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Modeling solvent environments [[electronic resource] ] : applications to simulations of biomolecules / / edited by Michael Feig
| Modeling solvent environments [[electronic resource] ] : applications to simulations of biomolecules / / edited by Michael Feig |
| Pubbl/distr/stampa | Weinheim, : Wiley-VCH Verlag GmbH, c2010 |
| Descrizione fisica | 1 online resource (336 p.) |
| Disciplina | 541.3482011 |
| Altri autori (Persone) | FeigMichael |
| Soggetto topico |
Solvents
Biomolecules |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-282-47232-1
9786612472329 3-527-62925-4 3-527-62926-2 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Modeling Solvent Environments: Applications to Simulations of Biomolecules; Contents; Preface; List of Contributors; 1: Biomolecular Solvation in Theory and Experiment; 1.1 Introduction; 1.2 Theoretical Views of Solvation; 1.2.1 Equilibrium Thermodynamics of Solvation; 1.2.2 Radial Distribution Functions; 1.2.3 Integral Equation Formalisms; 1.2.4 Kirkwood-Buff Theory; 1.2.5 Kinetic Effects of Solvation; 1.3 Computer Simulation Methods in the Study of Solvation; 1.3.1 Molecular Dynamics and Monte Carlo Simulations; 1.3.2 Water Models; 1.3.3 Solvent Structure and Dynamics from Simulations
1.3.4 Free Energy Simulations1.4 Experimental Methods in the Study of Solvation; 1.4.1 X-Ray/Neutron Diffraction and Scattering; 1.4.2 Nuclear Magnetic Relaxation; 1.4.3 Optical Spectroscopy; 1.4.4 Dielectric Dispersion; 1.5 Hydration of Proteins; 1.5.1 Protein Folding and Peptide Conformations in Aqueous Solvent; 1.5.2 Molecular Properties of Water Near Protein Surfaces; 1.5.3 Water Molecules at Protein-Ligand and Protein-Protein Interfaces; 1.6 Hydration of Nucleic acids; 1.7 Non-Aqueous Solvation; 1.7.1 Alcohols; 1.7.2 Urea; 1.7.3 Glycerol; 1.8 Summary; References 2: Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids2.1 Introduction; 2.2 Outline of the RISM and 3D-RISM theories; 2.3 Partial Molar Volume of Proteins; 2.4 Detecting Water Molecules Trapped Inside Protein; 2.5 Selective Ion Binding by Protein; 2.6 Water Molecules Identified as a Substrate for Enzymatic Hydrolysis of Cellulose; 2.7 CO Escape Pathway in Myoglobin; 2.7.1 Effect of Protein Structure on the Distribution of Xe; 2.7.2 Partial Molar Volume Change Through the CO Escape Pathway of Myoglobin; 2.8 Perspective; References 3: Developing Force Fields From the Microscopic Structure of Solutions: The Kirkwood-Buff Approach3.1 Introduction; 3.2 Biomolecular Force Fields; 3.3 Examples of Problems with Current Force Fields; 3.4 Kirkwood-Buff Theory; 3.5 Applications of Kirkwood-Buff Theory; 3.6 The General KBFF Approach; 3.7 Technical Aspects of the KBFF Approach; 3.8 Results for Urea and Water Binary Solutions; 3.9 Preferential Interactions of Urea; 3.10 Conclusions and Future Directions; Acknowledgments; References; 4: Osmolyte Influence on Protein Stability: Perspectives of Theory and Experiment; 4.1 Introduction 4.2 Denaturing Osmolytes4.2.1 Does Urea Weaken Water Structure?; 4.2.2 Effect of Urea on Hydrophobic Interactions; 4.2.3 Direct Interaction of Urea with Proteins; 4.3 Protecting Osmolytes; 4.3.1 Do Protecting Osmolytes Increase Water Structure?; 4.3.2 Effect of Protecting Osmolytes on Hydrophobic Interactions; 4.4 Mixed Osmolytes; 4.5 Conclusions; Acknowledgments; References; 5: Modeling Aqueous Solvent Effects through Local Properties of Water; 5.1 The Role of Water and Cosolutes on Macromolecular Thermodynamics; 5.2 Forces Induced by Water in Aqueous Solutions 5.2.1 Interactions in Water-Accessible Regions of Proteins |
| Record Nr. | UNINA-9910139545203321 |
| Weinheim, : Wiley-VCH Verlag GmbH, c2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Modeling solvent environments [[electronic resource] ] : applications to simulations of biomolecules / / edited by Michael Feig
| Modeling solvent environments [[electronic resource] ] : applications to simulations of biomolecules / / edited by Michael Feig |
| Pubbl/distr/stampa | Weinheim, : Wiley-VCH Verlag GmbH, c2010 |
| Descrizione fisica | 1 online resource (336 p.) |
| Disciplina | 541.3482011 |
