EPJ Web of Conferences 30, 04001 (2012)

DOI: 10.1051/epjconf/20123004001
Owned by the authors, published by EDP Sciences, 2012
This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which
permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Organized by
Thibault Charpentier thibault.chapentier@cea.fr
Patrick Berthault patrick.berthault@cea.fr
Constantin Meis constantin.meis@cea.fr
Lxper|ment and Mode|||ng |n Structura| NMk
November 28th - December 2
nd
2011
INS1N - CLA Sac|ay, Irance
Marc Meunier
Accelrys
Introduction to
Materials Studio
[04001]
Article available at http://www.epj-conferences.org or http://dx.doi.org/10.1051/epjconf/20123004001
04001-p.2
IntroductIon to
haterIaIs StudIo
haterIaIs StudIo
FIgures
E Tables
FIles E
Folders
Tools
Jobs
runnIng
PropertIes
04001-p.3
0Ifferent uIIders
uIId PoIymers
04001-p.4
uIId a
HomopoIymer
uIId Iock CopoIymer
04001-p.5
uIId Pandom CopoIymer

04001-p.6
uIId CrystaIs
TooIs for buIIdIng nanostructures wIth the
haterIaIs VIsuaIIzer
04001-p.7
NanocIuster uIIders
- WIde range of
shapes
- Element substItutIon
functIon (lInear,
quadratIc or
exponentIal) along
symmetry dIrectIons.
- 7acancy functIon.
- DptIonal cappIng of
broken bonds
- 7arIous styles
- Scale factor
dIsplay length () = scale * vector
magnItude
- Use wIth 7ectors dIalog
to select specIfIc
vectors
0IspIay StyIe
04001-p.8
Now wIth vectors!
VIbratIonaI AnaIysIs
Part II: IntroductIon to haterIaIs hodeIIng
04001-p.9
Why modeIIng!
- structures, processes and propertIes are numerIcally
sImulated based fully or In part on fundamental laws of
physIcs
- besIdes modelIng stable molecules, some methods may
be used to model also shortlIved specIes (unstable
IntermedIates and transItIon states)
- Important In supportIng or replacIng experImental
studIes
hotIvatIon for modeIIng and sImuIatIon
hore effIcIent use of P0 resources
etter understandIng of how and why a
product or a process Is workIng
Faster deIIvery of products to market
"TrIaI and error" experIment Is
tIme-consumIng
SoIutIons to crItIcaI research probIems
(SheIf-IIfe, StabIIIty, CompatIbIIIty.)
SoIutIons often come from adaptIng or
controIIIng moIecuIar IeveI behavIour
04001-p.10
What Is materIaIs sImuIatIon!
!mpossible d'afficher l'image.
eIectronIcs, cataIysIs
e.g., morphoIogy,
drug deIIvery
permeatIon, crystaIIIsatIon
ScaIe
huItI-ScaIe modeIIng
Atomistic/QM
Simulation + Analytical Instruments
Mesoscale
Simulation +
Analytical Instruments
QSAR/QSPR
Descriptors
Correlations
04001-p.11
- FeactIvIty, ElectronIcDptIc|agnetIc.
- |IscIbIlIty/CompatIbIlIty, SolubIlIty.
- 0IffusIon, permeatIon, membrane transport.
- AdhesIon (I.e., InteractIons wIth surfaces)
- CrystallIzatIon and polymorphIsm
- |Icelle or vesIcle formatIon and propertIes
- EmulsIons, kInetIcs and propertIes
- PolymerIc mIcrospheres, release profIles
- CorrelatIve methods (e.g. QSAF)
Issues that sImuIatIon can address.
Increasing Scale
of Study
Atomistic
Simulation
Mesoscale
Simulation
Quantum
Mechanics
A
c
c
u
r
a
c
y
hodeIIng and sImuIatIon methods In hS
- Quantum |echanIcs
- AtomIstIc |odelIng
- |esoscale |odelIng
- Crystal |odelIng
- CorrelatIon |ethods QSAF
04001-p.12
uantum hechanIcs
- The SchrodInger equatIon
- |ethods dIffer In how H and are descrIbed
H . kInetIc energy + potentIal energy + Exc
. descrIbed wIth electronIc wave -functIons
(numerIcal, STD, CTD) or plane waves
H = E
uantum hechanIcs: 0FT
0ensIty FunctIonal Theory (0FT) All groundstate propertIes of
a system are functIon of the charge densIty
}) ({ }) ({ }) ({
2
2
i i i
E V
m
r r r =

