chapter 1. introduction, perspectives, and aims. on the science of simulation and modelling....
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![Page 1: Chapter 1. Introduction, perspectives, and aims. On the science of simulation and modelling. Modelling at bulk, meso, and nano scale. (2 hours). Chapter](https://reader033.vdocuments.net/reader033/viewer/2022061305/551421c8550346ec488b5875/html5/thumbnails/1.jpg)
Chapter 1. Introduction, perspectives, and aims. On the science
of simulation and modelling. Modelling at bulk, meso, and nano
scale. (2 hours).
Chapter 2. Experimental Techniques in Nanotechnology. Theory
and Experiment: “Two faces of the same coin” (2 hours).
Chapter 3. Introduction to Methods of the Classic and Quantum
Mechanics. Force Fields, Semiempirical, Plane-Wave
pseudpotential calculations. (2 hours)
Chapter 4. Introduction to Methods and Techniques of Quantum
Chemistry, Ab initio methods, and Methods based on Density
Functional Theory (DFT). (4 hours)
Chapter 5. Visualization codes, algorithms and programs.
GAUSSIAN; CRYSTAL, and VASP. (6 hours)
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. Chapter 6. Calculation of physical and chemical properties of
nanomaterials. (2 hours).
Chapter 7. Calculation of optical properties. Photoluminescence.
(3 hours).
Chapter 8. Modelization of the growth mechanism of
nanomaterials. Surface Energy and Wullf architecture (3 hours)
Chapter 9. Heterostructures Modeling. Simple and complex
metal oxides. (2 hours)
Chapter 10. Modelization of chemical reaction at surfaces.
Heterogeneous catalysis. Towards an undertanding of the
Nanocatalysis. (4 hours)
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Chapter 6. Calculation of physical and
chemical properties of nanomaterials
Juan Andrés
Departamento de Química-Física y AnalíticaUniversitat Jaume I
Spain&
CMDCM, Sao CarlosBrazil
Sao Carlos, Octubro 2011
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- High-pressure phase transitions in crystalline systems
Applications in front-line research
- Li Diffusion in Crystalline Systems
- Two State Reactivity and heterogeneous catalysis
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Computational and Theoretical Chemistry (CTC)
Solid State Chemistry
Structrural properties of ceramic materials. Substitution and doping processes.
Adsorption processes on metal oxide surfaces.
Electronic and optical properties of piezoelectric and catalytic materials.
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Cooperation
CTC Experimentalwork
Characterization of chemical species of difficult experimental detection
Prediction
Interpretation
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High Pressure High Pressure EffectsEffects
Chemical Chemical ReactivityReactivity
Diffusion ProcessesDiffusion Processes
crystalline structurescrystalline structures-CompressibilityCompressibility(polyhedra, bonds)(polyhedra, bonds)- polymorphism- polymorphism
- reaction pathsreaction paths- activation barriersactivation barriers
Atoms (C, Li) in metals Atoms (C, Li) in metals and metal oxidesand metal oxides
- stationary pointsstationary points- reaction pathsreaction paths- crossing pointscrossing points
PESs of differentPESs of differentspin multiplicitiesspin multiplicities
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• Properties :
- Geometry optimization, macroscopic parameters: equations of state, B0 , e , n
- Electronic properties: r , DOS, band structure, dEg/dP
- Theoretical vibrational spectra (Raman , IR), vibrational modes asignation, w, dw/dP.
