1
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Nottoli M, Vanich E, Cupellini L, Scalmani G, Pelosi C, Lipparini F. Importance of Polarizable Embedding for Computing Optical Rotation: The Case of Camphor in Ethanol. J Phys Chem Lett 2024:7992-7999. [PMID: 39078659 DOI: 10.1021/acs.jpclett.4c01550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Solvation effects on optical rotation are notoriously challenging to model for computational chemistry, as the specific rotatory power of a molecule can vary wildly going from apolar to polar or even protic solvents. To address such a problem, we present a polarizable embedding implementation of an electric and magnetic response property based on density functional theory and the AMOEBA polarizable force field, and apply such an implementation to the study of the optical rotation of camphor in ethanol. By comparing a continuum model, and electrostatic and polarizable embedding QM/MM models, we observe that accounting for the environment's polarization gives rise to not only a different quantitative prediction, in very good agreement with experiments for the QM/AMOEBA model, but also to a very different qualitative picture, with the values of the optical rotation computed along a classical molecular dynamics trajectory with electrostatic embedding being statistically uncorrelated to the ones obtained with the polarizable description.
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Affiliation(s)
- Michele Nottoli
- Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart, Pfaffenwaldring 57, D-70569, Stuttgart, Germany
| | - Edoardo Vanich
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac Street Building 40, Wallingford, Connecticut 06492, United States
| | - Chiara Pelosi
- 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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2
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Capone M, Romanelli M, Castaldo D, Parolin G, Bello A, Gil G, Vanzan M. A Vision for the Future of Multiscale Modeling. ACS PHYSICAL CHEMISTRY AU 2024; 4:202-225. [PMID: 38800726 PMCID: PMC11117712 DOI: 10.1021/acsphyschemau.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/29/2024]
Abstract
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first principles. Indeed, countless biological, catalytic and photophysical processes require ab initio treatments to be properly described, but the breadth of length and time scales involved makes it practically unfeasible. A way to address these issues is to couple theories and algorithms working at different scales by dividing the system into domains treated at different levels of approximation, ranging from quantum mechanics to classical molecular dynamics, even including continuum electrodynamics. This approach is known as multiscale modeling and its use over the past 60 years has led to remarkable results. Considering the rapid advances in theory, algorithm design, and computing power, we believe multiscale modeling will massively grow into a dominant research methodology in the forthcoming years. Hereby we describe the main approaches developed within its realm, highlighting their achievements and current drawbacks, eventually proposing a plausible direction for future developments considering also the emergence of new computational techniques such as machine learning and quantum computing. We then discuss how advanced multiscale modeling methods could be exploited to address critical scientific challenges, focusing on the simulation of complex light-harvesting processes, such as natural photosynthesis. While doing so, we suggest a cutting-edge computational paradigm consisting in performing simultaneous multiscale calculations on a system allowing the various domains, treated with appropriate accuracy, to move and extend while they properly interact with each other. Although this vision is very ambitious, we believe the quick development of computer science will lead to both massive improvements and widespread use of these techniques, resulting in enormous progresses in physical chemistry and, eventually, in our society.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, L’Aquila 67010, Italy
| | - Marco Romanelli
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Davide Castaldo
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Giovanni Parolin
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Alessandro Bello
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gabriel Gil
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Instituto
de Cibernética, Matemática y Física (ICIMAF), La Habana 10400, Cuba
| | - Mirko Vanzan
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, University of Milano, Milano 20133, Italy
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3
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Lafiosca P, Rossi F, Egidi F, Giovannini T, Cappelli C. Multiscale Frozen Density Embedding/Molecular Mechanics Approach for Simulating Magnetic Response Properties of Solvated Systems. J Chem Theory Comput 2024; 20:266-279. [PMID: 38109486 PMCID: PMC10782454 DOI: 10.1021/acs.jctc.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
We present a three-layer hybrid quantum mechanical/quantum embedding/molecular mechanics approach for calculating nuclear magnetic resonance (NMR) shieldings and J-couplings of molecular systems in solution. The model is based on the frozen density embedding (FDE) and polarizable fluctuating charges (FQ) and fluctuating dipoles (FQFμ) force fields and permits the accurate ab initio description of short-range nonelectrostatic interactions by means of the FDE shell and cost-effective treatment of long-range electrostatic interactions through the polarizable force field FQ(Fμ). Our approach's accuracy and potential are demonstrated by studying NMR spectra of Brooker's merocyanine in aqueous and nonaqueous solutions.
