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ABSTRACT: The Fourier transform Coulomb (FTC) method has been shown to be effective for the fast and accurate calculation of long-range Coulomb interactions between diffuse (low-energy cutoff) densities in quantum mechanical (QM) systems. In this work, we split the potential of a compact (high-energy cutoff) density into short-range and long-range components, similarly to how point charges are handled in the Ewald mesh methods in molecular mechanics simulations. With this linear scaling QM Ewald mesh method, the long-range potential of compact densities can be represented on the same grid as the diffuse densities that are treated by the FTC method. The new method is accurate and significantly reduces the amount of computational time on short-range interactions, especially when it is compared to the continuous fast multipole method.
The Journal of chemical physics 03/2012; 136(11):114112. · 3.09 Impact Factor
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ABSTRACT: Becke's B05 method for nondynamic correlation is simplified for self-consistent implementation. An alternative form is proposed for the nondynamic correlation factors that do not require solving a complicated nonlinear algebraic equation. The four linear parameters of B05 are re-optimized together with one extra parameter entering a modified expression for the second-order same-spin energy contribution. The latter is co-linear with the exact-exchange energy density and does not require higher moments of the relaxed exchange hole. Preliminary tests of this method show that it leads to a slight improvement over the resolution-of-identity B05 results reported previously for atomization energies, and to a definite improvement for reaction barriers of Hydrogen abstraction.
Chemical Physics Letters 02/2012; 525-526:150-152. · 2.34 Impact Factor
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ABSTRACT: In a recent letter [E. Proynov, Y. Shao, and J. Kong, Chem. Phys. Lett. 493, 381 (2010)], Becke's B05 model of nondynamic electron correlation in density functional theory was implemented self-consistently with computational efficiency (the "SCF-RI-B05" scheme). Important modifications of the algorithm were done in order to make the self-consistency feasible. In the present work, we give a complete account of the SCF-RI-B05 algorithm, including all the formulae for the analytical representation of the B05 functional and for its self-consistent field (SCF) potential. The average performance of the SCF-RI-B05 method reported in the above letter was somewhat less accurate, compared to the original B05 implementation, mainly because the parameters of the original B05 model were optimized with post-local-spin-density calculations. In this work, we report improved atomization energies with SCF-RI-B05, based on a SCF re-optimization of its four linear parameters. The re-optimized SCF-RI-B05 scheme is validated also on reaction barriers, and on the subtle energetics of NO dimer, an exemplary system of strong nondynamic correlation. It yields both the binding energy and the singlet-triplet splitting of the NO dimer correctly, and close to the benchmarks reported in the literature.
The Journal of chemical physics 01/2012; 136(3):034102. · 3.09 Impact Factor
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ABSTRACT: Recent biochemical studies have identified a cell surface receptor for thyroid and steroid hormones that bind near the arginine-glycine-aspartate (RGD) recognition site on the heterodimeric αvβ3 integrin. To further characterize the intermolecular interactions for a series of hormone analogues, combined quantum mechanical and molecular mechanical (QM/MM) methods were used to calculate their interaction energies. All calculations were performed in the presence of either calcium (Ca(2+)) or magnesium (Mg(2+)) ions. These data reveal that 3,5'-triiodothyronine (T(3)) and 3,5,3',5'-tetraiodothyroacetic acid (T(4)ac) bound in two different modes, occupying two alternate sites, one of which is along the Arg side chain of the RGD cyclic peptide site. These orientations differ from those of the other ligands whose alternate binding modes placed the ligands deeper within the RGD binding pocket. These observations are consistent with biological data that indicate the presence of two discrete binding sites that control distinct downstream signal transduction pathways for T(3).
Journal of Biomedicine and Biotechnology 01/2012; 2012:959057. · 2.44 Impact Factor
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Fenglai Liu,
Zhengting Gan,
Yihan Shao,
Chao-Ping Hsu,
Andreas Dreuw,
Martin Head-Gordon,
Benjamin T. Miller,
Bernard R. Brooks,
Jian-Guo Yu,
Thomas R. Furlani, Jing Kong
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ABSTRACT: We derived the analytic gradient for the excitation energies from a time-dependent density functional theory calculation within the Tamm–Dancoff approximation (TDDFT/TDA) using Gaussian atomic orbital basis sets, and introduced an efficient serial and parallel implementation. Some timing results are shown from a B3LYP/6-31G**/SG-1-grid calculation on zincporphyrin. We also performed TDDFT/TDA geometry optimizations for low-lying excited states of 20 small molecules, and compared adiabatic excitation energies and optimized geometry parameters to experimental values using the B3LYP and ωB97 functionals. There are only minor differences between TDDFT and TDA optimized excited state geometries and adiabatic excitation energies. Optimized bond lengths are in better agreement with experiment for both functionals than either CC2 or SOS-CIS(D0), while adiabatic excitation energies are in similar or slightly poorer agreement. Optimized bond angles with both functionals are more accurate than CIS values, but less accurate than either CC2 or SOS-CIS(D0) ones.
