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Lambros E, Link B, Chow M, Lipparini F, Hammes-Schiffer S, Li X. Assessing Implicit and Explicit Polarizable Solvation Models for Nuclear-Electronic Orbital Systems: Quantum Proton Polarization and Solvation Energetics. J Phys Chem A 2023; 127:9322-9333. [PMID: 37889479 DOI: 10.1021/acs.jpca.3c03153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Accurate simulations of many chemical processes require the inclusion of both nuclear quantum effects and a solvent environment. The nuclear-electronic orbital (NEO) approach, which treats electrons and select nuclei quantum mechanically on the same level, combined with a polarizable continuum model (PCM) for the solvent environment, addresses this challenge in a computationally practical manner. In this work, the NEO-PCM approach is extended beyond the IEF-PCM (integral equation formalism PCM) and C-PCM (conductor PCM) approaches to the SS(V)PE (surface and simulation of volume polarization for electrostatics) and ddCOSMO (domain decomposed conductor-like screening model) approaches. IEF-PCM, SS(V)PE, C-PCM, and ddCOSMO all exhibit similar solvation energies as well as comparable nuclear polarization within the NEO framework. The calculations show that the nuclear density does not leak out of the molecular cavity because it is much more localized than the electronic density. Finally, the polarization of quantized protons is analyzed in both continuum solvent and explicit solvent environments described by the polarizable MB-pol model, illustrating the impact of specific hydrogen-bonding interactions captured only by explicit solvation. These calculations highlight the relationship among solvation formalism, nuclear polarization, and energetics.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Benjamin Link
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mathew Chow
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | | | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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2
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Seenithurai S, Chai JD. TAO-DFT with the Polarizable Continuum Model. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13101593. [PMID: 37242010 DOI: 10.3390/nano13101593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023]
Abstract
For the ground-state properties of gas-phase nanomolecules with multi-reference character, thermally assisted occupation (TAO) density functional theory (DFT) has recently been found to outperform the widely used Kohn-Sham DFT when traditional exchange-correlation energy functionals are employed. Aiming to explore solvation effects on the ground-state properties of nanomolecules with multi-reference character at a minimal computational cost, we combined TAO-DFT with the PCM (polarizable continuum model). In order to show its usefulness, TAO-DFT-based PCM (TAO-PCM) was used to predict the electronic properties of linear acenes in three different solvents (toluene, chlorobenzene, and water). According to TAO-PCM, in the presence of these solvents, the smaller acenes should have nonradical character, and the larger ones should have increasing polyradical character, revealing striking similarities to the past findings in the gas phase.
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Affiliation(s)
- Sonai Seenithurai
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Jeng-Da Chai
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
- Center for Theoretical Physics and Center for Quantum Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
- Physics Division, National Center for Theoretical Sciences, Taipei 10617, Taiwan
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3
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Lambros E, Link B, Chow M, Hammes-Schiffer S, Li X. Solvent Induced Proton Polarization within the Nuclear-Electronic Orbital Framework. J Phys Chem Lett 2023; 14:2990-2995. [PMID: 36942912 DOI: 10.1021/acs.jpclett.3c00471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
To explicitly account for nuclear quantum effects and solvent environments in simulations of chemical processes, the nuclear-electronic orbital approach is coupled with a polarizable continuum model (PCM). This NEO-PCM approach is used to explore the influence of solvation on nuclear polarization through applications to a water dimer and a set of protonated water tetramers. Nuclear polarization in these species is analyzed in terms of changes in proton density and oxygen-hydrogen bond length. Solvation is shown to enhance nuclear polarization with increasing dielectric constant. For the water dimer, the internal, hydrogen-bonded proton is shown to polarize more than the external, free proton. Moreover, proton quantization leads to greater solvent polarization through their mutual polarization. These calculations highlight the complex interplay among electronic, nuclear, and solvent polarization in chemical systems.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Benjamin Link
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mathew Chow
