Title: Computational Chemical Dynamics of Complex Systems Abstract:

Transcription

1 Title: Computational Chemical Dynamics of Complex Systems Abstract: The objective of this project is to develop and apply innovative high-performance computing techniques and simulation methods in order to address computationally challenging problems in chemical dynamics, with special emphasis on the critical problems in environmental science and chemical engineering facing the DOE and the nation. The proposal is concerned with several fundamental areas of research including thermochemical kinetics and rate constants, photochemistry and spectroscopy, chemical and phase equilibria, and heterogeneous catalysis. These areas are important for solar energy, fuel-cell technology, environmental remediation, weather modeling, pollution modeling, and atmospheric chemistry. These computationally intensive studies will be carried out with new high-throughput integrated software that we have been developing. The development of compatible, portable, scalable, and user-friendly computational tools that combine electronic structure packages with dynamics codes and efficient sampling algorithms will be continued as part of this project. The proposal features four EMSL themes: atmospheric aerosol chemistry, biological interactions and dynamics, geochemistry and subsurface science, and science of interfacial phenomena. In the field of atmospheric aerosol chemistry, we propose a study of nucleation phenomena which play a pivotal role in many atmospheric and technological processes. We propose to develop paradigm-shifting, scalable computational approaches for modeling the nucleation, structure, and properties of nanodroplets. Another aspect of our research is the development of efficient and robust methods for analytical representations of multidimensional potential energy surfaces for photochemical reactions including those of environmental and energetic importance. In the field of biological interactions and dynamics, we will study explicit polarization effects in various molecules and biochemical systems, such as protein residues and hydrogen bond complexes using re-parametrized semiempirical models and molecular mechanics force fields. We will also explore Feynman path integral methods in order to incorporate quantum effects such as tunneling and zero-point energy into the treatment of large molecules. In the field of geochemistry and subsurface science, we propose large-scale Monte Carlo simulations of silica melts. Silica plays a significant role in the chemistry and mineralogy of the Earth s crust and mantle. In the field of interfacial phenomena, we propose to provide molecular-level insights on retention mechanisms in reversed-phase liquid chromatography. These mechanisms are not well understood and there remain many open questions on bonded-phase conformation, solvent penetration, solvophobic versus lipophilic interactions, and partition versus adsorption. We are interested in studying interfacial phenomena related to heterogeneous catalysis, especially, involving transitionmetal compounds and zeolite frameworks. In particular, we plan to study the electrochemistry of water oxidation by binuclear copper and ruthenium catalysts. The water oxidation process is a difficult component of the challenge to efficiently convert solar radiation into a chemical fuel. Another area of interest is a study of nano-gold clusters in order to relate their optical and structural properties to their enhanced catalytic activity in CO oxidation. We will also develop new potential energy functions for the study of adsorption isotherms of hydrocarbons in zeolites and we will interface the new potentials with a Monte Carlo Gibbs ensemble algorithm to calculate the adsorption isotherms. In addition, substantial efforts will be put in the modeling of ion solvation and ion transport through biological membranes, geological minerals, or in electrolytes.

