Multiscale Dynamics Simulations Nano and Nano-bio-Systems in Complex Environments

389 Pages·2022·14.841 MB·English

by  Salahub

Multiscale Dynamics Simulations
Nano and Nano-bio Systems in Complex Environments
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Theoretical and Computational Chemistry Series
Editor-in-chief:
Jonathan Hirst, University of Nottingham, Nottingham, UK
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46 Dongqing Wei, Shanghai Jiao Tong University, China
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91 Jeremy Smith, Oakridge National Laboratory, USA
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97 Titles in the series:
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3 1: Knowledge-based Expert Systems in Chemistry: Not Counting on
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2/2on 7: Theory of Molecular Collisions
11/2021 8: In Silico Medicinal Chemistry: Computational Methods to Support
d on ber 2 Drug Design
ownloade4 Septem 109::CSCioamtmaulpylaustitisantgioEnnalzyBmioepRheysaicctsivoitfy:MCeommbprauntaetiPornoatleiMnsethods in Enzyme
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Dynamics
15: Knowledge-based Expert Systems in Chemistry: Artificial Intelligence
in Decision Making
16: London Dispersion Forces in Molecules, Solids and Nano-structures:
An Introduction to Physical Models and Computational Methods
17: Machine Learning in Chemistry: The Impact of Artificial Intelligence
18: Tunnelling in Molecules: Nuclear Quantum Effects from Bio to Physical
Chemistry
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19: Understanding Hydrogen Bonds: Theoretical and Experimental Views
20: Computational Techniques for Analytical Chemistry and Bioanalysis
21: Effects of Electric Fields on Structure and Reactivity: New Horizons
in Chemistry
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Multiscale Dynamics
Simulations
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46 Preface
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oi: Over the past decade, great strides have been taken in developing quantum
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Pc. density functional theory (DFT) and its parameterized version DF tight
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1/22/221 on environments with good accuracy. Most recently, some of these methods
10 have benefitted from extraordinary acceleration afforded by incorporating
d on ber 2 thelatestadvancesinmachinelearning(ML).Thisbookaimstosummarize
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methodologies.
Leading experts have contributed in the following subfields:
1) DFT/MM-MD
In Chapter 1, Andreas Ko¨ster from Cinvestav, Mexico City has co-
ordinated the writing of co-authors from the deMon2k community to
provideanin-depthaccountofthetheoryforQM/MMimplementation
in deMon2k within the framework of auxiliary density functional the-
ory(ADFT).Workingequationsaregiven,andapracticaltoolforinput
preparationispresented.QM/MMmagneticshieldingandexcitedstate
calculations are emphasized.
TheoreticalandComputationalChemistrySeriesNo.22
MultiscaleDynamicsSimulations:NanoandNano-bioSystemsinComplexEnvironments
EditedbyDennisR.SalahubandDongqingWei
rTheRoyalSocietyofChemistry2022
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
viii
View Online
Preface ix
Chapter2fromtheCalabriagroup(NinoRussoetal.)illustratesthe
state of the art of computational enzymology with several examples of
the performance of cluster models and QM/MM methods along with
MD, tracing the free energy through the many steps of enzymatically-
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66 2) DFT/MMpol-MD
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16 SergeiNoskovandhisUniversityofCalgaryco-authorssetthequestion
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83 for Chapter 3, ‘‘Is explicit inclusion of polarization on the horizon?’’.
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78 They examine the performance of stand-alone MMpol, and QM/MM,
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2/2on of their electron clouds by an external stimulus.’’ They couple QMPol
1/221 with real-time, time-dependent DFT (RT-TDDFT) implemented in
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n Moving to even larger, more complex systems, beyond the purview of
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blis (Toulouse) (Chapter 5) situate DFTB in the context of traditional tight
u binding techniques, on the one hand, and DFT, on the other, and
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review various hybrid schemes involving higher- and lower-level
methods. The dynamics and thermodynamics of metal nanoparticles
arehighlighted,extendingtocomplexenvironmentsfoundinsolution
and at surfaces.
In Chapter 6, Samuele Giannini (Jochen Blumberger group at Uni-
versity College, London) and co-workers explore charge transport in
nanoscale materials with a mixed quantum/classical non-adiabatic
molecular dynamics method termed fragment orbital-based surface
hopping(FOB-SH).Concernssuchastrivialcrossingdetectionandthe
removalofspuriouschargetransferduetodecoherencecorrectionsare
addressed. The transport mechanisms across high-mobility planes of
molecular crystals are elucidated.
Mechanistic insight into nano-catalyzed reactions in complex en-
vironmentsisthegoalespousedinChapter7byTingyuLei,Xingchen
Liu and Xiaodong Wen (Taiyuan and Beijing). They reach it with two
different methodologies DFTB/MM-MD and DFTB nanoreactor-MD,
shedding light on important reactions for the upgrading of oil sands,
View Online
x Preface
the synthesis of graphene by the detonation of carbonaceous material
and Fischer–Tropsch synthesis with Fe nanoparticles.
4) Solvation/Embedding models
Chapter 8, by Tomasz Wesolowski (Geneva) ‘‘concerns Frozen Density
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66 Hohenberg–Kohn energy functional.’’ A comprehensive and detailed
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83 ational and non-variational approaches, going far beyond the original
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2/2on 5) Atomistic MD in complex environments
1/221 Choosing reaction coordinates (RC) to study the dynamics of complex
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In Chapter 11 Jutta Rogel (Berlin) and Mark Tuckerman (New York
and Shanghai) provide ‘‘a framework for combining ML for local
structure classification with the definition of a global classifier space
as a basis for enhanced sampling of structural transformations in
condensed-phase systems.’’ Path collective variables are defined,
yielding insight into mechanisms for such complex phenomena as
solid–solid phase transitions in transition metals.
Finally, in Chapter 12, Abbas Khan, Byu-Ri Sim and Dong-Qing Wei
(Shanghai) show how an array of ML tools can be fruitfully applied to
the analysis of MD trajectories. An extensive table compares the
advantages of the most prominent techniques. Applications to drug–
target interactions, infrared spectra and ligand binding energies are
highlighted.
In the original proposal for this book, we expressed our main motivation
as promoting cross-talk among the various subfields by gathering chapters
from leading experts in a single volume. Our second, co-equal, motivation
View Online
Preface xi
was to provide newcomers with a comprehensive menu of multiscale mod-
elingoptionssothattheycanbettercharttheircourseinthenano/bioworld.
The extent to which our motivations have been satisfied will be judged by
you, the reader. We are grateful to all of the authors who took up the chal-
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66 The dimensional stretch of systems treated in the book ranges from
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83 andbeyond.Ofcourse,notallofthetechniquesarefullyintegrated,butthe
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1/221 Dennis R. Salahub, University of Calgary, Canada
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