1
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Ullah SA, Yang X, Jones B, Zhao S, Geng W, Wei GW. Bridging Eulerian and Lagrangian Poisson-Boltzmann solvers by ESES. J Comput Chem 2024; 45:306-320. [PMID: 37830273 PMCID: PMC10993026 DOI: 10.1002/jcc.27239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/08/2023] [Accepted: 09/24/2023] [Indexed: 10/14/2023]
Abstract
The Poisson-Boltzmann (PB) model is a widely used electrostatic model for biomolecular solvation analysis. Formulated as an elliptic interface problem, the PB model can be numerically solved on either Eulerian meshes using finite difference/finite element methods or Lagrangian meshes using boundary element methods. Molecular surface generators, which produce the discretized dielectric interfaces between solutes and solvents, are critical factors in determining the accuracy and efficiency of the PB solvers. In this work, we investigate the utility of the Eulerian Solvent Excluded Surface (ESES) software for rendering conjugated Eulerian and Lagrangian surface representations, which enables us to numerically validate and compare the quality of Eulerian PB solvers, such as the MIBPB solver, and the Lagrangian PB solvers, such as the TABI-PB solver. Furthermore, with the ESES software and its associated PB solvers, we are able to numerically validate an interesting and useful but often neglected source-target symmetric property associated with the linearized PB model.
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Affiliation(s)
| | - Xin Yang
- Department of Mathematics, Southern Methodist University, Dallas, Texas, USA
| | - Ben Jones
- Department of Mathematics, Michigan State University, East Lansing, Michigan, USA
| | - Shan Zhao
- Department of Mathematics, University of Alabama, Tuscaloosa, Alabama, USA
| | - Weihua Geng
- Department of Mathematics, Southern Methodist University, Dallas, Texas, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, Michigan, USA
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2
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Zhai H, Lee S, Cui ZH, Cao L, Ryde U, Chan GKL. Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters. J Phys Chem A 2023; 127:9974-9984. [PMID: 37967028 PMCID: PMC10694817 DOI: 10.1021/acs.jpca.3c06142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023]
Abstract
Characterizing the electronic structure of the iron-sulfur clusters in nitrogenase is necessary to understand their role in the nitrogen fixation process. One challenging task is to determine the protonation state of the intermediates in the nitrogen fixing cycle. Here, we use a dimeric iron-sulfur model to study relative energies of protonation at C, S, or Fe. Using a composite method based on coupled cluster and density matrix renormalization group energetics, we converge the relative energies of four protonated configurations with respect to basis set and correlation level. We find that accurate relative energies require large basis sets as well as a proper treatment of multireference and relativistic effects. We have also tested ten density functional approximations for these systems. Most of them give large errors in their relative energies. The best performing functional in this system is B3LYP, which gives mean absolute and maximum deviations of only 10 and 13 kJ/mol with respect to our correlated wave function estimates, respectively, comparable to the uncertainty in our correlated estimates. Our work provides benchmark results for the calibration of new approximate electronic structure methods and density functionals for these problems.
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Affiliation(s)
- Huanchen Zhai
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Seunghoon Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Zhi-Hao Cui
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lili Cao
- Department
of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department
of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Garnet Kin-Lic Chan
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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3
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Remme R, Kaczun T, Scheurer M, Dreuw A, Hamprecht FA. KineticNet: Deep learning a transferable kinetic energy functional for orbital-free density functional theory. J Chem Phys 2023; 159:144113. [PMID: 37830452 DOI: 10.1063/5.0158275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
Orbital-free density functional theory (OF-DFT) holds promise to compute ground state molecular properties at minimal cost. However, it has been held back by our inability to compute the kinetic energy as a functional of electron density alone. Here, we set out to learn the kinetic energy functional from ground truth provided by the more expensive Kohn-Sham density functional theory. Such learning is confronted with two key challenges: Giving the model sufficient expressivity and spatial context while limiting the memory footprint to afford computations on a GPU and creating a sufficiently broad distribution of training data to enable iterative density optimization even when starting from a poor initial guess. In response, we introduce KineticNet, an equivariant deep neural network architecture based on point convolutions adapted to the prediction of quantities on molecular quadrature grids. Important contributions include convolution filters with sufficient spatial resolution in the vicinity of nuclear cusp, an atom-centric sparse but expressive architecture that relays information across multiple bond lengths, and a new strategy to generate varied training data by finding ground state densities in the face of perturbations by a random external potential. KineticNet achieves, for the first time, chemical accuracy of the learned functionals across input densities and geometries of tiny molecules. For two-electron systems, we additionally demonstrate OF-DFT density optimization with chemical accuracy.
