gridchem a computational chemistry cyber-infrastructure sudhakar pamidighantam ncsa, university of...
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GridChemA Computational Chemistry
Cyber-infrastructure
Sudhakar PamidighantamNCSA, University of Illinois at Urabana
Champaignsudhakar@ncsa.edu
MotivationSoftware - 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
Background
Qauntum Chemistry Remote Job Monitor( Quantum Chemistry Workbench)1998, NCSA
Chemviz1999-2001, NSF
TechnologiesWeb Based Client Server ModelsVisual InterfacesDistributed computing
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
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
User Community
Chemistry and Computational Biology
User BaseSep 03 – Oct 04
NRAC AAB Small Allocations
-------------------------------------------------------------
#PIs 26 23 64
#SUs 5,953,100 1,374,100 640,000
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
Computational Chemistry Grid
Integrated Cyber Infrastructure for Computational Chemistry
Integrates Applications, Middleware, HPC
resources, Scheduling and Data
management
Allocations, User Services and Training
Resources• Over 400 processors and 3,525,000 CPU hours available annually
System (Site) Procs Avail Total CPU Hours/Year
HP Intel Cluster (OSC) 12 100,000
Intel Cluster (OSC) 36 315,000
Intel Cluster (UKy) 96 840,000
HP Integrity Superdome 33 290,000
Intel Cluster (NCSA) 64 560,000
SGI Origin2000 (NCSA)IA32 Linux Cluster
12864
1,000,000560,000
Intel Cluster (LSU)Intel Cluster (LSU)
321024
280,0001,000,000
IBM Power4 (TACC) 16 140,000
Teragrid 30,000
Other Resources
Extant HPC resources at various
Supercomputer Centers (Interoperable)
Optionally Other Grids and Hubs/local/personal
resources
These may require existing allocations/Authorization
Grid Middleware Proxy Server
GridChem System
user user useruser user
PPortal Clientortal Client
Grid ServicesGrid Services
GridGrid
applicationapplicationapplicationapplication
Mass Storage
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0438312
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 …..
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…)
Eigen Function Visualization
• Molecular Orbital/Fragment Orbital
• MO Density Visualization
• MO Density Properties
• Other functions
Radial distribution functions
Spectra
• IR/Raman Vibrotational Spectra
• UV Visible Spectra
• Spectra to Normal Modes
• Spectra to Orbitals
GridChem Use
• Allocation
Community and External Registration
• Consulting/User Services
Ticket tracking, Allocation Management
• Documentation Training and Outreach
FAQ Extraction, Tutorials, Dissemination
Users and Usage
• 160 Users Include Academic PIs, two graduate classesAnd 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 wellMore than a 1.5 Mil Normalized units during 8
months since Jan 06.
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.
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.edu
http://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.
Metalla Crown Ether Modeling Via GridChem
Sudhakar PamidighantamNCSA, University of Illinois at Urbana-Champaign
Scott Brozell Ohio Supercompter Center
Crystal Structures
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
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
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 -40.4C1-C6-C7-C12 45.4 22.3 -22.3 -72.8C13-C22-C23-C32 75.6 74.7 -85.9 -81.2C32-O-C33-C34 -178.4 -140.8 159.7 -171.2O-C33-C34-O 62.4 -64.5 -87.3 -82.4C33-C34-O-C35 -80.6 -118.9 67.8 64.9C34-O-C35-C36 174.6 118.9 -153.4 60.1O-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
1H NMR Chemical Shift ComparisonFor Aromatic Protons
Reference 32ppm (from TMS B3LYP/6-31g*)Atom Exp. Abinitio Atom Exp. AbinitioH2 7.025 5.6 H25 6.578 5.7H3 7.026 5.8 H26 6.737 5.9H4 7.049 5.9 H27 7.018 6.1H5 7.181 6.0 H28 7.623 6.5
H8 7.110 6.1 H30 7.790 6.7H9 6.890 6.0 H31 7.289 6.9H10 6.721 6.0H11 6.237 5.7 H38 7.327 6.2
H39 7.274 6.1H14 7.925 5.8 H40 7.169 6.0H15 7.808 6.3 H41 7.350 6.3
H17 7.741 6.0 H44 7.360 6.1H18 7.254 5.6 H45 7.160 5.9H19 7.091 5.1 H46 7.176 6.0H20 6.989 4.6 H47 7.060 7.0
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 149.85 124.0C2 121.98 97.3 C18 124.74 96.5 C38 122.33 99.5C3 128.92 101.3 C19 126.15 99.9 C39 129.50 103.0C4 125.10 97.4 C20 126.13 99.5 C40 125.57 99.9C5 129.95 105.5 C21 134.08 108.9 C41 130.14 103.2C6 129.93 105.0 C22 123.88 92.9 C42 130.19 106.8C7 129.73 106.3 C23 118.62 104.5 C43 129.59 105.2C8 129.13 102.8 C24 134.02 101.9 C44 129.95 103.9C9 125.05 99.5 C25 125.05 100.0 C45 125.45 98.1C10 128.81 103.1 C26 126.10 99.4 C46 129.50 101.3C11 122.28 99.5 C27 123.06 101.0 C47 122.26 101.1C12 148.00 122.2 C28 127.62 103.2 C48 150.22 129.6C13 147.66 128.5 C29 128.88 103.2C14 121.06 95.9 C30 129.53 103.2C15 128.56 102.6 C31 114.35 98.6C16 130.65 101.0 C32 154.31 125.5
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).
31P and 95Mo Chemical Shifts
17O Chemical Shiftsfor Phosphonite/Ether Oxygens*
B3LYP/3-21G*(BPW91)
P-O-Ph Shielding Chemical ShiftO 8 162.3(147.7) 154.3(168.9)O 9 171.5(155.8) 145.1(160.8)O 10 153.9(139.4) 162.7(177.2) (Naphthyl)O 11 162.7(147.8) 153.9(168.8)O 12 171.7(156.1) 144.9(160.5)P-O-CO95 201.9(189.5) 114.7(127.1)Napth-O_CO57 215.1(202.8) 101.5(113.8)C-O-CO92 287.0(279.5) 29.6( 37.1)
With reference to B3LYP/6-31g* H2O 316.6
17O Chemical Shifts B3LYP/3-21G*(BPW91)
Carbon Monoxide Oxygens
Shielding Const. Chemical Shift*
O 4 -79.4(-61.5) 396.0(378.1)
O 5 -85.8(-68.1) 402.4(384.7)
O 6 -61.0(-42.8) 376.6(359.4)
O 7 -73.1(-55.5) 389.7(372.1)
*with reference to H2O(B3LYP/6-31G*) 316.6 ppm
Summary
• Mo Crown Ethers are tricky to converge in standard DFT and HF Methods due to degenerate set of states and fluxional crown ether moieties
• GridChem can be successfully used to access resources and applications for computational chemistry
Acknowledgments
• Rion Dooley• Stelios Kyriacou• Chona Guiang• Kent Milfeld• Kailash Kotwani• Antitsa Stoycheva• Terry Lang• Tack Kuntz, UCSF
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