Molecular Physics 10/2010; 108(Nos. 19-20):2791-2800. · 1.82 Impact Factor
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ABSTRACT: Becke's B05 method of describing nondynamic electron correlation in Density Functional Theory is implemented self-consistently with computational efficiency. Important modifications of the method are proposed in order to make the self-consistency feasible. Resolution-of-identity technique is used to reduce dramatically the cost of the required exact-exchange energy density. The method is briefly validated on a variety of properties. It describes accurately for the first time the subtle energetics of the NO dimer, an exemplary system of strong nondynamic correlation. The efficient algorithm for the exact-exchange energy density can be applied to other functionals that use this quantity.
Chemical Physics Letters 06/2010; 493(4-6):381-385. · 2.34 Impact Factor
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ABSTRACT: A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the "tip effect" in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method.
The Journal of chemical physics 01/2009; 129(21):214109. · 3.09 Impact Factor
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ABSTRACT: The unique meta-GGA (generalized gradient approximation) exchange functional of Becke and Roussel (BR89) and the correlation functional of Becke related to it (B94) are represented for the first time in an analytical form. All functional derivatives are then obtained analytically, which allows an efficient self-consistent implementation. A brief assessment of this "BR89B94" meta-GGA scheme is made considering molecular atomization energies and equilibrium geometries, with the latter being reported for the first time. The hybrid version of it yields one of the most accurate atomization energies to date, but its bond distances are less satisfactory. Some interesting features of the BR exchange hole are discussed.
Chemical Physics Letters 04/2008; 455(1-3):103-109. · 2.34 Impact Factor
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ABSTRACT: Combined QM/MM calculations of the active-site of cytochrome P450cam have been performed before and after the binding of P450cam to putidaredoxin. The calculations were carried out for both a 5-coordinated and a 6-coordinated active-site of cytochrome P450cam, with either a water molecule or a carbon monoxide molecule as a 6th distal ligand. An experimentally observed increase in the Fe-S stretching frequency that occurs after cytochrome P450cam binds to putidaredoxin, has been reproduced in our study. Experimentally observed changes in the Fe-C and C-O vibration frequencies that occur after binding of both proteins, have also been reproduced in our study. The computed increase of the Fe-S and Fe-C stretching frequencies is correlated with a corresponding decrease of the Fe-S and Fe-C interatomic distances. According to our calculations, for the active-site with carbon monoxide in the triplet electronic state, the binding process increases the spin densities on the iron and sulfur atoms, which changes the Fe-C and C-O stretching frequencies in opposite directions, in agreement with experimental data.
Journal of Inorganic Biochemistry 04/2008; 102(3):427-32. · 3.35 Impact Factor
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ABSTRACT: Large-scale combined quantum mechanical -molecular mechanical (QM/MM) calculations of an active-site of the photoactive yellow protein have been performed. The calculations are based on a 10 ns molecular dynamics simulation of the protein, and a 10 ns molecular dynamics of the protein chromophor in water solution, using AMBER force fields. For each of these simulations, 1,000 randomly chosen configurations were selected and individual combined QM/MM calculations for each configuration were performed. The QM/MM calculations included geometry optimization of the protein chromophor calculated at the AMBER/B3LYP/6 -31+ G* level of theory, and electronic-excitation calculations performed at the AMBER/TDDFT/B3LYP/aug-cc-pVTZ level of theory. Final results are reported as averaged data based on an ensemble of 1,000 structures obtained from the molecular dynamics simulations. The results of the calculations are compared with experimental data of electronic excitations of the protein photoreceptor in the protein, in water solution and in the gas phase.
Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on; 11/2007
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ABSTRACT: A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.
The Journal of Physical Chemistry A 06/2007; 111(18):3661-71. · 2.95 Impact Factor
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ABSTRACT: A new correlation functional of the Lap series is derived based on a more elaborated form of correlation wave vectors. Its validation is carried out within two different codes: deMon-KS3 and Q-Chem 3.0. In deMon the implementation in a post-SCF manner is similar to the preceding BLap3 and Bmτ1 schemes. In Q-Chem the new functional is programmed self-consistently using the integration by parts procedure for the matrix elements. The post-SCF version of the functional deals with three fitting parameters; the previous Lap3 and τ1 functionals have four and five parameters, respectively. The SCF implementation requires only two fitting parameters. Preliminary comparative tests are discussed.
