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Mark S Gordon - One of the best experts on this subject based on the ideXlab platform.
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Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method
Journal of Physical Chemistry A, 2014Co-Authors: Hiroya Nakata, Kazuo Kitaura, Michael W. I. Schmidt, Shinichiro Nakamura, Dmitri G Fedorov, Mark S GordonAbstract:The fully analytic Energy Gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF Energy Gradient is compared with the corresponding numerical Gradient, illustrating the accuracy of the analytic Gradient. The ROHF analytic Gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the Energy Gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.
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fragment molecular orbital molecular dynamics with the fully analytic Energy Gradient
Journal of Chemical Theory and Computation, 2012Co-Authors: Kurt R Brorsen, Noriyuki Minezawa, Theresa L Windus, Mark S GordonAbstract:Fragment molecular orbital molecular dynamics (FMO-MD) with periodic boundary conditions is performed on liquid water using the analytic Energy Gradient, the electrostatic potential point charge approximation, and the electrostatic dimer approximation. Compared to previous FMO-MD simulations of water that used an approximate Energy Gradient, inclusion of the response terms to provide a fully analytic Energy Gradient results in better Energy conservation in the NVE ensemble for liquid water. An FMO-MD simulation that includes the fully analytic Energy Gradient and two body corrections (FMO2) gives improved Energy conservation compared with a previously calculated FMO-MD simulation with an approximate Energy Gradient and including up to three body corrections (FMO3).
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fully analytic Energy Gradient in the fragment molecular orbital method
Journal of Chemical Physics, 2011Co-Authors: Takeshi Nagata, Kazuo Kitaura, Dmitri G Fedorov, Kurt R Brorsen, Mark S GordonAbstract:The Z-vector equations are derived and implemented for solving the response term due to the external electrostatic potentials, and the corresponding contribution is added to the Energy Gradients in the framework of the fragment molecular orbital (FMO) method. To practically solve the equations for large molecules like proteins, the equations are decoupled by taking advantage of the local nature of fragments in the FMO method and establishing the self-consistent Z-vector method. The resulting Gradients are compared with numerical Gradients for the test molecular systems: (H2O)64, alanine decamer, hydrated chignolin with the protein data bank (PDB) ID of 1UAO, and a Trp-cage miniprotein construct (PDB ID: 1L2Y). The computation time for calculating the response contribution is comparable to or less than that of the FMO self-consistent charge calculation. It is also shown that the Energy Gradients for the electrostatic dimer approximation are fully analytic, which significantly reduces the computational cost...
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implementation of the analytic Energy Gradient for the combined time dependent density functional theory effective fragment potential method application to excited state molecular dynamics simulations
Journal of Chemical Physics, 2011Co-Authors: Noriyuki Minezawa, Nuwan De Silva, Federico Zahariev, Mark S GordonAbstract:Excited-state quantum mechanics/molecular mechanics molecular dynamics simulations are performed, to examine the solvent effects on the fluorescence spectra of aqueous formaldehyde. For that purpose, the analytical Energy Gradient has been derived and implemented for the linear-response time-dependent density functional theory (TDDFT) combined with the effective fragment potential (EFP) method. The EFP method is an efficient ab initio based polarizable model that describes the explicit solvent effects on electronic excitations, in the present work within a hybrid TDDFT/EFP scheme. The new method is applied to the excited-state MD of aqueous formaldehyde in the n-π* state. The calculated π*→n transition Energy and solvatochromic shift are in good agreement with other theoretical results.
Hua-shu Dou - One of the best experts on this subject based on the ideXlab platform.
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A universal equation for calculating the Energy Gradient function in shear driven flows using the Energy Gradient theory.
arXiv: Fluid Dynamics, 2020Co-Authors: Hua-shu DouAbstract:The Energy Gradient theory was proposed in our previous studies. The mechanism of flow instability is very different in shear driven flows from pressure driven flows. In present paper, the relationship for the Energy variation, work done, and Energy dissipation in unit volumetric fluid of incompressible flow is derived. A universal equation for calculating the Energy Gradient function in shear driven flows is presented. With the calculation of the Energy Gradient function which is a field variable and is considered as a local Reynolds number, the stability of a basic flow can be analyzed. The method can be applied to parallel flows, curved flows, and various complex flows.
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Large eddy simulation of Energy Gradient field in a centrifugal pump impeller
Proceedings of the Institution of Mechanical Engineers Part C: Journal of Mechanical Engineering Science, 2018Co-Authors: Xiaoping Chen, Zuchao Zhu, Hua-shu DouAbstract:Large eddy simulation of the fluid flow in a centrifugal pump impeller is conducted at design load and quarter load, and the Energy Gradient field is analyzed to reveal the behavior of internal flo...