• Methodology: Density Functional Theory (DFT) Periodic Models Programs: CRYSTAL, VASP
• Characterization of phase transition mechanisms
Pressure effect
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• MgAl2O4
METHODOLOGY
CRYSTAL ProgramDFT (B3LYP)8-511G*- Mg, Al8-411G* -O
iif
p
ppVNV
POLYHEDRA ANALYSIS
Optimización de la geometría
Curva ET-V
código GIBBS: Ecuación de Estado
V0, B0 , B0’
V
P-V
1 B
T
Pressure effect Physical Review B 66, 224114 (2002)
L. Gracia, A. Beltrán, J. Andrés, R. Franco and J. M. Recio
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Occuped octahedra AlOAlO66 Occuped tetraheda MgOMgO
44
Unfilled octahedra OO66 Unfilled tetrahedra (O(O
44))11 y (O(O
44))22
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MgO+Al2O3
P(GPa)
6050
G (
kJ/
mol
)
cubica
tipo-ferrita tipo-titanita
100
150
50
0
-50
0 40302010
MgO y -Al2O3
titanita ferrita
cúbica
ESTABILIDAD GLOBAL
distancia Mg2+-O2-
empaquetamiento
MgO y -Al2O3
IC (Mg2+) 4 6 8
ortorrómbicascúbica
COMPRESIBILIDADES LINEALES Al-O/Mg-O
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• CdGa2Se4, CdCr2Se4
Cúbic Fd3m Cd2+ tetrahedraCr3+ octahedraTetragonal I4
POLYHEDRA ANALYSIS
CdCr2Se4CdGa2Se4B0 (GPa)
Exp
Teor
10148
92 (no magnetic)4480 (ferromagnetic)
Journal of Physics: Condensed Matter 16, 53-63 (2004).
A. Waskowska. L. Gerward, J. Staun Olsen, M. Feliz, R. Llusar, L. Gracia, M. Marqués and J. M. Recio
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• Polymorphs of CO2
CO2-I Pa3 CO2-III Cmca
Programa VASPPAW (LDA) Análisis topológico (AIM)
METHODOLOGY
ESTRUCTURES
J. Physics: Condensed Matter 16, s1263 (2004)
L. Gracia, M. Marqués, A. Beltrán, A. Martín Pendás, and J. M. Recio
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P212121I42dP42/mnmCO2-V CO2-V CO2-V
V0 (Å3)
B0 (GPa)
dC-O (Å)
36.87 36.97 37.05 22.95 22.28 17.44
16.6 15.0 16.9 133.6 142.7 327.2
1.168(2) 1.168(2) 1.265(2) 1.385(4) 1.385(4) 1.577(4)
1.679(2)
Pa3 Cmca(1) Cmca(2) P212121 I42d P42/mnm
Molecular to polymeric phase transition: CO2
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Punto crítico firma sentido químico
máximo -3 nucleosPunto de silla -1 enlaces
- / 2
(r) = 0
TEORÍA DE ATOMOS EN MOLECULAS (AIM)
carácter y fuerza del enlace
polar C=O conCO2-I y CO2-III (1) / 2 > 0
covalente C-O conCO2-V / 2 <0
Isocontornos de la laplaciana de CO2-III (2):Configuration T
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J. Phys. Chem. B 110, 23417 (2006)TiO2 polymorphs
(Å3)
AnataseBrookite
Rutile
G r
elat
ive
toru
tile
(Har
tree
)
-999.97
-999.965
-999.96
-999.955
-999.95
-999.945
-999.94
-999.935
26 28 30 32 34 36 38 40
E(H
artr
ee)
V
-10
-5
0
5
10
15
20
0 2 4 6 8 10 12 14P(GPa)
(Å3)
AnataseBrookite
Rutile
G r
elat
ive
toru
tile
(Har
tree
)
-999.97
-999.965
-999.96
-999.955
-999.95
-999.945
-999.94
-999.935
26 28 30 32 34 36 38 40
E(H
artr
ee)
V
-10
-5
0
5
10
15
20
0 2 4 6 8 10 12 14P(GPa)
ab
c
ab
c
b
c
a b
c
a ab
c
ab
c
anatase → brookite at 3.8 GParutile → brookite at 6.2 GPa.
