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1 Introduction

UNO-CAS

FRET

SHG in membranes

Very large scale MO

SAMFETs

Electronic Properties of Flexible Systems

Tim ClarkCentre for Molecular DesignUniversity of Portsmouth

Tim.Clark@port.ac.ukComputer-Chemie-Centrum andExcellence Cluster Engineering of Advanced MaterialsFriedrich-Alexander-Universitt Erlangen-NrnbergTim.Clark@chemie.uni-erlangen.de2AcknowledgementsDr. Harry LanigDr. Frank BeierleinDr. Catalin RusuDr. Matthias HennemannDr. Christof JgerDr. Olaf OthersenPavlo Dral M.Sc.

Prof. Siegfried Schneider (FRET)Prof. Carola Kryschi (SHG)Prof. Nigel Richards (EMPIRE)Prof. Markus Halik (SAMFETs)

Deutsche Forschungsgemeinschaft (DFG)Bavarian State Government (KONWIHR)

Introduction

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Cant do large systemsNo good for charge transferModeling3

The HamiltonianForce field no electronics, but good sampling and geometriesSemiempirical MO/CICC-DFTB/TD-CC-DFTBDFT/TDDFTAb initioSAMPLING !!!!Molecular dynamicsQM/MM electronics Introduction

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Semiempirical MO TheoryIs very fastCan therefore handle either very large systems or very many smaller onesGenerally gives very good one-electron propertiesbecause the semiempirical electron density is good because the parameterization probably used a related propertyBecause the MEP is good, solvent effects are also goodSemiempirical CI is good for excited statesAlso better for frontier orbital energies than higher levels of theoryIs therefore ideal for calculating the properties of many hot geometries (snapshots) from MD simulations to obtain ensemble properties4 Introduction

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TopicsUNO-CAS for Band GapsSimulating FRET in Biological SystemsSimulating SHG in Biological MembranesEMPIRE Very Large massively parallel Semiempirical MO calculationsSelf-Assembled Monolayer Field-Effect Transistors (SAMFETs)

5 Introduction

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Semiempirical UNO-CAS for Optical Band GapsPavlo Dral6

Introduction

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UNO-CASUHF Natural Orbital Complete Active Space configuration interaction

J. M. Bofill and P. Pulay, J. Chem. Phys. 1989, 90, 3637.

Semiempirical UNO-CAS and UNO-CI: Method and Applications in Nanoelectronics, P. O. Dral and T. Clark, J. Phys. Chem. A, 2011, 115, asap (DOI: 10.1021/jp204939x).

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UHF Natural Orbitals (UNOs)Diagonalize the total ( + ) UHF density matrixThe eigenvectors are the UHF Natural orbitals and the Eigenvalues are the UNO occupation numbers (0 or 2 for RHF, partial values between 0 and 2 for UHF)Significant Fractional Occupation Numbers (SFONs) between 0.02 and 1.98 define the active space8 Introduction

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AdvantagesThe active space defined by the SFONs is usually small enough to allow a full CI calculation (UNO-CAS)A CI-Singles (CIS) or CISD approach can be used for larger active spacesThe active space is defined automaticallyUNOs contain some multi-reference information derived from the components of the UHF wavefunction9 Introduction

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DisadvantagesIt is sometimes very difficult to find the correct UHF wavefunction (there may be many solutions close in energy)Only applicable for systems that exhibit RHF/UHF instability (symmetry breaking)10 Introduction

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Calculated Band Gaps: Polyynes11

Introduction

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Polyacene band gaps12

Introduction

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Optical PropertiesTwo examplesFluorescence resonant energy transfer (FRET) in TetR (S. Schneider)Second-harmonic generation (SHG) by dyes in biological membranes (C. Kryschi)

A Numerical Self-Consistent Reaction Field (SCRF) Model for Ground and Excited States in NDDO-Based Methods, G. Rauhut, T. Clark and T. Steinke, J. Am. Chem. Soc., 1993, 115, 9174.

NDDO-Based CI Methods for the Prediction of Electronic Spectra and Sum-Over-States Molecular Hyperpolarizabilities, T. Clark and J. Chandrasekhar, Israel J. Chem., 1993, 33, 435.