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Affiliation(s)
- Piero Lafiosca
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Federico Rossi
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Franco Egidi
- Software
for Chemistry and Materials BV, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | | | - Chiara Cappelli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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4
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Burger S, Lipparini F, Gauss J, Stopkowicz S. NMR chemical shift computations at second-order Møller-Plesset perturbation theory using gauge-including atomic orbitals and Cholesky-decomposed two-electron integrals. J Chem Phys 2021; 155:074105. [PMID: 34418917 DOI: 10.1063/5.0059633] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report on a formulation and implementation of a scheme to compute nuclear magnetic resonance (NMR) shieldings at second-order Møller-Plesset (MP2) perturbation theory using gauge-including atomic orbitals (GIAOs) to ensure gauge-origin independence and Cholesky decomposition (CD) to handle unperturbed and perturbed two-electron integrals. We investigate the accuracy of the CD for the derivatives of the two-electron integrals with respect to an external magnetic field and for the computed NMR shieldings, before we illustrate the applicability of our CD-based GIAO-MP2 scheme in calculations involving up to about 100 atoms and more than 1000 basis functions.
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Affiliation(s)
- Sophia Burger
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Stella Stopkowicz
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
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5
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Marrazzini G, Giovannini T, Scavino M, Egidi F, Cappelli C, Koch H. Multilevel Density Functional Theory. J Chem Theory Comput 2021; 17:791-803. [PMID: 33449681 PMCID: PMC7880574 DOI: 10.1021/acs.jctc.0c00940] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
Following recent
developments in multilevel embedding methods,
we introduce a novel density matrix-based multilevel approach within
the framework of density functional theory (DFT). In this multilevel
DFT, the system is partitioned in an active and an inactive fragment,
and all interactions are retained between the two parts. The decomposition
of the total system is performed upon the density matrix. The orthogonality
between the two parts is maintained by solving the Kohn–Sham
equations in the MO basis for the active part only, while keeping
the inactive density matrix frozen. This results in the reduction
of computational cost. We outline the theory and implementation and
discuss the differences and similarities with state-of-the-art DFT
embedding methods. We present applications to aqueous solutions of
methyloxirane and glycidol.