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Affiliation(s)
- R Remme
- IWR, Heidelberg University Im Neuenheimer Feld 205, 69120 Heidelberg Baden-Württemberg, Germany
| | - T Kaczun
- IWR, Heidelberg University Im Neuenheimer Feld 205, 69120 Heidelberg Baden-Württemberg, Germany
| | - M Scheurer
- IWR, Heidelberg University Im Neuenheimer Feld 205, 69120 Heidelberg Baden-Württemberg, Germany
| | - A Dreuw
- IWR, Heidelberg University Im Neuenheimer Feld 205, 69120 Heidelberg Baden-Württemberg, Germany
| | - F A Hamprecht
- IWR, Heidelberg University Im Neuenheimer Feld 205, 69120 Heidelberg Baden-Württemberg, Germany
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4
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Stahn M, Ehlert S, Grimme S. Extended Conductor-like Polarizable Continuum Solvation Model (CPCM-X) for Semiempirical Methods. J Phys Chem A 2023; 127:7036-7043. [PMID: 37567769 DOI: 10.1021/acs.jpca.3c04382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
We have developed a new method to accurately account for solvation effects in semiempirical quantum mechanics based on a polarizable continuum model (PCM). The extended conductor-like polarizable continuum model (CPCM-X) incorporates a computationally efficient domain decomposition conductor-like screening model (ddCOSMO) for extended tight binding (xTB) methods and uses a post-processing approach based on established solvation models, like the conductor-like screening model for real solvents (COSMO-RS) and the universal solvent model based on solute electron density (SMD). According to various benchmarks, the approach performs well across a broad range of systems and applications, including hydration free energies, non-aqueous solvation free energies, and large supramolecular association reactions of neutral and charged species. Our method for computing solvation free energies is much more accurate than the current methods in the xtb program package. It improves the accuracy of solvation free energies by up to 40% for larger supramolecular association reactions to match even the accuracy of higher-level DFT-based solvation models like COSMO-RS and SMD while being computationally more than 2 orders of magnitude faster. The proposed method and the underlying ddCOSMO model are readily available for a wide variety of solvents and are accessible in xtb for use in various computational applications.
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Affiliation(s)
- Marcel Stahn
- Mulliken Center of Theoretical Chemistry, 53115 Bonn, Germany
| | | | - Stefan Grimme
- Mulliken Center of Theoretical Chemistry, 53115 Bonn, Germany
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5
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Xu X. Constrained Nuclear-Electronic Orbital Density Functional Theory with a Dielectric Continuum Solvent Model. J Phys Chem A 2023. [PMID: 37470267 DOI: 10.1021/acs.jpca.3c02507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Solvent effects are crucial for simulating chemical and biological processes in solutions. The continuum solvation model is widely used for incorporating solvent effects with different levels of theoretical descriptions of solutes. For solutes and solutions containing hydrogen atoms, nuclear quantum effects can also be nonnegligible for reliable simulations. In this work, we couple our recently developed constrained nuclear-electronic orbital density functional theory with a dielectric continuum solvation model to cover nuclear quantum effects and solvent effects simultaneously. This approach is applied to the formate ion, where an anomalous solvatochromic shift in C-H stretch frequency was reported in experiments. By using this new approach to account for nuclear quantum effects and solvent effects, we show that the vibrational frequency of the C-H stretch and the solvatochromic shift are accurately described.
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Affiliation(s)
- Xi Xu
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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6
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Janesko BG. Core-Projected Hybrids Fix Systematic Errors in Time-Dependent Density Functional Theory Predicted Core-Electron Excitations. J Chem Theory Comput 2023. [PMID: 37437304 DOI: 10.1021/acs.jctc.3c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Linear response time-dependent density functional theory (TDDFT) is widely applied to valence, Rydberg, and charge-transfer excitations but, in its current form, makes large errors for core-electron excitations. This work demonstrates that the admixture of nonlocal exact exchange in atomic core regions significantly improves TDDFT-predicted core excitations. Exact exchange admixture is accomplished using projected hybrid density functional theory [ J. Chem. Theory Comput. 2023, 19, 837-847]. Scalar relativistic TDDFT calculations using core-projected B3LYP accurately model core excitations of second-period elements C-F and third-period elements Si-Cl, without sacrificing performance for the relative shifts of core excitation energies. Predicted K-edge X-ray near absorption edge structure (XANES) of a series of sulfur standards highlight the value of this approach. Core-projected hybrids appear to be a practical solution to TDDFT's limitations for core excitations, in the way that long-range-corrected hybrids are a practical solution to TDDFT's limitations for Rydberg and charge-transfer excitations.
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Affiliation(s)
- Benjamin G Janesko
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
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7
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Minenkov Y. Solv: An Alternative Continuum Model Implementation Based on Fixed Atomic Charges, Scaled Particle Theory, and the Atom-Atom Potential Method. J Chem Theory Comput 2023. [PMID: 37390470 DOI: 10.1021/acs.jctc.3c00410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
An alternative continuum model implementation is reported. The electrostatic contribution to the solvation Gibbs free energy utilizes the noniterative conductor-like screening model of Vyboishchikov and Voityuk (DOI: 10.1002/jcc.26531) based on the fixed partial atomic charges. The nonelectrostatic solute-solvent dispersion-repulsion energy is calculated through the Caillet-Claverie atom-atom potential method employing the grid-based approach. The nonelectrostatic cavitation energy is computed within the scaled particle theory (SPT) formalism with the solute hard-sphere radius obtained via the Pierotti-Claverie (PC) scheme, from the solute molecular surface (SPT-S) or volume (SPT-V). The solvent hard-sphere radius is derived through the fitting to the experimental total solvation free energies of 2530 neutral species in 92 solvents. Application of the model to reproduce both the absolute and relative (reaction net) solvation free energies indicates that the SPT-V approach based on the CM5 charges is the best performer. The method is suggested for the solvation free energy calculation in the nonaqueous solvents.
