Table Of ContentEDITORIAL BOARD
GuillerminaEstiu´ (University Park, PA, USA)
Frank Jensen (Aarhus,Denmark)
Mel Levy (Greensboro, NC, USA)
Jan Linderberg (Aarhus, Denmark)
William H. Miller (Berkeley,CA, USA)
John W. Mintmire (Stillwater, OK,USA)
ManojMishra (Mumbai, India)
Jens Oddershede (Odense,Denmark)
Josef Paldus (Waterloo, Canada)
PekkaPyykko¨ (Helsinki, Finland)
Mark Ratner (Evanston, IL,USA)
Dennis R. Salahub (Calgary, Canada)
Henry F. Schaefer III (Athens, GA, USA)
John Stanton (Austin, TX, USA)
Harel Weinstein (New York,NY, USA)
Advances in
QUANTUM CHEMISTRY
COMBINING QUANTUM MECHANICS AND MOLECULAR
MECHANICS. SOME RECENT PROGRESSES IN QM/MM
METHODS
59
VOLUME
Editors
JOHN R. SABIN
QuantumTheoryProject
UniversityofFlorida
Gainesville,Florida
ERKKI BR˜NDAS
DepartmentofQuantumChemistry
UppsalaUniversity
Uppsala,Sweden
Special Editor
SYLVIO CANUTO
InstitutodeF´ısica
UniversidadedeSa~oPaulo
Brazil
Amsterdam(cid:129)Boston(cid:129)Heidelberg(cid:129)London(cid:129)NewYork(cid:129)Oxford
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PREFACE
The last decade has seen an enormous increase in the use of QM/MM
methods and the trend for the coming years is certainly to have an even
larger increase. QM/MM is now the general name given for methods that
combinequantummechanicsandmolecularmechanics.Originallydevised
for dealing with the complex problem of proteins and enzymes, it is now
used in a wide variety of physicochemical problems. For the study of a
chemical reaction in an active site of an enzyme, it is conceivable that the
amino acids located far from the active site will have considerable less
importance. But QM/MM methods are also very important in the study of
thespectroscopyofliquidsystems.QMisneededtostudythequantization
oftheenergylevelsandMMcanbeusedtogeneratetheliquidstructureat
nonzero temperatures. QM/MM methods have seen an extraordinary
development allowing quantum chemistry to enter real everyday activity
inmostlaboratoriesinchemistryandbiochemistry.ThenecessityforaQM
treatment(neededinspectroscopyandreactions,forinstance)togetherwith
the difficulties of treating the entire system by QM imposes some compro-
mising. This compromising comes by adding classical mechanics in a
partition of the system. It is used in biomolecular structure and reactivity
and in studying solvent effects. It is also considered in excited state
dynamics, wherethefate of the excitationenergy depends on the environ-
mentaroundthechromophore.ThedevelopmentofQM/MMmethodsisa
very active research area with different nuances. This gave the idea of
editing a special issue of the Advances in Quantum Chemistry dedicated
to the subject. This issue focuses on some of the recent progresses in
QM/MM methods. Some leading research groups around the world have
joinedthisprojecttogiveareviewoftheircontributiontothefield,includ-
ing applications. In total, this issue is composed of 10 different chapters.
The first chapter, by Tu and Laaksonen, shows the partition of the system
into QM and MM parts; discusses the boundary and the coupling of these
two parts. Computational aspects are then considered. In Chapter 2,
Barone,Biczysko,andBrancatoextendtherangeofcomputationalspectro-
scopybyusingQM/MMapproachesusingbothtime-dependentandtime-
independent routes. Applications in this case consider electronic spectra
and magnetic properties and vibrational dynamics beyond the harmonic
ix
x Preface
approximation. An important computational strategy for dealing with the
large number of explicit solvent molecules and a multitude of configura-
tions is the use of a mean field approximation. This has been successfully
conductedbyAguilarandcoworkerswhoreplacedtheconfigurationaver-
age of a given property by an average solvent perturbation. This is the
subject treated in Chapter 3 where special attention is devoted to a combi-
nation of the mean field approximation with molecular dynamics. One of
themostimportantaspectsofthesolventinteractionwithareferencesolute
molecule is the understanding of the role played by the hydrogen bonds
formed between the solute and the solvent and among the solvent. This
specificinteractionisattheheartoftheproperexistenceofliquidwaterin
roomconditions.AttentiontothisisdevotedbyMataandCabralinChapter4,
wherethecombinedandsequentialuseofMMandQMisusedtounravelthe
electronicpropertiesofhydrogenbondedliquidsystems,includingwaterand
ammonia.Further,waterisresponsibleforeasingchemicalreactionsthatare
important in biochemical and environmental processes. Water is in very
important in host–guest chemistry and as such there is an increasing need
for understanding the properties of the inclusion compounds. In Chapter 5
Lima, Heine, and Duarte present, discuss, and explore the simulation of
polypeptide and their inclusion compounds with b-cyclodextrin.The theore-
tical tool used in this endeavor is the recent and successful dispersion-
corrected–self-consistent charge–density functional tight binding model. Of
course, biomolecular processes and properties are natural candidates for the
application of the QM/MM methodology. Thus in Chapter 6, Groenhof,
Boggio-Pasqua, Scha¨fer, and Robb discuss the computer simulation of the
effectoftheproteinenvironmentonphotobiologicalprocesses.Thetheoretical
concepts of photochemical reactions together with a practical simulation
scheme for photochemical reactions in biomolecular systems are reviewed.
