Table Of Content60775_cover 3/8/11 9:19 AM Page 1
C M Y CM MY CY CMY K
GENERAL CHEMISTRY A
l
l
i
s
o
n
|
C
o
METALLIC s
k
u
n
e
r
SYSTEMS |
G
o
n
z
á
l
e
Metallic systems are ubiquitous in daily life. They play key roles, for example, in the z
chemistry of many biomolecules, ionic solutions, nanoparticles and catalytic processes.
They may be in solid, liquid or gaseous form. The interactions of other molecules with
metal surfaces are of considerable importance. Each of these topics is addressed in Metallic
Systems. As we have entered the age where theoretical approaches are sufficiently mature
to complement and guide experiments in many areas, an understanding of the theoretical
tools and approaches to studying metallic systems is essential. Metallic Systems is concerned M
with enhancing our understanding of the diverse chemistry of metals and metal-containing
systems and the applicability of modern quantum chemistry methodologies to study them. E
T
Metallic Systems presents brief overviews of most of the popular approaches to quantum
chemical treatments and computations of chemical systems that include metals. Attention A
is given to the potentialities and limitations of first principles Density Functional Theory
L
and dynamics methods (e.g. QM/MM approaches). The book emphasizes the importance
L
of using methods that take into account crucial physical features such as explicit solvation,
temperature and dynamics of metal-containing systems, and emphasizes first principles I
calculations in providing reliable and detailed information concerning electronic structures, C
mechanisms and reaction energetics.
S
Accessible to newcomers to the field, Metallic Systems overviews theory underpinning
Y
current methodologies. It presents a practical set of modalities for studying metallic systems,
S
assesses the current technological barriers, and examines future challenges and topics
T
of exploration.
E
M
S
60775
6000 Broken Sound Parkway, NW
Suite 300, Boca Raton, FL 33487
270 Madison Avenue
an informa business New York, NY 10016
www.crcpress.com 2 Park Square, Milton Park w w w. c r c p r e s s . c o m
Abingdon, Oxon OX14 4RN, UK
Composite
METALLIC
SYSTEMS
A Quantum Chemist’s
Perspective
META LLIC
SYSTEMS
A Quantum Chemist’s
Perspective
Edited by
Thomas C. Allison
Orkid Coskuner
Carlos A. González
Boca Raton London New York
CRC Press is an imprint of the
Taylor & Francis Group, an informa business
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2011 by Taylor and Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business
No claim to original U.S. Government works
Printed in the United States of America on acid-free paper
10 9 8 7 6 5 4 3 2 1
International Standard Book Number-13: 978-1-4200-6086-7 (Ebook-PDF)
This book contains information obtained from authentic and highly regarded sources. Reasonable
efforts have been made to publish reliable data and information, but the author and publisher cannot
assume responsibility for the validity of all materials or the consequences of their use. The authors and
publishers have attempted to trace the copyright holders of all material reproduced in this publication
and apologize to copyright holders if permission to publish in this form has not been obtained. If any
copyright material has not been acknowledged please write and let us know so we may rectify in any
future reprint.
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced,
transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or
hereafter invented, including photocopying, microfilming, and recording, or in any information stor-
age or retrieval system, without written permission from the publishers.
For permission to photocopy or use material electronically from this work, please access www.copy-
right.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222
Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that pro-
vides licenses and registration for a variety of users. For organizations that have been granted a pho-
tocopy license by the CCC, a separate system of payment has been arranged.
Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are
used only for identification and explanation without intent to infringe.
Visit the Taylor & Francis Web site at
http://www.taylorandfrancis.com
and the CRC Press Web site at
http://www.crcpress.com
Contents
Introduction...............................................................................................................vii
Contributors............................................................................................................xiii
Chapter 1 First.Principles.DFT.Studies.of.Metal-Based.Biological.
and.Biomimetic.Systems.......................................................................1
Arturo Robertazzi, Alessandra Magistrato, Matteo Dal Peraro,
and Paolo Carloni
Chapter 2 Structural.and.Thermodynamic.Studies.of.α-Synuclein.Proteins.
Related.to.Parkinson’s.Disease:.Impact.of.Aqueous.Solution.and.
Fe3+.Coordination................................................................................29
Olivia M. Wise, Liang Xu, and Orkid Coskuner
Chapter 3 Carbohydrate.and.Trivalent.Iron.Ion.Interactions.in.the.Gas.
