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E-raamat: Quantum Modeling of Complex Molecular Systems

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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 including: methods adapted to the computation of systems containing hundreds of atoms; advances in hybrid Quantum Mechanical/Molecular Mechanical methods; studies of molecular solids, studies of molecular liquids and solutions and new methodologies, applications in particular to biomacromolecules. 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.

1 Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics
1(50)
Nohad Gresh
Krystel El Hage
Elodie Goldwaser
Benoit de Courcy
Robin Chaudret
David Perahia
Christophe Narth
Louis Lagardere
Filippo Lipparini
Jean-Philip Piquemal
2 Proton Transfer in Aqueous Solution: Exploring the Boundaries of Adaptive QM/MM
51(42)
T. Jiang
J.M. Boereboom
C. Michel
P. Fleurat-Lessard
R.E. Bulo
3 Recent Progress in Adaptive-Partitioning QM/MM Methods for Born-Oppenheimer Molecular Dynamics
93(22)
Soroosh Pezeshki
Hai Lin
4 Probing Proton Transfer Reactions in Molecular Dynamics---A Crucial Prerequisite for QM/MM Simulations Using Dissociative Models
115(20)
Thomas S. Hofer
5 Accelerating QM/MM Calculations by Using the Mean Field Approximation
135(18)
M. Elena Martin
M. Luz Sanchez
Aurora Munoz-Losa
Ignacio Fdez Galvan
Manuel A. Aguilar
6 Development of a Massively Parallel QM/MM Approach Combined with a Theory of Solutions
153(44)
Hideaki Takahashi
Nobuyuki Matubayasi
7 Structure and Electronic Properties of Liquids and Complex Molecular Systems in Solution: Coupling Many-Body Energy Decomposition Schemes to Born-Oppenheimer Molecular Dynamics
197(22)
Benedito J.C. Cabral
K. Coutinho
S. Canuto
8 Free Energy Gradient Method and Its Recent Related Developments: Free Energy Optimization and Vibrational Frequency Analysis in Solution
219(34)
Yukichi Kitamura
Norio Takenaka
Yoshiyuki Koyano
Masataka Nagaoka
9 Towards an Accurate Model for Halogens in Aqueous Solutions
253(22)
M.I. Bernal-Uruchurtu
A. Alcaraz Torres
F.A. Batista Romero
R. Hernandez-Lamoneda
10 Theoretical Studies of the Solvation of Abundant Toxic Mercury Species in Aqueous Media
275(28)
J.I. Amaro-Estrada
A. Ramirez-Solis
11 Advances in QM/MM Molecular Dynamics Simulations of Chemical Processes at Aqueous Interfaces
303(22)
Marilia T.C. Martins-Costa
Manuel F. Ruiz-Lopez
12 QM/MM Approaches for the Modeling of Photoinduced Processes in Biological Systems
325(18)
Benedetta Mennucci
13 The Non Empirical Local Self Consistent Field Method: Application to Quantum Mechanics/Molecular Mechanics (QM/MM) Modeling of Large Biomolecular Systems
343(24)
Jean-Louis Rivail
Antonio Monari
Xavier Assfeld
14 Computational Study of the Initial Step in the Mechanism of Dehaloperoxidase A: Determination of the Protonation Scheme at the Active Site and the Movement of the His55 Residue
367(16)
Fiorentina Bottinelli
Patricia Saenz-Mendez
Oscar N. Ventura
15 Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM Methods: An Application to Dihydrofolate Reductase
383(32)
J. Javier Ruiz-Pernia
Vicent Moliner
Inaki Tunon
16 Multiscale Modelling of In Situ Oil Sands Upgrading with Molybdenum Carbide Nanoparticles
415(32)
Xingchen Liu
Baojing Zhou
Farouq Ahmed
Alexander Tkalych
Akira Miyamoto
Dennis R. Salahub
17 Computational Spectroscopy in Solution: Methods and Models for Investigating Complex Systems
447(72)
Vincenzo Barone
Enrico Benassi
Ivan Carnimeo
Index 519
Present status: Emeritus Professor of Theoretical Chemistry, University of Lorraine (Nancy Campus). Research field: Theoretical modeling of complex molecular systems. Publications (more than 200).