1
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Sepali C, Lafiosca P, Gómez S, Giovannini T, Cappelli C. Effective fully polarizable QM/MM approaches to compute Raman and Raman Optical Activity spectra in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123485. [PMID: 37827000 DOI: 10.1016/j.saa.2023.123485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/22/2023] [Accepted: 10/01/2023] [Indexed: 10/14/2023]
Abstract
Raman and Raman Optical Activity (ROA) signals are amply affected by solvent effects, especially in the presence of strongly solute-solvent interactions such as Hydrogen Bonding (HB). In this work, we extend the fully atomistic polarizable Quantum Mechanics/Molecular Mechanics approach, based on the Fluctuating Charges and Fluctuating Dipoles force field to the calculation of Raman and ROA spectra. Such an approach is able to accurately describe specific HB interactions, by also accounting for anisotropic contributions due to the inclusion of fluctuating dipoles. To highlight the potentiality of the novel approach, Raman and ROA spectra of L-Serine and L-Cysteine dissolved in aqueous solution are computed and compared both with alternative theoretical approaches and experimental measurements.
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Affiliation(s)
- Chiara Sepali
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, Pisa, 56126, Italy
| | - Piero Lafiosca
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, Pisa, 56126, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, Pisa, 56126, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, Pisa, 56126, Italy.
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2
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Larsson ED, Reinholdt P, Hedegård ED, Kongsted J. Accuracy of One- and Two-Photon Intensities with the Extended Polarizable Density Embedding Model. J Phys Chem B 2023; 127:9905-9914. [PMID: 37948667 DOI: 10.1021/acs.jpcb.3c05029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The recently developed extended polarizable density embedding (PDE-X) model is evaluated for the spectroscopic properties of organic chromophores solvated in water, including both one- and two-photon absorption properties. The PDE-X embedding model systematically improves vertical excitation energies over the preceding polarizable density embedding model (PDE). PDE-X shows more modest improvements over existing embedding models for oscillator strengths and two-photon absorption cross-sections, which are more sensitive properties. We argue that the origin of these discrepancies is related to the description of polarization effects, suggesting directions for future development of the embedding model.
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Affiliation(s)
- Ernst Dennis Larsson
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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3
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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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4
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Sirimatayanant S, Andruniów T. Benchmarking two-photon absorption strengths of rhodopsin chromophore models with CC3 and CCSD methodologies: An assessment of popular density functional approximations. J Chem Phys 2023; 158:094106. [PMID: 36889953 DOI: 10.1063/5.0135594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
This work presents the investigations of the impact of an increasing electron correlation in the hierarchy of coupled-cluster methods, i.e., CC2, CCSD, and CC3, on two-photon absorption (2PA) strengths for the lowest excited state of the minimal rhodopsin's chromophore model-cis-penta-2,4-dieniminium cation (PSB3). For a larger chromophore's model [4-cis-hepta-2,4,6-trieniminium cation (PSB4)], CC2 and CCSD calculations of 2PA strengths were performed. Additionally, 2PA strengths predicted by some popular density functional theory (DFT) functionals differing in HF exchange contribution were assessed against the reference CC3/CCSD data. For PSB3, the accuracy of 2PA strengths increases in the following order: CC2 < CCSD < CC3, with the CC2 deviation from both higher-level methods exceeding 10% at 6-31+G* basis sets and 2% at aug-cc-pVDZ basis set. However, for PSB4, this trend is reversed and CC2-based 2PA strength is larger than the corresponding CCSD value. Among the DFT functionals investigated, CAM-B3LYP and BHandHLYP provide 2PA strengths in best compliance with reference data, however, with the error approaching an order of magnitude.
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Affiliation(s)
- Saruti Sirimatayanant
- Institute of Advanced Materials, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Tadeusz Andruniów
- Institute of Advanced Materials, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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5
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Horz M, Masood HMA, Brunst H, Cerezo J, Picconi D, Vormann H, Niraghatam MS, van Wilderen LJGW, Bredenbeck J, Santoro F, Burghardt I. Vibrationally resolved two-photon electronic spectra including vibrational pre-excitation: Theory and application to VIPER spectroscopy with two-photon excitation. J Chem Phys 2023; 158:064201. [PMID: 36792506 DOI: 10.1063/5.0132608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Following up on our previous work on vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation [von Cosel et al., J. Chem. Phys. 147, 164116 (2017)], we present a combined theoretical and experimental study of two-photon-induced vibronic transitions in polyatomic molecules that are probed in the VIbrationally Promoted Electronic Resonance experiment using two-photon excitation (2P-VIPER). In order to compute vibronic spectra, we employ time-independent and time-dependent methods based on the evaluation of Franck-Condon overlap integrals and Fourier transformations of time-domain correlation functions, respectively. The time-independent approach uses a generalized version of the FCclasses method, while the time-dependent approach relies on the analytical evaluation of Gaussian moments within the harmonic approximation, including Duschinsky rotation effects. For the Coumarin 6 dye, two-dimensional 2P-VIPER experiments involving excitation to the lowest-lying singlet excited state (S1) are presented and compared with corresponding one-photon VIPER spectra. In both cases, coumarin ring modes and a CO stretch mode show VIPER activity, albeit with different relative intensities. Selective pre-excitation of these modes leads to a pronounced redshift of the low-frequency edge of the electronic absorption spectrum, which is a prerequisite for the VIPER experiment. Theoretical analysis underscores the role of interference between Franck-Condon and Herzberg-Teller effects in the two-photon experiment, which is at the root of the observed intensity distribution.
