1
|
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.
Collapse
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
| |
Collapse
|
2
|
Kvedaravičiūtė S, Carrasco-Busturia D, Møller KB, Olsen JMH. Polarizable Embedding without Artificial Boundary Polarization. J Chem Theory Comput 2023; 19:5122-5141. [PMID: 37458793 DOI: 10.1021/acs.jctc.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
We present a fully self-consistent polarizable embedding (PE) model that does not suffer from unphysical boundary polarization. This is achieved through the use of the minimum-image convention (MIC) in the induced electrostatics. It is a simple yet effective approach that includes a more physically accurate description of the polarization throughout the molecular system. Using PE with MIC (PE-MIC), we shed new light on the limitations of commonly employed cutoff models, such as the droplet model, when used in PE calculations. Specifically, we investigate the effects of the unphysical polarization at the outer boundary by comparing induced dipoles and the associated electrostatic potentials, as well as some optical properties of solute-solvent and biomolecular systems. We show that the magnitude of the inaccuracies caused by the unphysical polarization depends on multiple parameters: the nature of the quantum subsystem and of the environment, the cutoff model and distance, and the calculated property.
Collapse
Affiliation(s)
| | | | - Klaus B Møller
- DTU Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | |
Collapse
|
3
|
Lu SY, Zuehlsdorff TJ, Hong H, Aguirre VP, Isborn CM, Shi L. The Influence of Electronic Polarization on Nonlinear Optical Spectroscopy. J Phys Chem B 2021; 125:12214-12227. [PMID: 34726915 DOI: 10.1021/acs.jpcb.1c05914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The environment surrounding a chromophore can dramatically affect the energy absorption and relaxation process, as manifested in optical spectra. Simulations of nonlinear optical spectroscopy, such as two-dimensional electronic spectroscopy (2DES) and transient absorption (TA), will be influenced by the computational model of the environment. We here compare a fixed point charge molecular mechanics model and a quantum mechanical (QM) model of the environment in computed 2DES and TA spectra of Nile red in water and the chromophore of photoactive yellow protein (PYP) in water and protein environments. In addition to simulating these nonlinear optical spectra, we directly juxtapose the computed excitation energy correlation function to the dynamic Stokes shift function often used to analyze environment dynamics. Overall, we find that for the three systems studied here the mutual electronic polarization provided by the QM environment manifests in broader 2DES signals, as well as a larger reorganization energy and a larger static Stokes shift due to stronger coupling between the chromophore and the environment.
Collapse
Affiliation(s)
- Shao-Yu Lu
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Hanbo Hong
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Vincent P Aguirre
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| |
Collapse
|
4
|
Nottoli M, Nifosì R, Mennucci B, Lipparini F. Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation. J Chem Theory Comput 2021; 17:5661-5672. [PMID: 34476941 PMCID: PMC8444335 DOI: 10.1021/acs.jctc.1c00555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
We present the implementation
of a fully coupled polarizable QM/MM/continuum
model based on the AMOEBA polarizable force field and the domain decomposition
implementation of the conductor-like screening model. Energies, response
properties, and analytical gradients with respect to both QM and MM
nuclear positions are available, and a generic, atomistic cavity can
be employed. The model is linear scaling in memory requirements and
computational cost with respect to the number of classical atoms and
is therefore suited to model large, complex systems. Using three variants
of the green-fluorescent protein, we investigate the overall computational
cost of such calculations and the effect of the continuum model on
the convergence of the computed properties with respect to the size
of the embedding. We also demonstrate the fundamental role of polarization
effects by comparing polarizable and nonpolarizable embeddings to
fully QM ones.
Collapse
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Riccardo Nifosì
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| |
Collapse
|
5
|
Zuehlsdorff TJ, Shedge SV, Lu SY, Hong H, Aguirre VP, Shi L, Isborn CM. Vibronic and Environmental Effects in Simulations of Optical Spectroscopy. Annu Rev Phys Chem 2021; 72:165-188. [DOI: 10.1146/annurev-physchem-090419-051350] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Including both environmental and vibronic effects is important for accurate simulation of optical spectra, but combining these effects remains computationally challenging. We outline two approaches that consider both the explicit atomistic environment and the vibronic transitions. Both phenomena are responsible for spectral shapes in linear spectroscopy and the electronic evolution measured in nonlinear spectroscopy. The first approach utilizes snapshots of chromophore-environment configurations for which chromophore normal modes are determined. We outline various approximations for this static approach that assumes harmonic potentials and ignores dynamic system-environment coupling. The second approach obtains excitation energies for a series of time-correlated snapshots. This dynamic approach relies on the accurate truncation of the cumulant expansion but treats the dynamics of the chromophore and the environment on equal footing. Both approaches show significant potential for making strides toward more accurate optical spectroscopy simulations of complex condensed phase systems.
