomenclature with Leibniz&#x27... more Abstract We analyze the connections of Lavoisier system of nomenclature with Leibniz's philosophy, pointing out to the resemblance between what we call Leibnizian and Lavoisian programs. We argue that Lavoisier's contribution to chemistry is something more subtle, in so doing we show that the system of nomenclature leads to an algebraic system of chemical sets. We show how Döbereiner and Mendeleev were able to develop this algebraic system and to find new interesting properties for it. We pointed out the resemblances between ...
Abstract: Mathematical chemistry is often thought to be a 20 th-century subdiscipline of chemistr... more Abstract: Mathematical chemistry is often thought to be a 20 th-century subdiscipline of chemistry, but in this paper we discuss several early chemical ideas and some landmarks of chemistry as instances of the mathematical way of thinking; many of them before 1900. By the mathematical way of thinking, we follow Weyl's description of it in terms of functional thinking, ie setting up variables, symbolizing them, and seeking for functions relating them.
ABSTRACT Advances in Mathematical Chemistry and Applications (eBook), Volume 2 Edited By Subhash ... more ABSTRACT Advances in Mathematical Chemistry and Applications (eBook), Volume 2 Edited By Subhash C. Basak, International Society of Mathematical Chemistry, and UMD-NRRI, Duluth MN, USA Guillermo Restrepo, Laboratorio de Química Teórica, Universidad de Pamplona, Colombia & José L. Villaveces, Universidad de los Andes, Bogotá, D. C., Colombia CONTENTS Foreword by Professor Lemont B. Kier page - i Preface by Subhash C. Basak, Guillermo Restrepo and José L. Villaveces Page - iii List of Contributors v CHAPTERS 1. Topological Efficiency Approach to Fullerene Stability – Case Study with C50, Ante Graovac, Ali Reza Ashrafi and Ottorino Ori 2. Similarity in Chemical Reaction Networks: Categories, Concepts and Closures, Andrés Bernal, Eugenio Llanos, Wilmer Leal and Guillermo Restrepo 3. Discrimination of Small Molecules Using Topological Molecular Descriptors, Chandan Raychaudhury and Debnath Pal 4. The Periodicity of Molecules Fanao Kong, Weiqiang Wu, Na Ji and C. L. Calson 5. The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences, Ashesh Nandy 6. Linear Regression, Model Averaging, and Bayesian Techniques for Predicting Chemical Activities from Structure, Jarad B. Niemi and Gerald J. Niemi 7. Marine Algal Toxicity Models with Dunaliella tertiolecta: In Vivo and In Silico, Melek T. Saçan, Marjana Novic, M. Doğa Ertürk and Nikola Minovski 8. Anti-Tubercular Drug Designing Using Structural Descriptors, Manish C. Bagchi and Payel Ghosh 9. Integrating Bioinformatics and Systems Biology for Exploring Novel Lipid Pathways in Infectious Diseases, Sonali Shinde, Vineetha Mandlik and Shailza Singh 10. Applications of Molecular Docking and Molecular Dynamics on the Inhibition of Quorum Sensing Systems, Santiago Medina, Susana Casas, Mariana Restrepo, Alejandro Alvarez, Adriana J. Bernal and Andrés F. González 11. Designing Models for Metalloenzymes, James F. Weston 12. The Multi-Factor Coupled Protein Folding: Insights from Molecular Dynamics Simulations, Xiaomin Wu, Gang Yang and Lijun Zhou 13. Generalized Topologies: Hypergraphs, Chemical Reactions, and Biological Evolution, Christoph lamm, Bärbel M. R. Stadler and Peter F. Stadler Subject Index List of Contributors: Alejandro Alvarez Mycology and plant disease Laboratory (LAMFU), Department of Biological Sciences, Universidad de los Andes Bogotá, Colombia Ali Reza Ashrafi Department of Pure Mathematics, Faculty of Mathematical Sciences, University of Kashan, Kashan 87317 – 51167, I. R., Iran Manish C. Bagchi School of Bioscience & Engineering, Jadavpur University, Kolkata 700032, India Adriana J. Bernal Mycology and plant disease Laboratory (LAMFU), Department of Biological Sciences, Universidad de los Andes Bogotá, Colombia Andrés Bernal Grupo de Química Teórica, Universidad Nacional de Colombia, Bogotá, Colombia C. L. Calson The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Susana Casas Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia M. Doğa Ertürk Boğaziçi University, Institute of Environmental Sciences, 34342, Hisar Campus, Bebek, Istanbul, Turkey Christoph Flamm Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A- 1090 Vienna, Austria Payel Ghosh Structural Biology Laboratory, Centre for DNA Fingerprinting and Diagnostics (Dept. of Biotechnology, Govt. of India), Nampally, Hyderabad 500001, India Andrés F. González Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia Ante Graovac Faculty of Science, University of Split, Nikole Tesle 12, HR-21000 Split, Croatia NA JI The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Fanao Kong The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Wilmer Leal Fundación Instituto de Inmunología de Colombia FIDIC, Bogotá, Colombia Eugenio Llanos Corporación Colombiana del