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Dai M.,Rutgers University | Kwon J.,University of Texas at Dallas | Halls M.D.,Accelrys Inc. | Gordon R.G.,Harvard University | Chabal Y.J.,University of Texas at Dallas
Langmuir | Year: 2010

The initial surface chemistry and growth mechanisms of the atomic layer deposition (ALD) of metallic copper on SiO2 surfaces are investigated using an amidinate precursor (copper(I) di-sec-butylacetamidinate, [Cu( sBu-amd)]2) and molecular hydrogen. Using in situ Fourier transform infrared spectroscopy together with calculations based on density functional theory, we show that the initial surface reaction of [Cu( sBu-amd)]2 with hydroxylated SiO2 takes place by displacement of one of the sec-butylacetamidinate ligands at a surface -OH site, thus forming a Si-O-Cu-(sBu-amd) surface species, evident by the stretching vibrations of Si-O-Cu and the chelating -NCN- bonds. Molecular hydrogen exposure during a subsequent pulse dissociates most of the sec-butylacetamidinate ligands bound to surface Cu, which releases free amidine vapor, leaving Cu atoms free to agglomerate on the surface and thus opening more reactive sites for the next [Cu(sBu-amd)]2 pulse. Copper agglomeration is evident in the IR absorbance spectra through the partial recovery of the intensity of SiO2 optical phonon modes upon H 2 reduction, which was lost after the reaction of [Cu( sBu-amd)]2 with the initial SiO2 surface. The thermally activated ligand rearrangement from a bridging to a monodentate structure occurs above 220 °C through hydrogenation of the ligand by surface hydroxyl groups after exposure to a [Cu(sBu-amd)]2 pulse. As Cu particles grow with furtherALDcycles, the activation temperature is lowered to 185 °C, and hydrogenation of the ligand takes place after H 2 pulses, catalyzed by Cu particles on the surface. The surface ligand rearranged into a monodentate structure can be removed during subsequent Cu precursor or H2 pulses. Finally, we postulate that the attachment of dissociated ligands to the SiO2 surface during the [Cu( sBu-amd)]2 pulse can be responsible for carbon contamination at the surface during the initial cycles of growth, where the SiO2 surface is not yet completely covered by copper metal. © 2010 American Chemical Society.

Halls M.D.,Accelrys Inc. | Tasaki K.,Mitsubishi Group
Journal of Power Sources | Year: 2010

Advances in the stability and efficiency of electronic structure codes along with the increased performance of commodity computing resources has enabled the automated high-throughput quantum chemical analysis of materials structure libraries containing thousands of structures. This allows the computational screening of a materials design space to identify lead systems and estimate critical structure-property limits which should prove an invaluable tool in informing experimental discovery and development efforts. Here this approach is illustrated for lithium ion battery additives. An additive library consisting of 7381 structures was generated, based on fluoro- and alkyl-derivatized ethylene carbonate (EC). Molecular properties (e.g. LUMO, EA, μ and η) were computed for each structure using the PM3 semiempirical method. The resulting lithium battery additive library was then analyzed and screened to determine the suitability of the additives, based on properties correlated with performance as a reductive additive for battery electrolyte formulations. © 2009 Elsevier B.V. All rights reserved.

Avramopoulos A.,National Hellenic Research Foundation | Avramopoulos A.,Lamia Institute of Technology | Serrano-Andres L.,University of Valencia | Li J.,Accelrys Inc. | Papadopoulos M.G.,National Hellenic Research Foundation
Journal of Chemical Theory and Computation | Year: 2010

The electronic ground state of H-Ng-Ng-F (Ng = Ar, Kr, Xe) has been studied theoretically by employing the ab initio complete active space valence bond (CASVB) and multi-state complete active space perturbation theory (MS-CASPT2) methods. Both levels of theory confirm the diradicaloid character (DC) of the HNg2F ground state, increasing in the order Ar > Kr > Xe. The very significant effect of the first and, even more, the second Xe atom on the (hyper)polarizabilities has been shown and interpreted. Thus, the present results demonstrate a mechanism for producing very large (hyper) polarizabilities. © 2010 American Chemical Society.

Schatschneider B.,Pennsylvania State University | Liang J.-J.,Accelrys Inc. | Reilly A.M.,Fritz Haber Institute | Marom N.,University of Texas at Austin | And 2 more authors.
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

We show that electrodynamic dipolar interactions, responsible for long-range fluctuations in matter, play a significant role in the stability of molecular crystals. Density functional theory calculations with van der Waals interactions determined from a semilocal "atom-in-a-molecule" model result in a large overestimation of the dielectric constants and sublimation enthalpies for polyacene crystals from naphthalene to pentacene, whereas an accurate treatment of nonlocal electrodynamic response leads to an agreement with the measured values for both quantities. Our findings suggest that collective response effects play a substantial role not only for optical excitations, but also for cohesive properties of noncovalently bound molecular crystals. © 2013 American Physical Society.

Yuan Q.H.,Chinese University of Hong Kong | Li J.,Accelrys Inc. | Liu Z.-F.,Chinese University of Hong Kong
Physical Chemistry Chemical Physics | Year: 2011

The icosahedral Al-13 is a "magic" cluster with remarkable stability due to its high symmetry and closed valence shells. Its reactivity has provided a molecular model for understanding oxidation and dissolution processes in bulk metals. By first principles calculations, we demonstrated the importance of dynamic factors in the Al-13 + HX reactions, with HX being either HCl or HI. There was a barrier to the dissociative adsorption of HX on the surface of an Al-13 cluster, which involved charge transfer from Al-13. Furthermore, the H atom could be bonded to the cluster in multiple ways, similar to the top, bridge and hollow adsorption sites on Al(111) surface. With a large amount of energy (∼40 kcal mol-1) deposited during the formation of Al13HX-, the H atom could easily migrate among these sites, similar to the diffusion of hydrogen on metal surfaces. These factors were therefore important considerations in the formation and dissociation of Al13HX-, and more generally in reactions involving other metal clusters. © 2011 the Owner Societies.