+

Kohn - Sham equatIon
[ ] [ ] [ ]
xc total
E U T E + + =
Hohenberg - Kohn equatIon
04001-p.13
uantum hechanIcs
- Strong poInts
- ChemIcal reactIons and transItIon state
- ElectronIc, optIcal and magnetIc propertIes
- LImItatIons
- SImulatIon tIme growths as N
J
where N Is
the number of electrons. There Is a
computatIonal lImIt of - 250 atoms or a few
pIcoseconds
0hoI3, CASTEP 0hoI3, CASTEP
What can be caIcuIated!
CASTEP (pIane waves)
- PerIodIc systems
- Structural PropertIes
- ElectronIc and |agnetIc
PropertIes
- 0IffusIon
- 8ulk and ElastIc PropertIes
- LST/QST
- ST| (scannIng tunnelIng
mIcroscopy) analysIs
- WorkfunctIons
- EELS/ELNES spectra
- Faman/ntensItIes
- 0IspersIon CorrectIon
0hDL
3
(numerIcaI functIons)
- |olecules In the gas phase/perIodIc
systems
- FeactIon |odelIng, (gas phase,
solutIon, on surfaces)
- ThermodynamIcs
- DptIcal Spectra (F spectra)
- T00FT (U7vIs and optIcal
propertIes)
- |olecular 0ynamIcs (0IffusIon)
- LST/QST
- Solvent effects
- workfunctIons
- 0IspersIon correctIon
Extra Tool: CASTEP solid state NMR
04001-p.14
SemIempIrIcaI methods
- They solve an approxImate form of the SchrodInger
equatIon
- Dnly valence electrons are consIdered
- These methods use parameters derIved from
experImental data to sImplIfy the computatIon
E C S C F = E C C F =
VAhP VAhP
SemIempIrIcaI methods
- Strong poInts
- They are relatIvely InexpensIve and
provIde reasonable qualItatIve descrIptIons
of molecular systems, can be used on a PC
- LImItatIons
- Can only be used for elements and
InteractIons for whIch It has been
parameterIsed
- P|6 covers 70 elements
04001-p.15
What can be caIcuIated!
- Fast structure DptImIzatIon
- Fast transItIon state localIzatIon
- Structural propertIes
- DptIcal spectra (U7vIs)
-
1J
C ChemIcal shIft
- ElectrostatIcs
- Solvent effects

Q| regIon:
electronIc structure
changes
|| regIon:
embeddIng of Q| regIon
envIronment effects
For Example: FeactIve centre on a zeolIte
Usual approach: selectIng a cluster comprIsIng enough framework to mImIc
the actIve sIte plus a bIt of the bulk
Problem: there Is vacuum all around and the electrostatIc InteractIons are
severely neglected
WIth Q|EFA, we can do the followIng:
04001-p.16
hoIecuIar hechanIcs (hh)
- A molecule Is descrIbed as a serIes of charged poInts (atoms)
lInked by sprIngs (bonds).
- A mathematIcal descrIptIon of thIs system Is known as a
forcefIeld
- The forcefIeld Is used to calculate the relatIve potentIal energy
of the molecule (relatIve to other conformatIons of the same
molecule).
hh - PepresentatIon of a forcefIeId

total
=
valence
+
crossterm
+
nonbond

valence
=
bond
+
angle
+
torsIon
+
oop
+
U8

nonbond
=
vdW
+
Coulomb
+
hbond
PotentIal Energy
7alence nteractIons
Nonbond nteractIons
04001-p.17
hh - PepresentatIon of a forcefIeId
hh - hoIecuIar 0ynamIcs (h0)
- |olecular 0ynamIcs (|0) solves the Newton's equatIons of
motIon for each atom
ClassIcal equatIons of motIon are determInIstIc!!!
ThIs allows us to study the evolutIon of systems as a functIon of
tIme, temperature and pressure whIch are related by
statIstIcal mechanIcs
i i i
m a f =
2
2
t
m
i
i i