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Affiliation(s)
- Yury Minenkov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russian Federation
- Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russian Federation
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8
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Jha A, Nottoli M, Mikhalev A, Quan C, Stamm B. Linear scaling computation of forces for the domain-decomposition linear Poisson-Boltzmann method. J Chem Phys 2023; 158:104105. [PMID: 36922147 DOI: 10.1063/5.0141025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
The Linearized Poisson-Boltzmann (LPB) equation is a popular and widely accepted model for accounting solvent effects in computational (bio-) chemistry. In the present article, we derive the analytical forces using the domain-decomposition-based LPB-method with a van-der Waals or solvent-accessible surface. We present an efficient strategy to compute the forces and its implementation, allowing linear scaling of the method with respect to the number of atoms using the fast multipole method. Numerical tests illustrate the accuracy of the computation of the analytical forces and compare the efficiency with other available methods.
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Affiliation(s)
- Abhinav Jha
- Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Michele Nottoli
- Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Aleksandr Mikhalev
- Applied and Computational Mathematics, RWTH Aachen University, Schinkelstraße 2, 52062 Aachen, Germany
| | - Chaoyu Quan
- Shenzhen International Center for Mathematics , Southern University of Science and Technology, Shenzhen, China
| | - Benjamin Stamm
- Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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9
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Nottoli M, Mikhalev A, Stamm B, Lipparini F. Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library. J Phys Chem B 2022; 126:8827-8837. [PMID: 36265187 PMCID: PMC9639080 DOI: 10.1021/acs.jpcb.2c04579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies. In this paper we present a preliminary interface between the molecular dynamics package Tinker and the ddX library. The interface was used to test a united atom coarse-graining strategy that allowed us to push ddCOSMO to its limits by computing solvation energies on systems with up to 7 million atoms. We first present benchmarks to find an optimal discretization, and then, we discuss the performance and results obtained with fine- and coarse-grained solvation energy calculations.
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Affiliation(s)
- Michele Nottoli
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, 56124Pisa, Italy
| | - Aleksandr Mikhalev
- Department
of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062Aachen, Germany
| | - Benjamin Stamm
- Department
of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062Aachen, Germany
| | - Filippo Lipparini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, 56124Pisa, Italy,E-mail:
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10
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Mikhalev A, Nottoli M, Stamm B. Linearly scaling computation of ddPCM solvation energy and forces using the fast multipole method. J Chem Phys 2022; 157:114103. [PMID: 36137796 DOI: 10.1063/5.0104536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This paper proposes the first linear scaling implementation for the domain decomposition approach of the polarizable continuum model (ddPCM) for the computation of the solvation energy and forces. The ddPCM-equation consists of a (non-local) integral equation on the van der Waals or solvent accessible surface of the solute's cavity resulting in a dense solution matrix, and, in turn, one matrix-vector multiplication has a quadratic arithmetic complexity with respect to the number of atoms of the solute molecule. The use of spherical harmonics as basis functions makes it natural to employ the fast multipole method (FMM) in order to provide an asymptotically linear scaling method. In this paper, we employ the FMM in a non-uniform manner with a clusterization based on a recursive inertial bisection. We present some numerical tests illustrating the accuracy and scaling of our implementation.
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Affiliation(s)
- A Mikhalev
- Department of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany
| | - M Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - B Stamm
- Institute of Applied Analysis and Numerical Simulations, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
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11
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On the Convergence of the Damped Additive Schwarz Methods and the Subdomain Coloring. MATHEMATICAL AND COMPUTATIONAL APPLICATIONS 2022. [DOI: 10.3390/mca27040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this paper, we consider that the subdomains of the domain decomposition are colored such that the subdomains with the same color do not intersect and introduce and analyze the convergence of a damped additive Schwarz method related to such a subdomain coloring for the resolution of variational inequalities and equations. In this damped method, a single damping value is associated with all the subdomains having the same color. We first make this analysis both for variational inequalities and, as a special case, for equations in an abstract framework. By introducing an assumption on the decomposition of the convex set of the variational inequality, we theoretically analyze in a reflexive Banach space the convergence of the damped additive Schwarz method. The introduced assumption contains a constant C0, and we explicitly write the expression of the convergence rates, depending on the number of colors and the constant C0, and find the values of the damping constants which minimize them. For problems in the finite element spaces, we write the constant C0 as a function of the overlap parameter of the domain decomposition and the number of colors of the subdomains. We show that, for a fixed overlap parameter, the convergence rate, as a function of the number of subdomains has an upper limit which depends only on the number of the colors of the subdomains. Obviously, this limit is independent of the total number of subdomains. Numerical results are in agreement with the theoretical ones. They have been performed for an elasto-plastic problem to verify the theoretical predictions concerning the choice of the damping parameter, the dependence of the convergence on the overlap parameter and on the number of subdomains.
