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DFT, Monte-Carlo and classical simulation studies of crystals, surfaces and zeolites

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Title: DFT, Monte-Carlo and classical simulation studies of crystals, surfaces and zeolites


1
DFT, Monte-Carlo and classical simulation studies
of crystals, surfaces and zeolites
2
Overview
  • Molecular Mechanics
  • Theory
  • Binding of molecules to surfaces
  • Monte-Carlo of Metal Organic Frameworks
  • MC of Hydrocarbons in Zeolites
  • Defect migration
  • QM Methods
  • Theory
  • DMol
  • Lanthanum Catalysis
  • Methanol to Gasoline in ZSM-5
  • CASTEP
  • Surface Binding
  • Catalyst degradation
  • DeSOx and DeNOx
  • Summary

3
Molecular Mechanics
Assumption Classical mechanical description is
adequate Empirical analytical representation of
energy Limitations Accuracy limited by
empirical parameters limited to parameterized
systems atom connectivity can not change
Advantages Very fast Works for 1000s of atoms
Typical applications Applications Biological
compounds, silicas, zeolites, polymers,
glasses Conformational energies Crystal
morphology Physisorption energy
properties Diffusion
4
Force Field Parameterization
5
Typical Force Field Interactions
Inter and intra molecular interactions are
modeled with bonding and non- bond interactions
6
Modelling of retarders on ettringite
Physisorption.
7
Modelling of phosphonate retarders
  • Schlumberger make a range of phosphonate cement
    retarders to control the setting of cements in
    oil wells.
  • Retarders are believed to work by a chelating to
    the surface of ettringite
  • What is the mechanism? How can we design more
    efficient ones?

Reference J. Chem. Soc. Faraday Trans., 1996,
(92), P831
8
Modelling of phosphonate retarders
  • Optimized structures of 8 experimentally used
    compounds
  • Examined the phosphate-phosphate distances
  • Calculated the morphology of Ettringite, found
    the most dominant face is the (001) plane.
  • Surface structure of plane shows that molecules
    are likely to bind to the sulphur atoms on the
    surface.

9
Modelling of phosphonate retarders
  • The best retarders are those with phosphate -
    phosphate distances which match the
    sulfur-sulfur distances on the (001).
  • This correlates with experiment

10
Modelling of phosphonate retarders
  • Minimisation and Dynamics run with the molecules
    docked on the surface.
  • Molecules with more flexible backbones tend to
    bind better.
  • Longer chains
  • Only one phosphonate group on each side is used.
    Other extends into space due to steric repulsion
  • Replace with smaller non-polar groups

11
Modelling of phosphonate retarders
  • Proposed new structures included
  • The cyclic compound was synthesized and proved
    to be a powerful retarding agent.

12
Sorbent Frameworks MOF-5
13
Demo Study MOF-5 Ar Loading using Sorption
  • Sorption
  • Characterizes the sorption behavior a pure
    sorbate (or mixture of sorbate components)
    absorbed in a sorbent framework
  • Uses classical force-field potential to
    represent framework-molecule interactions with a
    Monte-Carlo search to calculate properties
    including
  • adsorption isotherms
  • binding sites and binding energies
  • global minimum sorbate locations
  • density fields

14
Sorbent Frameworks MOF-5
Nature (1999) 402, 276-279.
  • Open metal-organic framework using carboxylate
    linkers and Zn2 ions
  • Possible substrate for gas-storage applications

MOF-5 cavity sphere diameter 18.5A
15
Demo Study MOF-5 Ar Loading using Sorption
  • Preliminary demo study using COMPASS forcefield
    and Sorption to predict the fixed pressure
    loading of Ar in MOF-5
  • The Ar loading at 101 KPa and 79K is 230 /unit
    cell which agrees with the experimental value of
    230 /unit cell
  • Adsorption density of Ar in MOF-5 (blue)
  • Calculated the lowest energy binding site for a
    single Ar Binding energy 3.382 kcal/mol