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | | | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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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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Alam B, Jiang H, Zimmerman PM, Herbert JM. State-specific solvation for restricted active space spin-flip (RAS-SF) wave functions based on the polarizable continuum formalism. J Chem Phys 2022; 156:194110. [PMID: 35597663 DOI: 10.1063/5.0091636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The restricted active space spin-flip (RAS-SF) formalism is a particular form of single-reference configuration interaction that can describe some forms of strong correlation at a relatively low cost and which has recently been formulated for the description of charge-transfer excited states. Here, we introduce both equilibrium and nonequilibrium versions of a state-specific solvation correction for vertical transition energies computed using RAS-SF wave functions, based on the framework of a polarizable continuum model (PCM). Ground-state polarization is described using the solvent's static dielectric constant and in the nonequilibrium solvation approach that polarization is modified upon vertical excitation using the solvent's optical dielectric constant. Benchmark calculations are reported for well-studied models of photo-induced charge transfer, including naphthalene dimer, C2H4⋯C2F4, pentacene dimer, and perylene diimide (PDI) dimer, several of which are important in organic photovoltaic applications. For the PDI dimer, we demonstrate that the charge-transfer character of the excited states is enhanced in the presence of a low-dielectric medium (static dielectric constant ɛ0 = 3) as compared to a gas-phase calculation (ɛ0 = 1). This stabilizes mechanistic traps for singlet fission and helps to explain experimental singlet fission rates. We also examine the effects of nonequilibrium solvation on charge-separated states in an intramolecular singlet fission chromophore, where we demonstrate that the energetic ordering of the states changes as a function of solvent polarity. The RAS-SF + PCM methodology that is reported here provides a framework to study charge-separated states in solution and in photovoltaic materials.
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Affiliation(s)
- Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Multireference Perturbation Theory Combined with PCM and RISM Solvation Models: A Benchmark Study for Chemical Energetics. J Phys Chem A 2021; 125:8324-8336. [PMID: 34516121 DOI: 10.1021/acs.jpca.1c05944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The polarizable continuum model (PCM) has been one of the most widely used approaches to take into account the solvation effect in quantum chemical calculations. In this paper, we performed a series of benchmark calculations to assess the accuracy of the PCM scheme combined with the second-order complete-active-space perturbation theory (CASPT2) for molecular systems in polar solvents. For solute molecules with extensive conjugated π orbitals, exemplified by elongated conjugated arylcarbenes, we have incorporated the ab initio density matrix renormalization group algorithm into the PCM-CASPT2 method. In the previous work, we presented a combination of the DMRG-CASPT2 method with the reference interaction site model (RISM) theory for describing the solvation effect using the radial distribution function and compared its performance to the widely used density-functional approaches (PCM-TD-DFT). The work here allows us to further show a more thorough assessment of the RISM model compared to the PCM with an equal level of the wave function treatment, the (DMRG-)CASPT2 theory, toward a high-accuracy electronic structure calculations for solvated chemical systems. With the exception that the PCM models are not capable of properly describing the hydrogen bondings, accuracy of the PCM-CASPT2 model is in most cases quite comparable to the RISM counterpart.
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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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Coons MP, Herbert JM. Quantum chemistry in arbitrary dielectric environments: Theory and implementation of nonequilibrium Poisson boundary conditions and application to compute vertical ionization energies at the air/water interface. J Chem Phys 2018; 148:222834. [DOI: 10.1063/1.5023916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Affiliation(s)
- Juan J. Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Wien, Austria;,
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Wien, Austria;,
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10
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Duchemin I, Jacquemin D, Blase X. Combining the GW formalism with the polarizable continuum model: A state-specific non-equilibrium approach. J Chem Phys 2017; 144:164106. [PMID: 27131530 DOI: 10.1063/1.4946778] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have implemented the polarizable continuum model within the framework of the many-body Green's function GW formalism for the calculation of electron addition and removal energies in solution. The present formalism includes both ground-state and non-equilibrium polarization effects. In addition, the polarization energies are state-specific, allowing to obtain the bath-induced renormalisation energy of all occupied and virtual energy levels. Our implementation is validated by comparisons with ΔSCF calculations performed at both the density functional theory and coupled-cluster single and double levels for solvated nucleobases. The present study opens the way to GW and Bethe-Salpeter calculations in disordered condensed phases of interest in organic optoelectronics, wet chemistry, and biology.
