Reviews in Computational Chemistry

424 Pages·2001·2.637 MB·English

by  Lipkowitz K.B., Boyd D.B. (eds.)

ReviewsinComputationalChemistry,Volume17.EditedbyKennyB.Lipkowitz,DonaldB.Boyd
Copyright(cid:1)2001JohnWiley&Sons,Inc.
ISBNs:0-471-39845-4(Hardcover);0-471-22441-3(Electronic)
Reviews in
Computational
Chemistry
Volume 17
Reviews in
Computational
Chemistry
Volume 17
Edited by
Kenny B. Lipkowitz and Donald B. Boyd
NEWYORK (cid:1) CHICHESTER (cid:1) WEINHEIM (cid:1) BRISBANE (cid:1) SINGAPORE (cid:1) TORONTO
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Preface
The aphorism ‘‘Knowledge is power’’ applies to diverse circumstances.
Anyonewhohasclimbedanorganizationalladderduringacareerunderstands
thisconceptandknowshowtoexploitit.Theproblemforscientists,however,
is that there may exist too much to know, overwhelming even the brightest
intellectual. Indeed, it is a struggle for most scientists to assimilate even a
tiny part of what is knowable. Scientists, especially those in industry, are
under enormous pressure to know more sooner. The key to using knowl-
edge to gain power is knowing what to know, which is often a question
of what some might call, variously, innate leadership ability, intuition, or
luck.
Attemptstomanagespecializedscientificinformationhavegivenbirthto
thenewdisciplineofinformatics.Thebranchofinformaticsthatdealsprimar-
ily with genomic (sequence) data is bioinformatics, whereas cheminformatics
deals with chemically oriented data. Informatics examines the way people
work with computer-based information. Computers can access huge ware-
housesofinformationintheformofdatabases.Effectiveminingofthesedata-
bases can, in principle, lead to knowledge.
In the area of chemical literature information, the largest databases are
producedbythe ChemicalAbstractsService(CAS) ofthe American Chemical
Society (ACS). As detailed on their website (www.cas.org), their principal
databases are the Chemical Abstracts database (CA) with 16 million docu-
ment records (mainly abstracts of journal articles and other literature) and
the REGISTRY database with more than 28 million substance records. In
an earlier volume of this series,* we discussed CAS’s SciFinder software for
mining these databases. SciFinder is a tool for helping people formulate
queries and view hits. SciFinder does not have all the power and precision
ofthecommand-linequerysystemofCAS’sSTN,asoftwaresystemdeveloped
earliertoaccesstheseandotherCASdatabases.ButwithSciFinderbeingeasy
*D.B.BoydandK.B.Lipkowitz,inReviewsinComputationalChemistry,K.B.Lipkowitz
andD.B.Boyd,Eds.,Wiley-VCH,NewYork,2000,Vol.15,pp.v–xxxv.Preface.
v
vi Preface
touseandwithfavorableacademicpricingfromCAS,nowmanyinstitutions
have purchased it.
ThisvolumeofReviewsinComputationalChemistryincludesanappen-
dix with a lengthy compilation of books on the various topics in computa-
tional chemistry. We undertook this task because as editors we were
occasionally asked whether such a listing existed. No satisfactory list could
befound,sowedevelopedourownusingSciFinder,supplementedwithother
resources.
Wewereanticipatingnotbeingabletoretrieveeverybookwewerelook-
ing for with SciFinder, but we were surprised at how many omissions were
encountered. For example, when searching specifically for our own book ser-
ies,ReviewsinComputationalChemistry,severaloftheexistingvolumeswere
not‘‘hit.’’Moreover,thesewerenotconsecutiveomissionslikeVolumes2–5,
but ratherthey were missing sporadically. Clearly, something aboutthe data-
base is amiss.
Whereas experienced chemistry librarians and information specialists
may fully appreciate the limitations of the CAS databases, a less experienced
user may wonder: How punctilious are the data being mined by SciFinder?
Certainly, for example, one could anticipate differences in spelling like
Mueller versus Mu¨ller, so that typing in only Muller would lead one to not
finding the former name. The developers of SciFinder foresaw this problem,
and the software does give the user the option to look for names that are
spelled similarly. Thus, there is some degree of ‘‘fuzzy logic’’ implemented
in the search algorithms. However, when there are misses of information
that should be in the database, the searches are either not fuzzy enough or
there may be wrong or incomplete data in the CAS databases. Presumably,
theseerrorswere generatedbytheCASstaffduring theprocessofdataentry.
