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Ji H.,KAIST | Shao Y.,Q-Chem, Inc. | Goddard W.A.,KAIST | Goddard W.A.,California Institute of Technology | Jung Y.,KAIST
Journal of Chemical Theory and Computation | Year: 2013

Analytic first derivative expression of opposite-spin (OS) ansatz-adapted quartic scaling doubly hybrid XYGJ-OS functional is derived and implemented into Q-Chem. The resulting algorithm scales quartically with system size as in OS-MP2 gradient, by utilizing the combination of Laplace transformation and density fitting technique. The performance of XYGJ-OS geometry optimization is assessed by comparing the bond lengths and the intermolecular properties in reference coupled cluster methods. For the selected nonbonded complexes in the S22 and S66 data sets used in the present benchmark test, it is shown that XYGJ-OS geometries are more accurate than M06-2X and RI-MP2, the two quantum chemical methods widely used to obtain accurate geometries for practical systems, and comparable to CCSD(T) geometries. © 2013 American Chemical Society. Source


Nasief N.N.,State University of New York at Buffalo | Tan H.,Buffalo Center of Excellence | Kong J.,Buffalo Center of Excellence | Kong J.,Q-Chem, Inc. | Hangauer D.,State University of New York at Buffalo
Journal of Medicinal Chemistry | Year: 2012

Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2′ pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO- reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2′ pocket and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding. © 2012 American Chemical Society. Source


Bernard Y.A.,University of Southern California | Shao Y.,Q-Chem, Inc. | Krylov A.I.,University of Southern California
Journal of Chemical Physics | Year: 2012

We report an implementation of the spin-flip (SF) variant of time-dependent density functional theory (TD-DFT) within the Tamm-Dancoff approximation and non-collinear (NC) formalism for local, generalized gradient approximation, hybrid, and range-separated functionals. The performance of different functionals is evaluated by extensive benchmark calculations of energy gaps in a variety of diradicals and open-shell atoms. The benchmark set consists of 41 energy gaps. A consistently good performance is observed for the Perdew-Burke-Ernzerhof (PBE) family, in particular PBE0 and PBE50, which yield mean average deviations of 0.126 and 0.090 eV, respectively. In most cases, the performance of original (collinear) SF-TDDFT with 50-50 functional is also satisfactory (as compared to non-collinear variants), except for the same-center diradicals where both collinear and non-collinear SF variants that use LYP or B97 exhibit large errors. The accuracy of NC-SF-TDDFT and collinear SF-TDDFT with 50-50 and BHHLYP is very similar. Using PBE50 within collinear formalism does not improve the accuracy. © 2012 American Institute of Physics. Source


Jagau T.-C.,University of Southern California | Zuev D.,University of Southern California | Bravaya K.B.,Boston University | Epifanovsky E.,University of Southern California | And 3 more authors.
Journal of Physical Chemistry Letters | Year: 2014

A new strategy of using complex absorbing potentials (CAPs) within electronic structure calculations of metastable electronic states, which are ubiquitous in chemistry and physics, is presented. The stumbling block in numerical applications of CAPs is the necessity to optimize the CAP strength for each system, state, and one-electron basis set, while there is no clear metric to assess the quality of the results and no simple algorithm of achieving numerical convergence. By analyzing the behavior of resonance wave functions, we found that robust results can be obtained when considering fully stabilized resonance states characterized by constant density at large η (parameter determining the CAP strength). Then the perturbation due to the finite-strength CAP can be removed by a simple energy correction derived from energy decomposition analysis and response theory. The utility of this approach is illustrated by CAP-augmented calculations of several shape resonances using EOM-EA-CCSD with standard Gaussian basis sets. © 2013 American Chemical Society. Source


Grant
Agency: Department of Energy | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 149.99K | Year: 2014

Q-Chem, Inc. is submitting a DOE SBIR Phase I project (topic 9a), titled the Development of an Integrated Web User Interface for Multiscale Chemical-Physics Simulations, with Dr. Yihan Shao serving as the Principal Investigator and Prof. Lee Woodcock of the University of South Florida as the co-PI. In the last couple of decades, simulation and modeling methodologies have advanced considerably in academic laboratories, but wide availability of these new capabilities has lagged significantly, especially in the commercial sector. In large part, this is due to the absence of a general platform for intuitively preparing, executing, managing, and analyzing Chemical-Physics based simulations. Further complicating matters is the lack of universal standards across a diverse array of software packages, which severely hinders transitioning between packages, data sharing, and collaboration. In order to meet these challenges and to facilitate the deployment of new state-of- the-art computational methods, we propose the development of a user-friendly, Web- based platform for accessing a wide variety of computational Chemistry/Physics software packages. The proposed integrated Web user interface will build on the already momentous efforts made by Q-Chem developers in recent years; i.e. the development of open source platforms targeting both quantum mechanical (QM) calculations for small to medium-size molecules and molecular mechanical (MM) simulations for macromolecules. At the end of this Phase I period, a prototype Web interface will be produced that independently manages MM and QM calculations. This will allow us, in further developments, to support a multitude of molecular and macromolecular simulation packages; ultimately achieving our long-term goals of creating a user-friendly, highly extensible, package and platform independent Web-interface that promotes multiscale simulations, new methodologies, data sharing, and collaboration.

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