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Affiliation(s)
- Ivan Duchemin
- INAC, SP2M/L_Sim, CEA/UJF Cedex 09, 38054 Grenoble, France
| | - Denis Jacquemin
- Laboratoire CEISAM - UMR CNR 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
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11
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You ZQ, Herbert JM. Reparameterization of an Accurate, Few-Parameter Implicit Solvation Model for Quantum Chemistry: Composite Method for Implicit Representation of Solvent, CMIRS v. 1.1. J Chem Theory Comput 2016; 12:4338-46. [DOI: 10.1021/acs.jctc.6b00644] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhi-Qiang You
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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12
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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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13
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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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14
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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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15
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Ho J. Are thermodynamic cycles necessary for continuum solvent calculation of pKas and reduction potentials? Phys Chem Chem Phys 2014; 17:2859-68. [PMID: 25503399 DOI: 10.1039/c4cp04538f] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Continuum solvent calculations of pKas and reduction potentials usually entail the use of a thermodynamic cycle to express the reaction free energy in terms of gas phase energies and free energies of solvation. In this work, we present a systematic study comparing the solution phase free energy changes obtained in this manner with those directly computed within the SMD solvation model against a large test set of 117 pKas and 42 reduction potentials in water and DMSO. The inclusion of vibrational contributions in the free energy of solvation has a negligible impact on the accuracy of thermodynamic cycle predictions of pKas and reduction potentials. Additionally, when gas phase energies in the thermodynamic cycle are computed at more accurate levels of theory, very similar results (mean unsigned difference of 0.5 kcal mol(-1)) can be achieved when the high-level computations (MP2/GTMP2Large and G3(MP2)-RAD(+)) are directly carried out within the continuum model. Increasing the accuracy of the electronic structure theory may or may not improve the agreement with experiment suggesting that the error is largely in the solvation model. For amino acids where their gas and solution phase species exist as different tautomers, the direct approach provided a significant improvement in calculated pKas. These results demonstrate that direct calculation of solution phase pKas and reduction potentials within the SMD model provides a general and reliable approximation to corresponding thermodynamic cycle based protocols, and is recommended for systems where solvation induced changes in geometry are significant. Further studies are necessary to ascertain whether the results are generalisable to other continuum solvation models.
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Affiliation(s)
- Junming Ho
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA.
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Caricato M. A comparison between state-specific and linear-response formalisms for the calculation of vertical electronic transition energy in solution with the CCSD-PCM method. J Chem Phys 2013; 139:044116. [DOI: 10.1063/1.4816482] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Lipparini F, Stamm B, Cancès E, Maday Y, Mennucci B. Fast Domain Decomposition Algorithm for Continuum Solvation Models: Energy and First Derivatives. J Chem Theory Comput 2013; 9:3637-48. [DOI: 10.1021/ct400280b] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Filippo Lipparini
- UPMC Université Paris
06, Institut du Calcul et de la Simulation, F-75005 Paris, France
| | - Benjamin Stamm
- UPMC Université Paris
06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France
| | - Eric Cancès
- Université Paris-Est, CERMICS, Project-team Micmac, INRIA-Ecole des Ponts, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée Cedex 2, France
| | - Yvon Maday
- UPMC Université Paris
06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France
- Institut Universitaire de France,
103 bd Saint-Michel 75005 Paris
- Brown University, Division of
Applied Maths, Providence, Rhode Island, United States
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
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18
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Mennucci B. Modeling environment effects on spectroscopies through QM/classical models. Phys Chem Chem Phys 2013; 15:6583-94. [DOI: 10.1039/c3cp44417a] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Ma H, Ma Y. Solvatochromic shifts of polar and non-polar molecules in ambient and supercritical water: A sequential quantum mechanics/molecular mechanics study including solute-solvent electron exchange-correlation. J Chem Phys 2012; 137:214504. [DOI: 10.1063/1.4769124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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20