A Semiempirical QM/MM Implementation and its Application to the Absorption of Organic Molecules in Zeolites, T. Clark, A. Alex, B. Beck, P. Gedeck and H. Lanig, J. Mol. Model. 1999, 5, 1. Introduction

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FRET in the Tetracycline RepressorFrank Beierlein, Prof. Siegfried Schneider, Harry Lanig, Olaf Othersen14Simulating FRET from Tryptophan: Is the Rotamer Model Correct? ,

F. R. Beierlein, O. G. Othersen, H. Lanig, S. Schneider and T. Clark, J. Am. Chem. Soc. , 2006 , 128 , 5142-5152. Introduction

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FRET (SFB 473)Tryptophan

Tetracycline

One monomer of the Tetracycline Repressor (TetR) Protein Introduction

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The Experimental ProblemFluorescence decay in the protein is biexponentialUsually treated using the rotamer modelEach individual exponential decay process can be attributed to a corresponding tryptophan rotamerDifferences in distance and, above all orientation, relative to the acceptor (tetracycline) give different decay rates (Frster theory)Is this model correct? Introduction

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Chromophores

TryptophanTwo low-lying excited states1La, polar, solvent sensitive, usually the emitting state (~350nM)1Lb, non-polarTetracycline:Mg2+BCD ChromopohoreAbsorption overlaps with tryptophan emission, making FRET possible Introduction

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Glycyltryptophan Absorbance Spectra (H2O)

Experimental SCRF ( = 78.36) QM/MM (explicit water) Introduction

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Tryptophan Transition Dipoles

From above the ringIn the ring plane10% of the calculated snapshots shown Introduction

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Rotamer Distribution

Introduction

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Einstein Coefficients (no FRET) Total Rotamer 1 Rotamer 2 Introduction

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FRET Rate Constants (Frster theory) Total Rotamer 1 Rotamer 2 Introduction

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Exponential FitsTotal without FRETRotamer 1 with FRETRotamer 2 with FRETTotal with FRETNo. of Exponentials1222 (ns)4.654.03, 1.763.65, 1.703.94, 1.74Coefficient(s) (%)10057, 4366, 3359, 41Fit for the total is approximated well by the weighted average of the parameters for the individual rotamers, not as two individual decay components. Introduction

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FRET ConclusionsIndividual rotamers with significant lifetimes can be identified in the MD simulationsIncluding FRET makes the decay curves biexponential for each rotamerBiexponentiality is caused by the distribution of the FRET rates, rather than by individual rotamersSpectroscopic Ruler distances may be in error by as much as 6 if the orientation factor is not considered explicitly

Simulating FRET from Tryptophan: Is the Rotamer Model Correct?, F. R. Beierlein, O. G. Othersen, H. Lanig, S. Schneider and T. Clark, J. Am. Chem. Soc., 2006, 128, 5142-5152. Introduction

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SHG in Biological MembranesCatalin Rusu, Prof. Carola Kryschi, Harry Lanig25Monitoring Biological Membrane-Potential Changes: a CI QM/MM Study

C. Rusu, H. Lanig, T. Clark and C. Kryschi, J. Phys. Chem. B , 2008 , 112 , 2445-2455 Introduction

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SHG in MembranesSecond-harmonic generation (SHG) has been used recently to monitor action potentials (AP) in cardiomyocytes or neuronsThe intensity of the SHG (ISHG) is monitored as a function of the trans-membrane potentialDi-8-ANEPPS was used as a typical lipophilic dye that is incorporated into the membraneThe simulation system consisted of one dye molecule, 63 DPCC lipid molecules and 3,840 water molecules

Introduction

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The Simulation System

Water: blue Lipids: green (head groups bold) Dye: red GROMOS force field with optimized Lennard-Jones parameters for lipids Periodic boundary conditions PME electrostatics, NPT ensemble 10 ns equilibration + 10 ns production MD 700 snapshots per trajectory (last 7 ns of the production phase) Introduction