=
r
f
04001-p.18
hoIecuIar hechanIcs
- Strong poInts
- We can deal wIth bIgger systems
- We can sImulate dynamIc processes (e.g. dIffusIon,
phase transItIon)
- LImItatIons
- ForcefIelds are valId for a 'lImIted' type of materIal
- There Is no bond breakIng or formIng Involved (I.e.
no chemIsorptIon)
- SIze of system - 10
4
atoms or a few nanoseconds (1 s
possIble)
0Iscover, CULP, ForcIte pIus 0Iscover, CULP, ForcIte pIus
What can be caIcuIated!
- Property calculatIons
- PaIr correlatIon functIon probIng specIfIc InteractIons
- Length, angle, dIhedral dIstrIbutIons effects on moIecuIar
geometry
- ConcentratIon profIles InterfacIaI propertIes
- DrIentatIonal correlatIon IIquId crystaIIIne phases
- 0ynamIc calculatIons
- |S0, velocIty autocorrelatIon, spacetIme correlatIon
transport
- 0Ipole autocorrelatIon vIbratIonal behavIour - spectroscopy
- Shearstress tIme correlatIon fIuId vIscosIty
- ElastIc constants mechanIcaI propertIes
- |ultIcomponent systems
- nteractIon energy - compatIbIIIty
04001-p.19
hesoscaIe modeIIng
- Smallest unIt Is a group of atoms called 'bead'
- Laws of classIcal physIcs
0P0 (0IssIpatIve PartIcle dynamIcs):
Newton's equatIons of motIon
|eso0YN: StochastIc 0IffusIon
equatIons
Longer tIme
and length
scales!!!!
( )

+ + =
i j
Random
ij
Disip
ij
Cons
ij i
F F F f
[ ]

+ =
B A B A
A
M
dt
d ) (r
hesoscaIe modeIIng
- Strong poInts
- n |eso methods atoms are not specIfIcally treated :
reach much larger length and tIme scales
- LImItatIons
- SpecIfIc InteractIons are harder to model, defInIng
the average forces that best represent a specIfIc
system can be dIffIcult
- |InImum of two components
heso0YN, 0P0 heso0YN, 0P0
04001-p.20
What can be caIcuIated!
- SegregatIon
- nterfacIal tensIon
- Stress tensor
- 8ulk vIscosIty
- Shear vIscosIty
- Temperature dependence of mIscIbIlIty
- CrItIcal |Icelle ConcentratIon (C|C)
- Pressure
- 8ead correlatIons
- 0IffusIvItIes
- combInes two bead based methods
- CoarsegraIned molecular dynamIcs (CC|0)
Hard body InteractIons, charged beads
ncludes sterIc effects, detaIled descrIptIon of
InteractIons requIred
- 0IssIpatIve partIcle dynamIcs (0P0)
Soft potentIals, fewer parameters, longer tIme
and length scales, long chaIn polymers
- Study propertIes at longer tIme and length scales
than atomIstIc sImulatIons (mesophase formatIon,
dIffusIon In bIlayers, nanotube orIentatIon etc.)