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Affiliation(s)
- Gioia Marrazzini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Marco Scavino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Henrik Koch
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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6
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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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7
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Lambros E, Lipparini F, Cisneros GA, Paesani F. A Many-Body, Fully Polarizable Approach to QM/MM Simulations. J Chem Theory Comput 2020; 16:7462-7472. [PMID: 33213149 PMCID: PMC8131112 DOI: 10.1021/acs.jctc.0c00932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum-mechanical contributions (e.g., exchange-repulsion and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Using the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit two-body and three-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 two-body and three-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | | | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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8
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Giovannini T, Egidi F, Cappelli C. Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems. Phys Chem Chem Phys 2020; 22:22864-22879. [PMID: 33043930 DOI: 10.1039/d0cp04027d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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9
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Hashem S, Cupellini L, Lipparini F, Mennucci B. A polarisable QM/MM description of NMR chemical shifts of a photoreceptor protein. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1771449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Shaima Hashem
- Department of Chemistry, University of Pisa, Pisa, Italy
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10
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Giovannini T, Riso RR, Ambrosetti M, Puglisi A, Cappelli C. Electronic transitions for a fully polarizable QM/MM approach based on fluctuating charges and fluctuating dipoles: Linear and corrected linear response regimes. J Chem Phys 2019; 151:174104. [PMID: 31703497 DOI: 10.1063/1.5121396] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The fully polarizable Quantum Mechanics/Molecular Mechanics (QM/MM) approach based on fluctuating charges and fluctuating dipoles, named QM/FQFμ [T. Giovannini et al., J. Chem. Theory Comput. 15, 2233 (2019)], is extended to the calculation of vertical excitation energies of solvated molecular systems. Excitation energies are defined within two different solvation regimes, i.e., linear response (LR), where the response of the MM portion is adjusted to the QM transition density, and corrected-Linear Response (cLR) in which the MM response is adjusted to the relaxed QM density, thus being able to account for charge equilibration in the excited state. The model, which is specified in terms of three physical parameters (electronegativity, chemical hardness, and polarizability) is applied to vacuo-to-water solvatochromic shifts of aqueous solutions of para-nitroaniline, pyridine, and pyrimidine. The results show a good agreement with their experimental counterparts, thus highlighting the potentialities of this approach.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | | | | | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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11
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Giovannini T, Grazioli L, Ambrosetti M, Cappelli C. Calculation of IR Spectra with a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles. J Chem Theory Comput 2019; 15:5495-5507. [DOI: 10.1021/acs.jctc.9b00574] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Laura Grazioli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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12
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Di Remigio R, Giovannini T, Ambrosetti M, Cappelli C, Frediani L. Fully Polarizable QM/Fluctuating Charge Approach to Two-Photon Absorption of Aqueous Solutions. J Chem Theory Comput 2019; 15:4056-4068. [DOI: 10.1021/acs.jctc.9b00305] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Roberto Di Remigio
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Luca Frediani
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
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13
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Giovannini T, Puglisi A, Ambrosetti M, Cappelli C. Polarizable QM/MM Approach with Fluctuating Charges and Fluctuating Dipoles: The QM/FQFμ Model. J Chem Theory Comput 2019; 15:2233-2245. [DOI: 10.1021/acs.jctc.8b01149] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | | | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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14
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Dziedzic J, Head-Gordon T, Head-Gordon M, Skylaris CK. Mutually polarizable QM/MM model with in situ optimized localized basis functions. J Chem Phys 2019; 150:074103. [PMID: 30795653 DOI: 10.1063/1.5080384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with onetep linear-scaling density functional theory and the classical subsystem - with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully mutually polarizable. A total energy minimization scheme is employed for the Hamiltonian of the coupled QM/MM system. We demonstrate that, compared to simpler models using fixed basis sets, the additional flexibility offered by in situ optimized basis functions improves the accuracy of the QM/MM interface, but also poses new challenges, making the QM subsystem more prone to overpolarization and unphysical charge transfer due to increased charge penetration. We show how these issues can be efficiently solved by replacing the classical repulsive van der Waals term for QM/MM interactions with an interaction of the electronic density with a fixed, repulsive MM potential that mimics Pauli repulsion, together with a modest increase in the damping of QM/MM polarization. We validate our method, with particular attention paid to the hydrogen bond, in tests on water-ion pairs, the water dimer, first solvation shells of neutral and charged species, and solute-solvent interaction energies. As a proof of principle, we determine suitable repulsive potential parameters for water, K+, and Cl-. The mechanisms we employed to counteract the unphysical overpolarization of the QM subsystem are demonstrated to be adequate, and our approach is robust. We find that the inclusion of explicit polarization in the MM part of QM/MM improves agreement with fully QM calculations. Our model permits the use of minimal size QM regions and, remarkably, yields good energetics across the well-balanced QM/MM interface.