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QM-CI/MM SnapshotsDi-8-ANEPPS used as the QM-part (chromophore, 91 atoms)MM surroundings (DCCP + water) consisted of 14,700 atoms18 active orbitals18 active electronsSingle + pair-double excitationsQM/MM = 4.0Excitation energy = 1.17 eV (for sum-over-states ) Introduction

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Trans-Membrane PotentialExternal potential applied to the QM-CI/MM calculationsChange in dye dipole moment in vacuo used to calibrate the systemExternal potential then adjusted to give a local potential at the dye of 0.1 VThree calculations at +0.1, 0.0 and 0.1 V for each snapshotTotal simulated AP is therefore 0.2 V (about twice as large as in the experiment) Introduction

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Dye Vertical Stability

Introduction

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Calculated ISHG (V = 0.2V)Simulation 1: ISHG = 41.6 11.1 %Simulation 2: ISHG = 43.2 13.0 %Experiment: ISHG 40 % Introduction

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SHG ConclusionsThe qualitative picture of the dye in the membrane is correct

The MD simulations give lateral diffusion rates several orders of magnitude higher than those deduced from experimentForce-field problem (van der Waals)?Experimental interpretation ?

SHG enhancement of the order found in the experimental studies is also found in the simulations

C. F. Rusu, H. Lanig, O. G. Othersen, C. Kryschi and T. Clark, to be submitted to J. Am. Chem. Soc. (2007) Introduction

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EMPIRE: A Very Large Scale Parallel Semiempirical SCF ProgramMatthias Hennemann33

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Develop a completely new semiempirical MO Program (EMPIRE) ; design specifications:Neither LMO nor D&CNeed to treat conjugated systemsMassively parallel:SCF50,000 Atoms using 1,000 coresConfiguration Interaction (CI)5,000 Atoms using 1,000 coresProgramDirect on-the-fly calculation of the 2-electron integrals and the one-electron matrixAvoid matrix diagonalization

34The Big Hammer Approach Introduction

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Comparison with VAMP35

910 Atoms1,960 Orbitals

VAMP11 Cycles59 Seconds(1 Core)

EMPIRE16 Cycles58 Seconds(1 Core)7.8 Seconds(12 Cores)

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Scaling on one Node36Dual-Hex-Core Xeon 5650 Westmere 2.66 GHz (@ 2.93 GHz) with 12 MB cache per chip und 24 GB RAM.

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Benchmark results: Adamantane 66637

11,232 Atoms24,192 Orbitals

412 Cores:78.4 Minutes

812 Cores:44.3 Minuten

1612 Cores:25.6 Minuten

22 Cycles Introduction

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Benchmark-Results: HLRB II38

HLRB II: 9,728 Cores - 512 per Partition: 1.6 GHz dual core Itanium 2 Montecito, 4 GB RAM per Core, NUMAlink 4 with 6,4 GByte/s per link und direction Introduction

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Hard Scaling (LiMa)39

LiMa500 Dual-Hex-Core Xeon 5650 Westmere 2,66 GHz (@ 2.93 GHz) 12 MB Cache per Chip24 GB RAM per NodeInfiniband with 40 Gbit/s per link and direction Introduction

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0

molecular scale electronic devices with pure and mixed SAMs relation of device characteristics on molecular structure and SAM composition SAMs as important dielectric and bifunctional layers in condensers and FETsApplication: Organic Field-Effect Transistors Introduction

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Nr.Application: Organic Field-Effect Transistors41Constructed of self-assembled monolayers (SAMs)Head groups such as fullerenes can function as the semiconductorNo additional semiconductor layer necessaryProperties vary widelyCan an adequate permanent semiconductor layer be attained?Classical MD simulations with AM1 single-points on snapshotsProf. Marcus Halik

C10PA + C60C18PA

C60C18PA Introduction

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C10PA + C60C18PA - Monolayer42

6,050 Atoms15,950 Orbitals

25 Minutes(812 Cores)

36 Cycles

At the moment:50 Snapshots Introduction

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Local Electron Affinity (EAL)43

Introduction

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Section through the SAM (EAL)44

Introduction

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Section through the SAM (EAL)45

Introduction

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