Presentation is loading. Please wait.

Presentation is loading. Please wait.

Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009.

Published byBeverly Gallagher Modified over 4 years ago

Similar presentations

Presentation on theme: "Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009."— Presentation transcript:

1 Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

2 The tautomerization of cytosine presents unsolved questions
Background: The tautomerization of cytosine presents unsolved questions This process can only occur with the aid of WATER. Ergo: water can be an important catalyst Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

3 Challenge for theory: completely different electronic structures!
What is TAUTOMERISM? intramolecular proton transfer, a special form of isomerism Prototype case: Challenge for theory: completely different electronic structures! Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

4 one of the four bases in DNA
What is CYTOSINE? one of the four bases in DNA Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

5 Significance in biological systems:
All four nucleotide bases are prototypes of molecules with many possible tautomeric forms If tautomerization occurs, this would totally destroy the hydrogen bond structure of the double helix  mutation Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

6 1: the “canonical” oxo form; 2b: enol; 3a: imino
The challenge 1: the “canonical” oxo form; 2b: enol; 3a: imino Theoretical results, e.g.: CCSD(T)[f.c.]/cc-pVTZ// rfg Watch out, black-box users!: DFT gives a qualitatively different picture! 1 2b 3a B3LYP/ G(2d,2p): B3PW91/ G(2d,2p): Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

7 Section 1. Test calculations
Check the reliability of several methods on small molecules. Test calculations on three systems: Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

8 Vinylalcohol Acetaldehyde
Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

9 Acetaldimine Vinylamine
Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

10 Formamide Formamidic acid
Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

11 Methods Electronic theory: RHF, B3LYP, MP2, CCSD(T) Basis sets:
from G(d,p) to G(3df, 3pd) from cc-PVTZ to aug-cc-PV5Z Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

12 Acetaldehyde – Vinylalcohol Tautomer Pair
Test 1. Acetaldehyde – Vinylalcohol Tautomer Pair a In calculations with Pople-type basis sets (6-31…) geometries and energies calculated at the same level. b E in atomic units. Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

13 Acetaldehyde – Vinylalcohol Tautomer Pair Contnd.
C Geometry selected as standard: MP2/aug-PVTZ Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

14 Acetaldimine - Vinylamine pair, incl. Trans. State
Test 2. Acetaldimine - Vinylamine pair, incl. Trans. State _________________________________________ a Energy relative to vinylamine Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

15 Acetaldimine - Vinylamine contnd.
______________________________________________________ aEnergy relative to vinylamine. bAt MP2/aug-PVTZ geometry. Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

16 Formamide – Formamidic acid
Test 3. Formamide – Formamidic acid Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

17 Formamide – Formamidic acid, contnd.
Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

18 CONCLUSIONS ON THE TESTS:
_________________________________________________________________ (Even) the best results are (un)certain to ~ 1 kcal/mol Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

19 Section 2. The effect of water
Model: supermolecule, a water molecule added explicitly Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

20 water may mediate proton transfer
Formamide plus water: water may mediate proton transfer Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

21 (Formamide – Formamidic acid) Monohydrate
Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

22 Barrier height decreased to half by water
1: b3lyp/6-31G(d,p), 2: b3lyp/ G(2d,2p) 3: MP2/6-31G(d,p), 4: MP2/aug-pVTZ, 5: CCSD/aug-PVTZ, 6: CCSD(T)/aug-PVTZ Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

23 Try to ‘see’ the process of water-mediated tautomerization
Section 3: Dynamics: Try to ‘see’ the process of water-mediated tautomerization Specifically: is there an intermediate state ? Method: ab initio dynamics* Contrary to Car-Parrinello, the wave function is truly recalculated at each point …. * Pulay, P., Fogarasi, G.: Fock matrix dynamics, CPL 386, (2004) Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

24 About ab initio dynamics
The notion of reaction mechanisms is based on the Born-Oppenheimer (B-O) approximation: atoms move on a potential energy surface (PES) defined by the electronic energy as a function of nuclear positions. In the simplest models reactions follow the minimum energy pathway (MEP), going through a transition state (TS). The MEP expressed in mass-weighted Cartesians is referred to as the internal reaction coordinate, IRC. Recent computations have shown that reactions may follow a route totally different from the IRC. (W.L. Hase, Science 2002; M. Dupuis, Science 2003). Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

25 True dynamics calculations require knowledge of the complete PES, and recent methods generate it "on the fly". The well-known Car-Parrinello method is most efficient computationally because the electronic wave function is "propagated", and not optimized, at the trajectory points. As a consequence, the system is moving close to, but not exactly on the B-O surface. In B-O dynamics, the wave function of a QC method is fully optimized in each step along the trajectory. Energy and first derivatives are determined from ab initio wf, and atomic movements calculated from them classically. This is the approach adopted here. Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

26 Dynamics procedure 1. Start geometry not too far from equilibrium
2. The atomic nuclei get a random kick such that the average kinetic energy corresponds to a selected temperature. 3. Energy and FORCES calculated from ab initio Quantum Chemistry ‘on the fly’ 4. Movement of atoms calculated classically 5. GOTO 3 Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

27 - just 200 steps per trajectory. - but: several hundred trajectories.
Actual details: - 1 fs time steps - just 200 steps per trajectory. - but: several hundred trajectories. The QC method: DFT(B3LYP)/6-31G** or: MP2/6-31G** Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

28 Formamide plus a water molecule
Formamide plus a water molecule. Snapshots from a ‘successful’ trajectory. Time step 1 fs, every 5th step shown Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

29 Formamide dynamics movie: Call PQS Two different cases:
1391c and 1397c Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

30 Section 4: Back to Cytosine
Try to ‘see’ the process of water-mediated tautomerization Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

31 Tautomerization captured!
Time range:  fs ( cf: T  10 fs for an X-H str.) Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

32 Movie .... The End Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009

Download ppt "Materials Oriented Modelling - Catalysis and Interactions in Solid and Condensed Phases Stockholm, Sweden on 28 June - 1 July, 2009."