04001-p.21
CrystaI structure determInatIon from
powder dIffractIon data
- Crystal structure Important for patentIng
- Crystal structure Important as prerequIsIte for
the understandIng of most solId state propertIes
- SIngle crystals large enough for dIffractIon
experIments are frequently dIffIcult or
ImpossIble to obtaIn
PefIex, PefIex PIus, PefIex PA, X-CeII PefIex, PefIex PIus, PefIex PA, X-CeII
Poutes to determIne crystaI structures
?
04001-p.22
0Irect space methods
Indexing
Pawley Refinement
Rietveld Refinement
Global Optimization
0
10000
20000
30000
40000
50000
60000
10 20 30 40 50
Dther crystaIIography tooIs
horphoIgy: predIctIon of the morphology of the
crystal startIng from the atomIc structure of a
crystal (crystal shape, surface stabIlIty, aIds the
development of taIlormade addItIves)
PoIymorph predIctor: predIctIon of potentIal
polymorphs dIrectly from the molecular
structure.
FaIlry rIgId, (non)IonIc molecules (C,N,D,H)
PossIble packIng arrangements are generated In
all reasonable space groups, searchIng for
mInImum lattIce energy
04001-p.23
What can be caIcuIated!
- Powder dIffractIon pattern of a crystal (Feflex Powder 0IffractIon)
- Crystal structure
- From powder data (Powder Solve)
- From a lIst of theoretIcal trIal structures (Polymorph)
- |orphology predIctIon (|orphology)
- ConsIder possIble effects (qualItatIvely) of taIlormade
addItIves and solvents by IdentIfyIng Important InteractIons at
key growth faces.
- PredIct the morphologIcal effects of modIfyIng the growth rates
of partIcular faces
- Felate predIcted morphology to experIment, enablIng IndexIng
of experImental data
CorreIatIve methods
- Addresses two questIons:
- What features of a molecule affect Its actIvIty:
- What can be modIfIed to enhance Its propertIes:
- QuantItatIve In that a mathematIcal model Is used to
account for the observed actIvIty.
Hcppness = ](money + love + ccr + holdcy..)
QSAR property = ]( no. o] ccrbon ctoms +
sur]cce crec +..)
QSAF, SynthIa (Polymers) QSAF, SynthIa (Polymers)
04001-p.24
CorreIatIve methods
- Strong poInts
Allows to cover tIme and sIze range over the
"standard" molecular modelIng (ageIng, odour,
brIllIance.)
- LImItatIons
- The correlatIons are lImIted to a very
specIfIc range of components
- Success of the correlatIons depend on
the qualIty of the data
SAP-uantItatIve Structure ActIvIty PeIatIonshIp
04001-p.25
Dther hoduIes In hS
- AdsorptIon Locator
- Amorphous Cell
- 8lends
- Conformers
- ScrIptIng
- SorptIon
AdsorptIon Locator
0etermInes energetIcally
favourable posItIons of a
adsorbate In perIodIc and
aperIodIc structures
?
04001-p.26
Amorphous CeII
ConstructIon of complex amorphous systems
ConstructIon
PackIng
ConfIned Layer
Iends
A tool to estImate the mIscIbIIIty behavIour of bInary
mIxtures
(solventsolvent, polymersolvent, and polymerpolymer
mIxtures)
the thermodynamIcs of mIxIng Is dIrectly predIcted from
the chemIcal structures of the two components
(molecular structures and a forcefIeld as Input)
Phase dIagrams (crItIcal poInts, bInodal and spInodal curves)
nteractIon parameter,
|IxIng energy
Free energy of mIxIng Isotherms
Energy dIstrIbutIon functIons
8IndIng confIguratIons sorted by energy
04001-p.27
Conformers
The module provIdes methods for searchIng the
conformatIonal space of nonperIodIc molecular systems
In order to derIve a reasonable samplIng of the low energy
conformatIons
The set of rotatable torsIon angles of the molecular
system Is explored systematIc and stochastIc (random)
searches
A a set of conformers Is obtaIned and a range of
descrIptors
enablIng to perform a detaIled analysIs of the structures
SImpIe! Not so sImpIe .
CIS
TRANS
04001-p.28
ScrIptIng In hS
-What Is It:
-Server sIde scrIptIng
-WIll be an evolvIng project, wIll be lookIng for feedback for
Improvements for the next release
-ChemIstry model and ForcIte, 0|ol, CC0C, 0FT8, Crystallography,
CASTEP, Amorphous Cell, |esocIte, 7A|P
-WIll be extended to Include other modules In future releases
-Access Is to a lot of |aterIals 7IsualIzer functIonalIty - chemIstry
model and assocIated objects
-Perl Is the scrIptIng language
-WrIte and test scrIpt on clIent before submIttIng to server
-Fully documented AP and example scrIpts and tutorIal
ScrIptIng EdItor
Bookmarks
Line
numbers
Syntax
highlighting
Syntax
Check
and Output
tabs
04001-p.29