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12
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Mancini G, Fusè M, Lipparini F, Nottoli M, Scalmani G, Barone V. Molecular Dynamics Simulations Enforcing Nonperiodic Boundary Conditions: New Developments and Application to the Solvent Shifts of Nitroxide Magnetic Parameters. J Chem Theory Comput 2022; 18:2479-2493. [PMID: 35257572 PMCID: PMC9009096 DOI: 10.1021/acs.jctc.2c00046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Multiscale methods
combining quantum mechanics and molecular mechanics
(QM/MM) have become the most suitable and effective strategies for
the investigation of the spectroscopic properties of medium-to-large
size chromophores in condensed phases. In this context, we are developing
a novel workflow aimed at improving the generality, reliability, and
ease of use of the available computational tools. In this paper, we
report our latest developments with specific reference to a general
protocol based on atomistic simulations, carried out under nonperiodic
boundary conditions (NPBC). In particular, we add to our in house
MD engine a new efficient treatment of mean field electrostatic contributions
to energy and forces, together with the capability of performing the
simulations either in the canonical (NVT) or in the
isothermal–isobaric (NPT) ensemble. Next,
we provide convincing evidence that the NBPC approach enhanced by
specific tweaks for rigid body propagation, allows for the simulation
of solute–solvent systems with a minimum number of degrees
of freedom and large integration time step. After its validation,
this new approach is applied to the challenging case of solvatochromic
effects on the electron paramagnetic resonance (EPR) spectrum of a
prototypical nitroxide radical. To this end, we propose and validate
also an automated protocol to extract and weight simulation snapshots,
making use of a continuous description of the strength of solute–solvent
hydrogen bridges. While further developments are being worked on,
the effectiveness of our approach, even in its present form, is demonstrated
by the accuracy of the results obtained through an unsupervised approach
characterized by a strongly reduced computational cost as compared
to that of conventional QM/MM models, without any appreciable deterioration
of accuracy.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Universitaá di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Universitaá di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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13
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Eriksen JJ. Electronic excitations through the prism of mean-field decomposition techniques. J Chem Phys 2022; 156:061101. [PMID: 35168332 DOI: 10.1063/5.0082938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The potential of mean-field decomposition techniques in interpreting electronic transitions in molecules is explored, in particular, the usefulness of these for offering computational signatures of different classes of such excitations. When viewed as a conceptual lens for this purpose, decomposed results are presented for ground- and excited-state energies and dipole moments of selected prototypical organic dyes, and the discrete nature of these properties as well as how they change upon transitioning from one state to another is analyzed without recourse to a discussion based on the involved molecular orbitals. On the basis of results obtained both with and without an account of continuum solvation, our work is further intended to shed new light on practical and pathological differences in between various functional approximations in orbital-optimized Kohn-Sham density functional theory for excited states, equipping practitioners and developers in the field with new probes and possible validation tools.
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Affiliation(s)
- Janus J Eriksen
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, DK-2800 Kgs. Lyngby, Denmark
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14
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Filser J, Reuter K, Oberhofer H. Piecewise Multipole-Expansion Implicit Solvation for Arbitrarily Shaped Molecular Solutes. J Chem Theory Comput 2021; 18:461-478. [PMID: 34935366 DOI: 10.1021/acs.jctc.1c00834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The multipole-expansion (MPE) model is an implicit solvation model used to efficiently incorporate solvent effects in quantum chemistry. Even within the recent direct approach, the multipole basis used in MPE to express the dielectric response still solves the electrostatic problem inefficiently or not at all for solutes larger than approximately ten non-hydrogen atoms. In existing MPE parametrizations, the resulting systematic underestimation of the electrostatic solute-solvent interaction is presently compensated for by a systematic overestimation of nonelectrostatic attractive interactions. Even though the MPE model can thus reproduce experimental free energies of solvation of small molecules remarkably well, the inherent error cancellation makes it hard to assign physical meaning to the individual free-energy terms in the model, raising concerns about transferability. Here we resolve this issue by solving the electrostatic problem piecewise in 3D regions centered around all non-hydrogen nuclei of the solute, ensuring reliable convergence of the multipole series. The resulting method thus allows for a much improved reproduction of the dielectric response of a medium to a solute. Employing a reduced nonelectrostatic model with a single free parameter, in addition to the density isovalue defining the solvation cavity, our method yields free energies of solvation of neutral, anionic, and cationic solutes in water in good agreement with experiment.
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Affiliation(s)
- Jakob Filser
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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15
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Nottoli M, Nifosì R, Mennucci B, Lipparini F. Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation. J Chem Theory Comput 2021; 17:5661-5672. [PMID: 34476941 PMCID: PMC8444335 DOI: 10.1021/acs.jctc.1c00555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
We present the implementation
of a fully coupled polarizable QM/MM/continuum
model based on the AMOEBA polarizable force field and the domain decomposition
implementation of the conductor-like screening model. Energies, response
properties, and analytical gradients with respect to both QM and MM
nuclear positions are available, and a generic, atomistic cavity can
be employed. The model is linear scaling in memory requirements and
computational cost with respect to the number of classical atoms and
is therefore suited to model large, complex systems. Using three variants
of the green-fluorescent protein, we investigate the overall computational
cost of such calculations and the effect of the continuum model on
the convergence of the computed properties with respect to the size
of the embedding. We also demonstrate the fundamental role of polarization
effects by comparing polarizable and nonpolarizable embeddings to
fully QM ones.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Riccardo Nifosì
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
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16
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Gale A, Hruska E, Liu F. Quantum chemistry for molecules at extreme pressure on graphical processing units: Implementation of extreme-pressure polarizable continuum model. J Chem Phys 2021; 154:244103. [PMID: 34241353 DOI: 10.1063/5.0056480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Pressure plays essential roles in chemistry by altering structures and controlling chemical reactions. The extreme-pressure polarizable continuum model (XP-PCM) is an emerging method with an efficient quantum mechanical description of small- and medium-sized molecules at high pressure (on the order of GPa). However, its application to large molecular systems was previously hampered by a CPU computation bottleneck: the Pauli repulsion potential unique to XP-PCM requires the evaluation of a large number of electric field integrals, resulting in significant computational overhead compared to the gas-phase or standard-pressure polarizable continuum model calculations. Here, we exploit advances in graphical processing units (GPUs) to accelerate the XP-PCM-integral evaluations. This enables high-pressure quantum chemistry simulation of proteins that used to be computationally intractable. We benchmarked the performance using 18 small proteins in aqueous solutions. Using a single GPU, our method evaluates the XP-PCM free energy of a protein with over 500 atoms and 4000 basis functions within half an hour. The time taken by the XP-PCM-integral evaluation is typically 1% of the time taken for a gas-phase density functional theory (DFT) on the same system. The overall XP-PCM calculations require less computational effort than that for their gas-phase counterpart due to the improved convergence of self-consistent field iterations. Therefore, the description of the high-pressure effects with our GPU-accelerated XP-PCM is feasible for any molecule tractable for gas-phase DFT calculation. We have also validated the accuracy of our method on small molecules whose properties under high pressure are known from experiments or previous theoretical studies.
