Book Chapters:
J. Hynes, D. Laage, I. Tuñón, V. Moliner
"A Transition State Theory Perspective for Enzymatic Reactions: Fundamentals and Applications" Simulating Enzyme Reactivity : Computational Methods in Enzyme Catalysis. I. Tuñón, V. Moliner Royal Soc. Chem. Publishing, (2017)
Description: The simulation of enzymatic processes is a well-established field within computational chemistry, as demonstrated by the 2013 Nobel Prize in Chemistry. It has been attracting increasing attention in recent years due to the potential applications in the development of new drugs or new environmental-friendly catalysts. Featuring contributions from renowned authors, including Nobel Laureate Arieh Warshel, this book explores the theories, methodologies and applications in simulations of enzyme reactions. It is the first book offering a comprehensive perspective of the field by examining several different methodological approaches and discussing their applicability and limitations. The book provides the basic knowledge for postgraduate students and researchers in chemistry, biochemistry and biophysics, who want a deeper understanding of complex biological process at the molecular level.
J. Ruiz-Pernia, V. Moliner, I. Tuñón.
"Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM methods: An Application to Dihydrofolate Reductase" Challenges and Advances in Computational Chemistry and Physics series. Vol 21. Quantum Modeling of Complex Molecular Systems. Jean-Louis Rivail, Manuel Ruiz-Lopez, Xavier Assfeld Eds. Springer, (2015)
Description: This multi-author contributed volume includes methodological advances and original applications to actual chemical or biochemical phenomena which were not possible before the increased sophistication of modern computers. The chapters contain detailed reviews of the developments of various computational techniques, used to study complex molecular systems such as molecular liquids and solutions (particularly aqueous solutions), liquid-gas, solid-gas interphase and biomacromolecular systems.
Quantum modeling of complex molecular systems is a useful resource for graduate students and fledgling researchers and is also an excellent companion for research professionals engaged in computational chemistry, material science, nanotechnology, physics, drug design, and molecular biochemistry. (see more)
S. Ferrer, J. Ruiz-Pernia, S. Martí, V. Moliner, I. Tuñón, J. Bertran and J. Andrés.
"Hybrid Schemes Based on Quantum Mechanics/Molecular Mechanics Simulations: Goals to Success, Problems and Perspectives" Advances in Protein Chemistry and Structural Biology. Vol 85. C. Christov Ed. Elsevier, Holland, (2011)
Description: Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This volume features articles on Computational Chemistry methods in Structural Biology. (see more)
S. Ferrer, S. Martí, V. Moliner e I. Tuñón.
"Computational Modelling of Biological Systems: The LDH Story"
Kinetics and Dynamics Springer, P. Paneth and A. Dybala-Defratyka Eds. (2010)
Description: "Kinetics and Dynamics" on molecular modeling of dynamic processes opens with an introductory overview before discussing approaches to reactivity of small systems in the gas phase. Then it examines studies of systems of increasing complexity up to the dynamics of DNA. This title has interdisciplinary character presenting wherever possible an interplay between the theory and the experiment. It provides basic information as well as the details of theory and examples of its application to experimentalists and theoreticians interested in modeling of dynamic processes in chemical and biochemical systems. All contributing authors are renowned experts in their fields and topics covered in this volume represent the forefront of today’s science. (see more)
S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón y J. Bertrán.
"Improving catalytic antibodies by means of computational techniques"
Modelling Molecular Structure and Reactivity in Biological Systems. Edited by: J. J. Naidoo, J. Brady, M. J. Field, J. Gao y M. Hann. Royal Soc. Chem. Publishing. ISBN 0 854046682 (2006).
Description: Computational and theoretical tools for understanding biological processes at the molecular level is an exciting and innovative area of science. Using these methods to study the structure, dynamics and reactivity of biomacromolecules in solution, computational chemistry is becoming an essential tool, complementing the more traditional methods for structure and reactivity determination. Modelling Molecular Structure and Reactivity in Biological Systems covers three main areas in computational chemistry; structure (conformational and electronic), reactivity and design. Initial sections focus on the link between computational and spectroscopic methods in the investigation of electronic structure. The use of Free Energy calculations for the elucidation of reaction mechanisms in enzymatic systems is also discussed. Subsequent sections focus on drug design and the use of database methods to determine ADME (absorption, distribution, metabolism, excretion) properties. This book provides a complete reference on state of the art computational chemistry practised on biological systems. It is ideal for researchers in the field of computational chemistry interested in its application to biological systems. (see more)
R. Castillo, M. Oliva, S. Martí, V. Moliner, I. Tuñón y J. Andrés
"Hybrid QM/MM studies on chemical reactivity"
Recent Research Developments in Quantum Chemistry, Vol 3, pp 51-74. Published by Transworld Research Network. ISBN 81-7895-043-X. (2002)
O. Tapia, J. Andrés, V. Moliner y F. Stamato.
"Theory of Solvent Effects and the Description of Chemical Reactions. Proton and Hydride Transfer Processes"
Theoretical Treatments of Hydrogen Bonding. Edited by Dusan Hadzi. Published by John Wiley and Sons. Wiley Research Series in Theoretical Chemistry, pp 143-164. New York. (1997)