Phase.and.in.Aqueous.Solution...........................................................83
Orkid Coskuner and Carlos A. González
Chapter 4 Aqueous.Solutions.of.Metal.Ions......................................................107
Orkid Coskuner and Thomas C. Allison
Chapter 5 Structure.of.Liquid.Metal.Surfaces:.A.First.Principles.
Perspective.......................................................................................135
Brent Walker, Nicola Marzari, and Carla Molteni
Chapter 6 Some.Practical.Considerations.for.Density.Functional.Theory.
Studies.of.Chemistry.at.Metal.Surfaces............................................163
Rudolph J. Magyar, Ann E. Mattsson, and Peter A. Schultz
Chapter 7 Computational.Investigations.of.Metal.Oxide.Surfaces...................201
Emily A. A. Jarvis and Cynthia S. Lo
Chapter 8 Tight.Binding.Methods.for.Metallic.Systems...................................225
Luis Rincón, Thomas C. Allison, and Carlos A. González
vii
© 2011 by Taylor & Francis Group, LLC
viii Contents
Chapter 9 Density.Functional.Calculations.of.Metal.Clusters:.Structure,.
Dynamics,.and.Reactivity.................................................................267
Dennis R. Salahub, Patrizia Calaminici, Gabriel U. Gamboa,
Andreas M. Köster, and J. Manuel Vásquez
Chapter 10 Density.Functional.Theory.Calculations.on.Cobalt.and.
Platinum.Transition.Metal.Clusters...................................................341
Ali Sebetci
Chapter 11 Exploring.the.Borderland.between.Physics.and.Chemistry:.
Theoretical.Methods.in.the.Study.of.Atomic.Clusters......................371
Yamil Simón-Manso, Carlos A. González,
and Patricio Fuentealba
© 2011 by Taylor & Francis Group, LLC
Introduction
The.chemistry.of.metals.is.rich.and.diverse..It.is.important.in.many.traditional.dis-
ciplines.such.as.inorganic.chemistry,.metallurgy,.geochemistry,.solid.state.physics,.
medicine,.and.biochemistry.among.others..It.spans.many.orders.of.magnitude.in.
size,.from.nanoclusters.containing.a.few.atoms.up.to.extended.macroscopic.sol-
ids..It.encompasses.studies.of.the.properties.of.pure.metals,.alloys,.nanoparticles,.
small.metal-containing.molecules.and.biomolecules,.as.well.as.the.interactions.that.
occur.on.and.between.metal.surfaces..Metals.and.metal-containing.compounds.may.
be.studied.in.all.three.phases..Other.properties.of.metals.of.particular.interest.are.
magnetism.and.electrical.conductivity..Bonding.with.and.between.metals.frequently.
involves.d.orbitals,.which.adds.to.the.complexity.of.structures.they.form..This.both.
enhances.the.variety.of.chemistry.that.these.compounds.may.exhibit.and.confounds.
simple.prediction.of.their.properties..Many.metals.are.of.sufficient.mass.that.relativ-
istic.effects.must.be.taken.into.account.
In.this.book,.we.explore.topics.that.touch.on.most,.if.not.all,.of.the.areas.listed.
above..The.topic.of.metals.and.metal-containing.molecules.will.be.presented.from.
the.viewpoint.of.the.quantum.chemist,.that.is,.we.are.interested.in.the.calculation.
of.properties.of.metals.and.metal-containing.molecules.using.first.principles.(or.
semiempirical).methods..From.the.perspective.of.the.chemist,.we.are.more.fre-
quently.interested.in.molecular.properties.as.opposed.to.properties.of.extended.
solids,.or,.rather,.we.are.interested.in.the.chemistry.that.occurs.on.the.surfaces.of.
metals..The.exploration.of.this.chemistry.will.take.place.via.calculations.of.the.static.
electronic.structure.and.via.dynamics.calculations.
The.book.begins.with.two.chapters.on.biological.studies.involving.metals..As.
biological.applications.frequently.take.place.in.solution,.the.next.chapters.consider.
metals.in.solution..A.chapter.on.liquid.metals.leads.to.the.consideration.of.systems.
that.are.mostly.or.entirely.metallic..There.are.several.chapters.on.metal.surfaces.fol-
lowed.by.a.presentation.of.the.theory.and.application.of.tight-binding.methods.that.
have.been.used.to.study.metals.for.a.long.time..The.chapter.on.tight-binding.methods.
includes.a.discussion.of.metallic.nanoparticles,.which.continues.through.the.remain-
der.of.the.book..The.chapters.are.largely.independent.and.may.be.read.in.any.order.
without.loss.of.continuity.