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Affiliation(s)
- Ariel Gale
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Eugen Hruska
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Fang Liu
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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17
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Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA
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18
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Chen J, Hu J, Xu Y, Krasny R, Geng W. Computing Protein pKas Using the TABI Poisson–Boltzmann Solver. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A common approach to computing protein pKas uses a continuum dielectric model in which the protein is a low dielectric medium with embedded atomic point charges, the solvent is a high dielectric medium with a Boltzmann distribution of ionic charges, and the pKa is related to the electrostatic free energy which is obtained by solving the Poisson–Boltzmann equation. Starting from the model pKa for a titrating residue, the method obtains the intrinsic pKa and then computes the protonation probability for a given pH including site–site interactions. This approach assumes that acid dissociation does not affect protein conformation aside from adding or deleting charges at titratable sites. In this work, we demonstrate our treecode-accelerated boundary integral (TABI) solver for the relevant electrostatic calculations. The pKa computing procedure is enclosed in a convenient Python wrapper which is publicly available at the corresponding author’s website. Predicted results are compared with experimental pKas for several proteins. Among ongoing efforts to improve protein pKa calculations, the advantage of TABI is that it reduces the numerical errors in the electrostatic calculations so that attention can be focused on modeling assumptions.
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Affiliation(s)
- Jiahui Chen
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Jingzhen Hu
- Department of Mathematics, Duke University, Durham, NC 27710, USA
| | - Yongjia Xu
- Department of Mathematics, Southern Methodist University, Dallas, TX 75275, USA
| | - Robert Krasny
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Weihua Geng
- Department of Mathematics, Southern Methodist University, Dallas, TX 75275, USA
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19
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Ren Y, Li MY, Song YX, Sui MY, Sun GY, Qu XC, Xie P, Lu JL. Refined standards for simulating UV–vis absorption spectra of acceptors in organic solar cells by TD-DFT. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Nottoli M, Lipparini F. General formulation of polarizable embedding models and of their coupling. J Chem Phys 2020; 153:224108. [PMID: 33317291 DOI: 10.1063/5.0035165] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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21
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Schwalbe S, Fiedler L, Kraus J, Kortus J, Trepte K, Lehtola S. PyFLOSIC: Python-based Fermi–Löwdin orbital self-interaction correction. J Chem Phys 2020; 153:084104. [DOI: 10.1063/5.0012519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sebastian Schwalbe
- Institute of Theoretical Physics, TU Bergakademie Freiberg, Leipziger Str. 23, D-09599 Freiberg, Germany
| | - Lenz Fiedler
- Institute of Theoretical Physics, TU Bergakademie Freiberg, Leipziger Str. 23, D-09599 Freiberg, Germany
| | - Jakob Kraus
- Institute of Theoretical Physics, TU Bergakademie Freiberg, Leipziger Str. 23, D-09599 Freiberg, Germany
| | - Jens Kortus
- Institute of Theoretical Physics, TU Bergakademie Freiberg, Leipziger Str. 23, D-09599 Freiberg, Germany
| | - Kai Trepte
- Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Susi Lehtola
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A. I. Virtasen Aukio 1), FI-00014 University of Helsinki, Finland
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22
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Sun Q, Zhang X, Banerjee S, Bao P, Barbry M, Blunt NS, Bogdanov NA, Booth GH, Chen J, Cui ZH, Eriksen JJ, Gao Y, Guo S, Hermann J, Hermes MR, Koh K, Koval P, Lehtola S, Li Z, Liu J, Mardirossian N, McClain JD, Motta M, Mussard B, Pham HQ, Pulkin A, Purwanto W, Robinson PJ, Ronca E, Sayfutyarova ER, Scheurer M, Schurkus HF, Smith JET, Sun C, Sun SN, Upadhyay S, Wagner LK, Wang X, White A, Whitfield JD, Williamson MJ, Wouters S, Yang J, Yu JM, Zhu T, Berkelbach TC, Sharma S, Sokolov AY, Chan GKL. Recent developments in the PySCF program package. J Chem Phys 2020; 153:024109. [DOI: 10.1063/5.0006074] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Qiming Sun
- AxiomQuant Investment Management LLC, Shanghai 200120, China
| | - Xing Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Samragni Banerjee
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peng Bao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Marc Barbry
- Simbeyond B.V., P.O. Box 513, NL-5600 MB, Eindhoven, The Netherlands
| | - Nick S. Blunt
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Nikolay A. Bogdanov
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - George H. Booth
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Jia Chen
- Department of Physics, University of Florida, Gainesville, Florida 32611, USA
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Zhi-Hao Cui
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Janus J. Eriksen
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Yang Gao
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, USA
| | - Sheng Guo
- Google Inc., Mountain View, California 94043, USA
| | - Jan Hermann
- FU Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
- TU Berlin, Machine Learning Group, Marchstr. 23, 10587 Berlin, Germany
| | - Matthew R. Hermes
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
| | - Kevin Koh
- Department of Chemistry and Biochemistry, The University of Notre Dame du Lac, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - Peter Koval
- Simune Atomistics S.L., Avenida Tolosa 76, Donostia-San Sebastian, Spain
| | - Susi Lehtola
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A. I. Virtasen aukio 1), FI-00014 Helsinki, Finland