In any event, there are errors, and we were curious how prevalent they are.
To probe this, we analyzed the hits from our SciFinder searches. Three
kindsoferrorswereconsidered:(1)wrong,meaningtherewerefactualerrors
in an entry which prevented the citation from being found by, say, an author
search (although more exhaustive mining of the database did eventually
uncover the entry); (2) incomplete, meaning that a hit could be obtained,
but there were missing pieces of data, for example, the publisher, the city of
publication, the year of publication, or the name of an author or editor; (3)
spelling, meaning that there were spelling or typographical errors apparent
in the entry, but the hit could nevertheless be found with SciFinder. In our
study, about 95% of the books abstracted in the CA database were satisfac-
tory; 1% had errors that could be ascribed to the data being wrong, 3% had
incomplete data,and1% hadspellingerrors.Theseerrorratesare lower lim-
its. There almost certainly exist errors in spellings of authors’ names or other
errors that we did not detect. Concerning the wrong entries, most of them
were recognized with the help of books on our bookshelves, but there are
probably others we did not notice. Many errors, such as missing volumes of
Preface vii
a series, became evident when books from the same author or on the same
topic were listed together.
If we noticed a variation of the spelling of an author’s name from year
to year or from edition to edition, especially when Russian and Eastern
European names are involved, we classified these entries as being wrong if
the infraction is serious enough to give a wrong outcome in a search. If one
is looking for books by I. B. Golovanov and A. K. Piskunov, for example,
one needs to search also for Golowanow and Piskunow, respectively. The
userdiscoversthatthespellingoftheirco-authorchangesfromN.M.Sergeev
to N. M. Sergejew! Should the user write Markovnikoff or Markovnikov?
(Bothspellingscanbefoundincurrentundergraduateorganicchemistrytext-
books.) More of the literature is being generated by people who have non-
English names. But even for very British names, such as R. McWeeney and
R. McWeeny, there are misspellings in the CAS database. Perhaps one of
the more frequent occurrences of misspellings and errors is bestowed on N.
Yngve O¨hrn. Some of the CAS spellings include: N. Yngve Oehrn, Yngve
Ohrn,YnaveOhrn,andevenYngveOehru!Therealsomaybeerrorsconcern-
ing the publishing houses, some not very familiar to American readers. For
example, aside from variability in their spellings, the Polish publisher Panst-
woweWydawnictwoNaukowe(PWN)isenteredasPANinoneoftheentries
of W. Kolos’ books, whereas the others are PWN.
Some of this analysis might be considered ‘‘nit-picking,’’ but an error is
certainlyseriousifitpreventsauserfromfindingwhatisactuallyinthedata-
base. Our exercises with SciFinder suggest that it would be helpful if CAS
strengthened their quality control and standardization processes. Cross-
checking and cleaning up the spellings in their databases would allow users
to retrieve desired data more reliably. It would also enhance the value of the
CAS databases if missing data were added retrospectively.
So, what level of data integrity is acceptable? The total percentage of
errors we found in our study was 5%. Is this satisfactory? Is this the best
wecanhopefor?Hopefullynot,especiallyasmorepeoplebecomedependent
on databases and the rate of production of data becomes ever faster. Clearly,
there is a need for a system that will better validate data being entered in the
most used CAS databases. It is desirable that the quality of the databases
increases at the same time as they are mushrooming in size.
A Tribute
Manyprominentcolleagueswhohaveworkedincomputationalchemis-
try have passed away since about the time this book series began. These
include (in alphabetical order) Jan Almlo¨f, Russell J. Bacquet, Jeremy K.
Burdett, Jean-Louis Calais, Michael J. S. Dewar, Russell S. Drago, Kenichi
Fukui, Joseph Gerratt, Hans H. Jaffe, Wlodzimierz Kolos, Bowen Liu, Per-
OlovLo¨wdin,AmatzyaY.Meyer,WilliamE.Palke,BernardPullman,Robert
viii Preface
Rein, Carlo Silipo, Robert W. Taft, Antonio Vittoria, Kent R. Wilson, and
MichaelC.Zerner.*Thesescientistsenrichedthefieldofcomputationalchem-
istryeachinhisownway.Threeoftheseindividuals(Almlo¨f,Wilson,Zerner)
were authors of past chapters in Reviews in Computational Chemistry.