| Altri autori (Persone) | FeigMichael |
| Soggetto topico |
Solvents
Biomolecules |
| ISBN |
1-282-47232-1
9786612472329 3-527-62925-4 3-527-62926-2 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Modeling Solvent Environments: Applications to Simulations of Biomolecules; Contents; Preface; List of Contributors; 1: Biomolecular Solvation in Theory and Experiment; 1.1 Introduction; 1.2 Theoretical Views of Solvation; 1.2.1 Equilibrium Thermodynamics of Solvation; 1.2.2 Radial Distribution Functions; 1.2.3 Integral Equation Formalisms; 1.2.4 Kirkwood-Buff Theory; 1.2.5 Kinetic Effects of Solvation; 1.3 Computer Simulation Methods in the Study of Solvation; 1.3.1 Molecular Dynamics and Monte Carlo Simulations; 1.3.2 Water Models; 1.3.3 Solvent Structure and Dynamics from Simulations
1.3.4 Free Energy Simulations1.4 Experimental Methods in the Study of Solvation; 1.4.1 X-Ray/Neutron Diffraction and Scattering; 1.4.2 Nuclear Magnetic Relaxation; 1.4.3 Optical Spectroscopy; 1.4.4 Dielectric Dispersion; 1.5 Hydration of Proteins; 1.5.1 Protein Folding and Peptide Conformations in Aqueous Solvent; 1.5.2 Molecular Properties of Water Near Protein Surfaces; 1.5.3 Water Molecules at Protein-Ligand and Protein-Protein Interfaces; 1.6 Hydration of Nucleic acids; 1.7 Non-Aqueous Solvation; 1.7.1 Alcohols; 1.7.2 Urea; 1.7.3 Glycerol; 1.8 Summary; References 2: Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids2.1 Introduction; 2.2 Outline of the RISM and 3D-RISM theories; 2.3 Partial Molar Volume of Proteins; 2.4 Detecting Water Molecules Trapped Inside Protein; 2.5 Selective Ion Binding by Protein; 2.6 Water Molecules Identified as a Substrate for Enzymatic Hydrolysis of Cellulose; 2.7 CO Escape Pathway in Myoglobin; 2.7.1 Effect of Protein Structure on the Distribution of Xe; 2.7.2 Partial Molar Volume Change Through the CO Escape Pathway of Myoglobin; 2.8 Perspective; References 3: Developing Force Fields From the Microscopic Structure of Solutions: The Kirkwood-Buff Approach3.1 Introduction; 3.2 Biomolecular Force Fields; 3.3 Examples of Problems with Current Force Fields; 3.4 Kirkwood-Buff Theory; 3.5 Applications of Kirkwood-Buff Theory; 3.6 The General KBFF Approach; 3.7 Technical Aspects of the KBFF Approach; 3.8 Results for Urea and Water Binary Solutions; 3.9 Preferential Interactions of Urea; 3.10 Conclusions and Future Directions; Acknowledgments; References; 4: Osmolyte Influence on Protein Stability: Perspectives of Theory and Experiment; 4.1 Introduction 4.2 Denaturing Osmolytes4.2.1 Does Urea Weaken Water Structure?; 4.2.2 Effect of Urea on Hydrophobic Interactions; 4.2.3 Direct Interaction of Urea with Proteins; 4.3 Protecting Osmolytes; 4.3.1 Do Protecting Osmolytes Increase Water Structure?; 4.3.2 Effect of Protecting Osmolytes on Hydrophobic Interactions; 4.4 Mixed Osmolytes; 4.5 Conclusions; Acknowledgments; References; 5: Modeling Aqueous Solvent Effects through Local Properties of Water; 5.1 The Role of Water and Cosolutes on Macromolecular Thermodynamics; 5.2 Forces Induced by Water in Aqueous Solutions 5.2.1 Interactions in Water-Accessible Regions of Proteins |
| Record Nr. | UNINA-9910830153503321 |
| Weinheim, : Wiley-VCH Verlag GmbH, c2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Modeling solvent environments : applications to simulations of biomolecules / / edited by Michael Feig
| Modeling solvent environments : applications to simulations of biomolecules / / edited by Michael Feig |
| Pubbl/distr/stampa | Weinheim, : Wiley-VCH Verlag GmbH, c2010 |
| Descrizione fisica | 1 online resource (336 p.) |
| Disciplina | 541.3482011 |
| Altri autori (Persone) | FeigMichael |
| Soggetto topico |
Solvents
Biomolecules |
| ISBN |
9786612472329
9781282472327 1282472321 9783527629251 3527629254 9783527629268 3527629262 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Modeling Solvent Environments: Applications to Simulations of Biomolecules; Contents; Preface; List of Contributors; 1: Biomolecular Solvation in Theory and Experiment; 1.1 Introduction; 1.2 Theoretical Views of Solvation; 1.2.1 Equilibrium Thermodynamics of Solvation; 1.2.2 Radial Distribution Functions; 1.2.3 Integral Equation Formalisms; 1.2.4 Kirkwood-Buff Theory; 1.2.5 Kinetic Effects of Solvation; 1.3 Computer Simulation Methods in the Study of Solvation; 1.3.1 Molecular Dynamics and Monte Carlo Simulations; 1.3.2 Water Models; 1.3.3 Solvent Structure and Dynamics from Simulations