Throughout.the.chapters,.there.is.presentation.of.the.underlying.theory.as.well.as.
practical.advice.for.the.application.of.these.methods..The.reader.will.gain.an.appre-
ciation.for.the.subtlety.and.complexity.of.many.calculations.while.learning.how.to.
approach.the.simulation.of.such.systems.
In.the.remainder.of.this.introduction,.we.will.briefly.discuss.the.theory.underly-
ing.the.methods.presented.in.this.book.and.give.a.brief.introduction.to.each.of.the.
chapters..We.acknowledge.that.while.the.material.presented.in.this.book.covers.a.
wide.range.of.topics,.it.is.by.no.means.a.complete.discussion.of.the.chemistry.of.met-
als..Likewise,.it.would.take.several.volumes.to.adequately.describe.the.theory.under-
lying.the.calculations.presented.in.this.book..We.will.content.ourselves.to.introduce.
ix
© 2011 by Taylor & Francis Group, LLC
x Introduction
a.few.of.the.salient.details.and.provide.references.that.the.unfamiliar.reader.may.
consult.for.a.deeper.discussion.of.this.important.topic.
The.fundamental.equation.of.quantum.chemistry.is,.of.course,.the.Schrödinger.
equation
. HΨ=EΨ. (I.1)
where
H.is.the.Hamiltonian.operator
Ψ.is.the.wavefunction
E.is.the.energy
The.main.occupation.of.the.quantum.chemist,.then,.is.to.solve.this.equation.for.the.
molecular.system.of.interest..There.is.lengthy.literature.on.the.Schrödinger.equa-
tion.and.methods.for.its.solution..The.unfamiliar.reader.may.wish.to.consult.an.
introductory.text.[1–3].for.a.solid.introduction.to.the.theory.and.practice.of.quantum.
chemistry.calculations..For.readers.desiring.a.more.in-depth.treatment.of.the.subject,.
several.advanced.texts.are.available.[4–6]..Several.chapters.in.this.book.also.contain.
discussions.of.the.theory.
Solution.of.the.Schrödinger.equation.usually.involves.the.Born–Oppenheimer.
approximation.that.separates.Equation.I.1.into.an.electronic.structure.problem.and.
a.dynamics.problem..This.approximation.gives.rise.to.the.concept.of.the.potential.
energy.surface.in.which.the.potential.energy.of.a.molecular.system.is.expressed.as.
a.function.of.the.positions.of.the.nuclei..The.electronic.structure.problem.is.solved.
under.the.assumption.that.the.nuclei.remain.in.a.fixed.position..The.dynamics.prob-
lem.then.considers.the.motion.of.the.nuclei.on.the.potential.energy.surface.
One.may.broadly.divide.the.methods.for.solution.of.the.electronic.structure.
problem.into.three.categories:.semiempirical.methods,.ab.initio.methods,.and.den-
sity.functional.theory.(DFT).methods..Semiempirical.methods.include.traditional.
semiempirical.methods.in.quantum.chemistry.(e.g.,.AM1,.PM3,.PM6).as.well.as.
extended.Hückel.and.tight-binding.methods..These.methods.generally.neglect.some.
terms.in.the.Hamiltonian.and.approximate.others.to.gain.computational.speed.at.the.
expense.of.rigorous.solution..The.loss.in.accuracy.is.usually.compensated.through.
parameterization.to.accurate.data.(either.from.experiment.or.higher-level.theory)..
Ab.initio.is.taken.to.mean.those.methods.based.on.the.Hartree–Fock.equations..
Examples.include.the.Hartree–Fock.method,.Møller–Plesset.perturbation.theory.
methods,.coupled-cluster.methods,.and.multi-reference.methods.[4,5]..Finally,.DFT,.
typically.realized.through.the.Kohn–Sham.method.[6],.will.form.the.basis.for.most.
of.the.calculations.presented.in.this.book.
It.is.difficult.to.overstate.the.importance.of.the.Kohn–Sham.DFT.method.in.the.
treatment.of.metallic.systems..There.are.many.functionals.available.that.permit.the.
efficient.and.accurate.treatment.of.metallic.systems..DFT.methods.are.the.driving.
force.behind.the.advances.made.in.this.area..Many.chapters.in.this.book.emphasize.
the.importance.of.DFT.and.discuss.the.underlying.theory..The.interested.reader.is.
directed.to.two.recent.reviews.for.a.comprehensive.review.of.many.topics.related.to.
the.subject.at.this.book.[7,8].
