Herramientas mecano-cuánticas basadas en DFT para el...
Transcript of Herramientas mecano-cuánticas basadas en DFT para el...
![Page 1: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/1.jpg)
Herramientas mecano-cuánticas basadas en DFT para el estudio de moléculas y
materiales en Materials Studio 7.0
Javier Ramos Biophysics of Macromolecular Systems group
(BIOPHYM)
Departamento de Física Macromolecular
Instituto de Estructura de la Materia – CSIC
Webinar, 26 de Junio 2014
![Page 2: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/2.jpg)
Anteriores webinars
Como conseguir los videos y las presentaciones de anteriores webminars:
Linkedin: Grupo de Química Computacional
http://www.linkedin.com/groups/Química-computacional-7487634
![Page 3: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/3.jpg)
Density Functional Theory (DFT)
The Jacob’s ladder
DFT modules in Maretials Studio
DMOL3, CASTEP and ONETEP
XC functionals
Basis functions
Interfaces in Materials Studio
Tasks
Properties
Example: n-butane conformations
Índice
![Page 4: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/4.jpg)
Density Functional Theory (DFT)
DFT is built around the premise that the energy of an electronic system can be defined in terms
of its electron probability density (ρ). (Hohenberg-Kohn Theorem)
By minimizing the total energy functional applying the variational principle it is
possible to get the SCF equations (Kohn-Sham)
E0[
0] T
e[
0] E
ne[
0] E
ee[
0]
( r )v ( r ) drKinetic Energy for
noninteracting
electrons(easy)
(easy) ?????
1
1 2 1 22
1 2
1[ ] ( ) ( ) [ ]
e e X CE r r d r d r E
r
Classic Term(Coulomb) Non-classic
Exchange &
Correlation
Kohn-Sham orbitals
![Page 5: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/5.jpg)
The Jacob’s Ladder
Accurate form of XC potential
Empirical (Fitting to
atomic properties)
Non-Empirical
(physics rules)
Local Density Approximation
Generalized Gradient Approx.
Meta GGA
![Page 6: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/6.jpg)
![Page 7: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/7.jpg)
DFT modules in Materials Studio
DMol3: Combine computational speed with the accuracy
of quantum mechanical methods to predict materials
properties reliably and quickly
CASTEP: CASTEP offers simulation capabilities not
found elsewhere, such as accurate prediction of phonon
spectra, dielectric constants, and optical properties.
Simulate the properties of solids, interfaces, and
surfaces for a wide range of materials classes, including
ceramics, semiconductors, and metals.
ONETEP: Accurately treat systems such as protein-
ligand complexes, grain boundaries, and nanoclusters
with this revolutionary quantum mechanics-based
program designed specifically for calculations on large
systems (>500 atoms)
![Page 8: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/8.jpg)
F u n c t io n a l D M O L 3 C A S T E P O N E T E P
L D A ( L o c a l D e n s it y A p p r o x im a t io n )
1 9 8 0 V W N (V o s k o -W ilk -N u s a ir ) X X
1 9 8 1 C A -P Z ( C e p e r le y -A ld e r -P e r d e w -Z u n g e r ) X X
1 9 9 2 P W C (P e r d e w -W a n g ) X
G G A ( G e n e r a liz e d G r a d ie n t A p p r o x im a t io n )
1 9 8 8 B P ( B e c k e -P e r d e w ) X
1 9 8 8 B L Y P (B e c k e , L e e - Y a n g -P a r r ) X X
1 9 9 2 P W 9 1 (P e r d e w a n d W a n g ) X X X
1 9 9 2 V W N -B P (V o s k o -W i lk -N u s a ir , B e c k e -P e r d e w ) X
1 9 9 6 P B E (P e r d e w -B u r k e -E r n z e r n o f ) X X X
1 9 9 8 R E V P B E X
1 9 9 9 B O P X
1 9 9 9 R P B E (R e v is e d P e r d e w - B u r k e -E r n z e r n o f ) X X X
2 0 0 1 H C T H X
2 0 0 4 X L Y P X
2 0 0 6 W C X X
2 0 0 8 P B E S O L X
H y b r id s
B 3 L Y P ( B e c k e 3 , L e e - Y a n g -P a r ) X X
P B E 0 ( P e r d e w - B u r k e -E r n z e r n o f ) X
V a n d e r W a a ls F u n c t io n a ls
2 0 0 4 V D W -D F X
2 0 1 0 V D W -D F 2 X
2 0 1 0 o p t P B E X
2 0 1 0 o p t B 8 8 X
2 0 1 0 V D W -D F K X
DMOL3, CASTEP and ONETEP. XC Funtionals
![Page 9: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/9.jpg)
DMOL3, CASTEP and ONETEP. Basis Function
• Gaussian: Gaussian and Slater Type Orbitals (GTO and STO), i.e. 6-311G*
• DMOL3: Numerical Basis Set. Small BSSE and best performance than GTO X No systematic way to improve basis set quality and careful tests required to
construct a basis set
• CASTEP: Plane wave basis set. Good description of periodic systems, no BSSE, mathematically simple. A
single parameter controls convergence of the basis (Energy cutoff) X Need many functions to converge result. They provide the same accuracy
at all points in space even if there is no electronic density there (pseudopotential approach addresses these issues). The periodicity is mandatory (supercell for isolated molecules).