| | - Zhendong Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Junzi Liu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Narbe Mardirossian
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, USA
| | | | - Mario Motta
- IBM Almaden Research Center, San Jose, California 95120, USA
| | - Bastien Mussard
- Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA
| | - Hung Q. Pham
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
| | - Artem Pulkin
- QuTech and Kavli Institute of Nanoscience, Delft University of Technology, The Netherlands
| | - Wirawan Purwanto
- Information Technology Services, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Paul J. Robinson
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Enrico Ronca
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), Via G. Moruzzi, 1, 56124 Pisa, Italy
| | - Elvira R. Sayfutyarova
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University of Heidelberg, 205 Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Henry F. Schurkus
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - James E. T. Smith
- Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA
| | - Chong Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Shi-Ning Sun
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, USA
| | - Shiv Upadhyay
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Lucas K. Wagner
- Department of Physics and Institute for Condensed Matter Theory, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - Xiao Wang
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
| | - Alec White
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - James Daniel Whitfield
- Department of Physics and Astronomy, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Mark J. Williamson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Jun Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jason M. Yu
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Tianyu Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Timothy C. Berkelbach
- Department of Chemistry, Columbia University, New York, New York 10027, USA
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
| | - Sandeep Sharma
- Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA
| | - Alexander Yu. Sokolov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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23
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Nottoli M, Stamm B, Scalmani G, Lipparini F. Quantum Calculations in Solution of Energies, Structures, and Properties with a Domain Decomposition Polarizable Continuum Model. J Chem Theory Comput 2019; 15:6061-6073. [DOI: 10.1021/acs.jctc.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benjamin Stamm
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Schinkelstraße 2, 52062 Aachen, Germany
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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24
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Corbella M, Cupellini L, Lipparini F, Scholes GD, Curutchet C. Spectral Variability in Phycocyanin Cryptophyte Antenna Complexes is Controlled by Changes in the α‐Polypeptide Chains. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marina Corbella
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry and Institute of Theoretical and Computational Chemistry (IQTC-UB), Faculty of Pharmacy and Food SciencesUniversity of Barcelona Av. Joan XXIII s/n 08028 Barcelona Spain
- Department of ChemistryUppsala University BMC Box 576 Uppsala S-751 23 Sweden
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica IndustrialeUniversity of Pisa Via Risorgimento 35 56126 Pisa Italy
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica IndustrialeUniversity of Pisa Via Risorgimento 35 56126 Pisa Italy
| | - Gregory D. Scholes
- Department of ChemistryPrinceton University Washington Road, Princeton New Jersey 08544 United States
| | - Carles Curutchet
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry and Institute of Theoretical and Computational Chemistry (IQTC-UB), Faculty of Pharmacy and Food SciencesUniversity of Barcelona Av. Joan XXIII s/n 08028 Barcelona Spain
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25
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Labat F, Civalleri B, Dovesi R. Implicit Solvation Using a Generalized Finite-Difference Approach in CRYSTAL: Implementation and Results for Molecules, Polymers, and Surfaces. J Chem Theory Comput 2018; 14:5969-5983. [PMID: 30347161 DOI: 10.1021/acs.jctc.8b00762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the implementation of an implicit solvation model in the CRYSTAL code. The solvation energy is separated into two components: the electrostatic contribution arising from a self-consistent reaction field treatment obtained within a generalized finite-difference Poisson model, augmented by a nonelectrostatic contribution proportional to the solvent-accessible surface area of the solute. A discontinuous dielectric boundary is used, along with a solvent-excluded surface built from interlocking atom-centered spheres on which apparent surface point charges are mapped. The procedure is general and can be performed at both the Hartree-Fock and density functional theory levels, with pure or hybrid functionals, for systems periodic in 0, 1, and 2 directions, that is, for isolated molecules and extended polymers and surfaces. The Poisson equation resolution and apparent surface charge formalism is first validated on model analytical test cases. The good agreement obtained on solvation free energies is further confirmed by calculations performed on a large test set of 501 neutral molecules, for which a mean unsigned error of 1.3 kcal/mol is obtained when compared to the available experimental data. Importantly, the self-consistent reaction field procedure converges well for all molecules tested. This is further verified for all polymers and surfaces considered. In particular, for periodic systems, results obtained on an infinite glycine chain and on the wettability parameters of SiO2 surfaces are in good agreement with previously published data. The size extensivity of the energetic terms involved in the electrostatic contribution to the solvation energy is also well verified. These encouraging results constitute a first step to take into account complex environments in the CRYSTAL code, potentially allowing for a more accurate modeling of complex processes for both periodic and nonperiodic systems.