03/2007;
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Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2007, October 14-17, 2007, Harvard Medical School, Boston, MA, USA; 01/2007
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ABSTRACT: The resolution-of-the-identity (RI) approximation has placed the onus of the cost of a second-order Moller-Plesset (MP2) calculation on the underlying self-consistent field (SCF) calculation for many moderately sized molecules. A dual-basis approach to the SCF calculation, based on previous methods demonstrated for density functional theory, is combined with RI-MP2 calculations, and small basis subsets for cc-pVTZ, cc-pVQZ, and 6-311++G(3df,3pd) are presented. These subsets provide time savings of greater than 90%, with negligible errors in absolute and relative energies, compared to the associated full-basis counterpart. The method is tested with a series of rotational barriers, relative conformational energies of alanine tetrapeptides, as well as the full G3/99 molecular set. RI-MP2 calculations on alanine octapeptides (40 heavy atoms, 3460 basis functions), using cc-pVQZ, are presented. Results improve upon previous methods that diagonalize the virtual space separately.
The Journal of Chemical Physics 09/2006; 125(7):074108. · 3.33 Impact Factor
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Yihan Shao,
Laszlo Fusti Molnar,
Yousung Jung,
Jörg Kussmann,
Christian Ochsenfeld,
Shawn T Brown,
Andrew T B Gilbert,
Lyudmila V Slipchenko,
Sergey V Levchenko,
Darragh P O'Neill, [......],
Arup K Chakraborty,
Daniel M Chipman,
Frerich J Keil,
Arieh Warshel,
Warren J Hehre,
Henry F Schaefer, Jing Kong,
Anna I Krylov,
Peter M W Gill,
Martin Head-Gordon
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ABSTRACT: Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
Physical Chemistry Chemical Physics 08/2006; 8(27):3172-91. · 3.57 Impact Factor
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ABSTRACT: A new algorithm is presented to improve the efficiency of the computation of exchange-correlation contributions, a major time-consuming step in a density functional theory (DFT) calculation. The new method, called multiresolution exchange correlation (mrXC), takes advantage of the variation in resolution among the Gaussian basis functions and shifts the calculation associated with low-resolution (smooth) basis function pairs to an even-spaced cubic grid. The cubic grid is much less dense in the vicinity of the nuclei than the atom-centered grid and the computation on the former is shown to be much more efficient than on the latter. MrXC does not alter the formalism of the current standard algorithm based on the atom-centered grid (ACG), but instead employs two fast and accurate transformations between the ACG and the cubic grid. Preliminary results with local density approximation have shown that mrXC yields three to five times improvement in efficiency with negligible error. The extension to DFT functionals with generalized gradient approximation is also briefly discussed.
The Journal of Chemical Physics 04/2006; 124(9):94109. · 3.33 Impact Factor
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Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology, BIOCOMP'06, Las Vegas, Nevada, USA, June 26-29, 2006; 01/2006
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ABSTRACT: A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.
Journal of Computational Chemistry 10/2005; 26(12):1270-8. · 4.58 Impact Factor
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ABSTRACT: Solving the coupled-perturbed Hartree±Fock (CPHF) equations is the most time consuming part in the analytical computation of second derivatives of the molecular energy with respect to the nuclei. This paper describes a unique parallelization approach for solving the CPHF equations. The computational load is divided by the nuclear perturbations and distributed evenly among the computing nodes. The parallel algorithm is scalable with respect to the size of the molecule, i.e. the larger the molecule, the greater the parallel speedup. The memory storage requirements are also distributed among the processors, with little communication among the processors. The method is implemented in the Q-Chem software package and its performance is discussed. This work represents the ®rst step in a research project to parallelize analytical frequency calculations at Hartree±Fock and density functional theory levels.
01/2002; 100:1755-1761.
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ABSTRACT: We have incorporated MPI based parallelism with dynamic load balance into the Hartree–Fock and DFT modules of Q-Chem. A series of benchmark calculations consisting of both single point energy and gradient calculations were carried out to gauge the performance of the parallel modules. Calculations were carried out on two different parallel computers, namely a shared memory Silicon Graphics Origin2000 and a distributed memory Cray T3E, to show the flexibility of the code and demonstrate the great utility of MPI. Scalability for the DFT and Hartree–Fock modules is demonstrated for up to 64 processors. © 2000 Elsevier Science B.V. All rights reserved.
Computer Physics Communications 01/2000; 128:170-177. · 3.27 Impact Factor