Dr.MichaelC.ZernerdiedfromcanceronFebruary2,2000.Othertri-
butes have already been paid to Mike, but we would like to add ours. Many
readers of this series knew Mike personally or were aware of his research.
Mike earned a B.S. degree from Carnegie Mellon University in 1961, an
A.M. from Harvard University in 1962, and, under the guidance of Martin
Gouterman, a Ph.D. in Chemistry from Harvard in 1966. Mike then served
his country in the United States Army, rising to the rank of Captain. After
postdoctoralworkinUppsala,Sweden,wherehemethiswife,heheldfaculty
positions at the University of Guelph, Canada, and then at the University of
Florida. At Gainesville he served as department chairman and was eventually
nameddistinguishedprofessor,apositionheldbyonly16otherfacultymem-
bers on the Florida campus.
Probably, Mike’s research has most touched other scientists through his
development of ZINDO, the semiempirical molecular orbital method and
*Afterthisvolumewasinpress,thefieldofcomputationalchemistrylostatleastfourmore
highlyesteemedcontributors:G.N.Ramachandran,GildaH.Loew,PeterA.Kollman,and
DonaldE.Williams.Wealongwithmanyothersgrievetheirdemise,butremembertheir
contributionswithgreatadmiration.ProfessorRamachandranlenthisnametotheplotsfor
displayingconformationalanglesinpeptidesandproteins.Dr.LoewfoundedtheMolecular
ResearchInstituteinCaliforniaandappliedcomputationalchemistrytodrugs,proteins,and
othermolecules.ShealongwithDr.JoyceJ.Kaufmanwereinfluentialfiguresinthebranch
ofcomputationalchemistrycalledbyitspractitioners‘‘quantumpharmacology’’duringthe
1960sand1970s.ProfessorKollman,likemanyinourfield,beganhiscareerasaquantum
chemistandthenexpandedhisintereststoincludeotherwaysofmodelingmolecules.Peter’s
workinmoleculardynamicsandhisAMBERprogramarewellknownandhelpedshapethe
fieldasitexiststoday.ProfessorWilliams,anauthorofachapterinVolume2ofReviewsin
ComputationalChemistry,wasfamedforhiscontributionstothecomputationofatomic
chargesandintermolecularforces.Drs.Ramachandran,Loew,andWilliamswereblessed
withlongcareers,whereasPeter’swascutshortmuchtooearly.
AlthoughseveralofPeter’sstudentsandcollaboratorshavewrittenchaptersforReviews
inComputationalChemistry,Peter’sassociationwiththebookserieswasareviewhewrote
aboutVolume13.AsatributetoPeter,wewouldliketoquoteafewwordsfromthisbook
review,whichappearedinJ.Med.Chem.,43(11),2290(2000).Whilealwaysobjectivein
hisevaluation,Peterwasalso generousin praiseof theindividualchapters(‘‘abeautiful
pieceofpedagogy,’’‘‘timelyandinteresting,’’‘‘valuable,’’and‘‘anenjoyableread’’).Hehad
theseadditionalcommentswhichweshalltreasure:
ThisvolumeofReviewsinComputationalChemistryisofthesame
very high standard as previous volumes. The editors have played a
keyroleincarvingoutthedisciplineofcomputationalchemistry,hav-
ingorganizedaseminalsymposiumin1983andhavingservedasthe
chairmenofthefirstGordonConferenceonComputationalChemistry
in1986.Thus,theyhaveabroadperspectiveonthefield,andthearti-
clesinthisandpreviousvolumesreflectthis.
WewouldliketoaddthatPeterwasaninvitedspeakerattheSymposiumonMolecular
Mechanics (held in Indianapolis in 1983) and was co-chairman of the second Gordon
ResearchConferenceonComputationalChemistryin1988.AswepointedoutinthePre-
faceofVolume13(p.xiii)ofthisbookseries,noonehadbeencitedmorefrequentlyin
ReviewsofComputationalChemistrythanPeter.Peter—andtheothers—willbemissed.
Preface ix
program for calculating the electronic structure of molecules. To relieve the
burdenofprovidingusersupport,Mikeletasoftwarecompanycommercialize
it,anditiscurrentlydistributedbyAccelrys(ne´eMolecularSimulations,Inc.)