Saber Científico SCIO, Bogotá, Colombia Vineetha Mandlik Computational and Systems Biology Laboratory, Lab 9, New Building, NCCS, Pune -411007, India Santiago Medina Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia Nikola Minovski National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia Ashesh Nandy Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India Gerald J. Niemi Natural Resources Research Institute and Department of Biology, University of Minnesota, 5013 Miller Trunk Highway, Duluth, MN 55811, USA Jarad B. Niemi Department of Statistics, Iowa State University, Ames, IA 50011, USA Marjana Novic National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia Ottorino Ori Actinium Chemical Research, Via Casilina 1626/A, 00133 Rome, Italy Debnath Pal Bioinformatics Centre, Indian Institute of Science, Bangalore 560012, India Chandan…
ABSTRACT Advances in Mathematical Chemistry and Applications (eBook), Volume 2 Edited By Subhash ... more ABSTRACT Advances in Mathematical Chemistry and Applications (eBook), Volume 2 Edited By Subhash C. Basak, International Society of Mathematical Chemistry, and UMD-NRRI, Duluth MN, USA Guillermo Restrepo, Laboratorio de Química Teórica, Universidad de Pamplona, Colombia & José L. Villaveces, Universidad de los Andes, Bogotá, D. C., Colombia CONTENTS Foreword by Professor Lemont B. Kier page - i Preface by Subhash C. Basak, Guillermo Restrepo and José L. Villaveces Page - iii List of Contributors v CHAPTERS 1. Topological Efficiency Approach to Fullerene Stability – Case Study with C50, Ante Graovac, Ali Reza Ashrafi and Ottorino Ori 2. Similarity in Chemical Reaction Networks: Categories, Concepts and Closures, Andrés Bernal, Eugenio Llanos, Wilmer Leal and Guillermo Restrepo 3. Discrimination of Small Molecules Using Topological Molecular Descriptors, Chandan Raychaudhury and Debnath Pal 4. The Periodicity of Molecules Fanao Kong, Weiqiang Wu, Na Ji and C. L. Calson 5. The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences, Ashesh Nandy 6. Linear Regression, Model Averaging, and Bayesian Techniques for Predicting Chemical Activities from Structure, Jarad B. Niemi and Gerald J. Niemi 7. Marine Algal Toxicity Models with Dunaliella tertiolecta: In Vivo and In Silico, Melek T. Saçan, Marjana Novic, M. Doğa Ertürk and Nikola Minovski 8. Anti-Tubercular Drug Designing Using Structural Descriptors, Manish C. Bagchi and Payel Ghosh 9. Integrating Bioinformatics and Systems Biology for Exploring Novel Lipid Pathways in Infectious Diseases, Sonali Shinde, Vineetha Mandlik and Shailza Singh 10. Applications of Molecular Docking and Molecular Dynamics on the Inhibition of Quorum Sensing Systems, Santiago Medina, Susana Casas, Mariana Restrepo, Alejandro Alvarez, Adriana J. Bernal and Andrés F. González 11. Designing Models for Metalloenzymes, James F. Weston 12. The Multi-Factor Coupled Protein Folding: Insights from Molecular Dynamics Simulations, Xiaomin Wu, Gang Yang and Lijun Zhou 13. Generalized Topologies: Hypergraphs, Chemical Reactions, and Biological Evolution, Christoph lamm, Bärbel M. R. Stadler and Peter F. Stadler Subject Index List of Contributors: Alejandro Alvarez Mycology and plant disease Laboratory (LAMFU), Department of Biological Sciences, Universidad de los Andes Bogotá, Colombia Ali Reza Ashrafi Department of Pure Mathematics, Faculty of Mathematical Sciences, University of Kashan, Kashan 87317 – 51167, I. R., Iran Manish C. Bagchi School of Bioscience & Engineering, Jadavpur University, Kolkata 700032, India Adriana J. Bernal Mycology and plant disease Laboratory (LAMFU), Department of Biological Sciences, Universidad de los Andes Bogotá, Colombia Andrés Bernal Grupo de Química Teórica, Universidad Nacional de Colombia, Bogotá, Colombia C. L. Calson The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Susana Casas Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia M. Doğa Ertürk Boğaziçi University, Institute of Environmental Sciences, 34342, Hisar Campus, Bebek, Istanbul, Turkey Christoph Flamm Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A- 1090 Vienna, Austria Payel Ghosh Structural Biology Laboratory, Centre for DNA Fingerprinting and Diagnostics (Dept. of Biotechnology, Govt. of India), Nampally, Hyderabad 500001, India Andrés F. González Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia Ante Graovac Faculty of Science, University of Split, Nikole Tesle 12, HR-21000 Split, Croatia NA JI The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Fanao Kong The Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China Wilmer Leal Fundación Instituto de Inmunología de Colombia FIDIC, Bogotá, Colombia Eugenio Llanos Corporación Colombiana del Saber Científico SCIO, Bogotá, Colombia Vineetha Mandlik Computational and Systems Biology Laboratory, Lab 9, New Building, NCCS, Pune -411007, India Santiago Medina Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia Nikola Minovski National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia Ashesh Nandy Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India Gerald J. Niemi Natural Resources Research Institute and Department of Biology, University of Minnesota, 5013 Miller Trunk Highway, Duluth, MN 55811, USA Jarad B. Niemi Department of Statistics, Iowa State University, Ames, IA 50011, USA Marjana Novic National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia Ottorino Ori Actinium Chemical Research, Via Casilina 1626/A, 00133 Rome, Italy Debnath Pal Bioinformatics Centre, Indian Institute of Science, Bangalore 560012, India Chandan…