Collapse
Affiliation(s)
- Tim J. Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Sapana V. Shedge
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Shao-Yu Lu
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hanbo Hong
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Vincent P. Aguirre
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Liang Shi
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Christine M. Isborn
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| |
Collapse
|
6
|
Abstract
The problem of resonant energy transfer (RET) between an electric dipole donor, D, and an electric dipole acceptor, A, mediated by a passive, chiral third-body, T, is considered within the framework of molecular quantum electrodynamics theory. To account for the optical activity of the mediator, magnetic dipole and electric quadrupole coupling terms are included in addition to the leading electric dipole interaction term. Fourth-order diagrammatic time-dependent perturbation theory is used to obtain the matrix element. It is found that the Fermi golden rule rate depends on pure multipole moment polarizabilities and susceptibilities of T, as well as on various mixed electric and magnetic multipole moment response functions. The handedness of T manifests through mixed electric-magnetic dipole and mixed electric dipole-quadrupole polarizabilities, which affect the rate and, respectively, require the use of fourth-rank and sixth-rank Cartesian tensor averages over T, yielding non-vanishing isotropic rate formulae applicable to a chiral fluid medium. Terms of a similar order of magnitude proportional to the product of electric dipole polarizability and either magnetic dipole susceptibility or electric quadrupole polarizability of T are also computed for oriented and freely tumbling molecules. Migration rates dependent upon the product of the pure electric dipole or magnetic dipole polarizability with the mixed electric-magnetic or electric dipole-quadrupole analogs, which require fourth- and fifth-rank Cartesian tensor averaging, vanish for randomly oriented systems. Asymptotically limiting rate expressions are also evaluated. Insight is gained into RET occurring in complex media.
Collapse
Affiliation(s)
- A Salam
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, USA
| |
Collapse
|
7
|
Abstract
Molecular quantum electrodynamics (QED) theory is employed to calculate the rate of resonance energy transfer (RET) between a donor, D, described by an electric dipole and quadrupole, and magnetic dipole coupling, and an identical acceptor molecule, A, that is mediated by a third body, T, which is otherwise inert. A single virtual photon propagates between D and T, and between T and A. Time-dependent perturbation theory is used to compute the matrix element, from which the transfer rate is evaluated using the Fermi golden rule. This extends previous studies that were limited to the electric dipole approximation only and admits the possibility of the exchange of excitation between a chiral emitter and absorber. Rate terms are computed for specific pure and mixed multipole-dependent contributions of D and A for both an oriented arrangement of the three particles and for the freely tumbling situation. Mixed multipole moment contributions, such as those involving electric–magnetic dipole or electric dipole–quadrupole coupling at one center, do not survive random orientational averaging. Interestingly, the mixed electric–magnetic dipole D and A rate term is non-vanishing and discriminatory, exhibiting a dependence on the chirality of the emitter and absorber, and is entirely retarded. It vanishes, however, if D and A are oriented perpendicularly to one another. Near- and far-zone asymptotes of isotropic contributions to the rate are also evaluated, demonstrating radiationless short-range transfer and inverse-square radiative exchange at very large separations.
Collapse
|
8
|
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
| |
Collapse
|
9
|
Affiliation(s)
- A. Salam
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| |
Collapse
|
10
|
Yang L, Jang SJ. Theoretical investigation of non-Förster exciton transfer mechanisms in perylene diimide donor, phenylene bridge, and terrylene diimide acceptor systems. J Chem Phys 2020; 153:144305. [PMID: 33086841 DOI: 10.1063/5.0023709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rates of exciton transfer within dyads of perylene diimide and terrylene diimide connected by oligophenylene bridge units have been shown to deviate significantly from those of Förster's resonance energy transfer theory, according to single molecule spectroscopy experiments. The present work provides a detailed computational and theoretical study investigating the source of such a discrepancy. Electronic spectroscopy data are calculated by time-dependent density functional theory and then compared with experimental results. Electronic couplings between the exciton donor and the acceptor are estimated based on both the transition density cube method and transition dipole approximation. These results confirm that the delocalization of the exciton to the bridge parts contributes to significant enhancement of donor-acceptor electronic coupling. Mechanistic details of exciton transfer are examined by estimating the contributions of the bridge electronic states, vibrational modes of the dyads commonly coupled to both donor and acceptor, inelastic resonance energy transfer mechanism, and dark exciton states. These analyses suggest that the contribution of common vibrational modes serves as the main source of deviation from Förster's spectral overlap expression.
Collapse
Affiliation(s)
- Lei Yang
- Center for Molecular Systems and Organic Devices, Key Laboratory for Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, USA and PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, USA
| |
Collapse
|
11
|
Conti I, Cerullo G, Nenov A, Garavelli M. Ultrafast Spectroscopy of Photoactive Molecular Systems from First Principles: Where We Stand Today and Where We Are Going. J Am Chem Soc 2020; 142:16117-16139. [PMID: 32841559 PMCID: PMC7901644 DOI: 10.1021/jacs.0c04952] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Computational spectroscopy is becoming a mandatory tool for the interpretation of the
complex, and often congested, spectral maps delivered by modern non-linear multi-pulse
techniques. The fields of Electronic Structure Methods,
Non-Adiabatic Molecular Dynamics, and Theoretical
Spectroscopy represent the three pillars of the virtual ultrafast
optical spectrometer, able to deliver transient spectra in
silico from first principles. A successful simulation strategy requires a
synergistic approach that balances between the three fields, each one having its very
own challenges and bottlenecks. The aim of this Perspective is to demonstrate that,
despite these challenges, an impressive agreement between theory and experiment is
achievable now regarding the modeling of ultrafast photoinduced processes in complex
molecular architectures. Beyond that, some key recent developments in the three fields
are presented that we believe will have major impacts on spectroscopic simulations in
the very near future. Potential directions of development, pending challenges, and
rising opportunities are illustrated.