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Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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15
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Egidi F, Giovannini T, Del Frate G, Lemler PM, Vaccaro PH, Cappelli C. A combined experimental and theoretical study of optical rotatory dispersion for (R)-glycidyl methyl ether in aqueous solution. Phys Chem Chem Phys 2019; 21:3644-3655. [PMID: 30383044 DOI: 10.1039/c8cp04445g] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The dispersive optical activity for aqueous solutions of non-rigid (R)-glycidyl methyl ether (R-GME) has been explored synergistically from experimental and theoretical perspectives. Density functional theory analyses performed with the polarizable continuum model for implicit solvation identified nine low-lying stable conformers that are interconverted by rotation about two large-amplitude torsional coordinates. The antagonistic chiroptical signatures predicted for these structural isomers were averaged under a Boltzmann-weighting ansatz to estimate the behavior expected for a thermally equilibrated ensemble. This led to optical rotatory dispersion profiles that reproduced the overall shape of observations but failed to achieve uniform agreement with measured specific-rotation values even when anharmonic vibrational corrections were applied. A mixed QM/FQ paradigm, whereby quantum-mechanical (QM) calculations of optical activity were combined with classical molecular dynamics simulations of explicit solvation that included mutual-polarization effects by means of fluctuating charges (FQ), was enlisted to elucidate the microsolvation environment and gauge its impact upon conformer distributions and response properties. Although quantitative accord with experiments remained elusive, this approach revealed strong variations in the magnitude and sign of rotatory powers for R-GME as the configuration of surrounding water molecules evolved, thereby highlighting the inherently dynamical nature of the solvated chiroptical response, calling into question the validity of "static" descriptions based on the presumption of distinct energy minima, and giving insight into the inherent complexity posed by the modeling of such properties for solvated systems.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, Italy
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16
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Puglisi A, Giovannini T, Antonov L, Cappelli C. Interplay between conformational and solvent effects in UV-visible absorption spectra: curcumin tautomers as a case study. Phys Chem Chem Phys 2019; 21:15504-15514. [PMID: 31259324 DOI: 10.1039/c9cp00907h] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a combined theoretical and experimental study on the UV-vis spectra of enol-keto (EK) and keto-keto (KK) tautomeric forms of curcumin dissolved in aqueous solution. Solvent effects have been investigated by resorting to the implicit polarizable continuum model (QM/PCM) and non-polarizable and fully polarizable QM/MM approaches, the latter based on the fluctuating charges (FQ) force-field. In particular, all methods are challenged to rationalize the contribution of conformational, electrostatic and polarization effects in the calculation of the vertical excitation spectra of curcumin tautomers. The obtained results highlight that for both tautomers specific solute-solvent hydrogen-bond interactions play a minor role with respect to conformational and electrostatic effects.
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Affiliation(s)
| | | | - Liudmil Antonov
- Bulgarian Academy of Sciences, Institute of Organic Chemistry with Centre of Phytochemistry, Acad. G. Bonchev str., Bldg. 9, Sofia 1113, Bulgaria
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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17
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Caprasecca S, Cupellini L, Jurinovich S, Loco D, Lipparini F, Mennucci B. A polarizable QM/MM description of environment effects on NMR shieldings: from solvated molecules to pigment–protein complexes. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2264-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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18
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On the nature of charge-transfer excitations for molecules in aqueous solution: a polarizable QM/MM study. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2259-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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A polarizable embedding approach to second harmonic generation (SHG) of molecular systems in aqueous solutions. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2247-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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20
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21
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Giovannini T, Del Frate G, Lafiosca P, Cappelli C. Effective computational route towards vibrational optical activity spectra of chiral molecules in aqueous solution. Phys Chem Chem Phys 2018; 20:9181-9197. [DOI: 10.1039/c8cp00487k] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A polarizable QM/MM approach to accurately compute the Vibrational Optical Activity (VOA) spectra of chiral systems is proposed and applied to aqueous solutions of (l)-methyl lactate and (S)-glycidol.