MOF-5 crystal structure FM-3M
16
Demo Study MOF-5 N2 Loading using Sorption
  • Preliminary demo study using COMPASS forcefield
    and Sorption to predict the fixed pressure
    loading of N2 in MOF-5
  • The N2 loading at 101 KPa and 79K is 205 /unit
    cell which agrees with the experimental value of
    183 /unit cell
  • Adsorption of N2 in MOF-5 (blue)
  • Calculated the lowest energy binding site for a
    single N2 Binding energy 3.457 kcal/mol

MOF-5 crystal structure FM-3M
17
Demo Study MOF-5 H2 Loading using Sorption
  • Preliminary demo study using Sorption to predict
    the fixed pressure loading of H2 in MOF-5
  • The HC2 loading at 101 KPa and 295K is predicted
    to be 162 /unit cell
  • Adsorption of H2 in MOF-5 is shown
  • Calculated the lowest energy binding site for a
    single CHCl3 Binding energy 1.469 kcal/mol

MOF-5 crystal structure FM-3M
18
Overview
  • Molecular Mechanics
  • Theory
  • Binding of molecules to surfaces
  • Monte-Carlo of Metal Organic Frameworks
  • MC of Hydrocarbons in Zeolites
  • Defect migration
  • QM Methods
  • Theory
  • DMol
  • Lanthanum Catalysis
  • Methanol to Gasoline in ZSM-5
  • CASTEP
  • Surface Binding
  • Catalyst degradation
  • DeSOx and DeNOx
  • Summary

19
Adsorption of hydrocarbons in microporous
materials
  • Sorption simulation to analyze the adsorption of
    hydrocarbons on microporous zeolites and on the
    Pt/g-Al2O3 catalyst
  • Agreement between docking energy and sorption
    energy
  • Pt catalyst displays greater ability to absorb
    substrate

Docking energies increase as
heptane lt
methylcyclohexane, ethylpentane lt toluene
Szczygiel, J. Szyja, B. Microp. Mesop. Mat.
76 (2004)247.
20
Adsorption of hydrocarbons in microporous
materials
  • Calculation of adsorption isotherms
  • at low pressure adsorption of toluene molecules
    is impaired because of high interaction energy
  • adsorption of heptane molecules preferred
  • only at the highest pressures adsorption of
    toluene becomes favourable.

Szczygiel, J. Szyja, B. Microp. Mesop. Mat.
76 (2004)247.
21
Adsorption of hydrocarbons in microporous
materials
  • Adsorption sites in the host structure
    (silicalite)
  • Ring and branched hydrocarbon accumulate at sites
    offering sufficient space
  • Heptane located at entire pore length due to
    greater flexibilty
  • Heptane has lower density at sites where other
    molecules accumulate
  • Stronger adsorption in channels between
    intersections caused by proximity of host atoms

Szczygiel, J. Szyja, B. Microp. Mesop. Mat.
76 (2004)247.
22
Defect Migration Lanthanium Oxide
23
Defects in La2O3
Doped La2O3 is used as an electrolyte in solid
oxide fuel cells and in oxygen sensors. Material
is a fast ion conductor. Controlling factor is
vacancy migration. Doping with mono and divalent
cations increases vacancy concentration.
A
B
Two possible vacancy migration routes A and
B Route A - 0.63 eV Route B - 4.79 eV Low energy
for Route A explains fast ion conduction and
implies single crystals will show anisotropic
behavior
Ref. D. J. Ilett and M. S. Islam - J. Chem. Soc.
Farad. Trans. 1993, 89 (20), 3833
24
Defects in La2O3
  • Doping with mono and divalent cations increases
    the number of oxygen vacancies in the lattice to
    maintain neutrality.
  • Defect Energy calculations carried out on alkali
    metals and alkaline earth metals
  • Li, Na, K, Rb
  • Mg2, Ca2, Sr2, Ba2
  • Results show Sr2, has the lowest solution
    energy is 1.71eV per ion.
  • Hence doping with Sr ions will improve
    electrolytic properties of La2O3