Five hydrogen abstraction reactions, CH4 + R ? CH3 + HR have been studied usingab initio SCF and ... more Five hydrogen abstraction reactions, CH4 + R ? CH3 + HR have been studied usingab initio SCF and CI methods. R was successively chosen as H, CH3, NH2, OH and F. Geometries were fully optimized at SCF level and energies were computed at CI level for products, reactants and transition states. Quadratic hypersurfaces were fitted in the neighborhood of the
A study was performed on the HLA-DRbeta1*0401-collagen II peptide complex using the computation o... more A study was performed on the HLA-DRbeta1*0401-collagen II peptide complex using the computation of electronic multipolar variables proposed by us previously. Furthermore, these results were compared with those obtained for the HLA-DRbeta1*0101-haemaglutinin peptide complex studied by us with the same tools, confirming that Pocket 1 for this new complex is also the most important pocket for the interaction between the presenting molecule and the presented peptide. The pocket hierarchy established for HLA-DRbeta1*0401 allele was P1 > P9 approximately P7 > P6 > P4, whilst a P1 > P4 > P9 approximately P7>P6 pocket hierarchy was found for HLA-DRbeta1*0101, showing how the relative importance of the pockets distinguishes the two alleles. There are high correlation levels with experimental results (when possible), again confirming the validity of using calculated values for electronic multipolar variables as a useful tool for studying interactions between immune system molecules and peptides.
Calculations for C chemisorption on a finely divided nickel catalyst modeled by Ni5, Ni7 and Ni14... more Calculations for C chemisorption on a finely divided nickel catalyst modeled by Ni5, Ni7 and Ni14 clusters were carried out by using the MINDOSR semiempirical method. Vertical adsorption on several sites in the border and in the center of these clusters were evaluated. The adsorption energy depends not only on the type of site but also on the cluster size,
Page 1. Precise Determination of the Absorption Maxima in Wide Bands In analytical chemistry and ... more Page 1. Precise Determination of the Absorption Maxima in Wide Bands In analytical chemistry and spectroscopy, the analys~r of ~olutionr hy spectroscopic methods, one frequentlv m-counters compcmndn wh ~ rh have vrn. ...
ABSTRACT In this article we propose a new topology, based on the stable attractors of the gradien... more ABSTRACT In this article we propose a new topology, based on the stable attractors of the gradient field of the potential energy hypersurface, that may be used as a general definition of a stable chemical structure. We further construct two examples of particular realizations of this abstract topology. One of them is closely related to the catchment–region topology of Mezey and the other one to the molecular–graph model of Bader. A particularly interesting point is that both topologies lead to equivalent definitions of molecular structure; in particular, they permit us to differentiate between cis-trans isomers and rotational conformers, that had equivalent structures in the definition proposed by Bader.
Abstract We analyze the connections of Lavoisier system of nomenclature with Leibniz&#x27... more Abstract We analyze the connections of Lavoisier system of nomenclature with Leibniz's philosophy, pointing out to the resemblance between what we call Leibnizian and Lavoisian programs. We argue that Lavoisier's contribution to chemistry is something more subtle, in so doing we show that the system of nomenclature leads to an algebraic system of chemical sets. We show how Döbereiner and Mendeleev were able to develop this algebraic system and to find new interesting properties for it. We pointed out the resemblances between ...
Abstract: Mathematical chemistry is often thought to be a 20 th-century subdiscipline of chemistr... more Abstract: Mathematical chemistry is often thought to be a 20 th-century subdiscipline of chemistry, but in this paper we discuss several early chemical ideas and some landmarks of chemistry as instances of the mathematical way of thinking; many of them before 1900. By the mathematical way of thinking, we follow Weyl's description of it in terms of functional thinking, ie setting up variables, symbolizing them, and seeking for functions relating them.
Uploads
Papers