posted Apr 24, 2013, 5:48 AM by Emilio Xavier Esposito
The COMP Division is excited to announce the Chemical Computing Group Excellence Award for Graduate Students winners for the Indianapolis ACS meeting (fall 2013). Please visit the COMP award winners and the other excellent COMP posters at the COMP Poster Session on Tuesday, September 10, 2013 from 6pm to 8pm at a location to be determined.
Theoretical investigation of ion diffusion pathways in II-VI semiconductor nanocrystals Joseph W May, Daniel R Gamelin and Xiaosong Li; Department of Chemistry, University of Washington Continued advances in the development of smaller, faster computer processors; cheaper, more efficient solar energy conversion; and environmentally conscious, high-capacity energy storage relies upon the design of new materials. Semiconducting nanocrystals such as II-VI (ZnO, CdSe, etc.) quantum dots (QDs) have shown promising application towards each of these endeavors. Electrically charged II-VI semiconductor nanocrystals have been successfully used in activating room-temperature magnetic ordering and as chemical reduction catalysts. It was hypothesized that the charge-compensating cations in an electrolytic solution, which serve to stabilize the conduction band electrons, are either absorbed to the QD surface or diffused into the QD lattice. This latter scenario happens to share the same mechanism underlying modern day lithium-ion batteries that rely on the intercalation (diffusion) of Li+ ions into the anode and cathode materials. This hypothesis also holds the greatest promise for the development of new materials for energy storage, that is, semiconducting nanocrystal based lithium-ion batteries. A solid understanding of the ion diffusion processes in QDs lends significant insight into the design of functional materials for reusable energy storage. In this work, computational methods such as electronic structure theory and molecular dynamics are used to examine the energetics, thermodynamics, and kinetics of charge compensating cations (H+ and Li+) in II-VI QDs. Ion diffusion pathways in II-VI semiconductor QDs are studied in an effort to understand the physical underpinnings (kinetics and thermodynamics) of ion diffusion pathways in II-VI semiconductor colloidal nanocrystals. More specifically, the kinetics and thermodynamics conditions for proton and lithium ions to diffuse in/out (charging/discharging) of the semiconductor nanocrystals are investigated.
Acceleration of ab initio quantum chemistry calculation on GPUs Yipu Miao and Kenneth M Merz; Department of Chemistry, University of Florida Quantum theory has been utilized in many roles, including interpreting chemical phenomena and predicting new molecular species with novel functions.For computational chemistry, the most widely used types of electronic structure calculation are Hatree-Fock (HF) and density functional theory (DFT). Typically, for these methods, Electron Repulsion Integral (ERI) calculations, together with basic linear algebraic operations dominate the computational time. We developed a series of mapping strategies to avoid global memory access latency and thread divergence. Our benchmark studies shows that GPU can speedup ERI calculation by 100 times over a traditional GPU. This speedup is achieved by optimizing the Fock formation scheme by atomic-operations in order to avoid data transfer, a well-known GPU architectural bottleneck.
Multi-receptor high-throughput virtual docking on supercomputers with VinaMPI Sally R Ellingson,1,3 Jerome Baudry2,3 and Jeremy C Smith2,3; 1. Genome Science & Technology, University of Tennessee, Knoxville; 2. Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville; 3. Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, Tennessee Virtual docking is a computational process that aims at predicting the bound conformation of a protein-ligand complex and how well it binds through a scoring algorithm. The scoring functions commonly used in docking applications use significant approximations to rapidly estimate protein-ligand binding affinities and the resulting computational efficiency make these applications useful for virtual high-throughput screens in which millions of molecules can be tested quickly. Most of the screening applications developed to date focus on docking a library of drug-like molecules into one protein target. However, inverse techniques of docking libraries of chemical compounds into a library of proteins are of significant interest, as these permit the investigation of many conformational states of a single protein thus increasing the chemical diversity of drug candidates, and of the effects of a single target compound against a range of different proteins permitting the exploration of toxicity/side-effects of the drug and polypharmacology capabilities.