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Affiliation(s)
- Frédéric Labat
- PSL Research University, Chimie Paristech-CNRS , Institut de Recherche de Chimie de Paris , 11 rue P. et M. Curie , 75005 Paris , France
| | - Bartolomeo Civalleri
- Dipartimento di Chimica IFM , Università di Torino and NIS - Nanostructured Interfaces and Surfaces - Centre of Excellence , Via P. Giuria 7 , 10125 Torino , Italy
| | - Roberto Dovesi
- Dipartimento di Chimica IFM , Università di Torino and NIS - Nanostructured Interfaces and Surfaces - Centre of Excellence , Via P. Giuria 7 , 10125 Torino , Italy
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26
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Klamt A, Diedenhofen M. A refined cavity construction algorithm for the conductor-like screening model. J Comput Chem 2018; 39:1648-1655. [DOI: 10.1002/jcc.25342] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46; Leverkusen 51379 Germany
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstraße 31; Regensburg 93053 Germany
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27
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Gatto P, Lipparini F, Stamm B. Computation of forces arising from the polarizable continuum model within the domain-decomposition paradigm. J Chem Phys 2017; 147:224108. [DOI: 10.1063/1.5008329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paolo Gatto
- Mathematics Division, Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benjamin Stamm
- Mathematics Division, Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany
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28
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Loco D, Lagardère L, Caprasecca S, Lipparini F, Mennucci B, Piquemal JP. Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding. J Chem Theory Comput 2017; 13:4025-4033. [DOI: 10.1021/acs.jctc.7b00572] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniele Loco
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Louis Lagardère
- UPMC Univ. Paris
06, Institut des Sciences du Calcul et des Données, F-75005, Paris, France
| | - Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Jean-Philip Piquemal
- UPMC Univ. Paris
06, UMR7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Institut Universitaire de France, Paris
Cedex 05, 75231, France
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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29
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Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP. Polarizable molecular dynamics in a polarizable continuum solvent. J Chem Theory Comput 2016; 11:623-34. [PMID: 26516318 DOI: 10.1021/ct500998q] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-term energy conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
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Affiliation(s)
- Filippo Lipparini
- UniversitéPierre et Marie Curie−Paris 06 (UPMC), UMR 7598, Laboratoire Jacques-Louis Lions, Sorbonne Universités, F-75005, Paris, France
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30
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Lipparini F, Mennucci B. Perspective: Polarizable continuum models for quantum-mechanical descriptions. J Chem Phys 2016; 144:160901. [DOI: 10.1063/1.4947236] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Filippo Lipparini
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D55128 Mainz, Germany
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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31
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Stamm B, Cancès E, Lipparini F, Maday Y. A new discretization for the polarizable continuum model within the domain decomposition paradigm. J Chem Phys 2016; 144:054101. [DOI: 10.1063/1.4940136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Goez A, Neugebauer J. A Local Variant of the Conductor-Like Screening Model for Fragment-Based Electronic-Structure Methods. J Chem Theory Comput 2015; 11:5277-90. [DOI: 10.1021/acs.jctc.5b00832] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Albrecht Goez
- Theoretische Organische Chemie,
Organisch-Chemisches Institut and Center for Multiscale Theory and
Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie,
Organisch-Chemisches Institut and Center for Multiscale Theory and
Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
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33
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Lipparini F, Scalmani G, Lagardère L, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum, classical, and hybrid QM/MM calculations in solution: general implementation of the ddCOSMO linear scaling strategy. J Chem Phys 2015; 141:184108. [PMID: 25399133 DOI: 10.1063/1.4901304] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We present the general theory and implementation of the Conductor-like Screening Model according to the recently developed ddCOSMO paradigm. The various quantities needed to apply ddCOSMO at different levels of theory, including quantum mechanical descriptions, are discussed in detail, with a particular focus on how to compute the integrals needed to evaluate the ddCOSMO solvation energy and its derivatives. The overall computational cost of a ddCOSMO computation is then analyzed and decomposed in the various steps: the different relative weights of such contributions are then discussed for both ddCOSMO and the fastest available alternative discretization to the COSMO equations. Finally, the scaling of the cost of the various steps with respect to the size of the solute is analyzed and discussed, showing how ddCOSMO opens significantly new possibilities when cheap or hybrid molecular mechanics/quantum mechanics methods are used to describe the solute.
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Affiliation(s)
- Filippo Lipparini
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac St. Bldg. 40, Wallingford, Connecticut 06492, USA
| | - Louis Lagardère
- Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
| | - Benjamin Stamm
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Eric Cancès
- Université Paris-Est, CERMICS, Ecole des Ponts and INRIA, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée Cedex 2, France
| | - Yvon Maday
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France
| | - Michael J Frisch
- Gaussian, Inc., 340 Quinnipiac St. Bldg. 40, Wallingford, Connecticut 06492, USA
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
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Caprasecca S, Jurinovich S, Lagardère L, Stamm B, Lipparini F. Achieving Linear Scaling in Computational Cost for a Fully Polarizable MM/Continuum Embedding. J Chem Theory Comput 2015; 11:694-704. [DOI: 10.1021/ct501087m] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 3, I-56124 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 3, I-56124 Pisa, Italy
| | - Louis Lagardère
- Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
| | - Benjamin Stamm
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
- CNRS, UMR
7598
and 7616, F-75005 Paris, France
| | - Filippo Lipparini
- Sorbonne Universités, UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France
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35
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Bugeanu M, Di Remigio R, Mozgawa K, Reine SS, Harbrecht H, Frediani L. Wavelet formulation of the polarizable continuum model. II. Use of piecewise bilinear boundary elements. Phys Chem Chem Phys 2015; 17:31566-81. [DOI: 10.1039/c5cp03410h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sparsity pattern obtained in the wavelet Galerkin boundary element representation of the PCM boundary integral operators. By employing a wavelet basis on a smooth solvent-excluded molecular surface the method is able to guarantee solutions with high accuracy at a linear cost in memory and computational time.