• ONETEP: non-orthogonal generalized Wannier functions (NGWFs). Linear scaling X It is still under development
![Page 10: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/10.jpg)
DMOL3. Basis Function
NUMERICAL BASIS FUNCTION
![Page 11: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/11.jpg)
CASTEP and ONETEP. Plane waves
Ecut-off ~ Number of plane waves
![Page 12: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/12.jpg)
DMOL3, CASTEP and ONETEP. Interface in Materials Studio.
![Page 13: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/13.jpg)
DMOL3 - Calculation
![Page 14: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/14.jpg)
DMOL3 - Electronic
![Page 15: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/15.jpg)
DMOL3 - Properties
![Page 16: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/16.jpg)
DMOL3 – Job Control
![Page 17: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/17.jpg)
DMOL3, CASTEP and ONETEP. Tasks
Task DMOL3 CASTEP ONETEP
Energy Single Point X X X Geometry Optimization X X X
Dynamics X X TS Search X X X
TS Optimization X TS Confirmation X X Elastic Constant X X
![Page 18: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/18.jpg)
DMOL3, CASTEP and ONETEP. Properties
![Page 19: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/19.jpg)
DMOL3, CASTEP and ONETEP. Properties
![Page 20: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/20.jpg)
Example: n-butane conformations
gauche- (~60º)
trans (~180º)
gauche+ (~300º)
![Page 21: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/21.jpg)
gauche- (~60º)
trans (~180º)
Experimental (gas phase) = 0.660 ± 0.022 kcal/mol High-level ab-initio QM = 0.59 - 0.68 kcal/mol (MP2, CCSD(T),…)
DMOL3 (LDA/DND) = 0.18 kcal/mol DMOL3 (BLYP/DND) = 0.76 kcal/mol DMOL3 (BLYP/TNP) = 0.91 kcal/mol DMOL3 (BLYP/TNP, ZPE) = 1.10 kcal/mol DMOL3(B3LYP/TNP) = 1.18 kcal/mol DMOL3(B3LYP/DNP+) = 0.73 kcal/mol CASTEP (B3LYP,680eV) = 0.78 kcal/mol CASTEP (PW81,680eV) = 0.86 kcal/mol ONETEP (PW81,700eV) = 0.72 kcal/mol ONETEP (BLYP,700eV) = 0.74 kcal/mol
a) M.J. Hafezi, F. Sharif Journal of Molecular Structure: THEOCHEM 814 (2007) 43–49
b) D. Gruzman, A. Karton, and J.M. L. Martin, J. Phys. Chem. A 113 (2009) 11974–11983
Example: n-butane conformations
Energy trans-gauche conformations
![Page 22: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/22.jpg)
MP2/
6-311G(2df-p) a)
LDA/
DND
BLYP/
TNP
BLYP/
DNP+ Exp (gauche)b)
C1-C2 (A) 1.522 (1.524) 1.508 (1.510) 1.539 (1.540) 1.538 (1.540) 1.530
C2-C3 (A) 1.522 (1.526) 1.510 (1.514) 1.539 (1.544) 1.540 (1.544) 1.532
C1-C2-C3 (º) 112.6 (113.5) 112.8 (113.1) 113.4 (114.7) 113.3 (114.2) 113.3
C1-C2-C3-C4 (º) 180.0 (62.7) 180.0 (62.5) 180.0 (65.4) 180.0 (66.4) 62.8
a) M.J. Hafezi, F. Sharif Journal of Molecular Structure: THEOCHEM 814 (2007) 43–49
b) W.F. Bradford, S. Fjtzwater, L.S. Bartell, J. Mol. Struct. 38 (1977) 185.
Example: n-butane conformations
Geometry trans and gauche conformations
![Page 23: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/23.jpg)
DMOL3(B3LYP/TNP)
f
DEgt (kcal/mol) = 1.16 CCSD(T)-CB:0.628b
DE#gt (kcal/mol) = 3.70 CCSD(T)-CB:3.303b
DE#ct (kcal/mol) = 6.07 CCSD(T)-CB:5.400a
a
b
Example: n-butane conformations
Scan Potential Energy Surface
![Page 24: Herramientas mecano-cuánticas basadas en DFT para el ...digital.csic.es/bitstream/10261/108172/1/Presentacion_MS_cJ_v01.pdf · Herramientas mecano-cuánticas basadas en DFT para](https://reader031.fdocument.pub/reader031/viewer/2022021820/5aef5dee7f8b9abc788beaf6/html5/thumbnails/24.jpg)
Example: n-butane conformations
Infrared Spectra DMOL3(BLYP/DNP+)