Similar presentations

Introduction to Computational Chemistry NSF Computational Nanotechnology and Molecular Engineering Pan-American Advanced Studies Institutes (PASI) Workshop.

Introduction to Computational Chemistry NSF Computational Nanotechnology and Molecular Engineering Pan-American Advanced Studies Institutes (PASI) Workshop.
Molecular Modeling of Structure and Dynamics in Fuel Cell Membranes A. Roudgar, Sudha N.P. and M.H. Eikerling Department of Chemistry, Simon Fraser University,

Molecular Modeling of Structure and Dynamics in Fuel Cell Membranes A. Roudgar, Sudha N.P. and M.H. Eikerling Department of Chemistry, Simon Fraser University,
Transfer FAS UAS SAINT-PETERSBURG STATE UNIVERSITY COMPUTATIONAL PHYSICS Introduction Physical basis Molecular dynamics Temperature and thermostat Numerical.

Transfer FAS UAS SAINT-PETERSBURG STATE UNIVERSITY COMPUTATIONAL PHYSICS Introduction Physical basis Molecular dynamics Temperature and thermostat Numerical.
Hydrates of Cytosine: The Order of Binding Water Molecules Géza Fogarasi, Péter G. Szalay Institute of Chemistry, Eötvös Loránd University, Budapest, H-1518,

Hydrates of Cytosine: The Order of Binding Water Molecules Géza Fogarasi, Péter G. Szalay Institute of Chemistry, Eötvös Loránd University, Budapest, H-1518,
Potential Energy Surface. The Potential Energy Surface Captures the idea that each structure— that is, geometry—has associated with it a unique energy.

Potential Energy Surface. The Potential Energy Surface Captures the idea that each structure— that is, geometry—has associated with it a unique energy.
CHE-30042 Inorganic, Physical & Solid State Chemistry Advanced Quantum Chemistry: lecture 4 Rob Jackson LJ1.16, 01782 733042

CHE Inorganic, Physical & Solid State Chemistry Advanced Quantum Chemistry: lecture 4 Rob Jackson LJ1.16,
New questions about Tautomerism in Cytosine Quantum chemical and matrix isolation spectroscopic studies Géza Fogarasi Research Laboratory of Theoretical.

New questions about Tautomerism in Cytosine Quantum chemical and matrix isolation spectroscopic studies Géza Fogarasi Research Laboratory of Theoretical.
Computational Chemistry

Computational Chemistry
Ab initio Calculations of Interfacial Structure and Dynamics in Fuel Cell Membranes Ata Roudgar, Sudha P. Narasimachary and Michael Eikerling Department.

Ab initio Calculations of Interfacial Structure and Dynamics in Fuel Cell Membranes Ata Roudgar, Sudha P. Narasimachary and Michael Eikerling Department.
Case Studies Class 5. Computational Chemistry Structure of molecules and their reactivities Two major areas –molecular mechanics –electronic structure.

Case Studies Class 5. Computational Chemistry Structure of molecules and their reactivities Two major areas –molecular mechanics –electronic structure.
Molecular Simulation. Molecular Simluation Introduction: Introduction: Prerequisition: Prerequisition: A powerful computer, fast graphics card, A powerful.

Molecular Simulation. Molecular Simluation Introduction: Introduction: Prerequisition: Prerequisition: A powerful computer, fast graphics card, A powerful.
Overview of Simulations of Quantum Systems Croucher ASI, Hong Kong, December 7 2005 Roberto Car, Princeton University.

Overview of Simulations of Quantum Systems Croucher ASI, Hong Kong, December Roberto Car, Princeton University.
Potential Energy Surfaces

Potential Energy Surfaces
Chapter 2 Chemical Foundations.

Chapter 2 Chemical Foundations.
ChE 452 Lecture 15 Transition State Theory 1. Conventional Transition State Theory (CTST) 2 TST  Model motion over a barrier  Use stat mech to estimate.

ChE 452 Lecture 15 Transition State Theory 1. Conventional Transition State Theory (CTST) 2 TST  Model motion over a barrier  Use stat mech to estimate.
Computational Chemistry. Overview What is Computational Chemistry? How does it work? Why is it useful? What are its limits? Types of Computational Chemistry.

Computational Chemistry. Overview What is Computational Chemistry? How does it work? Why is it useful? What are its limits? Types of Computational Chemistry.
Objectives of this course

Objectives of this course
Molecular Modeling Fundamentals: Modus in Silico C372 Introduction to Cheminformatics II Kelsey Forsythe.

Molecular Modeling Fundamentals: Modus in Silico C372 Introduction to Cheminformatics II Kelsey Forsythe.
Geometry Optimisation Modelling OH + C 2 H 4 *CH 2 -CH 2 -OH CH 3 -CH 2 -O* 3D PES.

Geometry Optimisation Modelling OH + C 2 H 4 *CH 2 -CH 2 -OH CH 3 -CH 2 -O* 3D PES.
$200 $400 $600 $800 $1000 $200 $400 $600 $800 $1000 $200 $400 $600 $800 $1000 $200 $400 $600 $800 $1000 HeatIdeal GasesKinetics / Equilibrium Oxidation.

$200 $400 $600 $800 $1000 $200 $400 $600 $800 $1000 $200 $400 $600 $800 $1000 $200 $400 $600 $800 $1000 HeatIdeal GasesKinetics / Equilibrium Oxidation.

Similar presentations

Ads by Google