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GridChem A Computational Chemistry Cyber-infrastructure

GridChem A Computational Chemistry Cyber-infrastructure. Sudhakar Pamidighantam NCSA, University of Illinois at Urabana Champaign sudhakar@ncsa.edu. Acknowledgements. Outline. Historical Background Current Status Science Stories Future. Motivation. Software

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GridChem A Computational Chemistry Cyber-infrastructure

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  1. GridChemA Computational Chemistry Cyber-infrastructure Sudhakar Pamidighantam NCSA, University of Illinois at Urabana Champaign sudhakar@ncsa.edu

  2. Acknowledgements

  3. Outline • Historical Background • Current Status • Science Stories • Future

  4. Motivation Software - Reasonably Mature and easy to use to address chemists questions of interest Community of Users - Need and capable of using the software Some are non traditional computational chemists Resources - Various in capacity and capability

  5. Background Qauntum Chemistry Remote Job Monitor ( Quantum Chemistry Workbench) 1998, NCSA Chemviz 1999-2001, NSF Technologies Web Based Client Server Models Visual Interfaces Distributed computing

  6. GridChem NCSA Alliance was commissioned 1998 Diverse HPC systems deployed both at NCSA and Alliance Partner Sites Batch schedulers different at sites Policies favored different classes and modes of use at different sites/HPC systems

  7. Extended TeraGrid Facility www.teragrid.org

  8. Grid and Gridlock Alliance lead to Physical Grid Grid lead to TeraGrid Homogenous Grid was planned but it was difficult to keep it homogenous Things got more complicated and we have heterogeneous grids now! Interoperability and Standards and Openness Are Critical

  9. Current Grid Status Interfaces Grid Hardware Scientific Applications Middleware

  10. User Community Chemistry and Computational Biology User Base Sep 03 – Oct 04 NRAC AAB Small Allocations ------------------------------------------------------------- #PIs 26 23 64 #SUs 5,953,100 1,374,100 640,000

  11. User Issues • New systems meant learning new commands • Porting Codes • Learning new job submissions and monitoring protocols • New proposals for time • Computational modeling became more popular and users increased • Batch queues are longer / waiting increased • Find resources where to compute - probably multiple distributed sites • Multiple proposals/allocations/logins • Authentication and Data Security • Data management

  12. Computational Chemistry Grid Integrated Cyber Infrastructure for Computational Chemistry Integrates Applications, Middleware, HPC resources, Scheduling and Data management Allocations, User Services and Training

  13. Resources • Over 400 processors and 3,525,000 CPU hours available annually

  14. Other Resources Extant HPC resources at various Supercomputer Centers (Interoperable) Optionally Other Grids and Hubs/local/personal resources These may require existing allocations/Authorization

  15. GridChem System user user user user user Portal Client application application Grid Middleware Proxy Server Grid Services MassStorage Grid http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0438312

  16. Applications • GridChem supports some apps already • Gaussian 98/03, GAMESS, NWChem, Molpro, QMCPack, Amber • Schedule of integration of additional software • ACES-2 • Crystal • Q-Chem • Wein2K • MCCCS Towhee • More …..

  17. Gridchem MiddlewareWeb Services Oriented

  18. Job Editor

  19. Job Monitoring

  20. Resource Status

  21. Gradient Monitoring

  22. Energy Monitoring

  23. Visualization Molecular Visualization Electronic Properties Spectra Vibrational Modes

  24. Molecular Visualization Better molecule representations (Ball and Stick/VDW/MS) In Nanocad Molecular Editor Third party visualizer integration Chime/VMD Export Possibilities to others interfaces Deliver standard file formats (XML,SDF,MSF,Smiles etc…)

  25. Eigen Function Visualization • Molecular Orbital/Fragment Orbital • MO Density Visualization • MO Density Properties • Other functions Radial distribution functions

  26. Some example VisualsArginine Gamess/6-31G*Total electronic density2D - Slices

  27. Electron Density in 3DInteractive (VRML)

  28. Orbital 2D DisplaysN2 6-31g* Gamess

  29. Orbital 3DVRML

  30. Spectra • IR/Raman Vibrotational Spectra • UV Visible Spectra • Spectra to Normal Modes • Spectra to Orbitals

  31. GridChem Use • Allocation Community and External Registration • Consulting/User Services Ticket tracking, Allocation Management • Documentation Training and Outreach FAQ Extraction, Tutorials, Dissemination

  32. Users and Usage • 160 Users Include Academic PIs, two graduate classes And about 15 training users • NCSA 57000 SUs + A 7 node dedicated system • UKy around 106766 SUs • OSC 13,820 SUs + A 14 node dedicated system • Usage at LSU and TACC as well More than a 1.5 Mil Normalized units during 8 months since Jan 06.

  33. Science Enabled • Chemical Reactivity of the Biradicaloid (HO...ONO) Singlet States of Peroxynitrous Acid. The Oxidation of Hydrocarbons, Sulfides, and Selenides. Bach, R. D.; Dmitrenko, O.; Estévez, C. M. J. Am. Chem. Soc. 2005, 127, 3140-3155. • The "Somersault" Mechanism for the P-450 Hydroxylation of Hydrocarbons. The Intervention of Transient Inverted Metastable Hydroperoxides. Bach, R. D.; Dmitrenko, O. J. Am. Chem. Soc. 2006, 128(5), 1474-1488. • The Effect of Carbonyl Substitution on the Strain Energy of Small Ring Compounds and their Six-member Ring Reference Compounds Bach, R. D.; Dmitrenko, O. J. Am. Chem. Soc. 2006,128(14), 4598.