VinaMPI, a massively parallel Message Passing Interface (MPI) and muti-threaded version of the virtual docking program Autodock Vina has been developed. MPI is used to distribute tasks while multi-threading is used to speed-up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high-throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time.
Unlocking the binding and reaction mechanism of hydroxyurea as a biological nitric oxide donor Sai Lakshmana Vankayala, Henry Lee Woodcock, and Jacqueline C Hargis; Department of Chemistry, University of South Florida Hydroxyurea is the only FDA approved treatment of sickle cell disease. It is believed the primary mechanism of action is associated with the pharmacological elevation of nitric oxide in the blood, however, the exact details of this mechanism is still unclear. HU interacts with oxy and deoxyHb resulting in slow NO production rates. However, this did not correlate with the observed increase of NO concentrations in patients undergoing HU therapy. The discrepancy can be attributed to the interaction of HU competing with other heme based enzymes such as catalase and peroxidases. In the current work, we investigate the atomic level details of this process using a combination of flexible-ligand / flexible-receptor virtual screening (i.e. induced fit docking, IFD) coupled with energetic analysis that decomposes interaction energies at the atomic level. Using these tools we were able to elucidate the previously unknown substrate binding modes of a series of hydroxyurea analogs to human hemoglobin, catalase and the concomitant structural changes of the enzymes. Our results are consistent with kinetic and EPR measurements of hydroxyurea-hemoglobin reactions and a full mechanism is proposed that offers new insights into possibly improving substrate binding and/or reactivity.
Mechanism of Homogeneous Reduction of CO2 by Pyridine: Proton Relay in Aqueous Solvent and Aromatic Stabilization Chern-Hooi Lim,1 Aaron M Holder1,2 and Charles B Musgrave1,2; 1. Chemical & Biological Engineering, University of Colorado at Boulder; 2. Chemistry and Biochemistry, University of Colorado at Boulder We employ quantum chemical calculations to investigate the mechanism of homogeneous CO2 reduction by pyridine (Py) in the Py/p-GaP system. We find that CO2 reduction by Py commences with PyCOOH0 formation where: a) protonated Py (PyH+) is reduced to PyH0, b) PyH0 then reduces CO2 by one electron transfer (ET) via nucleophilic attack by its N lone pair on the C of CO2 and finally c) proton transfer (PT) from PyH0 to CO2 produces PyCOOH0. The predicted enthalpic barrier for this proton coupled ET (PCET) reaction is 45.7 kcal/mol for direct PT from PyH0 to CO2. However, when PT is mediated by one to three water molecules acting as a proton relay the barrier decreases to 29.5, 20.4 and 18.5 kcal/mol, respectively. The water proton relay reduces strain in the transition state (TS) and facilitates more complete ET. For PT mediated by a three water molecule proton relay, adding water molecules to explicitly solvate the core reaction system reduces the barrier to 13.6 - 16.5 kcal/mol, depending on the number and configuration of the solvating waters. This agrees with the experimentally determined barrier of 16.5 ± 2.4 kcal/mol. We calculate a pKa for PyH0 of 31 indicating that PT preceding ET is highly unfavorable. Moreover, we demonstrate that ET precedes PT in PyCOOH0 formation, confirming PyH0's pKa as irrelevant for predicting PT from PyH0 to CO2. Furthermore, we calculate adiabatic electron affinities in aqueous solvent for CO2, Py and Py•CO2 of 47.4, 37.9, 66.3 kcal/mol respectively, indicating that the anionic complex PyCOO− stabilizes the anionic radicals CO2− and Py− to facilitate low barrier ET. As the reduction of CO2 proceeds through ET and then PT, the pyridine ring becomes aromatic and thus Py catalyzes CO2 reduction by stabilizing the PCET TS and the PyCOOH0 product through aromatic resonance stabilization.
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posted Apr 24, 2013, 5:42 AM by Emilio Xavier Esposito
The COMP Division is excited to announce the OpenEye Award winners for the Indianapolis ACS meeting (fall 2013). Please visit the COMP award winners and the other excellent COMP posters at the COMP Poster Session on Tuesday, September 10, 2013 from 6pm to 8pm at a location to be determined.
