1
|
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.
Collapse
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
| |
Collapse
|
2
|
Weng G, Pang A, Vlček V. Spatial Decay and Limits of Quantum Solute-Solvent Interactions. J Phys Chem Lett 2023; 14:2473-2480. [PMID: 36867592 DOI: 10.1021/acs.jpclett.3c00208] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular excitations in the liquid-phase environment are renormalized by the surrounding solvent molecules. Herein, we employ the GW approximation to investigate the solvation effects on the ionization energy of phenol in various solvent environments. The electronic effects differ by up to 0.4 eV among the five investigated solvents. This difference depends on both the macroscopic solvent polarizability and the spatial decay of the solvation effects. The latter is probed by separating the electronic subspace and the GW correlation self-energy into fragments. The fragment correlation energy decays with increasing intermolecular distance and vanishes at ∼9 Å, and this pattern is independent of the type of solvent environment. The 9 Å cutoff defines an effective interacting volume within which the ionization energy shift per solvent molecule is proportional to the macroscopic solvent polarizability. Finally, we propose a simple model for computing the ionization energies of molecules in an arbitrary solvent environment.
Collapse
Affiliation(s)
- Guorong Weng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Amanda Pang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Vojtěch Vlček
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
- Materials Department, University of California, Santa Barbara, California 93106-5050, United States
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Gómez S, Giovannini T, Cappelli C. Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution. ACS PHYSICAL CHEMISTRY AU 2022; 3:1-16. [PMID: 36718266 PMCID: PMC9881242 DOI: 10.1021/acsphyschemau.2c00050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
In this Perspective, we outline the essential physicochemical aspects that need to be considered when building a reliable approach to describe absorption properties of solvated systems. In particular, we focus on how to properly model the complexity of the solvation phenomenon, arising from dynamical aspects and specific, strong solute-solvent interactions. To this end, conformational and configurational sampling techniques, such as Molecular Dynamics, have to be coupled to accurate fully atomistic Quantum Mechanical/Molecular Mechanics (QM/MM) methodologies. By exploiting different illustrative applications, we show that an effective reproduction of experimental spectral signals can be achieved by delicately balancing exhaustive sampling, hydrogen bonding, mutual polarization, and nonelectrostatic effects.
Collapse
|
6
|
Paul AC, Folkestad SD, Myhre RH, Koch H. Oscillator Strengths in the Framework of Equation of Motion Multilevel CC3. J Chem Theory Comput 2022; 18:5246-5258. [PMID: 35921447 PMCID: PMC9476665 DOI: 10.1021/acs.jctc.2c00164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We present an efficient implementation of the equation
of motion
oscillator strengths for the closed-shell multilevel coupled cluster
singles and doubles with perturbative triples method (MLCC3) in the
electronic structure program eT. The orbital space is split into an active part treated with
CC3 and an inactive part computed at the coupled cluster singles and
doubles (CCSD) level of theory. Asymptotically, the CC3 contribution
scales as floating-point operations, where nV is the total number of virtual orbitals while nv and no are the
number of active virtual and occupied orbitals, respectively. The
CC3 contribution, thus, only scales linearly with the full system
size and can become negligible compared to the cost of CCSD. We demonstrate
the capabilities of our implementation by calculating the ultraviolet–visible
spectrum of azobenzene and a core excited state of betaine 30 with
more than 1000 molecular orbitals.
Collapse
Affiliation(s)
- Alexander C Paul
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway
| | - Sarai Dery Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway
| | - Rolf H Myhre
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavaleri 7, 56126 Pisa, Italy
| |
Collapse
|
7
|
Fedotov DA, Paul AC, Koch H, Santoro F, Coriani S, Improta R. Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study. Phys Chem Chem Phys 2022; 24:4987-5000. [PMID: 35142309 DOI: 10.1039/d1cp04340d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, namely, equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the ππ* states (one for pyrimidine, two for purines) associated with the lowest-energy absorption band, and for the close-lying nπ* state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effects by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the nπ* state. Finally, ESA spectra have been computed from the minima of the lowest energy ππ* state, and found in line with the available experimental transient absorption spectra of the nucleosides in solution, providing further validation of our computational approach.
