1. 1 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs Electronic Properties of Flexible Systems Tim Clark Centre for Molecular Design University of Portsmouth Tim.Clark@port.ac.uk Computer-Chemie-Centrum and Excellence Cluster “Engineering of Advanced Materials” Friedrich-Alexander-Universität Erlangen-Nürnberg Tim.Clark@chemie.uni-erlangen.de

2. 2 Acknowledgements Dr. Harry Lanig Dr. Frank Beierlein Dr. Catalin Rusu Dr. Matthias Hennemann Dr. Christof Jäger Dr. Olaf Othersen Pavlo 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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

3. Can‘t do large systems No good for charge transfer Modeling 3 The Hamiltonian –Force field – no electronics, but good sampling and geometries –Semiempirical MO/CI –CC-DFTB/TD-CC-DFTB –DFT/TDDFT –Ab initio SAMPLING !!!! –Molecular dynamics –QM/MM electronics Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

4. Semiempirical MO Theory Is very fast –Can therefore handle either very large systems or very many smaller ones Generally gives very good one-electron properties –because the semiempirical electron density is good –because the parameterization probably used a related property –Because the MEP is good, solvent effects are also good Semiempirical CI is good for excited states –Also better for frontier orbital energies than “higher” levels of theory Is therefore ideal for calculating the properties of many “hot” geometries (snapshots) from MD simulations to obtain ensemble properties 4 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

5. Topics UNO-CAS for Band Gaps Simulating FRET in Biological Systems Simulating SHG in Biological Membranes EMPIRE – Very Large massively parallel Semiempirical MO calculations Self-Assembled Monolayer Field-Effect Transistors (SAMFETs) 5 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

6. Semiempirical UNO-CAS for Optical Band Gaps Pavlo Dral 6 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

7. UNO-CAS UHF 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). 7 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

8. UHF Natural Orbitals (UNOs) Diagonalize the total (  +  ) UHF density matrix The 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 space 8 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

9. Advantages The 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 spaces The active space is defined automatically UNOs contain some multi-reference information derived from the components of the UHF wavefunction 9 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

10. Disadvantages It 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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

11. Calculated Band Gaps: Polyynes 11 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

12. Polyacene band gaps 12 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

13. Optical Properties Two examples –Fluorescence 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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

14. FRET in the Tetracycline Repressor Frank Beierlein, Prof. Siegfried Schneider, Harry Lanig, Olaf Othersen 14 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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

15. FRET (SFB 473) Tryptophan Tetracycline One monomer of the Tetracycline Repressor (TetR) Protein Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

16. The Experimental Problem Fluorescence decay in the protein is biexponential Usually treated using the “rotamer model” –Each individual exponential decay process can be attributed to a corresponding tryptophan rotamer –Differences in distance and, above all orientation, relative to the acceptor (tetracycline) give different decay rates (Förster theory) –Is this model correct? Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

17. Chromophores Tryptophan Two low-lying excited states 1 L a, polar, solvent sensitive, usually the emitting state (~350nM) 1 L b, non-polar Tetracycline:Mg 2+ “BCD” Chromopohore Absorption overlaps with tryptophan emission, making FRET possible Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

18. Glycyltryptophan Absorbance Spectra (H 2 O) - Experimental - SCRF ( = 78.36) - QM/MM (explicit water) Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

19. Tryptophan Transition Dipoles From above the ring In the ring plane 10% of the calculated snapshots shown Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

20. Rotamer Distribution Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

21. Einstein Coefficients (no FRET) - Total - Rotamer 1 - Rotamer 2 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

22. FRET Rate Constants (Förster theory) - Total - Rotamer 1 - Rotamer 2 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

23. Exponential Fits Total without FRET Rotamer 1 with FRET Rotamer 2 with FRET Total with FRET No. of Exponentials 1222  (ns) 4.654.03, 1.763.65, 1.703.94, 1.74 Coefficient(s) (%)10057, 4366, 3359, 41 Fit for the total is approximated well by the weighted average of the parameters for the individual rotamers, not as two individual decay components. Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

24. FRET Conclusions Individual rotamers with significant lifetimes can be identified in the MD simulations Including FRET makes the decay curves biexponential for each rotamer Biexponentiality is caused by the distribution of the FRET rates, rather than by individual rotamers “Spectroscopic Ruler” distances may be in error by as much as 6 Å 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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