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Helgaker T, Coriani S, Jørgensen P, Kristensen K, Olsen J, Ruud K. Recent Advances in Wave Function-Based Methods of Molecular-Property Calculations. Chem Rev 2012; 112:543-631. [DOI: 10.1021/cr2002239] [Citation(s) in RCA: 463] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Trygve Helgaker
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Sonia Coriani
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Giorgieri 1, I-34127 Trieste, Italy
| | - Poul Jørgensen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kasper Kristensen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Jeppe Olsen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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21
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Pomogaeva A, Chipman DM. Field-Extremum Model for Short-Range Contributions to Hydration Free Energy. J Chem Theory Comput 2011; 7:3952-60. [DOI: 10.1021/ct200575c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Pomogaeva
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556-5674, United States
| | - Daniel M. Chipman
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556-5674, United States
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Lange AW, Herbert JM. A smooth, nonsingular, and faithful discretization scheme for polarizable continuum models: the switching/Gaussian approach. J Chem Phys 2011; 133:244111. [PMID: 21197980 DOI: 10.1063/1.3511297] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Polarizable continuum models (PCMs) are a widely used family of implicit solvent models based on reaction-field theory and boundary-element discretization of the solute/continuum interface. An often overlooked aspect of these theories is that discretization of the interface typically does not afford a continuous potential energy surface for the solute. In addition, we show that discretization can lead to numerical singularities and violations of exact variational conditions. To fix these problems, we introduce the switching/Gaussian (SWIG) method, a discretization scheme that overcomes several longstanding problems with PCMs. Our approach generalizes a procedure introduced by York and Karplus [J. Phys. Chem. A 103, 11060 (1999)], extending it beyond the conductor-like screening model. Comparison to other purportedly smooth PCM implementations reveals certain artifacts in these alternative approaches, which are avoided using the SWIG methodology. The versatility of our approach is demonstrated via geometry optimizations, vibrational frequency calculations, and molecular dynamics simulations, for solutes described using quantum mechanics and molecular mechanics.
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Affiliation(s)
- Adrian W Lange
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Lange AW, Herbert JM. Response to “Comment on ‘A smooth, nonsingular, and faithful discretization scheme for polarizable continuum models: The switching/Gaussian approach’” [J. Chem. Phys. 134, 117101 (2011)]. J Chem Phys 2011. [DOI: 10.1063/1.3567490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lipparini F, Scalmani G, Mennucci B, Cancès E, Caricato M, Frisch MJ. A variational formulation of the polarizable continuum model. J Chem Phys 2010; 133:014106. [DOI: 10.1063/1.3454683] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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25
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Scalmani G, Frisch MJ. Continuous surface charge polarizable continuum models of solvation. I. General formalism. J Chem Phys 2010; 132:114110. [PMID: 20331284 DOI: 10.1063/1.3359469] [Citation(s) in RCA: 1761] [Impact Index Per Article: 125.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Continuum solvation models are appealing because of the simplified yet accurate description they provide of the solvent effect on a solute, described either by quantum mechanical or classical methods. The polarizable continuum model (PCM) family of solvation models is among the most widely used, although their application has been hampered by discontinuities and singularities arising from the discretization of the integral equations at the solute-solvent interface. In this contribution we introduce a continuous surface charge (CSC) approach that leads to a smooth and robust formalism for the PCM models. We start from the scheme proposed over ten years ago by York and Karplus and we generalize it in various ways, including the extension to analytic second derivatives with respect to atomic positions. We propose an optimal discrete representation of the integral operators required for the determination of the apparent surface charge. We achieve a clear separation between "model" and "cavity" which, together with simple generalizations of modern integral codes, is all that is required for an extensible and efficient implementation of the PCM models. Following this approach we are now able to introduce solvent effects on energies, structures, and vibrational frequencies (analytical first and second derivatives with respect to atomic coordinates), magnetic properties (derivatives with respect of magnetic field using GIAOs), and in the calculation more complex properties like frequency-dependent Raman activities, vibrational circular dichroism, and Raman optical activity.