2 1. Project Definition [Maximum 1 page] This project involves a consortium of several faculty members and scientists at the University of Minnesota, the University of Colorado at Denver, and at the Pacific Northwest National Laboratory. In accordance with the guidelines for computationally intensive research projects, our collaborative approach provides a mechanism to engage the expertise of world-class researchers from multiple institutions to be focused on the basic and applied research projects needed to advance DOE s energy, environment, and basic research missions. The proposed work is important in many aspects. Our project in computational chemical dynamics will address several problems of high priority to EMSL, in particular, atmospheric aerosol chemistry, biological interactions and dynamics, geochemistry and subsurface science, and the science of interfacial phenomena. Recent advances in computer power and multi-scale algorithms have enabled the prospects for accurate calculations of many equilibrium and kinetic chemical properties that were recently infeasible. Nonetheless, applications to complex chemical systems, such as reactive processes in the condensed phase, remain problematic due to the lack of a seamless integration of computational methods that allow modern quantum electronic structure calculations to be combined with state-of-the-art methods for chemical thermodynamics and reactive dynamics. These problems are often exacerbated by nonvalidated methods and limited software reliability. Our success in these endeavors will facilitate EMSL s mission as a national scientific user facility that relies on continued significant progress in fundamental chemical sciences and effective use of the resulting knowledge in a broad range of applications. On the other hand, EMSL offers unique computational and collaborative opportunities for us to accomplish the goals of the present proposal. Present terascale, and eventually petascale, computational hardware and software offer the opportunity to revolutionize the scope and rate at which chemical science research can produce vital new information. The design of multi-scale models for chemical dynamics will allow one to address new challenging problems that simultaneously span a broad range of spatial and temporal domains. The proposed work will be a direct outgrowth of fundamental research previously initiated by the research teams involved in the proposal and it will continue to a more advanced level the progress made within our current Computational Grand Challenge grant (which will expire by 10/2009). We have developed protocols for calculating relevant thermodynamic and kinetic parameters and computational software for carrying out calculations based on these protocols. We have developed an array of methods for multi-time-scale simulation. The algorithms being developed are general enough to apply to a variety of problems, for example, catalysis in zeolites, catalysis on surfaces of metals and metal oxides, catalysis by and on nanoparticles, and partitioning and reactivity of aqueous solutions containing electrolytes at metal/water interfaces. In the computational photochemistry area, we have developed methods and software for excited state energies in the gas phase and we are working on those for the solution phase, as required to address condensed-phase effects on the excitation energies and couplings, couplings between excited states in the gas phase and the liquid phase, and new dynamics methods for non-born- Oppenheimer processes in the gaseous and liquid phases. 1

3 2. Proposed First Year of Work [Maximum 2 pages] The first year of work will be primarily devoted to the projects described in this section. Nucleation of Atmospheric Aerosols and Controllable Nanodroplet Structures. Nucleation phenomena play a pivotal role in many atmospheric and technological processes. Understanding how liquid particles nucleate and grow in a multi-component gaseous mixture has important practical implications from climate to nanotechnology. For instance, the formation of atmospheric aerosols that significantly impact climate and human health is governed by multi-component nucleation of species including water, sulfuric acid, ammonia (or other bases), and volatile organics (and iodide species in coastal environments) [Weber et al., 1999; Kulmala, 2003; Zhang et al., 2004; Berndt et al., 2005]. However, nucleation is the least understood process influencing the concentrations of atmospheric aerosols and cloud condensation nuclei. Atmospheric nucleation adds complexity because of acid-base reactions and of disparate timescales