Collapse
Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| |
Collapse
|
12
|
Green D, Jones GA, Salam A. Polariton mediated resonance energy transfer in a fluid. J Chem Phys 2020; 153:034111. [PMID: 32716175 DOI: 10.1063/5.0011562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The focus of this work is on a microscopic quantum electrodynamical understanding of cumulative quantum effects in resonance energy transfer occurring in an isotropic and disordered medium. In particular, we consider quantum coherence, defined in terms of interferences between Feynman pathways, and analyze pure-amplitude and phase cross terms that appear in the Fermi golden rule rate equation that results from squaring the matrix element for mediated energy transfer. It is shown that pure-amplitude terms dominate in the near-zone when chromophores are close in proximity to one another (within a few nanometers), and phase cross terms dominate toward the far-zone when phase differences between different Feynman pathways begin to emerge. This can be understood in terms of physical attributes of the mediating photon, whose character becomes more real at long distances, coinciding with vanishing longitudinal components of the field, as transverse components begin to dominate.
Collapse
Affiliation(s)
- Dale Green
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Garth A Jones
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - A Salam
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, USA
| |
Collapse
|
13
|
Bondanza M, Nottoli M, Cupellini L, Lipparini F, Mennucci B. Polarizable embedding QM/MM: the future gold standard for complex (bio)systems? Phys Chem Chem Phys 2020; 22:14433-14448. [DOI: 10.1039/d0cp02119a] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We provide a perspective of the induced dipole formulation of polarizable QM/MM, showing how efficient implementations will enable their application to the modeling of dynamics, spectroscopy, and reactivity in complex biosystems.
Collapse
Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| |
Collapse
|
14
|
Ford JS, Salam A, Jones GA. A Quantum Electrodynamics Description of Quantum Coherence and Damping in Condensed-Phase Energy Transfer. J Phys Chem Lett 2019; 10:5654-5661. [PMID: 31483664 DOI: 10.1021/acs.jpclett.9b02183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Quantum coherence in condensed-phase electronic resonance energy transfer (RET) is described within the context of quantum electrodynamics (QED) theory. Mediating dressed virtual photons (polaritons) are explicitly incorporated into the treatment, and coherence is understood within the context of interfering Feynman pathways connecting the initial and final states for the RET process. The model investigated is that of an oriented three-body donor, acceptor, and mediator RET system embedded within a dispersive and absorbing polarizable medium. We show how quantum coherence can significantly enhance the rate of RET and give a rigorous picture for subsequent decoherence that is driven by both phase and amplitude damping. Energy-conserving phase damping occurs as a result of geometric and dispersive effects and is associated with destructive interference between Feynman pathways. Dissipative amplitude damping, on the other hand, is attributed to vibronic relaxation and absorptivity of the medium and can be understood as virtual photons (polaritons) leaking into the environment. This model offers insights into the emergence of coherence and subsequent decoherence for energy transfer in photosynthetic systems.
Collapse
Affiliation(s)
- Jack S Ford
- School of Chemistry , University of East Anglia , Norwich NR4 7TJ , U.K
| | - A Salam
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27109 , United States
- Physikalische Institut , Albert-Ludwigs-Universitat-Freiburg , Hermann-Herder-Strasse 3 , D-79104 Freiburg , Germany
- Freiburg Institute for Advanced Studies (FRIAS) , Albertstrasse 19 , D-79104 Freiburg , Germany
| | - Garth A Jones
- School of Chemistry , University of East Anglia , Norwich NR4 7TJ , U.K
| |
Collapse
|
15
|
Segatta F, Cupellini L, Garavelli M, Mennucci B. Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems. Chem Rev 2019; 119:9361-9380. [PMID: 31276384 PMCID: PMC6716121 DOI: 10.1021/acs.chemrev.9b00135] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Indexed: 01/21/2023]
Abstract
Multichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment-protein complexes to nucleic acids. The former are designed to capture, harvest, efficiently transport, and transform energy from sunlight for photosynthesis, while the latter should dissipate the absorbed radiation as quickly as possible to prevent photodamages and corruption of the carried genetic information. Because of the unique electronic and structural characteristics, the modeling of their photoinduced activity is a real challenge. Numerous approaches have been devised building on the theoretical development achieved for single chromophores and on model Hamiltonians that capture the essential features of the system. Still, a question remains: is a general strategy for the accurate modeling of multichromophoric systems possible? By using a quantum chemical point of view, here we review the advancements developed so far highlighting differences and similarities with the single chromophore treatment. Finally, we outline the important limitations and challenges that still need to be tackled to reach a complete and accurate picture of their photoinduced properties and dynamics.