© 2011 by Taylor & Francis Group, LLC
Introduction xi
Analogous.to.the.importance.of.DFT.in.the.solution.of.the.electronic.structure.
problem,.the.Car–Parrinello.method.[9].for.performing.molecular.dynamics.calcula-
tions.is.one.of.the.primary.tools.available.to.the.quantum.chemist..Car–Parrinello.
molecular.dynamics.(CPMD).calculations,.which.are.based.on.DFT.calculations,.
are.efficient.and.accurate.for.a.wide.variety.of.chemical.studies.of.metallic.systems..
These.methods.are.discussed.in.several.chapters.
At.the.heart.of.many.biological.processes.are.molecules.whose.function.depends.
on.the.metal.atoms.they.contain..Chapter.1.is.concerned.with.understanding.such.
molecules.with.molecular.detail..Topics.in.this.chapter.include.first.principles.calcu-
lations.of.biomolecules.and.pharmaceuticals,.the.incorporation.of.solvation.effects.
via.explicit.solvent.models,.and.studies.of.chemical.reactivity..These.topics.are.pre-
sented.through.several.interesting.applications.
Metal.ions.in.solution.can.have.significant.effects.on.nearby.molecules..In.
Chapter.2,.chemical.dynamics.calculations.are.used.to.investigate.interactions.
between.metal.ions.and.carbohydrates..The.importance.of.using.dynamics.methods.
that.are.based.on.ab.initio.calculations.of.the.potential.energy.surface.(as.opposed.
to.classical.force.field.methods).is.emphasized..Results.are.presented.both.in.the.gas.
phase.and.in.solution,.thus.highlighting.the.role.of.the.solvent.
The.techniques.introduced.in.Chapter.2.are.used.again.in.Chapter.3,.this.time.
to.explore.the.interactions.of.iron.ions.with.α-synuclein.proteins.and.the.role.that.
this.interaction.may.play.in.Parkinson’s.disease..This.chapter.highlights.the.value.
of.chemical.computation.in.obtaining.molecular.detail.about.important.biological.
processes.that.may.ultimately.lead.to.the.development.of.more.effective.treatments..
Significant.attention.is.given.to.classical.molecular.dynamics.calculations,.and.the.
value.and.limitations.of.these.calculations.versus.their.quantum.counterparts.are.
discussed..Again,.the.role.of.the.solvent.is.emphasized.
The.discussion.of.metal.ions.in.aqueous.solutions,.a.central.theme.in.the.preced-
ing.two.chapters,.culminates.in.Chapter.4..In.this.chapter,.the.effect.of.a.metal.ion.
on.surrounding.water.molecules.is.considered..Although.on.the.surface.this.seems.to.
be.simpler.than.the.systems.considered.in.the.preceding.chapters,.the.reader.will.dis-
cover.the.rich.and.detailed.dynamics.of.these.solutions..In.particular,.topics.such.as.
the.migration.of.a.proton.through.aqueous.solution.and.the.formation.of.Zundel.and.
Eigen.complexes.are.discussed..As.before,.the.primary.tool.is.chemical.dynamics.
calculations,.but.these.are.augmented.with.a.rare.event.sampling.technique.known.as.
transition.path.sampling.that.is.essential.to.the.study.of.these.systems.
The.focus.of.the.book.shifts.to.liquid.metal.surfaces.in.Chapter.5..Such.systems.
have.considerable.industrial.importance..In.this.chapter,.dynamics.simulations.
based.on.DFT.calculations.are.used.to.obtain.molecular.level.detail.of.the.layering.
of.various.liquid.metals..Attention.is.given.to.the.comparison.of.simulation.results.
with.experimental.results..Liquid.sodium.surfaces.are.presented.in.detail.with.an.
emphasis.on.the.role.played.by.geometrical.confinement.in.the.layering.of.these.
systems.
Chapter.6.presents.a.wealth.of.practical.advice.on.the.calculation.of.solid.metal.
surfaces..This.chapter.contains.a.detailed.discussion.of.the.importance.of.DFT.
in.calculations.on.metals..The.two.main.themes.in.this.chapter.are.the.choice.of.
the. exchange-correlation. potential. and. the. choice. of. pseudopotential. in. these.
© 2011 by Taylor & Francis Group, LLC