Quantifying biomolecular hydration thermodynamics A detailed knowledge of the role water plays in biomolecular interactions is crucial to understand protein folding or biomolecular recognition. Methodologies to compute the thermodynamic properties of discrete sets of water molecules are increasingly used to support drug-discovery efforts. However it is not always possible to rationalise biomolecular hydration thermodynamics with a simple discrete distributions of water molecules. This poster will describe ongoing efforts to develop the grid cell theory method to resolve and visualize the thermodynamic properties of water over arbitrarily complex regions of space in the vicinity of a biomolecule. The robustness and versatility of the methodology will be demonstrated on diverse systems, ranging from small molecules to proteins. I will discuss ongoing efforts to: enhance convergence of solvent distributions; characterise biomolecules-induced perturbations in water structure; estimate ligand-induced changes in binding site hydration thermodynamics.
Enabling Chemical Discovery through the Lens of a Computational Microscope With exascale computing power on the horizon, computational studies have the opportunity to make unprecedented contributions to drug discovery efforts. Steady increases in computational power, coupled with improvements in the underlying algorithms and available structural experimental data, are enabling new paradigms for discovery, wherein computationally predicted ensembles from large-scale biophysical simulations are being used in rational drug design efforts. Such investigations help drive discovery efforts and experimental work on these systems in collaboration with leading experimentalists. Our work in this area has provided key insights into the systematic incorporation of structural information resulting from state-of-the-art biophysical simulations into protocols for inhibitor and drug discovery. In addition to the scientific advances, my lab has also developed freely-distributed, open source tools and technologies that assist the broader community in ensemble-structural selection and analyses to support simulation-based discovery efforts.
In this poster, I will present the overall strategy to use structures generated from molecular dynamics simulations in combination with virtual screening, which I pioneered as a postdoctoral scholar. As an independent PI, the emphasis of my lab has been on the exploration of these “high risk” methods in discovery. We have made substantial progress in these areas, including new discoveries for influenza, trypanosomiasis, agents against emerging pathogens, and cancer. Work to improve these methods, including the incorporation of more rigorous statistical models, is ongoing. I will also present my work in open source tool development for the community. Here, we have created a VMD plugin that computes ensemble-averaged electrostatic potential maps for arbitrary biomolecules using DelPhi. Very recently, we also developed a tool that assists in the analysis of computational solvent mapping across ensembles of structures.
Elucidating the Signatures of Fano Interferences in Electron Energy-Loss and Cathodoluminescence Spectroscopies via Multiscale Electrodynamics Simulations Through numerical simulation we demonstrate the existence of the Fano interference effect in the electron energy-loss spectroscopy (EELS) and cathodoluminescence (CL) of symmetry-broken nanorod dimers that are heterogeneous in both material composition and length. The differing selection rules of the electron probe in comparison to the photon of a plane wave allow for the simultaneous excitation of both optically bright and dark plasmons of each monomer unit. Yet, interferences are manifested in the dimer's scattered near- and far-fields due to the rapid π-phase offset in the polarizations between super-radiant and sub-radiant hybridized plasmon modes of the dimer as a function of the energy loss suffered by the impinging electron. Depending upon the location of the electron beam, we predict the conditions under which Fano interferences will be present in both optical and electron spectroscopies (EELS and CL) as well as a new class of Fano interferences that are uniquely electron-driven and are absent in the optical response.