Collapse
Affiliation(s)
- Francesco Segatta
- Dipartimento
di Chimica Industriale “Toso Montanari” University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, University
of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari” University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University
of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| |
Collapse
|
16
|
Ren S, Lipparini F, Mennucci B, Caricato M. Coupled Cluster Theory with Induced Dipole Polarizable Embedding for Ground and Excited States. J Chem Theory Comput 2019; 15:4485-4496. [PMID: 31265278 DOI: 10.1021/acs.jctc.9b00468] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, we present the theory and implementation of the coupled cluster single and double excitations (CCSD) method combined with a classical polarizable molecular mechanics force field (MMPol) based on the induced dipole model. The method is developed to compute electronic excitation energies within the state specific (SS) and linear response (LR) formalisms for the interaction of the quantum mechanical and classical regions. Furthermore, we consider an approximate expression of the correlation energy, originally developed for CCSD with implicit solvation models, where the interaction term is linear in the coupled cluster density. This approximation allows us to include the explicit contribution of the environment to the CC equations without increasing the computational effort. The test calculations on microsolvated systems, where the CCSD/MMPol method is compared to full CCSD calculations, demonstrates the reliability of this computational protocol for all interaction schemes (errors < 2%). We also show that it is important to include induced dipoles on all atom centers of the classical region and that too diffuse functions in the basis set may be problematic due to too strong interaction with the environment.
Collapse
Affiliation(s)
- Sijin Ren
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66044 , United States
| | - Filippo Lipparini
- Department of Chemistry , Università di Pisa , Via Giuseppe Moruzzi , 13 56124 Pisa , Italy
| | - Benedetta Mennucci
- Department of Chemistry , Università di Pisa , Via Giuseppe Moruzzi , 13 56124 Pisa , Italy
| | - Marco Caricato
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66044 , United States
| |
Collapse
|
17
|
Corbella M, Cupellini L, Lipparini F, Scholes GD, Curutchet C. Spectral Variability in Phycocyanin Cryptophyte Antenna Complexes is Controlled by Changes in the α‐Polypeptide Chains. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marina Corbella
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry and Institute of Theoretical and Computational Chemistry (IQTC-UB), Faculty of Pharmacy and Food SciencesUniversity of Barcelona Av. Joan XXIII s/n 08028 Barcelona Spain
- Department of ChemistryUppsala University BMC Box 576 Uppsala S-751 23 Sweden
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica IndustrialeUniversity of Pisa Via Risorgimento 35 56126 Pisa Italy
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica IndustrialeUniversity of Pisa Via Risorgimento 35 56126 Pisa Italy
| | - Gregory D. Scholes
- Department of ChemistryPrinceton University Washington Road, Princeton New Jersey 08544 United States
| | - Carles Curutchet
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry and Institute of Theoretical and Computational Chemistry (IQTC-UB), Faculty of Pharmacy and Food SciencesUniversity of Barcelona Av. Joan XXIII s/n 08028 Barcelona Spain
| |
Collapse
|
18
|
Loco D, Lagardère L, Cisneros GA, Scalmani G, Frisch M, Lipparini F, Mennucci B, Piquemal JP. Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings. Chem Sci 2019; 10:7200-7211. [PMID: 31588288 PMCID: PMC6677116 DOI: 10.1039/c9sc01745c] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/08/2019] [Indexed: 12/17/2022] Open
Abstract
Hybrid DFT(Gaussian)/AMOEBA(Tinker/Tinker-HP) polarizable molecular dynamics including the QM/MM mutual polarization on large complex systems. Example of the thiazole orange dye buried in a DNA double helix, embedded in a sphere of water (16 500 atoms).
In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA polarizable force field to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions. We discuss in detail the implementation and demonstrate the global energy conservation of our QM/MM Born–Oppenheimer molecular dynamics approach using Density Functional Theory. Finally, the approach is assessed on the electronic absorption properties of a 16 500 atom complex encompassing an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent Density Functional Theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.
Collapse
Affiliation(s)
- Daniele Loco
- Sorbonne Université , CNRS , Laboratoire de Chimie Théorique, LCT , Paris , France . ;
| | - Louis Lagardère
- Sorbonne Université , CNRS , Institut Parisien de Chimie Physique et Théorique, IP2CT , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données, ISCD , Paris , France
| | | | | | | | - Filippo Lipparini
- Univerisita di Pisa , Dipartimento di Chimica e ChimicaIndustriale , Pisa , Italy
| | - Benedetta Mennucci
- Univerisita di Pisa , Dipartimento di Chimica e ChimicaIndustriale , Pisa , Italy
| | - Jean-Philip Piquemal
- Sorbonne Université , CNRS , Laboratoire de Chimie Théorique, LCT , Paris , France . ; .,Institut Universitaire de France, IUF , Paris , France.,The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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]
|
21
|
Boulanger E, Harvey JN. QM/MM methods for free energies and photochemistry. Curr Opin Struct Biol 2018; 49:72-76. [PMID: 29414514 DOI: 10.1016/j.sbi.2018.01.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/17/2017] [Accepted: 01/02/2018] [Indexed: 11/27/2022]
Abstract
Hybrid computational methods describing a small region of a biomolecular system with quantum mechanics and the bulk with molecular mechanics, referred to as QM/MM methods, are now a central part of computational biochemistry. This review considers developments in the QM/MM approach that make it easier to calculate free energies using accurate QM-based potential energy expressions. We also describe techniques to treat electronic coupling between the core region and the MM environment. Polarizability of the protein matrix is important but so is electronic coupling. Applications of these new methods, especially to photochemistry, are discussed.