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Analysis of vortex breakdown in an enclosed cylinder based on the Energy Gradient theory
European Journal of Mechanics - B Fluids, 2018Co-Authors: Meina Xiao, Hua-shu Dou, Zuchao Zhu, Xifeng Zhao, Songying Chen, Hongli Chen, Yikun WeiAbstract:Abstract Numerical simulation is carried out to study the phenomenon of vortex breakdown in an enclosed cylinder. The Energy Gradient theory is used to explain the vortex breakdown in the cylinder with consideration of centrifugal force, Coriolis force, angular momentum and azimuthal vorticity. The research results show that the large value of Energy Gradient function K is mainly located at the centerline and the region between the circulation vortices on both sides of the cylinder and the vortex breakdown bubbles at the centerline. It is found that the position of the local peak value of the Energy Gradient function K at the centerline corresponds to the location of vortex breakdown first occurrence. The position of the local peak value of K function in horizontal direction corresponds to the velocity inflection points except for the centerline. The vortex breakdown is mainly determined by the high K value at the centerline for low aspect ratio. The influence of the region of high K value between the circulation vortices on both sides of the cylinder and the vortex breakdown bubbles at the centerline becomes larger with the increase of the aspect ratio. The occurrence and development of the vortex breakdown bubble may be affected by the region of high K value between the circulation vortices on both sides of the cylinder and the vortex breakdown bubbles at the centerline for high aspect ratio.
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A universal equation for calculating the Energy Gradient function in the Energy Gradient theory
arXiv: Fluid Dynamics, 2016Co-Authors: Hua-shu DouAbstract:The relationship for the Energy variation, work done, and Energy dissipation in unit volumetric fluid of incompressible flow is derived. A universal equation for calculating the Energy Gradient function is presented for situations where both pressure driven flow and shear driven flow are present simultaneously.
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Numerical Investigation of Flow Instability in Centrifugal Pump Based on Energy Gradient Method
Volume 2D: Turbomachinery, 2016Co-Authors: Lulu Zheng, Hua-shu Dou, Xiaoping Chen, Zuchao Zhu, Baoling CuiAbstract:Simulation of turbulent flow in a pump is carried out with the RANS equations and the RNG k-epsilon turbulence model. Numerical simulation has been compared with the experimental data. The results show that separating vortex is firstly produced at the pressure side of the impeller passage near the tongue. Then it spreads to the inlet and outlet of the impeller passages and moved to the centre region of impeller passages from the boundaries. Finally, it almost occupies all the impeller passages and multiple vortices exist in impeller passages at small flow rate. It is found that the tongue has large effect on the flow in the impeller passage approaching to it. The impeller passage near the tongue is easily tending to be unstable comparing with others passages. The Energy Gradient theory is used to analyze the flow stability in the impeller. The region with larger value of Energy Gradient function K means the bigger turbulence intensity and poor flow stability. At small flow rate the regions with large value of K are enlarged and are mainly located at both sides of blade pressure and suction surfaces where the flow is easily tending to be unstable.
Noriyuki Minezawa - One of the best experts on this subject based on the ideXlab platform.
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fragment molecular orbital molecular dynamics with the fully analytic Energy Gradient
Journal of Chemical Theory and Computation, 2012Co-Authors: Kurt R Brorsen, Noriyuki Minezawa, Theresa L Windus, Mark S GordonAbstract:Fragment molecular orbital molecular dynamics (FMO-MD) with periodic boundary conditions is performed on liquid water using the analytic Energy Gradient, the electrostatic potential point charge approximation, and the electrostatic dimer approximation. Compared to previous FMO-MD simulations of water that used an approximate Energy Gradient, inclusion of the response terms to provide a fully analytic Energy Gradient results in better Energy conservation in the NVE ensemble for liquid water. An FMO-MD simulation that includes the fully analytic Energy Gradient and two body corrections (FMO2) gives improved Energy conservation compared with a previously calculated FMO-MD simulation with an approximate Energy Gradient and including up to three body corrections (FMO3).
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implementation of the analytic Energy Gradient for the combined time dependent density functional theory effective fragment potential method application to excited state molecular dynamics simulations
Journal of Chemical Physics, 2011Co-Authors: Noriyuki Minezawa, Nuwan De Silva, Federico Zahariev, Mark S GordonAbstract:Excited-state quantum mechanics/molecular mechanics molecular dynamics simulations are performed, to examine the solvent effects on the fluorescence spectra of aqueous formaldehyde. For that purpose, the analytical Energy Gradient has been derived and implemented for the linear-response time-dependent density functional theory (TDDFT) combined with the effective fragment potential (EFP) method. The EFP method is an efficient ab initio based polarizable model that describes the explicit solvent effects on electronic excitations, in the present work within a hybrid TDDFT/EFP scheme. The new method is applied to the excited-state MD of aqueous formaldehyde in the n-π* state. The calculated π*→n transition Energy and solvatochromic shift are in good agreement with other theoretical results.
Masataka Nagaoka - One of the best experts on this subject based on the ideXlab platform.