A. Beltrán, L. Gracia and J. Andrés
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Brookite Surfaces
stabilities (010) < (110) < (100)
the electronic structure: - direct band gap in all of
them- minimum gap energy:
(110)
(100)
Ti5c
Ti4c
Ti5c
[100][010]
[001]
[010][100]
[001]
[110][110]
[001]
(010)
(110)
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Journal of Physical Chemistry B 111, 6479-6485 (2007). SnO2 polymorphs
Highest bulk moduli values of 293 (pyrite) and 322 GPa (fluorite) phases
A. Beltrán, L. Gracia and J. Andrés
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SnO2 polymorphs
-35.53
-35.52
-35.51
-35.50
-35.49
-35.48
-35.47
-35.46
-35.45
26 28 30 32 34 36
V (Å3)
E (
Har
tree
)
PnnmPbcnPa3
Pnam
Pbca
Fm3m
P42/mnmP4
P42/mnmP4-35.53
-35.52
-35.51
-35.50
-35.49
-35.48
-35.47
-35.46
-35.45
26 28 30 32 34 36
V (Å3)
E (
Har
tree
)
PnnmPbcnPa3
Pnam
Pbca
Fm3m
P42/mnmP4
P42/mnmP4
P (GPa)
Ent
halp
yva
riatio
n
-40
-20
0
20
40
60
0 5 10 15 20 25 30 35 40
P (GPa)
Ent
halp
yva
riatio
n
-40
-20
0
20
40
60
0 5 10 15 20 25 30 35 40
a)
b)
The phase transition sequence is consistent with an increase of coordination number of the tin ions, from 6 in the first three phases to 6+2 in the pyrite phase, 7 in the ZrO2-type orthorhombic phase I, 8 in fluorite phase and 9 in cotunnite orthorhombic phase II.
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a) b) c)
ab
c
ab
c
a) CrVO4,-type b) zircon c) scheelite
TiSiO4
B3LYP calculations (CRYSTAL06 program)
Phys. Rev. B 80, 094105 (2009)
L. Gracia, A. Beltrán and D. Errandonea 45 50 55 60 65 70
V (Å3)
zircon
scheelite
CrVO4
-1439.82
-1439.81
-1439.0
-1439.79
-1439.78
-1439.77
-1439.76
-1439.75
-1439.74
E (
Har
tree
)
45 50 55 60 65 70
V (Å3)
zircon
scheelite
CrVO4
-1439.82
-1439.81
-1439.0
-1439.79
-1439.78
-1439.77
-1439.76
-1439.75
-1439.74
E (
Har
tree
)
H (
KJ/
mol
)
P (GPa)
-20
-10
0
10
20
0 1 2 3 4 5
H (
KJ/
mol
)
P (GPa)
-20
-10
0
10
20
0 1 2 3 4 5
enthalpy vs presión curve(CrVO4-type as reference)
Vt = [V2(Pt)-V1(Pt)] / V1(Pt) - 0.8 GPa → volume change of 11.8%. - 3.8 GPa → volume reduction of 8.5%.
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In scheelite the low frequency mode with < 0 , T(Bg), suggest the possibility of a transition to the post-scheelite structure, fergusonite or wolframite
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ThGeO4
zircon
scheelite
fergusonite
PBE calculations (VASP program)
Physical Review B 80, 094101 (2009)
D. Errandonea, R. S. Kumar, L. Gracia, A. Beltrán, S. N. Achary, and A. K. Tyagi
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Computations: Zircon as the most stable to 2 GPa Scheelite P > 2 GPaFergusonite (post-scheelite) at 31 Gpa
XRD:Zircon Scheelite Fergusonite 11 GPa 26GPa
Decompressionfergusonite – scheelite: no histeresis zircon-scheelita: not reversible.
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Bastide diagram for ABX4 structuresDashed lines: evolution of the ionic radii ratio with pressure
D. Errandonea, F.J. Manjón , Progress in Materials Science, 53, 711 (2008)
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1.958
Anhydrite
1.955
Scheelite
Barite
ab
c
MonaziteCaSO4
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E-V curve
MonazitaAnhidrita
BaritaScheelita
AgMnO4
StructureStructure anhydritanhydritee
monazitemonazite baritebarite scheelitescheelite AgMnOAgMnO44
BB00 (B (B00‘)‘) 67.7 (5.61)67.7 (5.61) 146.2 (4.28)146.2 (4.28) 64.8 (6.94)64.8 (6.94) 84.1 (5.86)84.1 (5.86) 144.9 (4.19)144.9 (4.19)BB00 ‡‡ 73.373.3 160.9160.9 77.177.1 102.6102.6 152.2152.2Exp BExp B00 (B(B00') ')
≈≈45 (-)45 (-) 149.4 (4.25)149.4 (4.25)
Exp BExp B00 ‡‡ -- 151.2 151.2 (±21.4)(±21.4)