- Put molecules (sorbates) Into a threedImensIonal

perIodIc structure wIth pores (sorbent)
- TypIcal examples of sorbents Include zeolItes,
alumInophosphates, clays, nanotubes, polymer
membranes, sIlIca gels, actIvated carbons, and metal
organIc frameworks.
- The InformatIon that can be obtaIned: adsorptIon
Isotherms, bIndIng sItes, bIndIng energIes, global
mInImum sorbate locatIons, densIty and energy fIelds,
energy dIstrIbutIons, sorptIon selectIvItIes, solubIlItIes,
IsosterIc heats, and Henry constants.
Part III: Case StudIes
04001-p.30
VIsuaIIsIng PeactIvIty
ESP
- ElectrostatIc potentIal (ESP)
- PosItIve regIons (red) correspond to electrondefIcIent areas -
subject to nucleophIlIc attack
- NegatIve regIons (blue) correspond to electronrIch areas - subject to
electrophIlIc attack
Towards mproved ZInc CorrosIon nhIbItors
UnderstandIng the Fole of SIlanes on ZnD
DutlIne:
The aIm Is to produce coatIngs whIch prevent
corrosIon of zInc as zInc oxIde forms as a thIn fIlm
under atmospherIc condItIons.
The behavIour of three sIlane molecules [1] on ZnD
oxIde surfaces has been studIed.
Amorphous Cell was used to create solventsIlane
cells whIch are placed on the oxIde substrate.
04001-p.31
Towards mproved ZInc CorrosIon nhIbItors
UnderstandIng the Fole of SIlanes on ZnD
Two configurations:
A - only the silane head group binds to
the surface
B - both the head and tail are in contact
with the surface
Both effects are only seen in the presence of
solvent, without the solvent, the B is the most
dominant for all of the silanes.
E
ads
correspond to the degree of polarity; amino >
thiol > octyl
PeactIon pathway. TransItIon State (TS)
- TransItIon State
- StatIonary poInt on
PES
- Energy gradIent
vanIshes
- HessIan matrIx has
one ImagInary
frequency
Reaction Coordinates
E
n
e
r
g
y
Reactants
Transition State
Products
E
a
H
f
04001-p.32
PIng-openIng poIymerIzatIon reactIon
Two possIble sItes for the rIng
openIng of caprolactone
the acylIc carbon
an alkylIc sIte
AnalysIs showed that the rIngopenIng at the acylIc sIte has a much
lower energy more favorable. Agreement wIth N|F results
CalculatIon of the potentIal
surface for a full set of
IntermedIates
CalculatIon of TransItIon State
(LST/QST)
hIcrophase formatIon - 0P0
- Fesearchers at UnIIever studIed the mesophase formatIon of lInear
(A
m
8
n
) dIblock melts (applIcatIons: food, detergents, personal care)
- ExplaInIng mIcrophase mechanIsms enables researchers to desIgn
materIals processes more easIly, savIng tIme and reducIng processIng
problems
|orphology of copolymer blends wIth varyIng ratIos of headtotaIl group sIze
04001-p.33
Part V:
ProbIem SoIvIng Approach In hoIecuIar
hodeIIng
.or what a modeIer does .
PesuIts -
what do
they mean!
WhIch
hethod!
How to
Choose!
!!!!!!!
WhIch method!
- All methods for everythIng:
FE|E|8EF
f larger tIme and space domaIns are accessed ,
specIfIcIty and accuracy are lost
Q|
AtomIstIc
|esoscale
TIme SIze Accuracy SpecIfIcIty
- t Is essentIal to choose the rIght method for gettIng the best
results. Fesults have to be analyzed. ThIs Is the work of a
modeler, too.
04001-p.34
How to choose!
- 0FT ElectronIc propertIes or chemIcal phenomena
- 8reak/form bonds
- ElectronIc propertIes
- Accuracy Is my maIn concern, tIme Is secondary
- The system Is small (about 100 atoms)
- SemIempIrIc ElectronIc propertIes or chemIcal phenomena
StIll Interested In breakIng/formIng bonds and
electronIc propertIes but.
nterested only In a fIrst guess
TIme Is more Important than accuracy
Need to deal wIth a bIg quantIty of atoms
How to choose!
- AtomIstIc PhysIcal phenomena
- Not Interested In electrons
- Huge quantIty of molecules/atoms
- TargetIng systems of 100 maxImum
- Processes InvolvIng 1 x 10
9
s
- |esoscale Soft materIals
- Not Interested In electrons
- Not Interested In conformatIons
- |y systems are not crystallIne/semIcrystallIne
- have at least 2 dIfferent components
- 'm targetIng systems sIze mIcrometer and tIme mIcrosecond
04001-p.35
PuIe of thumb - part 1
- How much tIme do you have:
- How accurately do you need your results to be: (or
what approxImatIons are acceptable and what
aren't)
- How many atoms do you have In your system:
- What computatIonal resources do you have access to:
- What |aterIals do you want to study:
PuIe of thumb - part 2
- Small organIc molecules - All technIques applIcable
- Polymers - Usually too bIg to use Q| technIques. Cenerally use
|olecular |echanIcs, |esoscale and QSAF tools to study them.
Fecently, have been able to use Q| methods to study small
olIgomers
- norganIc materIals - Quantum |echanIcs and |olecular |echanIcs.
LImIted applIcatIons of QSAF
- Pure metals - Quantum |echanIcs. Some lImIted studIes usIng
|olecular |echanIcs, CULP
04001-p.36
PuIe of thumb - part 3
When usIng forcefIelds.
- ForcefIeld parameters are derIved empIrIcally. TypIcally the
parameters are adjusted IteratIvely to match experImental data
- Not all materIals have been parameterIzed.
- Polymers - |ost forcefIelds do well. CD|PASS Is the preferred
approach (also good for molecular crystals)
- Small organIc molecules As above
- norganIc materIals - LImIted avaIlabIlIty, some parameters In
CD|PASS, some In cvff_aug. ForcefIelds from the open
lIterature.
- Pure metals - specIal forcefIelds