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Affiliation(s)
- Monica Bugeanu
- Department for Mathematics and Computer Science
- University of Basel
- Basel
- Switzerland
| | - Roberto Di Remigio
- Department of Chemistry
- Centre for Theoretical and Computational Chemistry
- University of Tromsø
- Tromsø
- Norway
| | - Krzysztof Mozgawa
- Department of Chemistry
- Centre for Theoretical and Computational Chemistry
- University of Tromsø
- Tromsø
- Norway
| | - Simen Sommerfelt Reine
- Department of Chemistry
- Centre for Theoretical and Computational Chemistry
- University of Oslo, Oslo
- Norway
| | - Helmut Harbrecht
- Department for Mathematics and Computer Science
- University of Basel
- Basel
- Switzerland
| | - Luca Frediani
- Department of Chemistry
- Centre for Theoretical and Computational Chemistry
- University of Tromsø
- Tromsø
- Norway
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Lipparini F, Lagardère L, Scalmani G, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach. J Phys Chem Lett 2014; 5:953-958. [PMID: 26270973 DOI: 10.1021/jz5002506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a new implementation of continuum solvation models for semiempirical Hamiltonians that allows the description of environmental effects on very large molecular systems. In this approach based on a domain decomposition strategy of the COSMO model (ddCOSMO), the solution to the COSMO equations is no longer the computational bottleneck but becomes a negligible part of the overall computation time. In this Letter, we analyze the computational impact of COSMO on the solution of the SCF equations for large to very large molecules, using semiempirical Hamiltonians, for both the new ddCOSMO implementation and the most recent, linear scaling one, based on the fast multipole method. A further analysis is on the simulation of the UV/visible spectrum of a light-harvesting pigment-protein complex. All of the results show how the new ddCOSMO algorithm paves the way to routine computations for large molecular systems in the condensed phase.
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Affiliation(s)
- Filippo Lipparini
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ‡Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, F-75005 Paris, France
- ¶Institut du Calcul et de la Simulation, Sorbonne Universités, UPMC Univ. Paris 06, F-75005 Paris, France
| | - Louis Lagardère
- ¶Institut du Calcul et de la Simulation, Sorbonne Universités, UPMC Univ. Paris 06, F-75005 Paris, France
| | - Giovanni Scalmani
- §Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Benjamin Stamm
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ∥CNRS, UMR 7598 and 7616, F-75005 Paris, France
| | | | - Yvon Maday
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- #Institut Universitaire de France, France
- ∇Division of Applied Maths, Brown University, Providence, Rhode Island 02912, United States
| | - Jean-Philip Piquemal
- †Laboratoire Jacques-Louis Lions, Sorbonne Universités, UPMC Univ. Paris 06, UMR 7598, F-75005 Paris, France
- ∥CNRS, UMR 7598 and 7616, F-75005 Paris, France
| | - Michael J Frisch
- §Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Benedetta Mennucci
- ◆Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
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37
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Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald. J Chem Theory Comput 2014; 10:1638-1651. [PMID: 26512230 DOI: 10.1021/ct401096t] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this paper, we present a scalable and efficient implementation of point dipole-based polarizable force fields for molecular dynamics (MD) simulations with periodic boundary conditions (PBC). The Smooth Particle-Mesh Ewald technique is combined with two optimal iterative strategies, namely, a preconditioned conjugate gradient solver and a Jacobi solver in conjunction with the Direct Inversion in the Iterative Subspace for convergence acceleration, to solve the polarization equations. We show that both solvers exhibit very good parallel performances and overall very competitive timings in an energy-force computation needed to perform a MD step. Various tests on large systems are provided in the context of the polarizable AMOEBA force field as implemented in the newly developed Tinker-HP package which is the first implementation for a polarizable model making large scale experiments for massively parallel PBC point dipole models possible. We show that using a large number of cores offers a significant acceleration of the overall process involving the iterative methods within the context of spme and a noticeable improvement of the memory management giving access to very large systems (hundreds of thousands of atoms) as the algorithm naturally distributes the data on different cores. Coupled with advanced MD techniques, gains ranging from 2 to 3 orders of magnitude in time are now possible compared to non-optimized, sequential implementations giving new directions for polarizable molecular dynamics in periodic boundary conditions using massively parallel implementations.
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Affiliation(s)
- Louis Lagardère
- UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
| | - Filippo Lipparini
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France ; UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France
| | - Étienne Polack
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
| | - Benjamin Stamm
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; CNRS, UMR 7598 and 7616, F-75005, Paris, France
| | - Éric Cancès
- Université Paris-Est, CERMICS, Ecole des Ponts and INRIA, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée, France
| | - Michael Schnieders
- Departments of Biomedical Engineering and Biochemistry, The University of Iowa, Iowa City, Iowa 52358, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yvon Maday
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; Institut Universitaire de France ; Brown Univ, Division of Applied Maths, Providence, RI, USA
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
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