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free Energy Gradient method and its recent related developments free Energy optimization and vibrational frequency analysis in solution
2015Co-Authors: Yukichi Kitamura, Masataka Nagaoka, Norio Takenaka, Yoshiyuki KoyanoAbstract:To obtain stable states (SS) and transition states (TS) of chemical reaction system in condensed state at a finite temperature, the free Energy Gradient (FEG) method was proposed in 1998 as an optimization method on a multidimensional free Energy surface (FES) . This is analogous to the method for the Born Oppenheimer potential Energy surface (PES) considered by ab initio molecular orbital (MO) calculation , and utilizes the force and Hessian on the FES with respect to the coordinates of a solute molecule, which can be adiabatically calculated by molecular dynamics (MD) method . In this chapter, we reviewed the FEG methodology that is the method for estimating molecular properties based on the free Energy (FE) landscape in condensed state and also discussed a future perspective for the improvement and the extension of the theoretical methods. We believe that a family of the FEG methodologies should become more efficient as one promising strategic setting and will play important roles to survey condensed state chemistry on the basis of recent supercomputing technology.
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reaction path optimization and vibrational frequency analysis via ab initio qm mm free Energy Gradient feg method application to isomerization process of glycine in aqueous solution
Theoretical Chemistry Accounts, 2011Co-Authors: Norio Takenaka, Toshio Asada, Yukichi Kitamura, Yoshiyuki Koyano, Masataka NagaokaAbstract:For the purpose to explore reaction paths accurately for chemical reaction systems in solution, we have proposed the free Energy Gradient (FEG) method combined with ab initio QM/MM–MD calculation, i.e., the ab initio QM/MM–FEG method. For demonstration, the method has been applied to the isomerization reaction of glycine in aqueous solution, i.e., the intramolecular proton transfer reaction from zwitterion (ZW) to the neutral form (NF). Including the solvent effect explicitly by the ab initio QM/MM–FEG method, those stable-state structures were found different from those obtained in gas phase and by an implicit dielectric continuum model at the same ab initio QM level. Additionally, by the vibration frequency analysis with the “free Energy (FE)” hessian in solution, the calculated vibrational frequencies were in good agreement with the experimental ones in the range from low to middle frequency of ZW. Furthermore, the FE of activation from ZW to NF was found in very good agreement with not only the estimation by the Car-Parrinello MD method but also by the previous experimental one. It is concluded that the ab initio QM/MM–FEG method is promising and should provide a better description of chemical reaction systems in solution in comparison with a number of conventional approaches by using the mean field approximations.
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structure optimization via free Energy Gradient method application to glycine zwitterion in aqueous solution
Journal of Chemical Physics, 2000Co-Authors: Naoto Okuyamayoshida, Ken Kataoka, Masataka Nagaoka, Tokio YamabeAbstract:The free Energy Gradient method was applied to the multidimensional geometry optimization of glycine zwitterion (ZW) in aqueous solution in order not only to demonstrate its applicability, but also to examine its efficiency. The method utilizes force on the free Energy surface that can be directly calculated by the molecular dynamics method and the free Energy perturbation theory. Then, the most stable ZW structure in aqueous solution was obtained within the tolerance assumed, and it was found that the free Energy (FE) and enthalpy changes of stabilization from the initial geometry optimized in the gas phase are −0.9 and −3.5 kcal/mol, respectively, and the amino and carboxyl groups are spatially separated by each other due to their solvating with water molecules. Comparing the contributions of enthalpy and entropy to FE, the former is attributed to the main origin of FE stabilization during the optimization procedure, and it was found that solvation entropy prevents water molecules from solvating the ZW ...
Kimihiko Hirao - One of the best experts on this subject based on the ideXlab platform.
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excited state geometry optimizations by analytical Energy Gradient of long range corrected time dependent density functional theory
Journal of Chemical Physics, 2006Co-Authors: Mahito Chiba, Takao Tsuneda, Kimihiko HiraoAbstract:An analytical excitation Energy Gradient of long-range corrected time-dependent density functional theory (LC-TDDFT) is presented. This is based on a previous analytical TDDFT Gradient formalism, which avoids solving the coupled-perturbed Kohn-Sham equation for each nuclear degree of freedom. In LC-TDDFT, exchange interactions are evaluated by combining the short-range part of a DFT exchange functional with the long-range part of the Hartree-Fock exchange integral. This LC-TDDFT Gradient was first examined by calculating the excited state geometries and adiabatic excitation energies of small typical molecules and a small protonated Schiff base. As a result, we found that long-range interactions play a significant role even in valence excited states of small systems. This analytical LC-TDDFT Gradient was also applied to the investigations of small twisted intramolecular charge transfer (TICT) systems. By comparing with calculated ab initio multireference perturbation theory and experimental results, we found that LC-TDDFT gave much more accurate absorption and fluorescence energies of these systems than those of conventional TDDFTs using pure and hybrid functionals. For optimized excited state geometries, LC-TDDFT provided fairly different twisting and wagging angles of these small TICT systems in comparison with conventional TDDFT results.