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22
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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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23
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Giovannini T, Olszówka M, Egidi F, Cheeseman JR, Scalmani G, Cappelli C. Polarizable Embedding Approach for the Analytical Calculation of Raman and Raman Optical Activity Spectra of Solvated Systems. J Chem Theory Comput 2017; 13:4421-4435. [DOI: 10.1021/acs.jctc.7b00628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | - Marta Olszówka
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Franco Egidi
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - James R. Cheeseman
- Gaussian
Inc., 340 Quinnipiac Street Building
40, Wallingford, Connecticut 06492, United States
| | - Giovanni Scalmani
- Gaussian
Inc., 340 Quinnipiac Street Building
40, Wallingford, Connecticut 06492, United States
| | - Chiara Cappelli
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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24
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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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25
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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26
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Remigio RD, Repisky M, Komorovsky S, Hrobarik P, Frediani L, Ruud K. Four-component relativistic density functional theory with the polarisable continuum model: application to EPR parameters and paramagnetic NMR shifts. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1239846] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
| | - Michal Repisky
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
| | - Stanislav Komorovsky
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
| | - Peter Hrobarik
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Luca Frediani
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
| | - Kenneth Ruud
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
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27
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Giovannini T, Olszòwka M, Cappelli C. Effective Fully Polarizable QM/MM Approach To Model Vibrational Circular Dichroism Spectra of Systems in Aqueous Solution. J Chem Theory Comput 2016; 12:5483-5492. [PMID: 27704812 DOI: 10.1021/acs.jctc.6b00768] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a methodology, based on the combination of classical Molecular Dynamics (MD) simulations with a fully polarizable Quantum Mechanical (QM)/Molecular Mechanics (MM)/Polarizable Continuum Model (PCM) Hamiltonian, to calculate Vibrational Circular Dichroism (VCD) spectra of chiral systems in aqueous solution. Polarization effects are included in the MM force field by exploiting an approach based on Fluctuating Charges (FQ). By performing the MD, the description of the solvating environment is enriched by taking into account the dynamical aspects of the solute-solvent interactions. On the other hand, the QM/FQ/PCM calculation of the VCD spectrum ensures an accurate description of the electronic density of the solute and a proper account for the specific interactions in solution. The application of our approach to (R)-methyloxirane and (l)-alanine in aqueous solution gives calculated spectra in remarkable agreement with their experimental counterparts and a substantial improvement with respect to the same spectra calculated with the PCM.
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Affiliation(s)
| | - Marta Olszòwka
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via Moruzzi 13, 56124 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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28
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Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. J Chem Phys 2016; 145:124106. [DOI: 10.1063/1.4962909] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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29
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Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal JP, Cisneros GA. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. J Comput Chem 2016; 37:1019-29. [PMID: 26781073 PMCID: PMC4808410 DOI: 10.1002/jcc.24295] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 12/23/2022]
Abstract
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.