25
Overview
  • Introduction
  • Molecular Mechanics
  • Theory
  • Binding of molecules to surfaces
  • Monte-Carlo of Metal Organic Frameworks
  • Defect migration
  • QM Methods
  • Theory
  • DMol
  • Lanthanum Catalysis
  • Methanol to Gasoline in ZSM-5
  • CASTEP
  • Surface Binding
  • Catalyst degradation
  • DeSOx and DeNOx
  • Summary

26
Need for QM methods
  • Force Fields give good estimates for
  • structures, conformations,
  • BUT an accurate determination of transition
    states requires highly sophisticated quantum
    mechanical methods
  • no empirical parameters
  • work for all elements
  • dissociate bonds

27
Quantum Mechanical Methods
Solution of Schrödingers equation, ab
initio Disadvantages Potentially
slow Applicable to 100 atoms
Advantages Applicable to any element Tunable
accuracy Models bond breaking Predicts absolute
energies Applications molecular
geometry chemisorption chemical reactivity UV
IR spectra Solubility and thermodynamic properties
28
DMol Understanding Catalysis
29
DMol
  • DFT program for molecules, crystals, surfaces
  • Uses Localized numerical basis sets
  • DMol3 has been one of the main QM engines of
    Biosym/MSI/Accelrys since 1988
  • Successful applications include
  • polymerization catalysis (metallocenes)
  • metal oxides
  • zeolites
  • CVD
  • molecular organic crystal structure
  • Platforms
  • NT, Linux, Irix, Windows 2000

30
DMol3 Linear Combination of Atomic Orbitals
Periodic and a periodic systems
Radial portion atomic DFT eqs. numerically
Angular Portion
Good for molecules, clusters, zeolites,
molecular crystals, polymers "open structures"
31
Case Study Lanthanide Catalysts using DMol3
32
Lanthanide Catalysts using DMol3
  • La2O3, LaOCl, LaCl3 used in commercial reactions,
  • Production of vinyl chloride, alkane conversion
    to chloride
  • Studied model reaction of
  • CCl4 2 H2O ? CO2 4 HCl
  • A collaboration between Dow Chemical and several
    Universities
  • Use experiment theory to link surface
    properties with catalytic activity
  • Detailed work from can be found in

JPCB 108 (2004) 15770 Chem. Euro. J 10 (2004)
1637 JPCB 109 (2005) 11634
33
Lanthanide Catalysts using DMol3
  • Use DFT to study decomposition reaction on
    surface of La2O3
  • Rate determining step
  • La3surf O2-surf CCl4 ? La-Clsurf O-CCl3 surf
  • Acidic La site initiates split by polarizing one
    of Cl atoms
  • Base site (typically surface oxygen) stabilizes
    CCl3 fragment
  • Study first reaction step on surface of LaOCl,
    LaCl3, and La2O3

34
Lanthanide Catalysts using DMol3
Reaction on La2O3
Reaction on LaOCl
Reaction on LaCl3
  • Initial and final configuration same as La2O3
  • Stronger interaction with acid site
  • No activation barrier
  • Intermediate reaction mechanism
  • Similar to La2O3 before transition state
  • Similar to LaOCl after transition state
  • Activation barrier is 109 KJ mol-1
  • Chlorine become anion and CCl3 loses charge
  • Stabilized above O site
  • Activation barrier is 147 KJ mol-1

35
Lanthanide Catalysts using DMol3
  • Conclusions
  • Bond breaking CCl4 ? CCl3 Cl- is rate limiting
  • Activation energy consistent with expt activity
  • LaOCl gt LaCl3 (with partial dechlorination of
    surface) gt La2O3
  • Explains activity in terms of surface features
  • C-Cl bond activated by acid site
  • CCl3 fragment stabilized by O-atom base site
  • Best catalyst will be characterized by both
  • Strong acid base sites
  • Geometrically favorable arrangement
  • Experiment provides raw results like relative
    ordering of sites, ordering of catalytic activity
  • Modeling provides critical insight for improved
    catalyst engineering