J. Andrés, V. Moliner, V.S. Safont y L. R. Domingo.
"Transition Structures Characterization and Kinetic Isotope Effects. Understanding Chemical Reactivity in Enzymes and Organic Reactions"
Recent Research Developments in Physical Chemistry, 1 pp 99-116. Published by Transworld Research Network. (1997)
J. Hynes, D. Laage, I. Tuñón, V. Moliner
"A Transition State Theory Perspective for Enzymatic Reactions: Fundamentals and Applications" Simulating Enzyme Reactivity : Computational Methods in Enzyme Catalysis. I. Tuñón, V. Moliner Royal Soc. Chem. Publishing, (2017)
Description: The simulation of enzymatic processes is a well-established field within computational chemistry, as demonstrated by the 2013 Nobel Prize in Chemistry. It has been attracting increasing attention in recent years due to the potential applications in the development of new drugs or new environmental-friendly catalysts. Featuring contributions from renowned authors, including Nobel Laureate Arieh Warshel, this book explores the theories, methodologies and applications in simulations of enzyme reactions. It is the first book offering a comprehensive perspective of the field by examining several different methodological approaches and discussing their applicability and limitations. The book provides the basic knowledge for postgraduate students and researchers in chemistry, biochemistry and biophysics, who want a deeper understanding of complex biological process at the molecular level.J. Ruiz-Pernia, V. Moliner, I. Tuñón.
"Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM methods: An Application to Dihydrofolate Reductase" Challenges and Advances in Computational Chemistry and Physics series. Vol 21. Quantum Modeling of Complex Molecular Systems. Jean-Louis Rivail, Manuel Ruiz-Lopez, Xavier Assfeld Eds. Springer, (2015)
Description: This multi-author contributed volume includes methodological advances and original applications to actual chemical or biochemical phenomena which were not possible before the increased sophistication of modern computers. The chapters contain detailed reviews of the developments of various computational techniques, used to study complex molecular systems such as molecular liquids and solutions (particularly aqueous solutions), liquid-gas, solid-gas interphase and biomacromolecular systems.Quantum modeling of complex molecular systems is a useful resource for graduate students and fledgling researchers and is also an excellent companion for research professionals engaged in computational chemistry, material science, nanotechnology, physics, drug design, and molecular biochemistry. (see more)
S. Ferrer, J. Ruiz-Pernia, S. Martí, V. Moliner, I. Tuñón, J. Bertran and J. Andrés.
"Hybrid Schemes Based on Quantum Mechanics/Molecular Mechanics Simulations: Goals to Success, Problems and Perspectives" Advances in Protein Chemistry and Structural Biology. Vol 85. C. Christov Ed. Elsevier, Holland, (2011)
Description: Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This volume features articles on Computational Chemistry methods in Structural Biology. (see more)S. Ferrer, S. Martí, V. Moliner e I. Tuñón.
"Computational Modelling of Biological Systems: The LDH Story"
Kinetics and Dynamics Springer, P. Paneth and A. Dybala-Defratyka Eds. (2010)
Description: "Kinetics and Dynamics" on molecular modeling of dynamic processes opens with an introductory overview before discussing approaches to reactivity of small systems in the gas phase. Then it examines studies of systems of increasing complexity up to the dynamics of DNA. This title has interdisciplinary character presenting wherever possible an interplay between the theory and the experiment. It provides basic information as well as the details of theory and examples of its application to experimentalists and theoreticians interested in modeling of dynamic processes in chemical and biochemical systems. All contributing authors are renowned experts in their fields and topics covered in this volume represent the forefront of today’s science. (see more)S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón y J. Bertrán.
"Improving catalytic antibodies by means of computational techniques"
Modelling Molecular Structure and Reactivity in Biological Systems. Edited by: J. J. Naidoo, J. Brady, M. J. Field, J. Gao y M. Hann. Royal Soc. Chem. Publishing. ISBN 0 854046682 (2006).
Description: Computational and theoretical tools for understanding biological processes at the molecular level is an exciting and innovative area of science. Using these methods to study the structure, dynamics and reactivity of biomacromolecules in solution, computational chemistry is becoming an essential tool, complementing the more traditional methods for structure and reactivity determination. Modelling Molecular Structure and Reactivity in Biological Systems covers three main areas in computational chemistry; structure (conformational and electronic), reactivity and design. Initial sections focus on the link between computational and spectroscopic methods in the investigation of electronic structure. The use of Free Energy calculations for the elucidation of reaction mechanisms in enzymatic systems is also discussed. Subsequent sections focus on drug design and the use of database methods to determine ADME (absorption, distribution, metabolism, excretion) properties. This book provides a complete reference on state of the art computational chemistry practised on biological systems. It is ideal for researchers in the field of computational chemistry interested in its application to biological systems. (see more)R. Castillo, M. Oliva, S. Martí, V. Moliner, I. Tuñón y J. Andrés
"Hybrid QM/MM studies on chemical reactivity"
Recent Research Developments in Quantum Chemistry, Vol 3, pp 51-74. Published by Transworld Research Network. ISBN 81-7895-043-X. (2002)
O. Tapia, J. Andrés, V. Moliner y F. Stamato.
"Theory of Solvent Effects and the Description of Chemical Reactions. Proton and Hydride Transfer Processes"
Theoretical Treatments of Hydrogen Bonding. Edited by Dusan Hadzi. Published by John Wiley and Sons. Wiley Research Series in Theoretical Chemistry, pp 143-164. New York. (1997)
J. Andrés, V. Moliner, V.S. Safont y L. R. Domingo.
"Transition Structures Characterization and Kinetic Isotope Effects. Understanding Chemical Reactivity in Enzymes and Organic Reactions"
Recent Research Developments in Physical Chemistry, 1 pp 99-116. Published by Transworld Research Network. (1997)