25. SHG in Biological Membranes Catalin Rusu, Prof. Carola Kryschi, Harry Lanig 25 Monitoring 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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

26. SHG in Membranes Second-harmonic generation (SHG) has been used recently to monitor action potentials (AP) in cardiomyocytes or neurons The intensity of the SHG (I SHG ) is monitored as a function of the trans- membrane potential Di-8-ANEPPS was used as a typical lipophilic dye that is incorporated into the membrane The simulation system consisted of one dye molecule, 63 DPCC lipid molecules and 3,840 water molecules Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

27. 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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

28. QM-CI/MM Snapshots Di-8-ANEPPS used as the QM-part (chromophore, 91 atoms) MM surroundings (DCCP + water) consisted of 14,700 atoms 18 active orbitals 18 active electrons Single + pair-double excitations  QM/MM = 4.0 Excitation energy = 1.17 eV (for sum-over- states  ) Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

29. Trans-Membrane Potential External potential applied to the QM-CI/MM calculations Change in dye dipole moment in vacuo used to calibrate the system External potential then adjusted to give a local potential at the dye of  0.1 V Three calculations at +0.1, 0.0 and  0.1 V for each snapshot Total simulated AP is therefore 0.2 V (about twice as large as in the experiment) Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

30. Dye – Vertical Stability Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

31. Calculated  I SHG (  V = 0.2V) Simulation 1:  I SHG = 41.6  11.1 % Simulation 2:  I SHG = 43.2  13.0 % Experiment:  I SHG  40 % Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

32. SHG Conclusions The 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 experiment –Force-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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

33. EMPIRE: A Very Large Scale Parallel Semiempirical SCF Program Matthias Hennemann 33 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

34. Develop a completely new semiempirical MO Program (EMPIRE) ; design specifications: Neither LMO nor D&C Need to treat conjugated systems Massively parallel: SCF 50,000 Atoms using 1,000 cores Configuration Interaction (CI) 5,000 Atoms using 1,000 cores Program Direct on-the-fly calculation of the 2-electron integrals and the one-electron matrix Avoid matrix diagonalization 34 The Big Hammer Approach Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

35. Comparison with VAMP 35 910 Atoms 1,960 Orbitals VAMP 11 Cycles 59 Seconds (1 Core) EMPIRE 16 Cycles 58 Seconds (1 Core) 7.8 Seconds (12 Cores) Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

36. Scaling on one Node 36 Dual-Hex-Core Xeon 5650 “Westmere” 2.66 GHz (@ 2.93 GHz) with 12 MB cache per chip und 24 GB RAM. Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

37. Benchmark results: Adamantane 6  6  6 37 11,232 Atoms 24,192 Orbitals 4  12 Cores: 78.4 Minutes 8  12 Cores: 44.3 Minuten 16  12 Cores: 25.6 Minuten 22 Cycles Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

38. Benchmark-Results: HLRB II 38 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 UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

39. Hard Scaling (LiMa) 39 LiMa 500 Dual-Hex-Core Xeon 5650 “Westmere” 2,66 GHz (@ 2.93 GHz) 12 MB Cache per Chip 24 GB RAM per Node Infiniband with 40 Gbit/s per link and direction Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

40. 40 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 FETs Application: Organic Field-Effect Transistors Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

41. Application: Organic Field-Effect Transistors 41 Constructed of self-assembled monolayers (SAMs) Head groups such as fullerenes can function as the semiconductor No additional semiconductor layer necessary Properties vary widely Can an adequate permanent semiconductor layer be attained? Classical MD simulations with AM1 single-points on snapshots Prof. Marcus Halik C10PA + C60C18PA C60C18PA Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

42. C 10 PA + C 60 C 18 PA - Monolayer 42 6,050 Atoms 15,950 Orbitals 25 Minutes (8  12 Cores) 36 Cycles At the moment: 50 Snapshots Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

43. Local Electron Affinity (EA L ) 43 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

44. Section through the SAM (EA L ) 44 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs

45. Section through the SAM (EA L ) 45 Introduction UNO-CAS FRET SHG in membranes Very large scale MO SAMFETs