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30
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Nørby MS, Vahtras O, Norman P, Kongsted J. Assessing frequency-dependent site polarisabilities in linear response polarisable embedding. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1177667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Morten S. Nørby
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Olav Vahtras
- KTH Royal Institute of Technology, School of Biotechnology, Division of Theoretical Chemistry and Biology, Stockholm, Sweden
| | - Patrick Norman
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
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31
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A computational approach to the resonance Raman spectrum of doxorubicin in aqueous solution. Theor Chem Acc 2016. [DOI: 10.1007/s00214-015-1781-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Carnimeo I, Cappelli C, Barone V. Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges. J Comput Chem 2015; 36:2271-90. [PMID: 26399473 PMCID: PMC5054946 DOI: 10.1002/jcc.24195] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/31/2015] [Accepted: 08/07/2015] [Indexed: 01/09/2023]
Abstract
A polarizable quantum mechanics (QM)/ molecular mechanics (MM) approach recently developed for Hartree-Fock (HF) and Kohn-Sham (KS) methods has been extended to energies and analytical gradients for MP2, double hybrid functionals, and TD-DFT models, thus allowing the computation of equilibrium structures for excited electronic states together with more accurate results for ground electronic states. After a detailed presentation of the theoretical background and of some implementation details, a number of test cases are analyzed to show that the polarizable embedding model based on fluctuating charges (FQ) is remarkably more accurate than the corresponding electronic embedding based on a fixed charge (FX) description. In particular, a set of electronegativities and hardnesses has been optimized for interactions between QM and FQ regions together with new repulsion-dispersion parameters. After validation of both the numerical implementation and of the new parameters, absorption electronic spectra have been computed for representative model systems including vibronic effects. The results show remarkable agreement with full QM computations and significant improvement with respect to the corresponding FX results. The last part of the article provides some hints about computation of solvatochromic effects on absorption spectra in aqueous solution as a function of the number of FQ water molecules and on the use of FX external shells to improve the convergence of the results. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Ivan Carnimeo
- Istituto Italiano Di Tecnologia (IIT), Compunet, via Morego, 30 I-16163 Genova, Italy and Scuola Normale Superiore, Piazza Dei Cavalieri, 7 I-56126, Pisa, Italy
| | - Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi, 13, I-56124, Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126, Pisa, Italy
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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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34
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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. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald. J Chem Theory Comput 2015; 11:2589-99. [DOI: 10.1021/acs.jctc.5b00171] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Louis Lagardère
- Institut
du Calcul et de la Simulation, UPMC Univ. Paris 06, F-75005, Paris, France
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
| | - Filippo Lipparini
- Institut
du Calcul et de la Simulation, UPMC Univ. Paris 06, F-75005, Paris, France
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
| | - Étienne Polack
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
| | - Benjamin Stamm
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, 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
- Laboratoire
Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598, F-75005, Paris, France
- Institut Universitaire de France, F-75005, Paris, France
- Division
of Applied Mathematics, Brown University, Providence, Rhode Island 02912, United States
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617, F-75005, Paris, France
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35
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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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36
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Egidi F, Russo R, Carnimeo I, D'Urso A, Mancini G, Cappelli C. The electronic circular dichroism of nicotine in aqueous solution: a test case for continuum and mixed explicit-continuum solvation approaches. J Phys Chem A 2015; 119:5396-404. [PMID: 25568940 DOI: 10.1021/jp510542x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this paper, we extend an integrated QM/MM/polarizable continuum model (PCM) method, which combines a fluctuating charge (FQ) approach to the MM polarization with the PCM, to describe electronic circular dichroism (ECD) spectra of systems in aqueous solution. The main features of the approach are presented, and then applications to the UV and ECD spectra of neutral (S)-nicotine in aqueous solution are reported. The performance of the QM/FQ/PCM is compared with that of the PCM against newly measured UV ECD spectra, which are in agreement with previous findings. The inclusion of specific solvation effects via the QM/FQ/PCM method leads to an improvement in the calculated spectra compared to the experimental findings, though the pure PCM results are still qualitatively correct and are a useful tool for the characterization of the states.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Rosario Russo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Ivan Carnimeo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Alessandro D'Urso
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
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37
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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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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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39
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Pedersen MN, Hedegård ED, Olsen JMH, Kauczor J, Norman P, Kongsted J. Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method. J Chem Theory Comput 2014; 10:1164-71. [DOI: 10.1021/ct400946k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Morten N. Pedersen
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
- Department
of Physics, Chemistry and Biology, Linköping University, Linköping SE-58183, Sweden
| | - Erik D. Hedegård
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus H. Olsen
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Joanna Kauczor
- Department
of Physics, Chemistry and Biology, Linköping University, Linköping SE-58183, Sweden
| | - Patrick Norman
- Department
of Physics, Chemistry and Biology, Linköping University, Linköping SE-58183, Sweden
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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