  34. Science Enabled • Azide Reactions for Controlling Clean Silicon Surface Chemistry:Benzylazide on Si(100)-2 1Semyon Bocharov, Olga Dmitrenko, Lucila P. Mendez De Leo, and Andrew V. Teplyakov*Department of Chemistry and Biochemistry, UniVersity of Delaware, Newark, Delaware 19716Received April 13, 2006; E-mail: andrewt@udel.eduhttp://pubs.acs.org.proxy2.library.uiuc.edu/cgi-bin/asap.cgi/jacsat/asap/pdf/ja0623663.pdf [May  require ACS access]Acknowledgment. This work was supported by the NationalScience Foundation (CHE-0313803 and CHE-0415979). GridChemis acknowledged for computational resources and services for theselected results used in this publication.

  35. Metalla Crown Ether Modeling Via GridChem Sudhakar Pamidighantam NCSA, University of Illinois at Urbana-Champaign Scott Brozell Ohio Supercompter Center

  36. Unsymmetrical Mo(CO)4 Crown Ethers

  37. Dibenzaphosphepin based a,w-bis(phosphorous)polyether chelated Mo(CO)4

  38. Crystal Structures CSD:DEQDOS cis-Tetracarbonyl-(P,P'-(6-(2'-oxy-2-biphenyl)-3,6-dioxa-hexanolato)-bis(dibenzo (d,f)(1,3,2)dioxaphosphepine)-P,P')-molybdenum C44 H32 Mo1 O12 P2 CSD:XAPZAP cis-(6,6'-((1,1'-Binaphthyl)-2,2'-diylbis(oxy))bis(dibenzo(d,f)(1,3,2)dioxaphosp hepin))-tetracarbonyl-molybdenum(0) C48 H28 Mo1 O10 P2

  39. Reference Structure for Comparison

  40. Starting Structure

  41. Optimized Structure

  42. Reference Structure for Comparison 7 8

  43. Structural ComparisonsC-C Torsion Angles for the OCH2CH2O Fragments and for the Axially Chiral Biaryl Groups Atoms PCMODEL* UFF Ab Initio Amber C37-C42-C43-C48 -49.9 -26.4 -43.0 -40.4 C1-C6-C7-C12 45.4 22.3 -22.3 -72.8 C13-C22-C23-C32 75.6 74.7 -85.9 -81.2 C32-O-C33-C34 -178.4 -140.8 159.7 -171.2 O-C33-C34-O 62.4 -64.5 -87.3 -82.4 C33-C34-O-C35 -80.6 -118.9 67.8 64.9 C34-O-C35-C36 174.6 118.9 -153.4 60.1 O-C35-C36-0 66.2 56.0 64.0 67.3 • *Hariharasarma, et al. Organomet., 1232-1238, 2000. • Ab Initio=B3LYP/3-21G* • Amber9 ff03, GAFF, chloroform, 300K, median over 1ns MD

  44. MD OCH2CH2O Structure 7 8

  45. MD Biaryl Structure

  46. 1H NMR Chemical Shift ComparisonFor Aromatic ProtonsReference 32ppm (from TMS B3LYP/6-31g*) Atom Exp. Abinitio Atom Exp. Abinitio H2 7.025 5.6 H25 6.578 5.7 H3 7.026 5.8 H26 6.737 5.9 H4 7.049 5.9 H27 7.018 6.1 H5 7.181 6.0 H28 7.623 6.5 H8 7.110 6.1 H30 7.790 6.7 H9 6.890 6.0 H31 7.289 6.9 H10 6.721 6.0 H11 6.237 5.7 H38 7.327 6.2 H39 7.274 6.1 H14 7.925 5.8 H40 7.169 6.0 H15 7.808 6.3 H41 7.350 6.3 H17 7.741 6.0 H44 7.360 6.1 H18 7.254 5.6 H45 7.160 5.9 H19 7.091 5.1 H46 7.176 6.0 H20 6.989 4.6 H47 7.060 7.0

  47. 13C Chemical Shift ComparisonReference 190ppm (B3LYP/6-31g* TMS) Atom Exp. Abinitio Atom Exp. Abinitio Atom Exp. Abinitio C1 149.57 127.3 C17 127.78 100.3 C37 149.85 124.0 C2 121.98 97.3 C18 124.74 96.5 C38 122.33 99.5 C3 128.92 101.3 C19 126.15 99.9 C39 129.50 103.0 C4 125.10 97.4 C20 126.13 99.5 C40 125.57 99.9 C5 129.95 105.5 C21 134.08 108.9 C41 130.14 103.2 C6 129.93 105.0 C22 123.88 92.9 C42 130.19 106.8 C7 129.73 106.3 C23 118.62 104.5 C43 129.59 105.2 C8 129.13 102.8 C24 134.02 101.9 C44 129.95 103.9 C9 125.05 99.5 C25 125.05 100.0 C45 125.45 98.1 C10 128.81 103.1 C26 126.10 99.4 C46 129.50 101.3 C11 122.28 99.5 C27 123.06 101.0 C47 122.26 101.1 C12 148.00 122.2 C28 127.62 103.2 C48 150.22 129.6 C13 147.66 128.5 C29 128.88 103.2 C14 121.06 95.9 C30 129.53 103.2 C15 128.56 102.6 C31 114.35 98.6 C16 130.65 101.0 C32 154.31 125.5

  48. 31P and 95Mo Chemical Shifts P1 and P2 Are around 166ppm with a P-P Coupling of 49 Hz. Isotropic Shielding Const P1 P2 B3LYP 248.6 261.0 BPW91 251.0 265.0 Mo Isotropic Shielding Const B3LYP 1396 BPW91 1510 (Mo(CO)6) Exp. -1856 B3LYP -2350 BPW91 -2294 B3LYP Hybrid Not satisfactory; BPW91 “Pure” functionals give better results; Buehl, Chem. Eur. J., 3514 (1999).

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