1.3.4 Free Energy Simulations1.4 Experimental Methods in the Study of Solvation; 1.4.1 X-Ray/Neutron Diffraction and Scattering; 1.4.2 Nuclear Magnetic Relaxation; 1.4.3 Optical Spectroscopy; 1.4.4 Dielectric Dispersion; 1.5 Hydration of Proteins; 1.5.1 Protein Folding and Peptide Conformations in Aqueous Solvent; 1.5.2 Molecular Properties of Water Near Protein Surfaces; 1.5.3 Water Molecules at Protein-Ligand and Protein-Protein Interfaces; 1.6 Hydration of Nucleic acids; 1.7 Non-Aqueous Solvation; 1.7.1 Alcohols; 1.7.2 Urea; 1.7.3 Glycerol; 1.8 Summary; References 2: Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids2.1 Introduction; 2.2 Outline of the RISM and 3D-RISM theories; 2.3 Partial Molar Volume of Proteins; 2.4 Detecting Water Molecules Trapped Inside Protein; 2.5 Selective Ion Binding by Protein; 2.6 Water Molecules Identified as a Substrate for Enzymatic Hydrolysis of Cellulose; 2.7 CO Escape Pathway in Myoglobin; 2.7.1 Effect of Protein Structure on the Distribution of Xe; 2.7.2 Partial Molar Volume Change Through the CO Escape Pathway of Myoglobin; 2.8 Perspective; References 3: Developing Force Fields From the Microscopic Structure of Solutions: The Kirkwood-Buff Approach3.1 Introduction; 3.2 Biomolecular Force Fields; 3.3 Examples of Problems with Current Force Fields; 3.4 Kirkwood-Buff Theory; 3.5 Applications of Kirkwood-Buff Theory; 3.6 The General KBFF Approach; 3.7 Technical Aspects of the KBFF Approach; 3.8 Results for Urea and Water Binary Solutions; 3.9 Preferential Interactions of Urea; 3.10 Conclusions and Future Directions; Acknowledgments; References; 4: Osmolyte Influence on Protein Stability: Perspectives of Theory and Experiment; 4.1 Introduction 4.2 Denaturing Osmolytes4.2.1 Does Urea Weaken Water Structure?; 4.2.2 Effect of Urea on Hydrophobic Interactions; 4.2.3 Direct Interaction of Urea with Proteins; 4.3 Protecting Osmolytes; 4.3.1 Do Protecting Osmolytes Increase Water Structure?; 4.3.2 Effect of Protecting Osmolytes on Hydrophobic Interactions; 4.4 Mixed Osmolytes; 4.5 Conclusions; Acknowledgments; References; 5: Modeling Aqueous Solvent Effects through Local Properties of Water; 5.1 The Role of Water and Cosolutes on Macromolecular Thermodynamics; 5.2 Forces Induced by Water in Aqueous Solutions 5.2.1 Interactions in Water-Accessible Regions of Proteins |
| Record Nr. | UNINA-9911019461203321 |
| Weinheim, : Wiley-VCH Verlag GmbH, c2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Molecular response functions for the polarizable continuum model : physical basis and quantum mechanical formalism / / Roberto Cammi
| Molecular response functions for the polarizable continuum model : physical basis and quantum mechanical formalism / / Roberto Cammi |
| Autore | Cammi Roberto |
| Edizione | [1st ed. 2013.] |
| Pubbl/distr/stampa | Cham [Switzerland] : , : Springer, , 2013 |
| Descrizione fisica | 1 online resource (xvi, 58 pages) |
| Disciplina |
530.41
541.3482011 |
| Collana | SpringerBriefs in Electrical and Magnetic Properties of Atoms, Molecules, and Clusters |
| Soggetto topico |
Quantum chemistry
Molecular biology |
| ISBN | 3-319-00987-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Introduction -- The PCM model for solvated molecules -- The definition of the basic model -- The basic energy functional -- The Quantum Mechanical problem -- The Coupled-cluster equations -- Analytical derivatives theory for molecular solute -- Solute molecular properties -- The coupled-cluster analytical derivatives -- Response theory for molecules in solution -- General response theory for the Polarizable Contiuum Model -- The coupled-cluster response theory. |
| Record Nr. | UNINA-9910741151403321 |
Cammi Roberto
|
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| Cham [Switzerland] : , : Springer, , 2013 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||