Collapse
Affiliation(s)
- Eliot Boulanger
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| |
Collapse
|
22
|
Fihey A, Russo R, Cupellini L, Jacquemin D, Mennucci B. Is energy transfer limiting multiphotochromism? answers from ab initio quantifications. Phys Chem Chem Phys 2018; 19:2044-2052. [PMID: 28009859 DOI: 10.1039/c6cp07458h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dithienylethenes (DTEs) can be assembled to form supramolecular multiphotochromic systems that are highly functional molecular architectures of potential interest for building complex optoelectronic devices. Yet even simple DTE dimers relying on an organic linker may suffer from a partial photoactivity, i.e., only one of the two switches does isomerise. Experimentally, this limited photochromism has been attributed to an excited state energy transfer (EET) between the two DTEs of the multimer; this EET taking place instead of the desired photoinduced cyclisation of the DTE. However, no clear evidences of this phenomenon have been provided so far. In this work we propose the first rationalisation of this potential parasite photoinduced event using a computational approach based on Time-Dependent Density Functional Theory (TD-DFT) for the calculation of the electronic coupling in DTE dimers. Besides quantifying EET in several systems, we dissect the role of through-bond and through-space mechanisms on this process and clarify their dependence on both the nature and length of the bridge separating the two photochromes. The theoretical data obtained in this framework are in full agreement with the experimental outcomes and pave the way toward a molecular design of coupled, yet fully functionals, DTE-based multiswitches.
Collapse
Affiliation(s)
- Arnaud Fihey
- Institut des Sciences Chimiques de Rennes, UMR 6226 CNRS, Université de Rennes1, 263 Av. du Général Leclerc, 35042, Cedex Rennes, France. and CEISAM, UMR CNRS 6230, Université de Nantes, 2, Rue de la Houssinière, BP 92208, 44322 Nantes, Cedex 3, France.
| | - Roberto Russo
- Dipartimento di Chimica e Chimica Industriale, Universitá di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Universitá di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230, Université de Nantes, 2, Rue de la Houssinière, BP 92208, 44322 Nantes, Cedex 3, France. and Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 5, France
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Universitá di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy.
| |
Collapse
|
23
|
Di Remigio R, Beerepoot MTP, Cornaton Y, Ringholm M, Steindal AH, Ruud K, Frediani L. Open-ended formulation of self-consistent field response theory with the polarizable continuum model for solvation. Phys Chem Chem Phys 2018; 19:366-379. [PMID: 27905594 DOI: 10.1039/c6cp06814f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of high-order absorption properties of molecules is a field of growing importance. Quantum-chemical studies can help design chromophores with desirable characteristics. Given that most experiments are performed in solution, it is important to devise a cost-effective strategy to include solvation effects in quantum-chemical studies of these properties. We here present an open-ended formulation of self-consistent field (SCF) response theory for a molecular solute coupled to a polarizable continuum model (PCM) description of the solvent. Our formulation relies on the open-ended, density matrix-based quasienergy formulation of SCF response theory of Thorvaldsen, et al., [J. Chem. Phys., 2008, 129, 214108] and the variational formulation of the PCM, as presented by Lipparini et al., [J. Chem. Phys., 2010, 133, 014106]. Within the PCM approach to solvation, the mutual solute-solvent polarization is represented by means of an apparent surface charge (ASC) spread over the molecular cavity defining the solute-solvent boundary. In the variational formulation, the ASC is an independent, variational degree of freedom. This allows us to formulate response theory for molecular solutes in the fixed-cavity approximation up to arbitrary order and with arbitrary perturbation operators. For electric dipole perturbations, pole and residue analyses of the response functions naturally lead to the identification of excitation energies and transition moments. We document the implementation of this approach in the Dalton program package using a recently developed open-ended response code and the PCMSolver libraries and present results for one-, two-, three-, four- and five-photon absorption processes of three small molecules in solution.
Collapse
Affiliation(s)
- Roberto Di Remigio
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Yann Cornaton
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Magnus Ringholm
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Arnfinn Hykkerud Steindal
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Luca Frediani
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| |
Collapse
|
24
|
Azarias C, Cupellini L, Belhboub A, Mennucci B, Jacquemin D. Modelling excitation energy transfer in covalently linked molecular dyads containing a BODIPY unit and a macrocycle. Phys Chem Chem Phys 2018; 20:1993-2008. [DOI: 10.1039/c7cp06814j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We model the singlet–singlet Excitation Energy Transfer (EET) process in a panel of large BODIPY–macrocycle dyads, including some azacalixphyrin derivatives.