Collapse
Affiliation(s)
- Daniil A Fedotov
- DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Alexander C Paul
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavalieri, 7, I-56126, Pisa, Italy.
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, I-56124 Pisa, Italy.
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark. .,Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, I-80134 Napoli, Italy.
| |
Collapse
|
8
|
Goletto L, Kjønstad EF, Folkestad SD, Høyvik IM, Koch H. Linear-Scaling Implementation of Multilevel Hartree-Fock Theory. J Chem Theory Comput 2021; 17:7416-7427. [PMID: 34747179 PMCID: PMC8675138 DOI: 10.1021/acs.jctc.1c00299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce a new algorithm for the construction of the two-electron contributions to the Fock matrix in multilevel Hartree-Fock (MLHF) theory. In MLHF, the density of an active molecular region is optimized, while the density of an inactive region is fixed. The MLHF equations are solved in a reduced molecular orbital (MO) basis localized to the active region. The locality of the MOs can be exploited to reduce the computational cost of the Fock matrix: the cost related to the inactive density becomes linear scaling, while the iterative cost related to the active density is independent of the system size. We demonstrate the performance of this new algorithm on a variety of systems, including amino acid chains, water clusters, and solvated systems.
Collapse
Affiliation(s)
- Linda Goletto
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Eirik F Kjønstad
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Sarai D Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Ida-Marie Høyvik
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Scuola Normale Superiore, Pisa 56126, Italy
| |
Collapse
|
9
|
Ambrosetti M, Skoko S, Giovannini T, Cappelli C. Quantum Mechanics/Fluctuating Charge Protocol to Compute Solvatochromic Shifts. J Chem Theory Comput 2021; 17:7146-7156. [PMID: 34619965 PMCID: PMC8582258 DOI: 10.1021/acs.jctc.1c00763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Despite the potentialities
of the quantum mechanics (QM)/fluctuating
charge (FQ) approach to model the spectral properties of solvated
systems, its extensive use has been hampered by the lack of reliable
parametrizations of solvents other than water. In this paper, we substantially
extend the applicability of QM/FQ to solvating environments of different
polarities and hydrogen-bonding capabilities. The reliability and
robustness of the approach are demonstrated by challenging the model
to simulate solvatochromic shifts of four organic chromophores, which
display large shifts when dissolved in apolar, aprotic or polar, protic
solvents.
Collapse
Affiliation(s)
| | - Sulejman Skoko
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Macetti G, Genoni A. Three-Layer Multiscale Approach Based on Extremely Localized Molecular Orbitals to Investigate Enzyme Reactions. J Phys Chem A 2021; 125:6013-6027. [PMID: 34190569 DOI: 10.1021/acs.jpca.1c05040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) calculations are widely used embedding techniques to computationally investigate enzyme reactions. In most QM/MM computations, the quantum mechanical region is treated through density functional theory (DFT), which offers the best compromise between chemical accuracy and computational cost. Nevertheless, to obtain more accurate results, one should resort to wave function-based methods, which however lead to a much larger computational cost already for relatively small QM subsystems. To overcome this drawback, we propose the coupling of our QM/ELMO (quantum mechanics/extremely localized molecular orbital) approach with molecular mechanics, thus introducing the three-layer QM/ELMO/MM technique. The QM/ELMO strategy is an embedding method in which the chemically relevant part of the system is treated at the quantum mechanical level, while the rest is described through frozen ELMOs. Since the QM/ELMO method reproduces results of fully QM computations within chemical accuracy and with a much lower computational effort, it can be considered a suitable strategy to extend the range of applicability and accuracy of the QM/MM scheme. In this paper, other than briefly presenting the theoretical bases of the QM/ELMO/MM technique, we will also discuss its validation on the well-tested deprotonation of acetyl coenzyme A by aspartate in citrate synthase.
Collapse
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| |
Collapse
|