Increasing the Efficiency and Accuracy of Ultrafast Time-Resolved Electronic Spectra Calculations with On-the-Fly ab Initio Quantum Dynamics Methods I will present several approaches increasing both the efficiency and accuracy of ultrafast spectra calculations. First, we prove that the number of trajectories needed for evaluating such spectra with the semiclassical Dephasing Representation (DR) is independent of dimensionality [1]. This general result justifies the feasibility of quantum calculations of time-resolved electronic spectra of large systems. The method is further accelerated by developing the Cellular Dephasing Representation in which the number of trajectories is drastically reduced—spectra based on a single semiclassical trajectory are in a remarkable agreement with the fully converged DR requiring 104 trajectories [2]. Second, the accuracy is improved by combining the DR with accurate on-the-fly ab initio electronic structure calculations, including nonadiabatic and spin-orbit couplings [3], and by removing the inherent semiclassical approximation [4]. By starting from an exact Gaussian basis method, the DR is derived together with ten new methods for computing time-resolved spectra with intermediate accuracy and efficiency. These methods include the Gaussian DR, an exact generalization of the DR, in which trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. Surprisingly, in chaotic systems the Gaussian DR can outperform the presumably more accurate Gaussian basis method. The newly developed methods are tested on several systems of increasing complexity. Our time-resolved stimulated emission spectrum of the 54-dimensional azulene is at present the largest ab initio semiclassical dynamics calculation of a coherent spectrum. Our Multiple Surface DR provides theoretical justification of the violation of Kasha's rule of excited-state photochemistry in azulene.
[1] C. Mollica and J. Vanicek, Phys. Rev. Lett. 107 , 214101 (2011). [2] M. Sulc and J. Vanicek, Mol. Phys. 110 , 945 (2012). [3] T. Zimmermann and J. Vanicek, J. Chem. Phys. 136 , 094106; 137 , 22A516 (2012). [4] M. Sulc, H. Mendiola, T. J. Martinez, and J. Vanicek, submitted.
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posted Mar 25, 2013, 4:35 AM by Emilio Xavier Esposito
The COMP Programming Board would like to remind you that abstract submissions for the COMP technical program at the Indianapolis ACS meeting closes at 11pm Central Time on Tuesday, April 2, 2013. Authors can submit their abstract via http://abstracts.acs.org .
Information about COMP events at the Indianapolis ACS Meeting (September 8-12, 2013) can be found at the following links:
COMP Symposia at the Indianapolis ACS meeting Member Contributed Symposia Invited Symposia
COMP Awards at the Indianapolis ACS meeting NVIDIA GPU Award Emerging Technologies in Computational Chemistry
Graduate Student and Post Doc Image Contest Images due by 5pm Eastern Time on Friday, April 12, 2013.
Submitting an abstract for the Indianapolis ACS meeting and Presenter Information
Organizing a symposium within COMP at a 2014 (or 2015) ACS National Meeting
The COMP Programming Board Emilio Xavier Esposito Michael Feig Maciej Haranczyk Eric V Patterson Yufeng Jane Tseng Scott A Wildman
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posted Mar 6, 2013, 6:10 AM by Emilio Xavier Esposito
The COMP Programming Board
is proud to announce the latest COMP Graduate Student and Post Doc
Image Competition winner, Tara Michels-Clark.
About the cover image. The image is a representation of the atomic structure of the β-NaLaF4
super cell floating on a section of its diffuse single crystal
diffraction honeycomb pattern. The structure view is oriented around a
central La column (green) connected to three strictly alternating Na –
La (yellow – red) and three strictly alternating Na – void (orange –
white) through a fluorine framework (turquoise) allowing variations of
the occupation sequence in next neighbor columns. Rare earth doped
members of this family of compounds show light up-conversion capability
used for applications in LED display devices and labels for
immunoassays.. The image was created using ParaView for the diffuse
X-Ray diffraction pattern background and CrystalMaker for the β-NaLaF 4 super cell; ZODS (Zürich Oak Ridge Disorder Simulation) is used for local structure analysis.