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Affiliation(s)
- Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac Street Building 40, Wallingford, Connecticut 06492, USA.
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Schlosser F, Moskaleva LV, Kremleva A, Krüger S, Rösch N. Comparative density functional study of the complexes [UO2(CO3)3]4− and [(UO2)3(CO3)6]6− in aqueous solution. Dalton Trans 2010; 39:5705-12. [DOI: 10.1039/c002788j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chipman DM. Vertical electronic excitation with a dielectric continuum model of solvation including volume polarization. I. Theory. J Chem Phys 2009; 131:014103. [DOI: 10.1063/1.3157464] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Vilkas MJ, Zhan CG. An efficient implementation for determining volume polarization in self-consistent reaction field theory. J Chem Phys 2009; 129:194109. [PMID: 19026047 DOI: 10.1063/1.3020767] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An efficient algorithm of the surface and volume polarization for electrostatics (SVPE) method in self-consistent reaction field (SCRF) theory, denoted by SV(1)PE, has been proposed to simulate direct volume polarization potential with a single layer of point charges outside the solute cavity while the indirect effects of volume polarization on surface polarization are still simulated with multiple layers of point charges. The free energies of solvation calculated using the SV(1)PE algorithm (implemented in GAUSSIAN03) reproduce the corresponding values calculated using the standard SVPE implementation within an error of only approximately 0.1% when the solute cavity is defined by the standard 0.001e/a(0) (3) solute charge isodensity contour. The SV(1)PE results are much less sensitive to the used cavity size in comparison with the well-established surface and simulated volume polarization for electrostatics [SS(V)PE] method which simulates volume polarization through an additional surface charge distribution on the cavity surface. The SCRF calculations using the SV(1)PE method are more efficient than those using the original SVPE method.
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Affiliation(s)
- Marius J Vilkas
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose Street, Lexington, Kentucky 40536, USA
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Hsieh C, Lin S. Determination of cubic equation of state parameters for pure fluids from first principle solvation calculations. AIChE J 2008. [DOI: 10.1002/aic.11552] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Theoretical modeling of spectroscopic properties of molecules in solution: toward an effective dynamical discrete/continuum approach. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0216-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lin ST, Hsieh CM. Efficient and accurate solvation energy calculation from polarizable continuum models. J Chem Phys 2006; 125:124103. [PMID: 17014162 DOI: 10.1063/1.2354489] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new approach is proposed to enhance the efficiency and accuracy for calculation of the long-range electrostatic interaction from implicit solvation models, i.e., the polarizable continuum model (PCM) and its variants, conductorlike PCM/conductorlike screening model and integral equation formalism PCM. In these methods the solvent electrostatics effects are represented by a set of discrete apparent charges distributed on tesserae of the molecular cavity surface embedding the solute. In principle, the accuracy of these methods is improved if the cavity surface is tessellated to finer tesserae; however, the computational time is increased rapidly. We show that such undesired dependency between accuracy and efficiency is a result of the inaccurate treatment of the apparent charge self-contribution to the potential and/or electric field. By taking into account the full effects due to the size and curvature of the segment occupied by each apparent charge, the error in calculated electrostatic solvation free energy is essentially zero for ions (point charge at the center of a sphere) regardless of the degree of tessellation used. For molecules where gradient of apparent charge density is nonzero at the cavity surface, we propose a multiple-sampling technique which significantly lowers the calculated error compared to the original PCM methods, especially when very few numbers of tesserae are used.
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Affiliation(s)
- Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan.
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Chipman DM. New formulation and implementation for volume polarization in dielectric continuum theory. J Chem Phys 2006; 124:224111. [PMID: 16784267 DOI: 10.1063/1.2203068] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the use of dielectric continuum theory to model bulk solvation effects on the electronic structure and properties of a solute, volume polarization contributions due to quantum mechanical penetration of the solute charge density outside the cavity nominally enclosing it are known to be significant. This work provides a new formulation and implementation of methods for solution of the requisite Poisson equation. In previous formulations the determination of the surface polarization contribution required evaluation of the difficult to calculate electric field generated by the volume polarization. It is shown that this problematic quantity can be eliminated in favor of other more easily evaluated quantities. That formal advance also opens the way for a more efficient apparatus to be implemented for calculation of the direct contribution of volume polarization to the solvation energy. The new formulation and its practical implementation are described, and illustrative numerical results are given for several neutral and ionic solutes to study the convergence and precision in practice.
