Chemistry Reference
In-Depth Information
Nowadays,. several. QM/MM. schemes. are. available:. for. a. detailed. description. of.
these.methods,.see.for.example.
50,55-58,86,89,90
.Among.these,.the.QM/MM.approach.in.
combination.with.the.Car-Parrinello.molecular.dynamics.(CPMD).scheme.has.been.
extensively. employed. for. the. studies. reported. below.
35,51,52,91
. Within. this. scheme,.
simulations. are. typically. performed. by. using. plane. wave. (PW). basis. sets. rather.
than.localized.functions.as.the.former.perform.better.for.irst.principles.molecular.
dynamics. of. large. systems.. PW. basis. sets. have. further. advantages,
40
. e.g.,. conver-
gence.can.be.easily.monitored.by.increasing.the.number.of.PWs.that,.unlike.local.
basis. sets,. depends. on. one. parameter,. i.e.,. the. cutoff. energy;. PWs. are. completely.
unbiased. and. do. not. suffer. from. basis. set. superposition. error. which. affects. local.
basis. sets.. Pseudopotentials. (which. can. be. applied. to. local. basis. sets. as. well). are.
employed.for.the.core.electrons,.providing.a.great.computational.advantage.as.only.
valence.electrons.are.explicitly.described..Relativistic.effects,.which.are.crucial.for.
heavy.metals.may.also.be.included.in.pseudopotentials..It.has.to.be.stressed.that.the.
choice. of. the. basis. sets. is. crucial. for. the. reliability. of. the. theoretical. description,.
and. special. care. has. to. be. taken. for. charged. molecules,. and. for. those. systems. in.
which. intermolecular. forces. (such. as. H-bonding. and/or. hydrophobic. interactions,.
vide.infra).play.an.important.role.
53,54
Albeit. widely. applied,. DFT. methods. as. implemented. suffer. severe. limitations..
Even.the.popular.B3LYP.and.BLYP.exchange-correlation.functionals.tend.to.under-
estimate.reaction.barriers.of.chemical.processes.compared.to.MP2.calculations.
36,92-94
.
This.may.be.due.to.the.failure.of.gradient-corrected.functionals.in.describing.three-
center,.two-electron.chemical.bonds.as.previously.reported.
40
.When.predicting.reac-
tion.barriers,.the.accuracy.of.DFT.functional.becomes.a.crucial.consideration.and.the.
functional.employed.should.always.be.compared.with.higher-level.calculations.(usu-
ally. HF-based. calculations. with. explicit. electron. correlation). and/or. experimental.
data..Moreover,.DFT.functionals.are.not.capable.of.rigorously.describing.dispersive.
forces.which.play.a.fundamental.role.in.many.aspects.of.chemistry.and.biochemis-
try.
95-97
.For.instance,.π-stacking.is.central.to.the.correct.function.of.proteins.and.in.
determining. the. packing. of. DNA. base. pairs.
98,99
. Current. implementations. of. gra-
dient-corrected. exchange-correlation. functionals. prevent. accurate. descriptions. of.
π-stacking.since.long-range.electron.correlation.is.not.included..Fortunately,.recent.
advances.allow.such.problems.to.be.partially.overcome.
100-110
A. further. issue. that. affects. DFT. calculations. is. the. so-called. self-interaction.
problem.
32,34,35
. Unlike. HF. theory,. the. self-interaction. term. in. Coulomb. interaction.
is.not.fully.cancelled.by.the.approximate.self-exchange.term.
75
.This.may.lead.to.an.
unphysical. localization. of. the. spin. densities. in. open. shell. systems. (such. as. heavy.
metals),. although. a. few. cases. of. reasonable. agreement. between. DFT. calculations.
and. experimental. spin. density. exist.
111-113
. Several. schemes. to. overcome. this. error.
have. been. proposed,. but. they. are. generally. too. computationally. demanding. to. be.
extensively.employed.in.QM/MM.molecular.dynamics.(QM/MM.MD).
40
The.inal.scenario.is.that.DFT.calculations.have.to.be.performed.carefully.and.
comparison. with. experimental. data. and/or. higher-level. calculations. is. essential. to.
provide.a.correct.picture.of.the.system.of.interest..Yet.once.the.model.has.been.built.
carefully,. the. exchange-correlation. performance. rigorously. checked,. the. suitable.
basis.set.chosen,.and.the.system.properly.partitioned.into.QM.and.MM.layers,.DFT.
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