H-P curve
anhydrite → monazite at Pt 5 GPa , reduction of volum -2% at 5GPa
monazite → barite (and/or scheelite) at 8 GPa
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SiO2 polymorphs
stihovite
-cristobalite
-cristobalite is 0.1 eV more stable than stishovite at P=0
transition as low as 0.5 GPa with a large volume collapse
L. Gracia, J. Contreras-García, A. Beltrán and J. M. Recio High Press Res 29, 93-96 (2009).
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SiO2 polymorphs
The atomic displacements connecting both polymorphs can be described under a martensitic approach (collective and concerted movements of all the atoms) in terms of a transition path of P41212 symmetry. The transition path is traced up using a normalized coordinate: x, that evolves continuously from 0 (-cristobalite, c) to 1 (stishovite, s)
sc
c
ac
ac
ac
ac
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Experimental StudyDAC Diamond Anvil
Cell
Sincrotrones ALBA
Nuevos Beamlines dedicados a altas presiones (APS/ESRF/SPring8/Diamond/Soleil/ALBA)
Electrones acelerados a una energía de 7 mil millones de electron-volts (7 GeV).
Radiación sincrotrón: radiación electromagnética producida por partículas cargadas que se mueven a alta velocidad (una fracción apreciable de la velocidad de la luz) en un campo magnético.
Ionización del aire producida por un haz de rayos X en un sincrotrón
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Diffusion Procesess
Structure Cleveage of adsorbates Catalysis
Alteration
Impurities in metals
VASP ProgramPlane waves / GGA
METHODOLOGY
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tet1
tet2
oct2tet1
Oct > Tet1 > Tet2Oct > Tet1 > Tet2 E(relative,eV):E(relative,eV): 0.000.00 >> 0.410.41 >>
0.520.52
oct1
• Stability of C in Pd(111)
Unit cell R30º
- subsurface interstices
L. Gracia, M. Calatayud, J. Andrés, C. Minot and M. Salmeron Physical Review B 71, 033407-1(-4) (2005).
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oct
0.340.32 y0.36 0.38 0.40 0.42 0.44 0.46 0.48 0.50
tet1
tet2
ts1
ts2 -0.17
-0.13
1.9-0.75
2.8
oct
1.90
-0.53-0.15
0.41
0.52
0.86
0.74
0.0
E (eV)
-0.92
2.4
1.9
1.9
-0.74
-0.352.0
2.0
Horizontal Diffusion
tet1tet2
oct2
9
10
11
oct17
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To bulk Diffusion
oct1
0.80.6
y
0.4
1 1.5 2 2.5 3 3.5
ts1ts2
E (eV)
1.93
1.80
tet1
tet2
0.0
0.63
1.14
0.27
oct2
z
0.63
tet1
tet2
oct2
oct17
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• Li in WO3
WOLi
ab
cd
eO1
O2
WOLi
ab
cd
eO1
O2
Maximum energy barrier
Minimum energy pathdistortion d(O1-O2)
2.65 Å without Li - 4.25 Å
d(Li-O)= d(Li-W)=2.09 Å
4 O, 2 W
Cell 2x2Pm3m
Electrochemical and Solid State Letters. 8, J21 (2005)
L. Gracia, J. García Cañadas, G. García-Belmonte, A. Beltrán, J. Andrés and J. Bisquert
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xTckE ln B
(●) experimental data of DJ.
(○) theoretical calculations
Energy barrier variation with x
Rect lines relation
with c=1.55 (simulation) and 1.25 (experiment).
Process more favorable for low doped systems
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Intercalation and diffusion of Li: Li1+xTi2O4 (spinel )
Phys Rev. B 77, 085112 (2008) M. Anicete-Santos, L. Gracia, A. Beltrán and J. Andrés
Li diffusion processes from tetrahedral 8a sites to ctahedral 16c sites are thermodynamically favorable only in the compositions x > 0.250.
