1
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Giovannini T, Scavino M, Koch H. Time-Dependent Multilevel Density Functional Theory. J Chem Theory Comput 2024; 20:3601-3612. [PMID: 38648031 DOI: 10.1021/acs.jctc.4c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We present a novel three-layer approach based on multilevel density functional theory (MLDFT) and polarizable molecular mechanics to simulate the electronic excitations of chemical systems embedded in an external environment within the time-dependent DFT formalism. In our method, the electronic structure of a target system, the chromophore, is determined in the field of an embedded inactive layer, which is treated as frozen. Long-range interactions are described by employing the polarizable fluctuating charge (FQ) force field. The resulting MLDFT/FQ thus accurately describes both electrostatics (and polarization) and non-electrostatic target-environment interactions. The robustness and reliability of the approach are demonstrated by comparing our results with experimental data reported for various organic molecules in solution.
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Affiliation(s)
| | - Marco Scavino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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2
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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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3
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Mashkovtsev D, Orimoto Y, Aoki Y. Fast and Accurate Calculation of the UV-Vis Spectrum with the Modified Local Excitation Approximation. J Chem Theory Comput 2023; 19:5548-5562. [PMID: 37471461 DOI: 10.1021/acs.jctc.3c00266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The local excitation approximation (LEA), a method for the calculation of electronic excitations localized in a specific region of a molecule, has been modified with new approaches to enhance the accuracy of the original method. The primary concept behind LEA involves isolating the region of interest as a submolecule from the full molecule using a localization method, followed by calculating electronic excitations solely within this submolecule. In this study, we examined approaches that improve the accuracy in describing the region of interest, particularly its molecular orbital energies. Additionally, the localization method was extended with a new projection technique to accelerate calculations. These approaches were studied in time-dependent density functional theory (TDDFT) calculations applied to four testing systems with a chromophore as the region of interest: two basic linear molecules, acrolein surrounded by 24 water molecules, and a model of a green fluorescent protein. For all studied systems, the results of TDDFT calculations combined with LEA exhibited near-zero error when groups of atoms adjacent to the chromophore were explicitly included in the submolecule. This was achieved with at least a quadratic speedup of the calculation time as a function of the submolecule size.
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Affiliation(s)
- Denis Mashkovtsev
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
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4
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Rojas-Valencia N, Gómez S, Giovannini T, Cappelli C, Restrepo A, Núñez Zarur F. Water Maintains the UV-Vis Spectral Features During the Insertion of Anionic Naproxen and Ibuprofen into Model Cell Membranes. J Phys Chem B 2023; 127:2146-2155. [PMID: 36877579 DOI: 10.1021/acs.jpcb.2c08332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
UV-vis spectra of anionic ibuprofen and naproxen in a model lipid bilayer of the cell membrane are investigated using computational techniques in combination with a comparative analysis of drug spectra in purely aqueous environments. The simulations aim at elucidating the intricacies behind the negligible changes in the maximum absorption wavelength in the experimental spectra. A set of configurations of the systems constituted by lipid, water, and drugs or just water and drugs are obtained from classical Molecular Dynamics simulations. UV-vis spectra are computed in the framework of atomistic Quantum Mechanical/Molecular Mechanics (QM/MM) approaches together with Time-Dependent Density Functional Theory (TD-DFT). Our results suggest that the molecular orbitals involved in the electronic transitions are the same, regardless of the chemical environment. A thorough analysis of the contacts between the drug and water molecules reveals that no significant changes in UV-vis spectra are a consequence of ibuprofen and naproxen molecules being permanently microsolvated by water molecules, despite the presence of lipid molecules. Water molecules microsolvate the charged carboxylate group as expected but also microsolvate the aromatic regions of the drugs.
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Affiliation(s)
- Natalia Rojas-Valencia
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia, UdeA, Calle 70 No. 52-21 050010, Medellín, Colombia
| | - Francisco Núñez Zarur
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026, Medellín, Colombia
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5
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Giovannini T, Marrazzini G, Scavino M, Koch H, Cappelli C. Integrated Multiscale Multilevel Approach to Open Shell Molecular Systems. J Chem Theory Comput 2023; 19:1446-1456. [PMID: 36780359 PMCID: PMC10018740 DOI: 10.1021/acs.jctc.2c00805] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
We present a novel multiscale approach to study the electronic structure of open shell molecular systems embedded in an external environment. The method is based on the coupling of multilevel Hartree-Fock (MLHF) and Density Functional Theory (MLDFT), suitably extended to the unrestricted formalism, to Molecular Mechanics (MM) force fields (FF). Within the ML region, the system is divided into active and inactive parts, thus describing the most relevant interactions (electrostatic, polarization, and Pauli repulsion) at the quantum level. The surrounding MM part, which is formulated in terms of nonpolarizable or polarizable FFs, permits a physically consistent treatment of long-range electrostatics and polarization effects. The approach is extended to the calculation of hyperfine coupling constants and applied to selected nitroxyl radicals in an aqueous solution.
