Metallic Systems: A Quantum Chemist's Perspective

412 Pages·2011·20.261 MB·English

by  Thomas Clayton Allison, Orkid Coskuner, Carlos A González

60775_cover 3/8/11 9:19 AM Page 1
C M Y CM MY CY CMY K
GENERAL CHEMISTRY A
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METALLIC s
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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
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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
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and dynamics methods (e.g. QM/MM approaches). The book emphasizes the importance
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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.

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Accessible to newcomers to the field, Metallic Systems overviews theory underpinning
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current methodologies. It presents a practical set of modalities for studying metallic systems,
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assesses the current technological barriers, and examines future challenges and topics
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of exploration.
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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
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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