About the cover image artist, Tara Michels-Clark. Tara
received her BS in Mathematics and a minor in Physics from King College
and a MS in Mathematics from East Tennessee State University. She
taught undergraduate Mathematics for five years at Nashville State
Community College and Middle Tennessee State University until 2009,
before pursuing a PhD in Theoretical Physical Chemistry with a minor in
computational sciences at the University of Tennessee, Knoxville. She is
jointly mentored by Robert Harrison (UTK), Christina Hoffmann
(Spallation Neutron Source, ORNL) and collaborating with the University
of Zürich, University of Bern and ETH Zürich. Tara’s PhD research
focuses on “Employing high performance computing for structure
elucidation of locally disturbed crystalline materials using Monte Carlo
crystal modeling and evolutionary algorithms” and is funded by the Oak
Ridge National Laboratory, supported by the Division of Scientific User
Facilities, Office of Basic Energy Sciences, US Department of Energy,
under contract DE-AC05-00OR22725 with UT Battelle, LLC. and the Swiss
National Science Foundation. Connect with Tara on LinkedIn (direct link to her public LinkedIn page).
Are you interested in participating? Submissions for the Indianapolis ACS meeting (fall 2013) The COMP
Graduate Student and Post Doc Image Competition are now being
accepted! Images are due by 5pm Eastern Time on Friday, April 12, 2013.
Please email your image to emilio.esposito AT gmail.com . One image per
artist. The creator of the winning image will be notified via email by
May 1, 2013.
More information and to view images of past winners, please visit The COMP Graduate Student and Post Doc Image Competition website. |
posted Jan 7, 2013, 1:13 PM by Emilio Xavier Esposito
[
updated Jan 7, 2013, 2:45 PM
]
The COMP Division is excited to announce the OpenEye Award winners for the New Orleans ACS meeting (spring 2013). Please visit the COMP award winners and the other excellent COMP posters at the COMP Poster Session on Tuesday, April 9, 2013 from 6pm to 8pm at a location to be determined.
Molecular Simulation of Biomolecules in Non-Aqueous Media The potential for non-aqueous solvents to endow biological catalysts with improved or previously unknown properties is exciting and could transform their use in industry. In spite of this great promise, our incomplete understanding of the relationship between solvent, enzyme structure, and reactivity has hampered significant scientific technological development in this arena. Specifically, we lack the ability to relate molecular features of the solvent to its effect on enzyme stability and activity. This poster describes our efforts to study biomolecular structure and dynamics of two enzymes (Candida Rugosa Lipase A and glycoside hydrolase 11) in four different solvents. We use classical MD simulations to probe the solvent structure and equilibrium fluctuations. These results are used to understand enzyme deactivation that was observed in our lab with various experiments. Additionally, we apply the metadynamics method to study the thermodynamics of protein folding in ionic liquids on the model system tryptophan cage.
Partition Energy Functionals: Avoiding the Delocalization Error of Approximate Density Functionals We show how the delocalization error that plagues density-functional calculations of bond stretching processes can be avoided by approximating the partition energy of Partition Density Functional Theory (PDFT) via simple functionals of the set of fragment densities. These functionals involve the overlap between the relevant fragment densities, and can be used in combination with any approximate exchange-correlation functional. I also describe our progress understanding the behavior of the fragment energies as a function of fragment occupations, the formulation of the partition energy as an implicit functional of the total spin-densities, derivative discontinuities, practical implementation, and application of PDFT to small molecules.
Dissecting electrostatic potentials: Understanding anion/π interactions and the nature of electron-deficient arenes Although strong interactions between cations and the faces of aromatic systems have long been recognized (i.e.: cation/π interactions), only in the last decade have favorable interactions between anions and electron deficient arenes been reported. That is, arenes heavily substituted with electron-withdrawing substituents, as well as N-heteroaromatic systems, have been shown computationally and experimentally to exhibit strong avidities for anions, with important applications in biology, supramolecular chemistry, and crystal engineering. Previously, we showedd that prototypical anion/π interactions between halide ions and the faces of substituted benzenes arise from the direct interactions of the anion with the local multipole moments associated with the substituents; the interaction of the anion with the phenyl ring itself remained repulsive regardless of the substituents. Here, we examine the interaction of anions with a number of heteroaromatic systems using symmetry-adapted perturbation theory (SAPT) and electrostatic potentials (ESPs). Notably, we introduce dissected ESPs, which enable the rigorous division of electrostatic potentials of planar arenes into contributions from the σ- and π-systems. These dissected ESPs provide critical insight into the factors that govern the strength of prototypical anion/π interactions and the nature of electron-deficient aromatic systems in general. They also provide, indirectly, a means of quantifying the contribution of the σ- and π-electron systems to Hammett substituent constants. |
posted Jan 7, 2013, 1:09 PM by Emilio Xavier Esposito
The COMP Division is excited to announce the Chemical Computing Group Excellence Award for Graduate Students winners for the New Orleans ACS meeting (spring 2013). Please visit the COMP award winners and the other excellent COMP posters at the COMP Poster Session on Tuesday, April 9, 2013 from 6pm to 8pm at a location to be determined.