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Intercalation and diffusion of Li: Li1+xTi2O4 (spinel )
Phys Rev. B 77, 085112 (2008) M. Anicete-Santos, L. Gracia, A. Beltrán and J. Andrés
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Chemical Reactivity
R’ P’
TS’
R
TS
P
PCPC
R
TS
P
R’
P’
TS’
PC
TS
TS’
R
R’
P
P’
PC
Program GAUSSIANDFT (B3LYP)6-311G(2d,p)
•Vibrational Analysis
•IRC
METHODOLOGY
• MECP by Harvey et al.
Ei y q
Ei GradientsParallel to SEPsortogonal to CP
• IRCs by Yoshizawa et al. IRC minimum TS closer
Single-point energy calculation with the other spin electronic state
geometries
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V(OH)2+ + C3H4
VO+ + CO(CH3)2 / CHOC2H5
C3H6+
VO2+
VO+ + CHOCH3C2H4+
V(OH)2+ + C2H4
VO+ + H2O + C2H4C2H6+
NbO3- + H2O + O2
MO(H2O)+ M(OH)2+ M=(V, Nb, Ta)
Reaction mechanisms Spin inversion processes crossing points Topological analysis of electron density
NbO5- + H2O
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VO2+ + C2H4 VO+ + CHOCH3
G (kcal/mol)
-80
-60
-40
-20
0
20
40
s-TS2/3
s-TS1/2
s-3 s-2
s-VO2+ + s-C2H4
t-VO+ + s-CHOCH3
s-1
s-4s-TS1/4
s-TS4/5 s-5 s-TS5/3
s-3s-1
t-TS4/5 t-5 t-TS5/3
t-3
t-TS2/3
t-3
t-2
‡ ‡ ‡ ‡‡
t-VO+ + s-CHOCH3
Mecanismo 1
CP2
CP1
Mecanismo 2
J. Phys. Chem. A 107, 3107 (2003)L. Gracia, J. R. Sambrano, V. S. Safont, M. Calatayud, A, Beltrán and J. Andrés
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t-VO++ s-H2O + s-C2H4
s-VO+ + s-H2O + s-C2H4
-70
-50
-30
-10
10
30
50
s-1
t-1
s-TS1/2
s-TS2/3
t-TS2/3
t-TS1/2
s-3
s-2
t-2
t-4
t-TS3/4
s-TS3/4
t-3
s-4
s-5
s-6
t-6
t-TS5
s-TS5
t-5
G (kcal/mol)
7.3
t-VO2+ + s-C2H6
s-VO2+ s-C2H6
CP
‡
+
‡‡‡
VO2+ + C2H6
VO+ + H2O + C2H4
V(OH)2+ + C2H4
s-V(OH)2+ + s-C2H4
t-V(OH)2+ + s-C2H4
Organometallics 23, 730 (2004). Gracia, J. Andrés, J. R. Sambrano, V. S. Safont, and A. Beltrán
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s-propene +
S-VO2+
t-1
s-TS1Al
s-1Als-3
s-2
s-1
t-1Al
t-2/3
t-TS1P
t-TS1Ac
s-TS1Al
s-TS1P
s-TS1Ac
t-2Ac
s-2Al
t-2P
t-2Al
s-2Ac
s-2P
s-TS2Al
t-TS2Al
s-Propanal + s-VO+
s-Acetona + s-VO+
s-Aleno + s-V(OH)2+
s-Propanal + t-VO+
s-Acetona + t-VO+
s-Aleno + t-V(OH)2+
G (kcal/mol)
-70
-60
-50
-40
-30
-20
-10
0
10
20
‡ ‡
CP
VO2+ + C3H6
V(OH)2+ + C3H4
VO+ + CO(CH3)2
CHOC2H5
Organometallics 25, 1643 (2006)
L. Gracia, J. R. Sambrano, J. Andrés and A. Beltrán
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t-NbO2(OH)2-
G (kcal/mol)
t-NbO3-
+ H2O
t-TS1
41.5
-59.0
43.9
35.7
t-NbO3(H2O)-
t-NbO4(OH)2--A
-22.4
-12.0
-23.1
-1.9-4.0
t-NbO5 (H2O)- s-NbO5
-
+ H2O
26.0
+O2
0.0
-12.4 -13.4
17.9
-19.2 -12.1 -23.0
1.3-2.3
-4.4
-80
-60
-40
-20
0
20
40
60
-3.7
s-NbO3-
+ H2O
s-NbO2(OH)2-
s-TS1 s-NbO3(H2O)-
t-TS2
t-NbO4(OH)2--B
t-TS3
+O2
‡
‡ ‡
+O2
•
CP1