In addition, a version of the ZINDO method has been written separately by
scientists at Hypercube in their modeling software HyperChem. Likewise,
ZINDO calculations can be done with the CAChe (Computer-Aided Chemis-
try) software distributed by Fujitsu. Several thousand academic, government,
andindustriallaboratorieshaveusedZINDOinoneformoranother.ZINDO
is even distributed by several publishing companies to accompany their text-
books, including introductory texts in chemistry.
Mikepublishedover225researcharticlesinwell-respectedjournalsand
20bookchapters,oneofwhichwasinthesecondvolumeofReviewsinCom-
putational Chemistry. It still remains a highly cited chapter in our series. In
addition, Mike edited 35 books or proceedings, many of which were asso-
ciated with the very successful Sanibel Symposia that he helped organize
with his colleagues at Florida’s Quantum Theory Project (QTP). If you have
never organized a conference or edited a book, it may be hard to realize how
much work is involved. Not only was Mike doing basic research, teaching
(includingatworkshopsworldwide),andservingonnumerousuniversitygov-
ernance and service committees, he was also consulting for Eastman Kodak,
Union Carbide, and others. A little known fact is that Mike is a co-inventor
of eight patents related to polymers and polymer coatings.
Mike’s interests and abilities earned him invitations to many meetings.
He attended four Gordon Research Conferences (GRCs) on Computatio-
nal Chemistry (1988, 1990, 1994, and 1998).* Showing the value of cross-
fertilization,Mikesubsequentlybroughtsomeofthetopicsandideasofthese
GRCstotheSanibelSymposia.MikealsolongedtoserveaschairoftheGRC.
The GRCs are organized so that the job of chair alternates between someone
from academia and someone from industry. The participants at each biennial
conference elect someone to be vice-chair at the next conference (two years
later),andthenthatpersonmovesuptobecomechairfouryearsaftertheelec-
tion.Mikewasacandidatein1988and1998,whichwereyearswhennonin-
dustrial participants could run for election. He and Dr. Bernard Brooks
(NationalInstitutesofHealth)wereelectedco-vice-chairsin1998.Sadly,Mike
diedbeforehewasabletofulfillhisdream.AttheGRCinJuly2000,y tributes
werepaidtoMikebyDr.TerryR.Stouch(Bristol-MyersSquibb),Chairman,
andbyDr.Brooks.Inaddition,Dr.JohnMcKelvey,Mike’scollaboratordur-
ing the Eastman Kodak consulting days, beautifully recounted Mike’s many
fine accomplishments.
Ourscienceofcomputationalchemistryowesmuchtothecontributions
of our departed friends and colleagues.
*D.B.BoydandK.B.Lipkowitz,inReviewsinComputationalChemistry,K.B.Lipkowitz
andD.B.Boyd,Eds.,Wiley-VCH,NewYork,2000,Vol.14,pp.399–439.Historyofthe
GordonResearchConferencesonComputationalChemistry.
ySeehttp://chem.iupui.edu/rcc/grccc.html.
x Preface
This Volume
As with our earlier volumes, we ask our authors to write chapters that
canserveastutorialsontopicsofcomputationalchemistry.Inthisvolume,we
havefourchapterscoveringarangeofissuesfrommoleculardockingtospin–
orbit coupling to cellular automata modeling.
Thisvolumebeginswithtwochaptersondocking,thatis,theinteraction
and intimate physical association of two molecules. This topic is highly ger-
mane to computer-aided ligand design. Chapter 1, written by Drs. Ingo
Muegge and Matthias Rarey, describes small molecule docking (to proteins
primarily).Theauthorsputthedockingproblemintoperspectiveandprovide
a brief survey of docking methods, organized by the type of algorithms used.
Theauthorsdescribetheadvantagesanddisadvantagesofthemethods.Rigid
dockingincludinggeometrichashingandposeclusteringisdescribed.Tomo-
delnaturemoreclosely,onereallyneedstoaccountforflexibilityofbothhost
and guest during docking. The authors delineate the various categories of
treating flexible ligands and explain how each works. Then an evaluation of
how to handle protein flexibility is given. Docking of molecules from combi-
natoriallibrariesisdescribednext,andthevalueofconsensusscoringiniden-
tifying potentially interesting bioactive compounds from large sets of
molecules is pointed out. Of particular note in Chapter 1 are explanations
of the multitude of scoring functions used in this realm of computational
chemistry: shape and chemical complementary scoring, force field scoring,
empiricalandknowledge-basedscoring,andsoon.Theneedforreliablescor-
ing functions underlies the role that docking can play in the discovery of
ligands for pharmaceutical development.