This provides not only experimentally accessible information but also quan-
tities that are more difficult to measure. Applications include photoactive
yellow protein and reversible switchable fluorescent proteins. Molecular
dynamics based on first-principle methods would be the ideal choice if it
were not computationally very demanding for liquid systems of chemical
interest. QM/MM methods are alternatives to a full QM dynamics. But
simplifiedandefficientabinitiodynamicscanstillbeperformedforsystems
of interest. In this direction an ab initio quantum mechanics charge field
moleculardynamicshasbeendevelopedbyRodeandcollaborators.InChap-
ter 7 Hofer, Pribil, Randolf, and Rode present this methodology that over-
comes the necessity of solute–solvent potentials. Comparison with other
molecular dynamics simulation approaches are made and applications are
shown for difficult cases of anions and cations in solution. Chapter 8 by
Pierdominici-Sottile, Alberti, and Palma is dedicated to one very important
aspectofchemicalreactionthatisthenuclearquantumeffects.Theydiscuss
and use mixed-quantum/classical trajectories to study the effects of the
Preface xi
nuclear quantum effects in chemical reactions and vibrational relaxation
processes. Hence they study proton transfer in gas and condensed phases
and vibrational relaxation processes. In chemical reactions in solution the
essential quantity is the variation of the free energy along the process. A
recent theory has been developed by the Osaka and Kyoto groups, where
they use an energy representation for the hybrid QM/MM method. In this,
the distribution function of the solute–solvent interaction is a fundamental
quantitytoobtainthesolvationfreeenergy.ThisisdescribedinChapter9by
Takahashi, Matubayasi, and Nakano where they review this QM/MM-ER
and describe important applications making also comparison with more
traditional procedures. Interesting, they also introduce a novel implementa-
tion for redox reactions in biological molecules. Chapter 10 closes this issue
withareviewbyZhang,Lev,Cuervo,Noskov,andSalahub,thatisalsosome
guide to QM/MM methods. Essential and basic concepts with the related
techniques are introduced, applications are discussed, and some possible
answers tothe utilizationof QM/MM techniquesindifferent studiestaking
placeincondensedphaseareprovided.
Altogether this issue involves some of the recent progresses including
different and complementary aspects of the QM/MM methodology for
different applications inbiochemistry and in solution chemistry.
I take this opportunity to thank the editors of the Advances in Quantum
Chemistry for support and for the invitation to carry on this project. I
specially thank all contributors for accepting my invitation. It is my hope
that this issue will be useful to both the beginners and the experienced
scientists, and thus contribute and stimulate further developments in this
excitingand fast expanding research topic.
Sylvio Canuto
Sa~o Paulo, Brazil
CONTRIBUTORS
Numbersin parentheses indicate the pages where the authors’
contributions can be found.
Manuel A.Aguilar(59)
A´readeQu´ımicaF´ısica,UniversidaddeExtremadura,Avda. deElvass/n,
06071 Badajoz, Spain
Sebastia´nFerna´ndez Alberti (247)
Universidad Nacional de Quilmes, Sa´enz Pen˜a 352, Bernal, B1876BXD, Bs.