for the evaporation of H 2 O and H 2 SO 4. We propose here to develop paradigm-shifting, scalable computational approaches for modeling the nucleation, structure and properties on nanodroplets. We will focus on understanding recent experimental atmospheric observations which demonstrate that critical clusters found in diverse continental and marine atmospheric environments contain two H 2 SO 4 molecules [Kuang et al., 2008], and on engineering core-shell and multi-shell nanoparticles that can be used for sensing and delivery of a single molecule. Our research will not only lead to transformative advances for atmospheric and nanodroplet sciences, but our new methodologies will be applicable to nanomaterial synthesis, semiconductor manufacturing, pharmaceutics, and other application areas that involve complex nucleation processes. The proposed computational approach builds upon an extremely efficient Monte Carlo (MC) method developed by us [Chen et al., 2005] that has led to our recent successes in understanding vapor liquid nucleation pathways [e.g., Nellas et al., 2007]. The advantage of this method in studying nucleation events lies in its ability to overcome the large free energy barriers or low probabilities for clusters near the critical nucleus size through the use of self-adaptive umbrella sampling and the slow evolution inherent to microheterogeneous systems, i.e., coexistence of clusters and monomers, through aggregation-volume-bias MC concepts. We will apply our novel methodologies to understanding why a critical nucleus containing two H 2 SO 4 molecules is essential for many atmospheric nucleation processes [Kuang et al., 2008]. The evaporation rates will be computed (as is done in dynamic nucleation theory [Kathmann et al., 2008]) from selected pre-critical aggregates through variational transition state dynamical nucleation theory [Schenter et al., 1999] and ensemble-averaged variational transition state theory [Truhlar et al., 2004]. In addition, we will investigate the influence of volatile organics on aqueous nucleation pathways [Zhang et al., 2004]. In this subproject we will obtain accurate potential energies by employing electrostaticallyembedded many-body (EE-MB) theory which has been proven to be successful in the treatment of moderately large systems of non-covalently interacting particles [Dahlke and Truhlar, 2007; Sorkin et al., 2008; Dahlke et al., 2008]. EE-MB theory has been especially developed because of its suitability for large-scale parallel computation on this project. CP2K and NWChem will be used for these calculations. Multi-Scale Modeling of Chemical Transformations in Complex Environments. Multi-scale based methodologies present a natural evolution of conventional computational chemistry applications. These methods recognize the natural decomposition of the chemical system into distinct regions and the advantages, both computational and conceptual, of an integrated approach that uses different theoretical models that can be associated be associated with different parts of the overall chemical system different layers of the system. The main focus of the present multi-scale project is the development of scalable multi-scale algorithms utilizing a task pool management system that we have recently developed [Nieplocha et al., 2008]. Our initial focus will be on utilization of simple layered multi-scale ideas [Nieplocha et al., 2008; Valiev et al., 2008; Kamiya et al. 2008; Hirata et al., 2005] in conjunction with high-level coupled cluster methods. Taking an advantage of fully parallel constructs in the context of processor groups, a single-point coupled cluster-based free energy calculation has the ability to scale beyond 10 6 processors. This capability alone can be extremely useful to number of application areas 2

4 requiring the knowledge of a free energy surface to study reaction pathways, electron transfer, excited states in many different application areas. We will build prototype applications of calculating reaction rates and excited state properties in condensed phase systems. In the next step of the project more sophisticated simulations involving multiple interacting subdomains will be investigated. NWChem will be used for these calculations. Adaptive schemes will be employed for dynamics [Heyden and Truhlar, 2008], and in some cases charge response kernels will be used for further efficiency [Higashi and Truhlar, 2008]. Interfacing POLYRATE and NWChem. POLYRATE is a computer program for calculating chemical reaction rates. The latest version of POLYRATE has capabilities for variational transition state theory calculations on