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Affiliation(s)
- Maximiliane Horz
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Hafiz M A Masood
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Hendrik Brunst
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David Picconi
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Hannah Vormann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Madhava Shyam Niraghatam
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Luuk J G W van Wilderen
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche - CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
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6
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Gómez S, Lafiosca P, Egidi F, Giovannini T, Cappelli C. UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA. J Chem Inf Model 2023; 63:1208-1217. [PMID: 36745496 PMCID: PMC9976284 DOI: 10.1021/acs.jcim.2c01495] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomolecular receptors. The extraction of information at the molecular level from experimental RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramolecular system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/molecular mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with experimental data, thus confirming the reliability of the computational protocol.
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Affiliation(s)
- Sara Gómez
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy,E-mail:
| | - Piero Lafiosca
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Franco Egidi
- Software
for Chemistry and Materials BV, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - 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,E-mail:
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7
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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.
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8
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Theoretical study of the one- and two-photon absorption cross-section of substituted polyaryl pyridine-based compounds. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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de Wergifosse M, Beaujean P, Grimme S. Ultrafast Evaluation of Two-Photon Absorption with Simplified Time-Dependent Density Functional Theory. J Phys Chem A 2022; 126:7534-7547. [PMID: 36201255 DOI: 10.1021/acs.jpca.2c02395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work presents the theoretical background to evaluate two-photon absorption (2PA) cross-sections in the framework of simplified time-dependent density functional theory (sTD-DFT). Our new implementation allows the ultrafast evaluation of 2PA cross-sections for large molecules based on a regular DFT ground-state determinant as well as a variant employing our tight-binding sTD-DFT-xTX flavor for very large systems. The method is benchmarked against higher-level calculations for trans-stilbene and typical fluorescent protein chromophores. For eGFP, a quadrupolar chromophore and its branched version, the flavine mono-nucleotide, and the iLOV protein, we compare sTD-DFT 2PA spectra to experimental ones. This includes extension and testing of our all-atom quantum chemistry methodology for the evaluation of 2PA for a system of ∼2000 atoms, providing striking agreement with the experimental spectrum.
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Affiliation(s)
- Marc de Wergifosse
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115Bonn, Germany
| | - Pierre Beaujean
- Laboratory of Theoretical Chemistry, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000Namur, Belgium
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115Bonn, Germany
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10
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Asido M, Hamerla C, Weber R, Horz M, Niraghatam MS, Heckel A, Burghardt I, Wachtveitl J. Ultrafast and efficient energy transfer in a one- and two-photon sensitized rhodamine-BODIPY dyad: a perspective for broadly absorbing photocages. Phys Chem Chem Phys 2022; 24:1795-1802. [PMID: 34985062 DOI: 10.1039/d1cp04528h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In view of the demand for photoactivatable probes that operate in the visible (VIS) to near infrared (NIR) region of the spectrum, we designed a bichromophoric system based on a rhodamine fluorophore and a BODIPY photocage. Two-photon excited fluorescence (TPEF) measurements and quantum chemical calculations reveal excellent two-photon properties of the employed rhodamine derivative. Excitation of the rhodamine unit via a one- or two-photon process leads to excitation energy transfer (EET) onto the BODIPY part, which is followed by the liberation of the leaving group. Ultrafast transient absorption spectroscopy provides evidence for a highly efficient EET dynamics on a sub-500 femtosecond scale. Complementary quantum dynamical calculations using the multi-layer multiconfiguration time-dependent Hartree (ML-MCTDH) approach highlight the quantum coherent character of the EET transfer. Photorelease of p-nitroaniline (PNA) was investigated by UV/vis absorption spectroscopy by either excitation of the rhodamine or the BODIPY moiety. Even though a quantitative assessment of the PNA yield could not be achieved for this particular BODIPY cage, the present study provides a design principle for a class of photocages that can be broadly activated between 500 and 900 nm.