Schatschneider B.,Pennsylvania State University | Monaco S.,Pennsylvania State University | Liang J.-J.,Accelrys Inc. | Tkatchenko A.,Fritz Haber Institute
Journal of Physical Chemistry C | Year: 2014

The quest for cheap, light, flexible materials for use in electronics applications has resulted in the exploration of soft organic materials as possible candidates, and several polycyclic aromatic hydrocarbons (PAHs) have been shown to be versatile (semi)conductors. In this investigation, dispersion inclusive density functional theory is used to explore all of the current crystalline PAHs within the Cambridge Structure Database (CSD) from both structural and electronic standpoints. Agreement is achieved between the experimental and calculated crystalline structures, as well as the electronic properties. Specifically, variation between the mass densities, unit cell parameters, and intermolecular close contact fractions were within +5%, ±2%, and ±1% of experiment, respectively. It is found that a simple addition of a ∼1 eV constant to the DFT-PBE gaps provides good agreement with the experimental optical gaps of both gas phase (within ±2.6%) and crystalline (within ±3.5%) PAHs. Structural and electronic analysis revealed several correlations/trends, where ultimately limits in the band gaps as a function of structure are established. Finally, analysis of the difference between band gaps of the isolated molecules and crystals (ΔEgXtal-Mol) demonstrates that ΔEgXtal-Mol can be captured qualitatively by PBE and PBE0 functionals, yet significant quantitative deviations remain between these functionals and experiment. © 2014 American Chemical Society.

Chen W.L.,Accelrys Inc. | Chen D.Z.,Yale University | Taylor K.T.,Accelrys Inc.
Wiley Interdisciplinary Reviews: Computational Molecular Science | Year: 2013

A reaction center is the part of a chemical reaction that undergoes changes, the heart of the chemical reaction. The reaction atom-atom mapping indicates which reactant atom becomes which product atom during the reaction. Automatic reaction mapping and reaction center detection are of great importance in many applications, such as developing chemical and biochemical reaction databases and studying reaction mechanisms. Traditional reaction mapping algorithms are either based on extended-connectivity or maximum common substructure (MCS) algorithms. With the development of several biochemical reaction databases (such as KEGG database) and increasing interest in studying metabolic pathways in recent years, several novel reaction mapping algorithms have been developed to serve the new needs. Most of the new algorithms are optimization based, designed to find optimal mappings with the minimum number of broken and formed bonds. Some algorithms also incorporate the chemical knowledge into the searching process in the form of bond weights. Some new algorithms showed better accuracy and performance than the MCS-based method. © 2013 John Wiley & Sons, Ltd.

Sahini L.,ChimericBio Incorporated | Tempczyk-Russell A.,Accelrys Inc. | Agarwal R.,ChimericBio Incorporated
PLoS ONE | Year: 2010

Background: Influenza A viral surface protein, hemagglutinin, is the major target of neutralizing antibody response and hence a main constituent of all vaccine formulations. But due to its marked evolutionary variability, vaccines have to be reformulated so as to include the hemagglutinin protein from the emerging new viral strain. With the constant fear of a pandemic, there is critical need for the development of anti-viral strategies that can provide wider protection against any Influenza A pathogen. An anti-viral approach that is directed against the conserved regions of the hemaggutinin protein has a potential to protect against any current and new Influenza A virus and provide a solution to this ever-present threat to public health. Methodology/Principal Findings: Influenza A human hemagglutinin protein sequences available in the NCBI database, corresponding to H1, H2, H3 and H5 subtypes, were used to identify highly invariable regions of the protein. Nine such regions were identified and analyzed for structural properties like surface exposure, hydrophilicity and residue type to evaluate their suitability for targeting an anti-peptide antibody/anti-viral response. Conclusion/Significance: This study has identified nine conserved regions in the hemagglutinin protein, five of which have the structural characteristics suitable for an anti-viral/anti- peptide response. This is a critical step in the design of efficient anti-peptide antibodies as novel anti-viral agents against any Influenza A pathogen. In addition, these anti-peptide antibodies will provide broadly cross-reactive immunological reagents and aid the rapid development of vaccines against new and emerging Influenza A strains. © 2010 Sahini et al.

Green N.J.B.,University of Oxford | Robertson S.H.,Accelrys Inc.
Chemical Physics Letters | Year: 2014

A formulation of the master equation for reversible association/ dissociation reactions where one of the reactants is not in thermal equilibrium is presented and its detailed balance properties are discussed. This formulation incorporates the distribution of states immediately following a dissociation reaction and generalizes some earlier specific results. © 2014 Elsevier B.V. All rights reserved.

Accelrys Inc. | Date: 2010-03-31

The disclosed embodiments contemplate an electronic storage system able to be rapidly deployed and subsequently used to receive and organize data entries. The system comprises a knowledge schema able to organize entries into a coherent form facilitating revision and review. The system may be implemented across a computer network such that users from a variety of locations may asynchronously review and update the database.

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