What If you want to study the evolutIon of a system durIng hours or
a phenomena that has a sIze of 1 cm:
- Try to study the problem from another angle
- What about studyIng the "InItIal" and the "fInal"
systems (before and after a reactIon):
- What about studyIng the Interface:
- f reducIng the tIme/sIze scale does not gIve you the InformatIon
- QSAF
- f you have a lot of data but lIttle chemIcal or physIcal
knowledge of the system
- Useful to generate correlatIons In systems or to fInd
out whIch factors control a certaIn property
04001-p.37
Steps requIred for moIecuIar modeIIng
- |olecular |odelIng (In most cases) Involves four maIn steps
|odel 8uIldIng
|odel FefInement
SImulatIon AlgorIthm
AnalysIs
Sketch molecule, 8uIld Surface,
Crystal, Polymer - Clean
(0ata 8ase, LIterature)
FefIne, DptImIze, |InImIze wIth
the chosen method
|InImIze + 0ynamIcs
ProductIon stage
CalculatIon, 0ynamIcs
CalculatIon of PropertIes,
Spectra, DrbItals
How to proceed !
0efIne the topIc
0efIne the questIon
Choose the technIque/model
|ake calculatIons
SatIsfIed :
ND
YES
|odIfIcatIons
7alIdatIon |ake more calculatIons
Analyse Fesults
Answer to the questIon
04001-p.38

- SometImes not only one technIque wIll gIve all the answers
- 0Ifferent technIques wIll tackle dIfferent angles
of the problem
- You need scIentIfIc background on the domaIn of study
- FIght choIce of model/sImulatIon tool
- Correct analysIs of the results
- You want to keep the referees happy
- |InImum computer requIrements are ok but.
- |emory the more FA| your computer has, the
better
- CPU speed the faster, the better
|ore nformatIon
Dur WebsItes:
www.accelrys.com
www.accelrys.org
04001-p.39
04001-p.40