reactions with both tight and loose transition states. We have recently successfully parallelized this program [Zheng et al., 2008a, 2008b; Zhang et al., 2008] to perform direct dynamics in conjunction with Gaussian 03. The resulting scalability on an SGI Altix XE 1300 Linux cluster is nearly 100% for running on up to 150 processors in studies of the methyl association reaction over 8192 Monte Carlo samples per a test run. We propose to interface the POLYRATE program with the latest version of NWChem for the use in multi-scale direct dynamics calculations on EMSL s Chinook. The code will be parallelized in order to be used predominantly for large-scale parallel calculations that will scale efficiently with both the number of processors and size of problem. This parallelization work is expected to provide a good showcase for the most effective use of EMSL s computing facilities. Importing POLYRATE to EMSL s supercomputers in an efficient parallel fashion may open a new era in modeling atmospheric reactions and other environmentally important processes. Computational Photochemistry of Complex Systems. We will pursue the following avenues in computational photochemistry: (i) development and improvement of the semi-automated multiconfiguration molecular mechanics (MCMM) protocol [Kim et al., 2000; Tishchenko and Truhlar, 2009, Tishchenko et al. 2009] for constructing sets of multidimensional coupled diabatic and adiabatic potential energy surfaces; (ii) application of the new computational tools to photochemical reactions that are important in the environment and for energy. As input, MCMM calculations require potential energies and their gradients and Hessians at a selected number of nuclear geometries, called Shepard points. These will be obtained via high level ab initio calculations; in particular, using the quasi-degenerate multiconfiguration perturbation theory [Nakano, 1993], for which the diabatization procedure has been implemented [Nakamura and Truhlar, 2001]. Due to unavailability of analytical gradients and Hessians at this computational level, the gradients and Hessians need to be obtained numerically. This task is computationally expensive and will require the use of many processors in parallel, but the work is ideally suited for a CIR grant. We will create a special interface for running such large-scale calculations on EMSL s high-performance platforms most efficiently in terms of scalability and productivity. In these calculations we will use GAMESS, NWChem, and MC-TINKER. QM/MM Molecular Dynamics Modeling of Ion Solvation and Transport. Ion solvation and transport is critical to many engineering and biological processes [Kreuer, 2001; Warren and Haack, 2001; Hille, 2001; Huetz et al., 2006]. Extensive experimental and theoretical studies in recent decades have provided important insights into the molecular basis of ion solvation structures and transport mechanisms. However, many problems remain unresolved. We propose a molecular dynamics (MD) simulation of the transport of Li +, Na +, K +, Ca 2+, Cl, and NH 4 + through the ion channels of various size [Zhou et al., 2001; Dutzler et al., 2002; Wang et al., 2001] with the use of accurate potential functions evaluated at an affordable cost by means of a combination of the revisited QM/MM method taking efficiently on polarization and charge transfer effects [Lin and Truhlar, 2007; Zhang and Lin, 2008] and the recently developed electrostatically-embedded many-body expansion [Dahlke and Truhlar, 2007]. We will use our QMMM computer program in conjunction with GAMESS, NWChem, and TINKER. Other projects. Other projects (see abstract) cannot be described in detail due to space limitations. 3

5 3. References Albu, T. V.; Tishchenko, O.; Corchado, J. C.; Kim, Y.; Villà, J.; Xing, J.; Lin, H.; Higashi, M.; Truhlar, D. G MC-TINKERATE version 2008; University of Minnesota, Minneapolis. Anderson, K. E.; Siepmann, J. I.; McMurry, P. H.; Vande Vondele, J Importance of the number of acid molecules and the strength of the base for double-ion formation in (H 2 SO 4 ) m base (H 2 O) 6 clusters. Journal of the American Chemical Society, 130, Berndt, T.; Boge, O.; Stratmann, F.; Heintzenberg, J.; Kulmala, M Rapid formation of sulfuric acid particles at near-atmospheric conditions. Science, 307, Bylaska, E. J.; de Jong, W. A.; Kowalski, K.; Straatsma, T. P.; Valiev, M.; Wang, D.; Apra, E.; Windus, T. L.; Hirata, S.; Hackler, M. T.; Zhao, Y.; Fan, P.