36
Case Study Methanol to Gasoline Conversion
37
Zeolite-Catalyzed Hydocarbon Formation from
Methanol
  • Reaction studied conversion of methanol to
    gasoline (MTG) developed by Mobil in the 1970s
  • Study of mechanisms of C-O bond cleavage and
    formation of first C-C bond
  • Open questions
  • Clusters of H-bonded methanols form in zeolite
    cage leading to dimethylether (DME) formation ?
  • Is C-O bond cleaved through formation of methoxyl
    or by surface ylide ?
  • ? Study of reaction mechanism using periodic
    models

Govind, N. Andzelm, J. Reindel, K.
Fitzgerald, G. Int. J. Mol. Sci. 3 (2002) 423.
38
Zeolite-Catalyzed Hydocarbon Formation from
Methanol
  • Single methanol adsorbs via H-bonds
  • Surface methoxyl formation occurs via concerted
    reaction of C-O bond breaking in methanol and C-O
    bond formation on the surface
  • Energy barrier of 54 kcal/mol

Govind, N. Andzelm, J. Reindel, K.
Fitzgerald, G. Int. J. Mol. Sci. 3 (2002) 423.
39
Zeolite-Catalyzed Hydocarbon Formation from
Methanol
  • Second methanol lowers barrier to 44 kcal/mol
  • Methoxonium forms spontaneously by capture of
    proton from Bronsted acid site

Govind, N. Andzelm, J. Reindel, K.
Fitzgerald, G. Int. J. Mol. Sci. 3 (2002) 423.
40
Zeolite-Catalyzed Hydocarbon Formation from
Methanol
  • Ethanol formation New pathway with water as
    spectator
  • Concerted reaction Methanol gives up proton to
    Bronsted site
  • Barrier (50 kcal/mol) similar to previously
    reported scheme (competing reactions). Overall
    reaction exothermic.

Govind, N. Andzelm, J. Reindel, K.
Fitzgerald, G. Int. J. Mol. Sci. 3 (2002) 423.
41
Zeolite-Catalyzed Hydocarbon Formation from
Methanol
  • Ylide species formation has substantially higher
    barrier (78 kcal/mol)
  • Substantial lattice distortion around Bronsted
    site and zeolite cage
  • Rules out possibility of ylide formation

Govind, N. Andzelm, J. Reindel, K.
Fitzgerald, G. Int. J. Mol. Sci. 3 (2002) 423.
42
Overview
  • Molecular Mechanics
  • Theory
  • Binding of molecules to surfaces
  • Monte-Carlo of Metal Organic Frameworks
  • Defect migration
  • QM Methods
  • Theory
  • DMol
  • Lanthanum Catalysis
  • Methanol to Gasoline in ZSM-5
  • CASTEP
  • Surface Binding
  • Catalyst degradation
  • DeSOx and DeNOx
  • Summary

43
CASTEP Facts at a Glance
Technology First-principles plane-wave
pseudopotential code Periodic Boundary
Conditions Application Solids and surfaces, all
material types (metals, semiconductors and
insulators) Origin Mike Paynes group
Cambridge University plus world-wide
developers club Information Wealth of
applications including defects, surface
chemistry, zeolites, diffusion 240
publications Platforms SGI, Linux, NT, Windows
2000
CASTEPCAmbridge Serial Total Energy Program
44
Plane Wave Basis Set
  • Blocks theorem states
  • The cell-periodic part can then be expanded using
    a basis set consisting of a discrete set of plane
    waves. Then each electronic wave function can be
    written as a sum of plane waves
  • G reciprocal lattice vectors

Wavelike part Cell-periodic part
45
Case Study DeSox Catalysts
46
DeSOx Catalyst Design using Simulation
  • Back ground
  • SO2 is a major air pollutant arising from sulfur
    in fuels
  • Causes acid rain with negative impact on
    ecosystem, human health and buildings and
    monuments
  • Oxides can be used to catalyze DeSOx reactions
  • Key goal is activation of the S-O bond in SO2
  • Simulations and experiments have been used to
    understand the chemistry of SO2 on oxide surfaces