Toward effective CO2/CH4 separations by sulfur-containing PIMs: insight from molecular simulations
Kyle E Hart and Coray M Colina (Advisor), Department of Materials Science and Engineering, Penn State University
The separation of CO2 from CH4 is an industrially important process, and polymeric membranes have the potential to greatly increase the efficiency of current separation techniques. In this work, we evaluate four novel sulfur-containing polymers of intrinsic microporosity (PIMs) for use in CO2/CH4 gas separation membranes through the use of molecular simulations. Using a three-step multi-scale approach, we found that the CO2/CH4 separation ability of PIMs is directly correlated with the number of polar groups per repeat unit, and sulfur PIMs may be profoundly improved upon by a post-polymerization oxidation to contain sulfonyl functionalities. In addition, a quantitative structure-property relationship model was constructed to correlate the polymer's essential characteristic to the selectivity under those conditions, which, moving forward, will allow for the predictive screening of many PIM functionalities. The results presented in this work should facilitate the design of new intrinsically microporous polymer membranes with increased CO2/CH4 gas separation performance.
Examining the 4d transition metals and the lower p-block with a pseudopotential-based composite method: Atomic and molecular applications of rp-ccCA
Marie L Laury and Angela K Wilson (Advisor), Department of Chemistry, University of North Texas
By combining relativistic pseudopotentials and the correlation consistent composite approach (ccCA), a first-principles-based composite approach for main group and first-row transition metal species, accurate energetic and thermodynamic data for heavier elements, including transition metals and lower p-block (5p and 6p) elements, are obtainable. Relativistic pseudopotential ccCA (rp-ccCA) is formulated and tested on a subset of the G3/05 set that contains 4p elements (Ga-Kr). The time savings and accuracy of the methodology, as compared to ccCA and ccCA-TM, is gauged before extending the method to the 4d transition metals and lower p-block elements. The TM-4d set, composed of 30 experimental enthalpies of formation, is employed for the second row transition metal study, while the LP80 set, composed of atomic ionization potentials and electron affinities and molecular dissociation energies and enthalpies of formation, is utilized for the lower p-block study. The accuracy and utility of rp-ccCA for energetic and thermodynamic studies of elements further down the periodic table will be demonstrated for 4d metals and lower p-block molecules.
Effect of trans and cis conformational defects on the localization of electronic excitations in ∏-conjugated organic polymers
Iffat H Nayyar,1,2 Enrique R Batista,1 Sergei Tretiak (Advisor),1 Avadh Saxena,1 Darryl L Smith,1 and Richard L Martin1
1Los Alamos National Laboratory; 2University of Central Florida
Electro-optical devices with ∏-conjugated polymers are in demand for use in light-emitting diodes (LED), solar cells and lasers. A recent study predicted differences in the response of the hyperfine field by opposite charges in organic LEDs. The improved fluorescence exhibited by different isomeric forms of PPV derivatives in optoelectronic devices motivated us to investigate the influence of various conformational distortions of trans and cis nature on the energetics and localization of positive (P+) and negative (P-) polarons. We observe the P+ and P- states are highly sensitive on the structural conformation and atomic charge distributions. The P- state is observed to be more localized than P+ in consistent with experiment with the inclusion of the polarizable dielectric environment. These defects not only break the particle-hole symmetry but demonstrate higher charge-carrier mobilities for holes than electrons. Thus, we can tune the charge-transport and photo-physical properties in organic materials by understanding their structure-property correlations for technological applications.