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Affiliation(s)
- Daniel M Chipman
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556-5674, USA.
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Iozzi MF, Cossi M, Improta R, Rega N, Barone V. A polarizable continuum approach for the study of heterogeneous dielectric environments. J Chem Phys 2006; 124:184103. [PMID: 16709093 DOI: 10.1063/1.2188392] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a computational method, exploiting some features of the polarizable continuum model (PCM) to describe heterogeneous media; it belongs to the family of electrostatic embedding mixed methods, such as the more common quantum-mechanical (QM)/molecular mechanics approaches, with the electrostatic long range effects accounted for by a polarized continuum instead of atomic point charges. Provided effective dielectric constants are determined for the various parts of the system, the method is much faster than its atomistic counterpart, and allows for high-level QM calculations on the fragment of interest, using all the highly efficient computational tools developed for homogeneous PCM. Two case studies (the calculation of the pKa of solvent exposed acidic residues in a model protein, and the calculation of the electron spin resonance spectrum of a typical spin probe partially embedded in a membrane) are analyzed in some detail, to illustrate the application of the method to complex systems.
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Affiliation(s)
- Maria Francesca Iozzi
- Dipartimento di Chimica, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
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Frediani L, Agren H, Ferrighi L, Ruud K. Second-harmonic generation of solvated molecules using multiconfigurational self-consistent-field quadratic response theory and the polarizable continuum model. J Chem Phys 2005; 123:144117. [PMID: 16238384 DOI: 10.1063/1.2055180] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present the first implementation of the quadratic response function for multiconfigurational self-consistent-field wave functions of solvated molecules described by a polarizable continuum model employing a molecule-shaped cavity. We apply the methodology to the first hyperpolarizability beta and, in particular, the second-harmonic generation process for a series of conjugated push-pull oligomers, as well as for para-nitroaniline. The effect of solvation on the dispersion of the hyperpolarizability and the change in the hyperpolarizability for increasing chain length of the oligomers in vacuum and in solution is considered. The effect of a correlated description is analyzed by comparing the Hartree-Fock hyperpolarizabilities to the multiconfigurational self-consistent-field hyperpolarizabilities. The effect of geometry relaxation in the solvent on the properties of the solvated molecules are also investigated.
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Affiliation(s)
- Luca Frediani
- Laboratory of Theoretical Chemistry, The Royal Institute of Technology, Stockholm Center for Physics, Astronomy, and Biotechnology (SCFAB), Sweden.
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Affiliation(s)
- Jacopo Tomasi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
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Zhan CG, Deng SX, Skiba JG, Hayes BA, Tschampel SM, Shields GC, Landry DW. First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine. J Comput Chem 2005; 26:980-6. [PMID: 15880781 PMCID: PMC2875688 DOI: 10.1002/jcc.20241] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, approximately 4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.
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Affiliation(s)
- Chang-Guo Zhan
- Division of Clinical Pharmacology and Experimental Therapeutics, College of Physicians & Surgeons, Columbia University, 630 West 168th Street, New York, New York 10032, USA.
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Chen X, Zhan CG. Theoretical Determination of Activation Free Energies for Alkaline Hydrolysis of Cyclic and Acyclic Phosphodiesters in Aqueous Solution. J Phys Chem A 2004. [DOI: 10.1021/jp049938v] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xi Chen
- College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 907 Rose Street, Lexington, Kentucky 40536
| | - Chang-Guo Zhan
- College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 907 Rose Street, Lexington, Kentucky 40536
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Abstract
Improved methods are formulated for solution of the linearized Poisson-Boltzmann equation, to be used in conjunction with electronic structure calculation on a solute together with dielectric continuum representation of the salt-containing solvent. Volume polarization effects due to quantum mechanical penetration of solute charge density outside the cavity that excludes solvent are treated by exact and by approximate methods analogous to those previously developed for the salt-free case. With boundary element approaches, exact solutions lead to coupled equations for a pair of cavity surface distributions that mimic the polarization of the solvent dielectric and the ionic atmosphere. A novel means is found to effectively decouple these equations, yielding more efficient practical methods for their numerical solution. Detailed comparisons are given to related boundary element formulations previously reported in the literature, which neglect volume polarization, and analogous decoupling is also found for the pair of surface distributions invoked there. Illustrative results are provided for a simple spherical example.