As., Argentina
Vincenzo Barone (17)
Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy, E-mail:
[email protected]
Malgorzata Biczysko (17)
Dipartimento di Chimica, Universita` di Napoli “Federico II,” Complesso
Univ. Monte S.Angelo,via Cintia, 80126 Napoli,Italy
MartialBoggio-Pasqua(181)
Laboratoire de Chimie et Physique Quantiques, IRSAMC, CNRS et
Universite´ de Toulouse,118 Route de Narbonne, 31062 Toulouse,France
Giuseppe Brancato (17)
Italian Institute of Technology, IIT@NEST Center for Nanotechnology
Innovation, Piazza San Silvestro 12, 56125 Pisa, Italy
B.J.Costa Cabral(99)
Grupo de F´ısica-Matema´tica da Universidade de Lisboa, Avenue Professor
Gama Pinto 2, 1649-003 Lisboa, Portugal
JavierEduardo Cuervo (353)
Department of Chemistry; Institute for BioComplexity and Informatics—
University of Calgary, Calgary, Alberta, Canada
xiii
xiv Contributors
Ignacio Fdez. Galva´n (59)
A´readeQu´ımica F´ısica,Universidad deExtremadura,Avda. deElvass/n,
06071Badajoz, Spain
Guilherme Ferreirade Lima (145)
Departamento de Qu´ımica, ICEx, Universidade Federal de Minas Gerais,
UFMG, 31270-901Belo Horizonte, MG, Brazil
He´lioAnderson Duarte(145)
Departamento de Qu´ımica, ICEx, Universidade Federal de Minas Gerais,
UFMG, 31270-901Belo Horizonte, MG, Brazil, E-mail: [email protected]
Gerrit Groenhof (181)
ComputationalBiomolecularChemistry,DepartmentofComputationaland
Theoretical Biophysics, Max-Planck-Institute for Biophysical Chemistry,
Am Fassberg11,D-37077, Go¨ttingen, Germany
Thomas Heine (145)
School ofEngineering and Science,Jacobs University, Bremen, 28759
Bremen, Germany
Thomas S.Hofer (213)
TheoreticalChemistryDivision,InstituteofGeneral,InorganicandTheore-
tical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck,
Austria,E-mail: [email protected]
Aatto Laaksonen(1)
Division of Physical Chemistry, Arrhenius Laboratory, Stockholm Univer-
sity, 106 91Stockholm, Sweden.E-mail: [email protected]
Bogdan Lev (353)
Department of Biological Sciences;Institute for BioComplexity and
Informatics—University of Calgary, Calgary, Alberta, Canada
M.Elena Mart´ın (59)
A´readeQu´ımica F´ısica,Universidad deExtremadura,Avda. deElvass/n,
06071Badajoz, Spain
Ricardo A.Mata (99)
Grupo de F´ısica-Matema´tica da Universidade de Lisboa, Avenue Professor
Gama Pinto2, 1649-003 Lisboa, Portugal
Contributors xv
Nobuyuki Matubayasi(283)
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011,
Japan, E-mail: [email protected]
Aurora Mun˜oz-Losa(59)
A´readeQu´ımicaF´ısica,UniversidaddeExtremadura,Avda. deElvass/n,
06071 Badajoz, Spain
Masayoshi Nakano (283)
DepartmentofMaterialsEngineeringScience,GraduateSchoolofEngineer-
ing Science,Osaka University, Toyonaka, Osaka 560-8531,Japan
SergeiYuNoskov (353)
Department of Biological Sciences; Institute for BioComplexity and Infor-
matics—University of Calgary, Calgary, Alberta, Canada, E-mail: snosko-
[email protected]
Juliana Palma (247)
Universidad Nacional de Quilmes, Sa´enz Pen˜a 352, Bernal, B1876BXD, Bs.
As., Argentina
Gustavo Pierdominici-Sottile (247)
Universidad Nacional de Quilmes, Sa´enz Pen˜a 352, Bernal, B1876BXD, Bs.
As., Argentina
Andreas B. Pribil (213)
TheoreticalChemistryDivision,InstituteofGeneral,InorganicandTheore-
tical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck,
Austria
Bernhard R. Randolf(213)
TheoreticalChemistryDivision,InstituteofGeneral,InorganicandTheore-
tical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck,
Austria
Michael A.Robb (181)
DepartmentofChemistry,ImperialCollegeLondon,LondonSW72AZ,UK
BerndM. Rode (213)
TheoreticalChemistryDivision,InstituteofGeneral,InorganicandTheore-
tical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck,
Austria