Fast protein refolding observed in pressure-jump molecular dynamics simulation
Yanxin Liu, Martin Gruebele and Klaus Schulten (Advisor), Department of Physics, University of Illinois at Urbana-Champaign
Pressure jump is known to induce fast protein folding. For a five-helix bundle λ-repressor fragment, a short refolding time of ~2 μs was reported in an earlier pressure-jump experiment. To investigate this pressure-jump induced fast folding behavior, all-atom molecular dynamics simulations of more than 33 μs in explicit solvent were carried out on the same λ-repressor construct. High-pressure denatured states, generated through a high-temperature unfolding and high-pressure equilibration simulation procedure, were found to contain a significant amount of helical structure. Upon pressure drop, the protein refolded into the native state in 20 μs. The folding in the simulation is slower than the one measured in pressure-jump experiment, but faster than the folding time of 80 μs measured in temperature-jump experiment. A complete unfolding and refolding process was observed in the trajectory, which permitted the characterization of high-pressure denatured states and refolding pathway. The pressure jump simulations carried out for this study can be employed in the future to investigate slow-folding proteins through 10∼100 μs molecular dynamics simulations by inducing a fast folding phase.
Development and Application of the generalized Connectivity-Based Hierarchy: Accurate Thermochemistry for Organic Molecules
Raghunath O Ramabhadran and Krishnan Raghavachari (Advisor), Department of Chemistry, Indiana University
The long-standing problem of constructing a reliable and automated computational procedure to obtain the various thermochemical properties of organic molecules have been solved by our Connectivity-Based Hierarchy (CBH) – an automated method developed by us recently.
The excellent performance of our hierarchy offers scope to accurately compute thermochemical properties for important systems such as biologically relevant amino acids and carbohydrates. In an initial application on amino acids, we have calculated the enthalpies of formation of the two naturally occurring sulfur containing amino acids. Our results confirm that MP2 or B3LYP methods with modest sized basis-sets are adequate in yielding reliable geometries and thermochemistry.
The poster presents a detailed account of (a) the construction of the hierarchy, (b) results for reaction energies and heats of formations, (c) applications to amino acids and (d) future directions in CBH.
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posted Nov 1, 2012, 1:54 PM by Emilio Xavier Esposito
[
updated Nov 1, 2012, 1:58 PM
]
Due to the compounding circumstances of the PACSystem being down and Hurricane Sandy, the COMP Programming Board has moved the abstract submission deadline for the New Orleans ACS meeting (spring 2013) to Monday, November 12, 2012 at 11pm Central Time. |
posted Oct 28, 2012, 5:11 PM by Emilio Xavier Esposito
The ACS abstract server ( http://abstracts.acs.org ) is now available for abstract submission for the New Orleans National ACS meeting. COMP’s abstract submission deadline is Thursday, November 1, 2012 at 11pm Central Time. Thank you for your patience and understanding over the past week. The COMP Programming Board |
posted Oct 23, 2012, 4:53 AM by Emilio Xavier Esposito
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updated Oct 23, 2012, 8:47 PM
]
On the morning of Monday, October 22 the abstract submission server at the ACS failed. The ACS is working to put the server back online and is continually informing the COMP Programming Board -- and the Programming Board of other ACS Divisions -- of their progress.
More information, when it becomes available, will be posted on the COMP website ( http://www.acsCOMP.org ) and on Twitter ( http://twitter.com/acsCOMPprog ). The abstract submission deadline will be updated later this week and will provide sufficient time to submit your abstract(s).
Thank you for your patience. |
posted Oct 19, 2012, 1:57 PM by Emilio Xavier Esposito
From a total of six tutorials that were submitted in four categories, an overall winner and three runners-up have been determined. Additional details can be found here: http://www.teach-discover-treat.org/winners
All four winners will be recognized at the Award Symposium at the New Orleans ACS National Meeting (April 7-11, 2013) where they will have an opportunity to present their work. All materials submitted to the competition will be made available through the TDT website at the time of the Award Symposium.
See you in New Orleans!
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