-D.; Harrison, R. J.; Dupuis, M.; Smith, D. M. A.; Nieplocha, J.; Tipparaju, V.; Krishnan, M.; Auer, A. A.; Nooijen, M.; Brown, E.; Cisneros, G.; Fann, G. I.; Frochtl, H.; Garza, J.; Hirao, K.; Kendall, R.; Nichols, R. A.; Tsemekhman, K.; Wolinski, K.; Anchell, J.; Bernholdt, D.; Borowski, P.; Clark, T.; Clerc, D.; Dachsel, H.; Deegan, M.; Dyall, K.; Elwood, D.; Glendening, E.; Gutowski, M.; Hess, A.; Jaffe, J.; Johnson, B.; Ju, J.; Kobayashi, R.; Kutteh, R.; Lin, Z.; Littlefield, R.; Long, X.; Meng, B.; Nakajima, T.; Niu, S.; Pollack, L.; Rosing, M.; Sandrone, G.; Stave, M.; Taylor, H.; Thomas, G.; van Lenthe, J.; Wong, A.; Zhang, Z NWChem, A Computational Chemistry Package for Parallel Computers, Version 5.1; Pacific Northwest National Laboratory: Richland, WA. Chen, B.; Siepmann, J. I.; Klein, M. L Simulating vapor-liquid nucleation of water: A combined histogramreweighting and aggregation-volume-bias Monte Carlo investigation for fixed-charge and polarizable models. Journal of Physical Chemistry A, 109, Dahlke, E. E.; Truhlar, D. G Electrostatically embedded many-body expansion for large systems, with applications to water clusters. Journal of Chemical Theory and Computation, 3, Dahlke, E. E.; Leverentz, H. R.; Truhlar, D. G Evaluation of the electrostatically embedded many-body expansion and the electrostatically embedded many-body expansion of the correlation energy by applications to low-lying water hexamers. Journal of Chemical Theory and Computation, 4, Dutzler, R.; Campbell, E. B.; Cadene, M.; Chait, B. T.; MacKinnon, R X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity. Nature, 415, Heyden, A.; Truhlar, D. G A conservative algorithm for an adaptive change of resolution in mixed atomistic / coarse-grained multiscale simulations. Journal of Chemical Theory and Computation 4, Higashi, M.; Truhlar, D. G Combined electrostatically embedded multiconfiguration molecular mechanics and molecular mechanical method. Journal of Chemical Theory and Computation 4, Hille, B Ion channels of excitable membranes, 3rd ed.; Sinauer Associates: Sunderland, MA; p 814. Hirata, S.; Valiev, M.; Dupuis, M.; Xantheas, S. S.; Sugiki, S.; Sekino, H Fast electron correlation methods for molecular clusters in the ground and excited states. Molecular Physics, 103, Huetz, P.; Boiteux, C.; Compoint, M.; Ramseyer, C.; Girardet, C Incidence of partial charges on ion selectivity in potassium channels. Journal of Chemical Physics, 124, Kamiya, M.; Hirata, S.; Valiev, M Fast electron correlation methods for molecular clusters without basis set superposition errors. Journal of Chemical Physics, 128, Kathmann, S. M.; Schenter, G. K.; Garrett, B. C.; Chen, B.; Siepmann, J. I The thermodynamics and kinetics of nanoclusters controlling gas-to-particle nucleation. Journal of Physical Chemistry A; Article ASAP; DOI: /jp Kendall, R.A.; Apra, E.; Bernholdt, D.E.; Bylaska, E.J.; Dupuis, M.; Fann, G.I.; Harrison, R.J.; Ju, J.; Nichols, J.A.; Nieplocha, J.; Straatsma, T.P.; Windus, T.L.; Wong, A.T High performance computational chemistry: an overview of NWChem a distributed parallel application. Computer Physics Communications, 128, Kim, Y.; Corchado, J. C.; Villa, J.; Xing, J.; Truhlar, D. G Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions. Journal of Chemical Physics. 112, Kreuer, K. D On the development of proton conducting polymer membranes for hydrogen and methanol fuel cells. Journal of Membrane Science, 185, Kuang, C.; McMurry, P. H.; McCormick, A. V.; Eisele, F. L Dependence of nucleation rates on sulfuric acid concentration. Journal of Geophysical Research, 113, D Kulmala, M Atmospheric science: How particles nucleate and grow. Science. 302, Lin, H.; Zhang, Y.; Truhlar, D. G QMMM version 1.3.5; University of Minnesota, Minneapolis. 4

6 Lin, H.; Truhlar, D. G QM/MM: What have we learned, where are we, and where do we go from here? Theoretical Chemistry Accounts, 117, Nakamura, H.; Truhlar, D. G The direct calculation of diabatic states based on configurational uniformity. Journal of Chemical Physics, 115, Nakano, H Quasidegenerate perturbation theory with multiconfigurational self-consistent-field reference functions. Journal of Chemical Physics, 99, Nellas, R. B.; Chen, B.; Siepmann, J. I Dumbbells and onions in ternary nucleation. Physical Chemistry Chemical Physics, 9, Nieplocha, J.; Krishnamoorthy, S.; Valiev, M.; Krishnan, M. K.; Palmer, B. J.; Sadayappan, P Integrated data and task management for scientific applications. In Proceedings of ICCS: Lecture Notes in Computer Science; Springer-Verlag: Berlin, Germany,; vol. 5101, pp Schenter, G. K.; Kathmann, S. M.; Garrett, B. C Dynamical nucleation theory: A new molecular approach to vapor-liquid nucleation. Physical Review Letters, 82, Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A., Jr General atomic and molecular