CP2
NbO3- (1A1)+ H2O + O2 (3g) NbO5
- (1A’)+ H2O
J. Phys. Chem. A 108, 10850 (2004) R. Sambrano, L. Gracia, J. Andrés, S. Berski and A. Beltrán
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E (
kca
l /mo
l)
E (
kca
l /mo
l)
-40
-20
0
20
40
60
-12.8
M1 M2
8.1
0.0
M5 + H2O+ CH2O
58.8
35.1
M4 + H2OTS1
22.5
TS2
39.3
33.0
M3
19.5
52.9MECP1
T
CSS
36.331.7
OSSLS
35.3
23.6
E (
kca
l /mo
l)
E (
kca
l /mo
l)
-40
-20
0
20
40
60
-12.8
M1 M2
8.1
0.0
M5 + H2O+ CH2O
58.8
35.1
M4 + H2OTS1
22.5
TS2
39.3
33.0
M3
19.5
52.9MECP1
T
CSS
36.331.7
OSSLS
35.3
23.6
Oxidation of Methanol to Formaldehydeon a Hydrated Vanadia Cluster
P. González-Navarrete, L. Gracia, M. Calatayud and J. AndrésJ Comput Chem 31, 2493-2501(2010).
The main effect of hydration can be associated to the destabilization of the methoxy-intermediates
five-fold V
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Two intermediates, a five-fold coordinate and a tetrahedral vanadium, have been considered with C-H bond breaking barriers of 23.6 kcal/mol and 45.3 kcal/mol respectively. The penta-coordinate species, although it is 11.5 kcal/mol less stable than the tetrahedral one, might be regarded as a potential reactive intermediate
-40
-20
0
20
40
60
TS3 M8 + H2O
-1.60.0
M5 + H2O+ CH2O
58.8
TS4 + H2O
7.04
51.0
-9.6
M6 M7
-12.2
67.9
48.1
35.1
M4 + H2O
MECP2
T
CSS
48.643.7
OSSLS
E (
kcal
/mo
l)
E (
kcal
/mo
l)
16.6
45.3
-40
-20
0
20
40
60
TS3 M8 + H2O
-1.60.0
M5 + H2O+ CH2O
58.8
TS4 + H2O
7.04
51.0
-9.6
M6 M7
-12.2
67.9
48.1
35.1
M4 + H2O
MECP2
T
CSS
48.643.7
OSSLS
E (
kcal
/mo
l)
E (
kcal
/mo
l)
16.6
45.3
Modelo HidratadoActividad investigadora: Resultados
tetrahedral V
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-10
-5
0
5
10
15
20
25
30
35
on V-O-Ti
4.9
14.9
-7.5
Int4
on V-O-Ti
TS
on V=O
TS
V-O-Ti site leads to lower barrier, more stable dissociation product
Int1
Int4
on V=O
29.3
17.2
Int1
P. González-Navarrete, L. Gracia, M. Calatayud and J. Andrés J. Phys. Chem. C, Vol. 114, No. 13, 2010
The vanadia/titania catalystsThe vanadia/titania catalysts
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-20,0
-15,0
-10,0
-5,0
0,0
5,0
10,0
15,0
20,0
25,0
30,0E
+Z
PE
(kca
l/mol
)
PATH1PATH2
+ Methanol
40.9
10.7
25.2
20.1
5.0
-7.0
18.2
15.4
25.1
19.5
-7.0
3.7
-17.2
23.7
15.4
19.5
Reactive complex
Int1
TS1a
Int2b
Int3b
Int2b
Int3b
Int1
Int4
Int4
TS2a
Comparison between both B3LYP/6-311G(2d,p) energy profiles. Path1 and Path2. a Broken-symmetry transition states and projected energies. bTriplet intermediates.
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Read
Structural Stability of High-Pressure Polymorphs in In2O3 Nanocrystals: Evidence of Stress-Induced Transition?**
A. Gurlo, Angew. Chem. Int. Ed. 2010, 49, 2–5