Collapse
Affiliation(s)
- Cloé Azarias
- Chimie Et Interdisciplinarité
- Synthèse, Analyse, Modélisation (CEISAM)
- UMR CNRS no. 6230
- BP 92208
- Université de Nantes
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale
- University of Pisa
- 56124 Pisa
- Italy
| | - Anouar Belhboub
- Chimie Et Interdisciplinarité
- Synthèse, Analyse, Modélisation (CEISAM)
- UMR CNRS no. 6230
- BP 92208
- Université de Nantes
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- University of Pisa
- 56124 Pisa
- Italy
| | - Denis Jacquemin
- Chimie Et Interdisciplinarité
- Synthèse, Analyse, Modélisation (CEISAM)
- UMR CNRS no. 6230
- BP 92208
- Université de Nantes
| |
Collapse
|
25
|
Cupellini L, Giannini S, Mennucci B. Electron and excitation energy transfers in covalently linked donor–acceptor dyads: mechanisms and dynamics revealed using quantum chemistry. Phys Chem Chem Phys 2018; 20:395-403. [DOI: 10.1039/c7cp07002k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A quantum chemical strategy is developed to study photoinduced electron and energy transfer processes in covalently linked dyads. The strategy is applied to two zinc and free-based porphyrin–naphthalenediimide dyads in solution.
Collapse
Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale
- University of Pisa
- 56124 Pisa
- Italy
| | - Samuele Giannini
- Dipartimento di Chimica e Chimica Industriale
- University of Pisa
- 56124 Pisa
- Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- University of Pisa
- 56124 Pisa
- Italy
| |
Collapse
|
26
|
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
| |
Collapse
|
27
|
Sæther S, Kjærgaard T, Koch H, Høyvik IM. Density-Based Multilevel Hartree–Fock Model. J Chem Theory Comput 2017; 13:5282-5290. [DOI: 10.1021/acs.jctc.7b00689] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sandra Sæther
- Department
of Chemistry, The Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Thomas Kjærgaard
- qLEAP
Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Henrik Koch
- Department
of Chemistry, The Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Ida-Marie Høyvik
- Department
of Chemistry, The Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Azarias C, Russo R, Cupellini L, Mennucci B, Jacquemin D. Modeling excitation energy transfer in multi-BODIPY architectures. Phys Chem Chem Phys 2017; 19:6443-6453. [PMID: 28197587 DOI: 10.1039/c7cp00427c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The excitation energy transfer (EET) allowing the concentration of the energy has been investigated in several multi-BODIPY architectures with the help of an approach coupling time dependent density functional theory to an implicit solvation scheme, the polarizable continuum model. We have first considered several strategies to compute the electronic coupling in a dyad varying the size of the donor/acceptor units, the bridge, the geometries and conformations. We have next studied the electronic coupling in three different architectures for which the EET rate constants have been experimentally measured both from luminescence and transient absorption data and from Förster theory. A good agreement with experimental values was obtained. Finally, in an effort to further improve these systems, we have designed several series of BODIPY triads, investigating the effect of acidochromism, core modifications, the position of the linkage and chemical substitutions on the EET coupling and rate constant. We show that several architectures allow us to increase the EET rate by one order of magnitude compared to the original compound.
Collapse
Affiliation(s)
- Cloé Azarias
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS no. 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes, France.
| | - Roberto Russo
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi 3, 56124 Pisa, Italy.
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi 3, 56124 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi 3, 56124 Pisa, Italy.
| | - Denis Jacquemin
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS no. 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes, France. and Institut Universitaire de France, 1 rue Descartes, F-75231 Paris Cedex 05, France
| |
Collapse
|
30
|
Nishimoto Y, Fedorov DG. Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding. J Comput Chem 2017; 38:406-418. [DOI: 10.1002/jcc.24693] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/14/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry, Kyoto University; 34-4 Takano Nishihiraki-cho Sakyo-ku Kyoto 606-8103 Japan
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat); National Institute of Advanced Industrial Science and Technology (AIST); 1-1-1 Umezono Tsukuba Ibaraki 305-8568 Japan
| |
Collapse
|
31
|
Varsano D, Caprasecca S, Coccia E. Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.