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Affiliation(s)
| | - Gioia Marrazzini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Scavino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Henrik Koch
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.,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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6
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Hégely B, Szirmai ÁB, Mester D, Tajti A, Szalay PG, Kállay M. Performance of Multilevel Methods for Excited States. J Phys Chem A 2022; 126:6548-6557. [PMID: 36095318 PMCID: PMC9511572 DOI: 10.1021/acs.jpca.2c05013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The performance of multilevel quantum chemical approaches,
which
utilize an atom-based system partitioning scheme to model various
electronic excited states, is studied. The considered techniques include
the mechanical-embedding (ME) of “our own N-layered integrated
molecular orbital and molecular mechanics” (ONIOM) method,
the point charge embedding (PCE), the electronic-embedding (EE) of
ONIOM, the frozen density-embedding (FDE), the projector-based embedding
(PbE), and our local domain-based correlation method. For the investigated
multilevel approaches, the second-order algebraic-diagrammatic construction
[ADC(2)] approach was utilized as the high-level method, which was
embedded in either Hartree–Fock or a density functional environment.
The XH-27 test set of Zech et al. [, 2018, 14, 402829906111] was used for the assessment,
where organic dyes interact with several solvent molecules. With the
selection of the chromophores as active subsystems, we conclude that
the most reliable approach is local domain-based ADC(2) [L-ADC(2)],
and the least robust schemes are ONIOM-ME and ONIOM-EE. The PbE, FDE,
and PCE techniques often approach the accuracy of the L-ADC(2) scheme,
but their precision is far behind. The results suggest that a more
conservative subsystem selection algorithm or the inclusion of subsystem
charge-transfers is required for the atom-based cost-efficient methods
to produce high-accuracy excitation energies.
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Affiliation(s)
- Bence Hégely
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary.,ELKH-BME Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Ádám B Szirmai
- Laboratory of Theoretical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, P.O. Box 32, H-1518 Budapest 112, Hungary
| | - Dávid Mester
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary.,ELKH-BME Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Attila Tajti
- Laboratory of Theoretical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, P.O. Box 32, H-1518 Budapest 112, Hungary
| | - Péter G Szalay
- Laboratory of Theoretical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, P.O. Box 32, H-1518 Budapest 112, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary.,ELKH-BME Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
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7
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Uribe L, Gómez S, Giovannini T, Egidi F, Restrepo A. An efficient and robust procedure to calculate absorption spectra of aqueous charged species applied to NO 2. Phys Chem Chem Phys 2021; 23:14857-14872. [PMID: 34223573 DOI: 10.1039/d1cp00652e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Accurate calculation of absorption spectra of aqueous NO2- requires rigorously sampling the quantum potential energy surfaces for microsolvation of NO2- with at least five explicit water molecules and embedding the resulting clusters in a continuum solvent accounting for the statistical weighted contributions of individual isomers. This method, which we address as ASCEC + PCM, introduces several desired features when compared against MD simulations derived QM/MM spectra: comparatively fewer explicit solvent molecules to be treated with expensive QM methods, the identification of equilibrium structures in the quantum PES to be used in further vibrational spectroscopy, and the unequivocal identification of cluster orbitals undergoing electronic transitions and charge transfer that originate the spectral bands.
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Affiliation(s)
- Lina Uribe
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Franco Egidi
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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8
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Egidi F, Angelico S, Lafiosca P, Giovannini T, Cappelli C. A polarizable three-layer frozen density embedding/molecular mechanics approach. J Chem Phys 2021; 154:164107. [PMID: 33940798 DOI: 10.1063/5.0045574] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We present a novel multilayer polarizable embedding approach in which the system is divided into three portions, two of which are treated using density functional theory and their interaction is based on frozen density embedding (FDE) theory, and both also mutually interact with a polarizable classical layer described using an atomistic model based on fluctuating charges (FQ). The efficacy of the model is demonstrated by extending the formalism to linear response properties and applying it to the simulation of the excitation energies of organic molecules in aqueous solution, where the solute and the first solvation shell are treated using FDE, while the rest of the solvent is modeled using FQ charges.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Angelico
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Piero Lafiosca
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - 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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9
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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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10
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Giovannini T, Koch H. Energy-Based Molecular Orbital Localization in a Specific Spatial Region. J Chem Theory Comput 2021; 17:139-150. [PMID: 33337150 DOI: 10.1021/acs.jctc.0c00737] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present a novel energy-based localization procedure able to localize molecular orbitals into predefined spatial regions. The method is defined in a multiscale framework based on the multilevel Hartree-Fock approach. In particular, the system is partitioned into active and inactive fragments. The localized molecular orbitals are obtained maximizing the repulsion between the two fragments. The method is applied to several cases including both conjugated and non-conjugated systems. Our multiscale approach is compared with reference values for both ground-state properties, such as dipole moments, and local excitation energies. The proposed approach is useful to extend the application range of high-level electron correlation methods. In fact, the reduced number of molecular orbitals can lead to a large reduction in the computational cost of correlated calculations.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Henrik Koch
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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11
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Goletto L, Giovannini T, Folkestad SD, Koch H. Combining multilevel Hartree–Fock and multilevel coupled cluster approaches with molecular mechanics: a study of electronic excitations in solutions. Phys Chem Chem Phys 2021; 23:4413-4425. [DOI: 10.1039/d0cp06359b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the coupling of different quantum-embedding approaches with a third molecular-mechanics layer, which can be either polarizable or non-polarizable.
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Affiliation(s)
- Linda Goletto
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- 7491 Trondheim
- Norway
| | - Tommaso Giovannini
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- 7491 Trondheim
- Norway
| | - Sarai D. Folkestad
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- 7491 Trondheim
- Norway
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