GridChemA Computational Chemistry

Cyber-infrastructure

Sudhakar PamidighantamNCSA, University of Illinois at Urabana

Champaignsudhakar@ncsa.edu

Acknowledgements

Outline

• Historical Background

• Current Status

• Science Stories

• Future

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

Extended TeraGrid Facility

www.teragrid.org

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

Current Grid Status

Grid Hardware

Middleware

Scientific Applications

InterfacesInterfaces

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 …..

Gridchem Middleware

Web Services Oriented

Job Editor

Job Monitoring

Resource Status

Gradient Monitoring

Energy Monitoring

Visualization

Molecular Visualization

Electronic Properties

Spectra

Vibrational Modes

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

Some example VisualsArginine Gamess/6-31G*Total electronic density

2D - Slices

Electron Density in 3DInteractive (VRML)

Orbital 2D DisplaysN2 6-31g* Gamess

Orbital 3DVRML

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

Unsymmetrical Mo(CO)4 Crown Ethers

Dibenzaphosphepin based bis(phosphorous)polyether chelated Mo(CO)4

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

Reference Structure for Comparison

Starting Structure

Optimized Structure

Reference Structure for Comparison

8

7

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

MD OCH2CH2O Structure

8

7

MD Biaryl Structure

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

Acknowledgements

Job Monitoring

Vacuum MD

Vacuum MD

Vacuum MD

Third Year Plans

• Post Processing

• New Application Support

• Expansion of Resources

• Extension Plan