Collapse
Affiliation(s)
- Daniele Varsano
- S3 Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | | | | |
Collapse
|
32
|
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
| |
Collapse
|
33
|
Nørby MS, Steinmann C, Olsen JMH, Li H, Kongsted J. Computational Approach for Studying Optical Properties of DNA Systems in Solution. J Chem Theory Comput 2016; 12:5050-5057. [DOI: 10.1021/acs.jctc.6b00706] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Morten Steen Nørby
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Casper Steinmann
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - Hui Li
- Department
of Chemistry and Nebraska Center for Materials and Nanoscience, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
34
|
Tosi I, Segado Centellas M, Campioli E, Iagatti A, Lapini A, Sissa C, Baldini L, Cappelli C, Di Donato M, Sansone F, Santoro F, Terenziani F. Excitation Dynamics in Hetero-bichromophoric Calixarene Systems. Chemphyschem 2016; 17:1686-706. [PMID: 26867716 DOI: 10.1002/cphc.201501065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/22/2016] [Indexed: 11/06/2022]
Abstract
In this work, the dynamics of electronic energy transfer (EET) in bichromophoric donor-acceptor systems, obtained by functionalizing a calix[4]arene scaffold with two dyes, was experimentally and theoretically characterized. The investigated compounds are highly versatile, due to the possibility of linking the dye molecules to the cone or partial cone structure of the calix[4]arene, which directs the two active units to the same or opposite side of the scaffold, respectively. The dynamics and efficiency of the EET process between the donor and acceptor units was investigated and discussed through a combined experimental and theoretical approach, involving ultrafast pump-probe spectroscopy and density functional theory based characterization of the energetic and spectroscopic properties of the system. Our results suggest that the external medium strongly determines the particular conformation adopted by the bichromophores, with a direct effect on the extent of excitonic coupling between the dyes and hence on the dynamics of the EET process itself.
Collapse
Affiliation(s)
- Irene Tosi
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy
| | | | - Elisa Campioli
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy
| | - Alessandro Iagatti
- LENS (European Laboratory for Non Linear Spectroscopy), via N. Carrara 1, 50019, Sesto Fiorentino (FI), Italy.,INO (Istituto Nazionale di Ottica), Largo Fermi 6, 50125, Firenze, Italy
| | - Andrea Lapini
- LENS (European Laboratory for Non Linear Spectroscopy), via N. Carrara 1, 50019, Sesto Fiorentino (FI), Italy.,Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 13, 50019, Sesto Fiorentino (FI), Italy
| | - Cristina Sissa
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy
| | - Laura Baldini
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy.
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy.
| | - Mariangela Di Donato
- LENS (European Laboratory for Non Linear Spectroscopy), via N. Carrara 1, 50019, Sesto Fiorentino (FI), Italy. .,INO (Istituto Nazionale di Ottica), Largo Fermi 6, 50125, Firenze, Italy. .,Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 13, 50019, Sesto Fiorentino (FI), Italy.
| | - Francesco Sansone
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca via G. Moruzzi 1, I-56124, Pisa, Italy
| | - Francesca Terenziani
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/a, 43124, Parma, Italy.
| |
Collapse
|
35
|
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.
Collapse
|
36
|
Banerjee S, Baiardi A, Bloino J, Barone V. Vibronic Effects on Rates of Excitation Energy Transfer and Their Temperature Dependence. J Chem Theory Comput 2016; 12:2357-65. [DOI: 10.1021/acs.jctc.6b00157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shiladitya Banerjee
- Scuola Normale
Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale
delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR),
UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Alberto Baiardi
- Scuola Normale
Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Julien Bloino
- Consiglio Nazionale
delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR),
UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale
Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
| |
Collapse
|
37
|
Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
Collapse
Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
| |
Collapse
|
38
|
Höfener S, Visscher L. Wave Function Frozen-Density Embedding: Coupled Excitations. J Chem Theory Comput 2016; 12:549-57. [DOI: 10.1021/acs.jctc.5b00821] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Sebastian Höfener
- Amsterdam Center for Multiscale
Modelling (ACMM), VU University Amsterdam, Theoretical Chemistry Section, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Amsterdam Center for Multiscale
Modelling (ACMM), VU University Amsterdam, Theoretical Chemistry Section, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
39
|
Nishimoto Y, Fedorov DG. The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model. Phys Chem Chem Phys 2016; 18:22047-61. [DOI: 10.1039/c6cp02186g] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electronic gap in proteins is analyzed in detail, and it is shown that FMO-DFTB/PCM is efficient and accurate in describing the molecular structure of proteins in solution.
Collapse
Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry
- Kyoto University
- Sakyo-ku, Kyoto 606-8103
- Japan
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat)
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tsukuba
- Japan
| |
Collapse
|
40
|
Nakano H, Sato H. An Ab Initio QM/MM-Based Approach to Efficiently Evaluate Vertical Excitation Energies in Condensed Phases Including the Nonequilibrium Solvation Effect. J Phys Chem B 2015; 120:1670-8. [DOI: 10.1021/acs.jpcb.5b08455] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hiroshi Nakano
- Department
of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department
of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
| |
Collapse
|
41
|
Zgarbová M, Rosnik AM, Luque FJ, Curutchet C, Jurečka P. Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields. J Comput Chem 2015. [DOI: 10.1002/jcc.24012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science; Palacky University; 17. listopadu 12 Olomouc 77146 Czech Republic
| | - Andreana M. Rosnik
- Department de Fisicoquímica; Facultat de Farmàcia, Universitat de Barcelona; Av. Joan XXIII s/n Barcelona 08028 Spain
| | - F. Javier Luque
- Department de Fisicoquímica and Institut de Biomedicina (IBUB); Facultat de Farmàcia, Universitat de Barcelona; Avgda Prat de la Riba 171, Santa Coloma de Gramenet 08921 Spain
| | - Carles Curutchet
- Department de Fisicoquímica; Facultat de Farmàcia, Universitat de Barcelona; Av. Joan XXIII s/n Barcelona 08028 Spain
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science; Palacky University; 17. listopadu 12 Olomouc 77146 Czech Republic
| |
Collapse
|
42
|
Lasorne B, Fihey A, Mendive-Tapia D, Jacquemin D. A curve-crossing model to rationalize and optimize diarylethene dyads. Chem Sci 2015; 6:5695-5702. [PMID: 29910863 PMCID: PMC5975843 DOI: 10.1039/c5sc01960e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 06/27/2015] [Indexed: 12/01/2022] Open
Abstract
Extra crossing points play a key role in the photochemistry of diarylethene dyads.
