Fragmentation: Toward Accurate Calculations on Complex Molecular Systems

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems

Mark S. Gordon

Iowa State University, USA 

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system.

Topics covered include:

          Fragmentation methods

          Embedding methods

          Explicitly correlated local electron correlation methods

          Fragment molecular orbital method

          Methods for treating large molecules

This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.

Preface

1. Explicitly correlated local electron correlation Methods
Hans–JoachimWerner, Christoph Koppl, Qianli Ma, and Max Schwilk

2. Density and Potential Functional Embedding: Theory and Practice
Kuang Yu, Caroline M. Krauter, Johannes M. Dieterich, and Emily A. Carter

3. Modeling and visualization for the fragment molecular orbital method with the graphical user interface FU, and analyses of protein–ligand binding
Dmitri G. Fedorov and Kazuo Kitaura

4. Molecules–in–Molecules Fragment–Based Method for the Accurate Evaluation of Vibrational and Chiroptical Spectra for Large Molecules
K. V. Jovan Jose and Krishnan Raghavachar

5. Effective Fragment Molecular Orbital Method
Casper Steinmann and Jan H Jensen

6. Effective Fragment Potential method: past, present and future
Lyudmila V. Slipchenko and Pradeep K. Gurunathan

7. Nucleation using the effective fragment potential and two–level parallelism
Ajitha Devarajan, Alexander Gaenko, Mark S. Gordon, and Theresa L. Windus

8. Five years of density matrix embedding theory
Sebastian Wouters, Carlos A. Jiménez–Hoyos and Garnet K.–L. Chan

9. Ab initio ice, dry ice, and liquid water
So Hirata, Kandis Gilliard, Xiao He, Murat Keçeli, Jinjin Li, Michael A. Salim, Olaseni Sode, and Kiyoshi Yagi

10. A linear–scaling divide–and–conquer quantum chemical method for open–shell systems and excited states
Takeshi Yoshikawa and Hiromi Nakai

11. MFCC based fragmentation methods for biomolecules
Jinfeng Liu, Tong Zhu, Xiao he, and John Z. H. Zhang

Index