ThefirstchaptersetsthestageforChapter2whichcoversprotein–protein
docking.Drs.LutzP.EhrlichandRebeccaC.Wadepresentatutorialonhow
to predict the structure of a protein–protein complex. This topic is important
becauseasweentertheeraofproteomics(thestudyofthefunctionandstruc-
ture of gene products) there is increasing need to understand and predict
‘‘communication’’ between proteins and other biopolymers. It is made clear
at the outset of Chapter 2 that the multitude of approaches used for small
molecule docking are usually inapplicable for large molecule docking; the
generation of putative binding conformations is more complex and will
most likely require new algorithms to be applied to these problems. In
this review, the authors describe rigid-body and flexible docking (with an
emphasis on methods for the latter). Geometric hashing techniques, confor-
mational search methodologies, and gradient approaches are explained and
put into context. The influence of side chain flexibility, backbone confor-
mational changes, and other issues related to protein binding are described.
Contrasts and comparisons between the various computational methods are
made, and limitations of their applicability to problems in protein science
are given.
Preface xi
Chapter 3, by Dr. Christel Marian, addresses the important issue of
spin–orbit coupling. This is a quantum mechanical relativistic effect, whose
impact on molecular properties increases with increasing nuclear charge in a
waysuchthattheelectronicstructureofmoleculescontainingheavyelements
cannotbedescribedcorrectlyifspin–orbitcouplingisnottakenintoaccount.
Dr.Marianprovidesahistoryandthequantummechanicalimplicationsofthe
Stern–Gerlach experiment and Zeeman spectroscopy. This review is followed
by a rigorous tutorial on angular momenta, spin–orbit Hamiltonians, and
transformationsbasedonsymmetry.Tipsandtricksthatcanbeusedbycom-
putational chemists are given along with words of caution for the nonexpert.
Computational aspects of various approaches being used to compute spin–
orbiteffectsare presented,followedbyasection oncomparisons ofpredicted
and experimental fine-structure splittings. Dr. Marian ends her chapter with
descriptions of spin-forbidden transitions, the most striking phenomenon in
which spin–orbit coupling manifests itself.
Chapter 4 moves beyond studying single molecules by describing how
one can predict and explain experimental observations such as physical and
chemical properties, phase transitions, and the like where the properties are
averagedoutcomesresultingfromthebehaviorsofalargenumberofinteract-
ing particles. Professors Lemont B. Kier, Chao-Kun Cheng, and Paul G.
Seyboldprovideatutorialoncellularautomatawithafocusonaqueoussolu-
tion systems. This computational technique allows one to explore the less-
detailed and broader aspects of molecular systems, such as variations in
speciespopulationswithtimeandthestatisticalandkineticdetailsofthephe-
nomenon beingobserved.Themethodologycantreatchemicalphenomenaat
a level somewhere between the intense scrutiny of a single molecule and the
averaged treatment of a bulk sample containing an infinite population. The
authorsprovideabackgroundonthedevelopmentanduseofcellularautoma-
ta, their general structure, the governing rules, and the types of data usually
collected from such simulations. Aqueous solution systems are introduced,
and studies of water and solution phenomena are described. Included here
are the hydrophobic effect, solute dissolution, aqueous diffusion, immiscible
liquids and partitioning, micelle formation, membrane permeability, acid dis-
sociation,andpercolationeffects.Theauthorsexplainhowcellularautomata
areusedforsystemsoffirst-andsecond-orderkinetics,kineticandthermody-
namic reaction control, excited state kinetics, enzyme reactions, and chroma-
tographic separation. Limitations of the cellular automata models are made
clearthroughout.Thiskindofcoarse-grainedmodelingcomplementstheideas
consideredintheotherchaptersinthisvolumeandpresentsthebasicconcepts
needed to carry out such simulations.
Lastly, we provide an appendix of books published in the field of com-
putationalchemistry.The number islarge, morethan1600. Rather thansim-
plypresenting all these books inone longlist sortedby authororby date, we
have partitioned them into categories. These categories range from broad