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The Resource Large-Scale Quantum-Mechanical Enzymology

Large-Scale Quantum-Mechanical Enzymology

Label
Large-Scale Quantum-Mechanical Enzymology
Title
Large-Scale Quantum-Mechanical Enzymology
Creator
Subject
Language
eng
Summary
This work establishes linear-scaling density-functional theory (DFT) as a powerful tool for understanding enzyme catalysis, one that can complement quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics simulations. The thesis reviews benchmark studies demonstrating techniques capable of simulating entire enzymes at the ab initio quantum-mechanical level of accuracy. DFT has transformed the physical sciences by allowing researchers to perform parameter-free quantum-mechanical calculations to predict a broad range of physical and chemical properties of materials. In principle, similar methods could be applied to biological problems. However, even the simplest biological systems contain many thousands of atoms and are characterized by extremely complex configuration spaces associated with a vast number of degrees of freedom. The development of linear-scaling density-functional codes makes biological molecules accessible to quantum-mechanical calculation, but has yet to resolve the complexity of the phase space. Furthermore, these calculations on systems containing up to 2,000 atoms can capture contributions to the energy that are not accounted for in QM/MM methods (for which the Nobel prize in Chemistry was awarded in 2013) and the results presented here reveal profound shortcomings in said methods
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Cataloging source
MiAaPQ
Literary form
non fiction
Nature of contents
dictionaries
Series statement
Springer Theses Ser
Large-Scale Quantum-Mechanical Enzymology
Label
Large-Scale Quantum-Mechanical Enzymology
Link
http://libproxy.rpi.edu/login?url=https://ebookcentral.proquest.com/lib/rpi/detail.action?docID=2120653
Publication
Copyright
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Carrier category
online resource
Carrier category code
cr
Carrier MARC source
rdacarrier
Color
multicolored
Content category
text
Content type code
txt
Content type MARC source
rdacontent
Contents
  • Publications Related to this Work -- Supervisor's Foreword -- Abstract -- Acknowledgments -- Contents -- 1 Introduction -- 1.1 Modelling and Simulation: In Silico Techniques -- 1.2 Synergy Between Theory and Experiment -- 1.3 Dissertation Outline -- References -- 2 Proteins, Enzymes and Biological Catalysis -- 2.1 Amino Acids -- 2.2 Protein Structure -- 2.3 Enzyme Catalysis -- 2.4 Summary -- References -- 3 Computational Techniques -- 3.1 Many-Body Quantum Mechanics -- 3.2 Density-Functional Theory -- 3.2.1 Exchange and Correlation -- 3.2.2 Basis Sets -- 3.2.3 The Pseudopotential Approximation -- 3.3 Linear-Scaling DFT -- 3.4 The onetep Code -- 3.4.1 The Periodic Cardinal Sine Function Basis Set -- 3.4.2 Cutoff Coulomb Interactions -- 3.4.3 Implicit Solvation -- 3.4.4 Calculating the Local/Partial Density of States -- 3.4.5 Empirical Dispersion Corrections -- 3.4.6 Electrostatic Embedding and the QM/EE Approach -- 3.4.7 Natural Bond Orbital Analysis -- 3.4.8 Density Derived Electrostatic and Chemical Method for Computing Net Atomic Charges -- 3.5 Structural Optimisation -- 3.5.1 Calculation of Forces -- 3.5.2 Normal Mode Analysis -- 3.5.3 Transition State Searching -- 3.5.4 Linear and Quadratic Synchronous Transit Methods -- 3.5.5 The Eigenvector-Following Approach -- 3.6 Classical Force Fields -- 3.7 Hybrid Quantum Mechanics/Molecular Mechanics Approaches -- 3.8 Summary -- References -- 4 Validation Studies -- 4.1 Ethene -- 4.2 Alanine Dipeptide -- 4.3 Pericyclic Chorismate Rearrangement -- 4.4 Summary -- References -- 5 Explaining the Closure of Calculated HOMO-LUMO Gaps in Biomolecular Systems -- 5.1 Introduction -- 5.2 Vanishing HOMO-LUMO Gaps -- 5.3 Water Clusters -- 5.4 Protein Systems -- 5.5 Summary -- References -- 6 A Density-Functional Perspective on the Chorismate Mutase Enzyme -- 6.1 Introduction
  • 6.2 General Preparation and Optimisation of Systems -- 6.2.1 Specific Preparation of the Enzyme System -- 6.2.2 Specific Preparation of System in Solution -- 6.3 Rearrangement in Enzyme -- 6.4 Natural Bond Orbital Analysis -- 6.5 Structural Analysis -- 6.6 Rearrangement in Solution -- 6.7 DDEC and NPA Charge Analysis -- 6.8 Discussion -- 6.9 Summary -- References -- 7 Concluding Remarks -- 7.1 Summary of Dissertation -- 7.2 Suggestions for Further Work -- References
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{'f': 'http://opac.lib.rpi.edu/record=b4383411'}
Extent
1 online resource (162 pages)
Form of item
online
Isbn
9783319193519
Media category
computer
Media MARC source
rdamedia
Media type code
c
Sound
unknown sound
Specific material designation
remote

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