electronic structure system. Journal of Computational Chemistry, 14, Sorkin, A.; Dahlke, E. E.; Truhlar, D. G Application of the electrostatically embedded many-body expansion to microsolvation of ammonia in water clusters. Journal of Chemical Theory and Computation, 4, Tishchenko, O.; Truhlar, D. G Efficient global representations of potential energy functions: Trajectory calculations of bimolecular gas-phase reactions by multiconfiguration molecular mechanics. Journal of Chemical Physics, 130, Tishchenko, O.; Higashi, M.; Albu, T. V.; Corchado, J. C.; Kim, Y.; Vill, J.; Xing, J.; Lin, H.; Truhlar, D. G MC-TINKER version 2009; University of Minnesota, Minneapolis,. Truhlar, D. G.; Gao, J.; Garcia-Viloca, M.; Alhambra, C.; Corchado, J. C.; Sanchez, M. L.; Poulsen, T. D Ensemble-averaged variational transition state theory with optimized multidimensional tunneling for enzyme kinetics and other condensed-phase reactions. International Journal of Quantum Chemistry, 100, Valiev, M.; Bylaska, E. J.; Dupuis, M.; Tratnyek, P. G Combined quantum mechanical and molecular mechanics studies of the electron-transfer reactions involving carbon tetrachloride in solution. Journal of Physical Chemistry A, 112, Wang, J.; Kim, S.; Kovacs, F.; Cross, T. A Structure of the transmembrane region of the M2 protein H+ channel. Protein Science, 10, Warren, L. A.; Haack, E. A Biogeochemical controls on metal behaviour in freshwater environments. Earth- Science Reviews, 54, Weber, R. J.; McMurry, P. H.; Mauldin, R. L.; Tanner, D. J.; Eisele, F. L.; Clarke, A. D.; Kapustin, V. N New particle formation in the remote troposphere: A comparison of observations at various sites. Geophysical Research Letters, 26, Zhang, R.; Suh, I.; Zhao, J.; Zhang, D.; Fortner, E. C.; Tie, X.; Molina, L. T.; Molina, M. J. S Atmospheric new particle formation by organic acids. Science, 304, Zhang, S.; Zheng, J.; Truhlar, D. G Massively parallel variational transition state theory calculations for association reactions with POLYRATE. In Supercomputing Conference Proceedings; Austin, TX, November 15-21, Zhang, Y.; Lin, H Flexible-boundary quantum-mechanical/molecular-mechanical calculations: Partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems. Journal of Chemical Theory and Computation, 4, Zheng, J.; Iron, M. A.; Ellingson, B. A.; Corchado, J. C.; Chuang, Y. Y.; Truhlar, D. G NWCHEMRATE version 2007; University of Minnesota, Minneapolis,. Zheng, J.; Zhang, S.; Truhlar, D. G. 2008a. Density functional study of methyl radical association kinetics. J. Phys. Chem. A, 112, Zheng, J.; Zhang, S.; Lynch, B. J.; Corchado, J. C.; Chuang, Y.-Y.; Fast, P. L.; Hu, W.-P.; Liu, Y.-P.; Lynch, G. C.; Nguyen, K. A.; Jackels, C. F.; Ramos, A. F.; Ellingson, B. A.; Melissas, V. S.; Villà, J.; Rossi, I.; Coitino, E. L.; Pu, J.; Albu, T. V.; Steckler, R.; Garrett, B. C.; Isaacson, A. D.; Truhlar, D. G., 2008b. POLYRATE version 2009; University of Minnesota, Minneapolis. Zhou, Y.; Morais-Cabral, J. H.; Kaufman, A.; MacKinnon, R Chemistry of ion coordination and hydration revealed by a K+ channel-fab complex at 2.0 Å resolution. Nature, 414,

7 1. Software [Maximum 1 page] NWChem. NWChem is a computational chemistry package designed to run on high-performance parallel supercomputers. NWChem is scalable, both in its ability to treat large problems efficiently and in its utilization of available parallel computing resources. POLYRATE. POLYRATE is a computer program for computing chemical reaction rates using Monte Carlo methods. POLYRATE version 2008 is an enhanced parallel version with improved capabilities for direct dynamics and curvilinear coordinates. It was designed with a Message-Passing Interface (MPI) protocol in the single program multiple data paradigm. POLYRATE requires no communication between the MPI processes unless all the electronic structure calculations are done and a global averaging over all the Monte Carlo nuclear configurations is needed. Since up to 99% of the CPU time is consumed by electronic structure calculations, POLYRATE can scale up linearly for massively parallel applications. However, typical electronic structure calculations require intensive I/O operations and the scalability of a file system equipped on a cluster is critical for POLYRATE to achieve its full potential if no local disks are available. Since EMSL s Chinook comprises 2,310 nodes with a local file system of 365 GB on each, POLYRATE should be able to scale up very well over the cluster. We have tested POLYRATE on an SGI Linear Scaling 4096 Samples 8192 Samples Number of Processors Altix XE 1300 Linux cluster at Minnesota Supercomputing Institute