Claus reaction
2H2S SO2 -gt 2H2O 3Ssolid
J. A. Rodriguez et al. JACS, 122, 12362 (2000).
Reduction of SO2 by CO
SO2 2CO -gt 2CO2 Ssolid
47
DeSOx Catalyst Design
SO2 2CO ? 2C2O Ssolid at 500 C
O
Mg
Cr
  • Why is Cr0.06Mg0.94O so active?
  • What metal could be user to replace Cr?
  • Health hazard, environmental impact, cost

48
Calculation of SO2 Adsorption on Surfaces
h1-O
Cr
49
Origins of SO2 Activation
  • Cr0.06Mg0.94O is a good catalyst for the
    reduction of SO2 by CO because
  • Occupied electronic states appear well above the
    valence band edge of MgO
  • The Cr atoms in Cr0.06Mg0.94O are in a lower
    oxidation state than the atoms in Cr2O3

Design rule that can now be applied to look for
alternative dopants to chromium!
50
How can Cr be replaced?
  • Candidates to replace Cr Mn, Fe, Co, Ni, Zn Sn
  • INMATEL rank according to non-chemical factors
  • Approach compute electronic structure and
    measure dopant level position above Valence Band
    (VB) edge

Mn lt Ni lt Co lt Sn lt Zn lt Fe
Worst
Best
Iron looks like best choice!
Dopant position above VB edge in eV
51
Catalyst Test at INMATEL
SO2 Conversion
Zn0.05Mg0.95O
Fe0.06Mg0.94O K
Cr0.06Mg0.94O
Fe0.06Mg0.94O
SO2 2CO ? 2CO2 Ssolid at 500 C

52
Case Study Phase transistion of CsI
53
Phase transition in CsI B. Winkler, V. Milman, J.
Phys. 9 (1997) 9811
  • Simple structure, but
  • transition at 50 GPa has just been discovered
    experimentally
  • exact transition pressure is not known (P-V curve
    is smooth)
  • symmetry of the high-pressure phase is still
    controversial
  • CASTEP results
  • identify transition pressure as 47 GPa (all
    properties are discontinuous)
  • identify space group as Pmma (tetragonal,
    corresponds to distorted hexagonal)

54
Pressure dependence of cell parameters in CsI
  • Cubic structure has a/bc/b?21.41
  • Ideal hexagonal structure has a/b1.63,
    c/b?31.73
  • Transition pressure is 47 Gpa
  • At higher pressures there will be a transition
    from tetragonal to hexagonal structure.

Cubic
Pmma
55
CsI structural change with pressure
Bulk modulus 13.2 GPa (13.5 exp.)
  • Internal fractional coordinate changes
    discontinuously at the transition pressure

There is practically no discontinuity in the P-V
curve.
56
Density of states as a function of pressure
Cs 5s
I 5s
VB (Cs 6s, I 5p)
  • Total DOS after transition (red) shows that
    nominally core states become broadened - some of
    them even start overlapping.
  • DOS at 0 (yellow), 40 (black) and 60 GPa (red)
    are shown

Cs 5p
57
Charge density distribution
  • This plot shows the charge density distribution
    of Cs 5p electrons (semi-core states) in the
    plane containing I atoms. The maximum value in
    the left plot (40 GPa, before the transition) is
    0.01 compared to 0.13 on the right (60 GPa, after
    the transition) which illustrates the conclusion
    that the hybridization of semi-core states is the
    major driving force for the observed hexagonal
    distortions under pressure.

58
Summary
  • Computational chemistry offers a range of tools
    for studying materials properties
  • We can calculate a range of properties
  • It is a useful tool in increasing our
    understanding of the atomistic behaviour of
    systems and can be used to do more efficient
    experiments
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