Going from photochromic compounds presenting a single switchable function to multi-addressable photochromic multimers remains an extremely difficult task notably because the interactions of several photochromic units through a linker generally result in a substantial loss of photoactivity. Due to their size and the intrinsic complexity of their electronic structure, coupled photochromes also constitute a fundamental challenge for theoretical chemistry. We present here an effective curve-crossing model that, used in connection with easily accessible ab initio data, allows a first understanding of the difficulty to obtain efficient multiphotochromes. Indeed, we demonstrate that extra crossing points, specific to multiphotochromes, have to be passed to ensure reactivity. In addition, the proposed approach allows the definition of an intuitive tilt criterion that can be used to screen a large number of substitution patterns and hence help in the design of new compounds, an aspect that is also developed here. The compatibility of this tilt criterion with previously proposed static Franck–Condon parameters is discussed as well.
Collapse
Affiliation(s)
- Benjamin Lasorne
- Institut Charles Gerhardt Montpellier , UMR 5253 , CNRS-UM , CTMM , Université Montpellier , CC 1501, Place Eugène Bataillon , 34095 Montpellier , France .
| | - Arnaud Fihey
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM) , UMR CNRS no. 6230 , BP 92208 , Université de Nantes , 2, Rue de la Houssinière , 44322 Nantes Cedex 3 , France .
| | - David Mendive-Tapia
- Institut Charles Gerhardt Montpellier , UMR 5253 , CNRS-UM , CTMM , Université Montpellier , CC 1501, Place Eugène Bataillon , 34095 Montpellier , France .
| | - Denis Jacquemin
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM) , UMR CNRS no. 6230 , BP 92208 , Université de Nantes , 2, Rue de la Houssinière , 44322 Nantes Cedex 3 , France . .,Institut Universitaire de France , 103 bd St. Michel , 75005 Paris Cedex 5 , France
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
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
| |
Collapse
|
45
|
Olsen JMH, Steinmann C, Ruud K, Kongsted J. Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy. J Phys Chem A 2015; 119:5344-55. [DOI: 10.1021/jp510138k] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Laboratory of
Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Casper Steinmann
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Kenneth Ruud
- Centre for Theoretical
and Computational Chemistry, Department of Chemistry, University of Tromsø—The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| |
Collapse
|
46
|
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
| |
Collapse
|
47
|
Di Remigio R, Bast R, Frediani L, Saue T. Four-Component Relativistic Calculations in Solution with the Polarizable Continuum Model of Solvation: Theory, Implementation, and Application to the Group 16 Dihydrides H2X (X = O, S, Se, Te, Po). J Phys Chem A 2014; 119:5061-77. [DOI: 10.1021/jp507279y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø
, N-9037 Tromsø, Norway
| | - Radovan Bast
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center
, S-10691 Stockholm, Sweden
- PDC Center for High Performance Computing, Royal Institute of Technology
, S-10044 Stockholm, Sweden
| | - Luca Frediani
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø
, N-9037 Tromsø, Norway
| | - Trond Saue
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), CNRS/Université de Toulouse III (Paul Sabatier)
, 118 route de Narbonne, 31062 Toulouse, France
| |
Collapse
|
48
|
Li X, Chung LW, Morokuma K, Li G. Theoretical Study on the UVR8 Photoreceptor: Sensing Ultraviolet-B by Tryptophan and Dissociation of Homodimer. J Chem Theory Comput 2014; 10:3319-30. [DOI: 10.1021/ct5003362] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xin Li
- State
Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Lung Wa Chung
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
- Department
of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Guohui Li
- State
Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian 116023, China
| |
Collapse
|
49
|
Biancardi A, Burgalassi A, Terenzi A, Spinello A, Barone G, Biver T, Mennucci B. A Theoretical and Experimental Investigation of the Spectroscopic Properties of a DNA-Intercalator Salphen-Type ZnIIComplex. Chemistry 2014; 20:7439-47. [DOI: 10.1002/chem.201304876] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 01/22/2023]
|
50
|
Caprasecca S, Mennucci B. Excitation Energy Transfer in Donor-Bridge-Acceptor Systems: A Combined Quantum-Mechanical/Classical Analysis of the Role of the Bridge and the Solvent. J Phys Chem A 2014; 118:6484-91. [DOI: 10.1021/jp502815r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Stefano Caprasecca
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| |
Collapse
|