and the results are very encouraging. The figure shows the scalability benchmark for POLYRATE used in a study of the CH 3 + CH 3 reaction by direct dynamics (in regard to the number of processors and Monte Carlo samples). In this case in order to perform electronic structure calculations we have interfaced POLYRATE with Gaussian 03. Here we propose to interface POLYRATE with NWChem by means of an interface protocol called NWChemRate. The latter generates input files for NWChem electronic structure calculations for each Monte Carlo configuration. NWChemRate is available at for free download. POLYRATE also needs SPRNG (2.0 or newer) which is a Scalable Parallel Random Number Generator library used for generating unique random configurations in parallel. SPRNG is freely available software. QMMM. QMMM is a computer program for performing geometry optimizations and calculating singlepoint energies, gradients, and/or Hessians using combined quantum mechanics (QM) and molecular mechanics (MM) methods. QMMM calls a QM package and an MM package to perform required singlelevel calculations. It was tested with Gaussian 03, GAMESS, and ORCA for the QM packages and TINKER for the MM package. We propose to develop a version of QMMM that runs in conjunction with NWChem used as a QM package. MC-TINKERATE and MC-TINKER. MC-TINKERATE is a computer program for carrying out direct dynamics calculations of chemical reaction rates for polyatomic species by using single-configuration molecular mechanics (SCMM) methods or multi-configuration molecular mechanics (MCMM) methods available in MC-TINKER to calculate the potential energy surface and by using POLYRATE for the dynamics. MC-TINKER is based on TINKER by J. W. Ponder. CP2K. CP2K is a freely available (General Public License) program, written in Fortran 95, to perform atomistic and molecular simulations of solid-state, liquid, molecular and biological systems. It provides a general framework for different methods such as density functional theory using a mixed Gaussian and plane waves approach and classical pair and many-body potentials. GAMESS. GAMESS is a program for ab initio molecular quantum chemistry. The program is well documented at Most computations can be performed in parallel using the Distributed Data Interface (DDI). GAMESS will be used only if NWChem cannot be used. 1

8 2. Proposed MSC Computational Resources [Maximum 1 page] First year request: 800,000 node-hours Nucleation of Atmospheric Aerosols and Controllable Nanodroplet Structures. This subproject requires time-consuming Monte Carlo simulations. We are budgeting 175,000 node-hours for this project. Multi-Scale Modeling of Chemical Transformations in Complex Environments. Based on the usage in the past years, we evaluate that we need 150,000 node-hours to complete this subproject. Interfacing POLYRATE and NWChem. We plan to run extensive calculations for testing POLYRATE. When we did these tests on Minnesota supercomputers we spent about 400,000 CPU-hours that is equivalent to 50,000 node-hour on Chinook. We plan to spend four times as much. For instance, we plan to run POLYRATE on 64 nodes for four months. Thus, our request for the POLYRATE project is 64 nodes x 2880 wall-clock hours = 184,320 node-hours. Computational Photochemistry of Complex Systems. In the past we ran similar calculations on Minnesota supercomputers, and we spent about 560,000 CPU-hours that is equivalent to 70,000 nodehour on Chinook. We plan to spend approximately twice as much. In particular, we are budgeting enough units to run NWChem single-point energy calculations distributed over 32 nodes for 5.5 months. Thus, our request for this subproject is 32 nodes x 4015 wall-clock hours = 128,480 node-hours. QM/MM Molecular Dynamics Modeling of Ion Solvation and Transport. Molecular dynamics simulations within this subproject are budgeted for 70,000 node-hours. Other projects. A total of 65,000 node-hours is reserved for other projects (smaller projects and exploratory work, for example, the path integral project, water splitting by binuclear copper and ruthernium complexes, zeolite and gold catalysis, revere-phase liquid-chromatography, and the explicitpolarization protein simulations) which could grow in importance in a later year. Contingency and new developments. We added 27,200 node-hours for contingency and new developments. 2

9 3. Proposed MSC Archival Storage Requirements [Half page Maximum] Maximum Short-term Disk Storage Year 1: 60GB Cumulative Long-term Storage Year 1: 500 GB 3

10 4. Curriculum Vitae for Team Leader and Team Members [Maximum 2 pages each] See an additional attachment. 4