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Affiliation(s)
- Daniel M Chipman
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Chen F, Chipman DM. Boundary element methods for dielectric cavity construction and integration. J Chem Phys 2003. [DOI: 10.1063/1.1615232] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Curutchet C, Cramer CJ, Truhlar DG, Ruiz-López MF, Rinaldi D, Orozco M, Luque FJ. Electrostatic component of solvation: comparison of SCRF continuum models. J Comput Chem 2003; 24:284-97. [PMID: 12548720 DOI: 10.1002/jcc.10143] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report a systematic comparison of the electrostatic contributions to the free energy of solvation from three different kinds of quantum mechanical self-consistent reaction field (SCRF) methods. We also compare the liquid-phase dipole moments as a measure of the solute's response to the reaction field of the solvent. In particular, we compare these quantities for the generalized Born model as implemented in the SM5.42R method, the multipolar expansion model developed at Nancy, and the MST version of the polarizable continuum model. All calculations are carried out at the HF/6-31G(d) level. The effects of various choices of solute cavities and representations of the charge density are examined. The test set consists of 18 molecules containing prototypical polar groups, and three different values of the dielectric permittivity are considered.
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Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, 08028 Barcelona, Spain
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Senn HM, Margl PM, Schmid R, Ziegler T, Blöchl PE. Ab initio molecular dynamics with a continuum solvation model. J Chem Phys 2003. [DOI: 10.1063/1.1528890] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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van Duijnen PT, de Vries AH, Swart M, Grozema F. Polarizabilities in the condensed phase and the local fields problem: A direct reaction field formulation. J Chem Phys 2002. [DOI: 10.1063/1.1512278] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chipman DM. Energy correction to simulation of volume polarization in reaction field theory. J Chem Phys 2002. [DOI: 10.1063/1.1477928] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Zhan CG, Landry DW. Theoretical Studies of Competing Reaction Pathways and Energy Barriers for Alkaline Ester Hydrolysis of Cocaine. J Phys Chem A 2001. [DOI: 10.1021/jp0023157] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chang-Guo Zhan
- Department of Medicine, College of Physician & Surgeons, Columbia University, New York, New York 10032
| | - Donald W. Landry
- Department of Medicine, College of Physician & Surgeons, Columbia University, New York, New York 10032
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Zhan CG, Landry DW, Ornstein RL. Energy Barriers for Alkaline Hydrolysis of Carboxylic Acid Esters in Aqueous Solution by Reaction Field Calculations. J Phys Chem A 2000. [DOI: 10.1021/jp001459i] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chang-Guo Zhan
- Department of Medicine, College of Physician & Surgeons, Columbia University, New York, New York 10032 and the Pacific Northwest National Laboratory, Battelle-Northwest, Environmental Technology Division, Mailstop K2-21, Richland, Washington 99352
| | - Donald W. Landry
- Department of Medicine, College of Physician & Surgeons, Columbia University, New York, New York 10032 and the Pacific Northwest National Laboratory, Battelle-Northwest, Environmental Technology Division, Mailstop K2-21, Richland, Washington 99352
| | - Rick L. Ornstein
- Department of Medicine, College of Physician & Surgeons, Columbia University, New York, New York 10032 and the Pacific Northwest National Laboratory, Battelle-Northwest, Environmental Technology Division, Mailstop K2-21, Richland, Washington 99352
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Affiliation(s)
- John Bentley
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
| | - Jesse Y. Collins
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
| | - Daniel M. Chipman
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556
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