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Affiliation(s)
- Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Carsten Hamerla
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Rebekka Weber
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Maximiliane Horz
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Madhava Shyam Niraghatam
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
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11
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Zhang C, Sun YT, Gao LX, Feng B, Yan X, Guo XH, Ren AM, Zhou YB, Li J, Wang WL. Theoretical study and application of 2-phenyl-1,3,4-thiadiazole derivatives with optical and inhibitory activity against SHP1. Phys Chem Chem Phys 2022; 24:861-874. [PMID: 34908073 DOI: 10.1039/d1cp04268h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Src homology-2 domain-containing protein tyrosine phosphatase 1 (SHP1) is mainly restricted to hematopoietic and epithelial cells and widely accepted as a convergent node for oncogenic cell-signaling cascades. The development of efficient methods for rapidly tracing and inhibiting the SHP1 activity in complex biological systems is of considerable significance for advancing the integration of diagnosis and treatment of the related disease. With this aim, we designed and synthesized five 2-phenyl-1,3,4-thiadiazole derivatives (PT2, PT5, PT8, PT9 and PT10) here based on the reported SHP1 inhibitors (PT1, PT3, PT4, PT6 and PT7). The photophysical properties and inhibitory activities of these 2-phenyl-1,3,4-thiadiazole derivatives (PT1-PT10) against SHP1 were thoroughly studied from the theoretical simulation and experimental application aspects. The representative compound PT10 exhibited a larger quantum yield than the other molecules because of the smaller geometric relaxation and reorganization energy of the excited state, which was consistent with the results from the fluorescence experiments in organic solvents. In addition, PT10 showed a selective fluorescence response for SHP1 activity and low cytotoxicity in HeLa cells. Lastly, it indicated the potential application in two-photon cell fluorescence imaging in the future according to the calculated excellent two-photon absorption properties. In this contribution, firstly, we offered the fluorescent and activated molecule PT10 against SHP1, which achieved the integration of visualization and inhibitory activity of SHP1 preliminarily at the enzyme molecular level.
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Affiliation(s)
- Chun Zhang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, China.
| | - Yi-Tao Sun
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, China.
| | - Li-Xin Gao
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, China. .,National Center for Drug Screening, State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Bo Feng
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, China. .,National Center for Drug Screening, State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Xue Yan
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, China.
| | - Xue-Hui Guo
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road 2#, Changchun, 130061, P. R. China.
| | - Ai-Min Ren
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Liutiao Road 2#, Changchun, 130061, P. R. China.
| | - Yu-Bo Zhou
- National Center for Drug Screening, State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan, Guangdong, 528400, P. R. China
| | - Jia Li
- National Center for Drug Screening, State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan, Guangdong, 528400, P. R. China
| | - Wen-Long Wang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, China.
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12
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Loco D, Lagardère L, Adjoua O, Piquemal JP. Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity. Acc Chem Res 2021; 54:2812-2822. [PMID: 33961401 PMCID: PMC8264944 DOI: 10.1021/acs.accounts.0c00662] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/20/2022]
Abstract
The computational modeling of realistic extended systems, relevant in, e.g., Chemistry and Biophysics, is a fundamental problem of paramount importance in contemporary research. Enzymatic catalysis and photoinduced processes in pigment-protein complexes are typical problems targeted by computer-aided approaches, to complement experiments as interpretative tools at a molecular scale. The daunting complexity of this task lies in between the opposite stringent requirements of results' reliability for structural/dynamical properties and related intermolecular interactions, and a mandatory principle of realism in the modeling strategy. Therefore, in practice, a truly realistic computational model of a biologically relevant system can easily fail to meet the accuracy requirement, in order to balance the excessive computational cost necessary to reach the desired precision.To address such an "accuracy vs reality" dualistic requirement, mixed quantum mechanics/classical mechanics approaches within Atomistic (i.e., preserving the discrete particle configuration) Polarizable Embeddings (QM/APEs) methods have been proposed over the years. In this Account, we review recent developments in the design and application of general QM/APE methods, targeting situations where a local intrinsically quantum behavior is coupled to a large molecular system (i.e., an environment), often involving processes with different dynamical time scales, in order to avoid brute-force, unpractical quantum chemistry calculations on the complete system.In the first place, our interest is devoted to the available APEs models presently implemented in computational software, highlighting the quantum chemistry methods that can be used to treat the QM subsystem. We review the coupling strategy between the QM subsystem and the APE, which requires to examine the way the QM/MM mutual interactions are accounted for and how the polarization of the classical environment is considered with respect to (wrt) the quantum variables. Because of the need of reliable molecular and macromolecular structures, a pivotal aspect to address here is the handling of the system dynamics (i.e., gradients wrt nuclear positions are required), especially for large molecular assemblies composed by an overwhelming number of atoms, exploring many conformations on a complex energy landscape.Alongside, we highlight our views on the necessary steps to take toward more accurate general-purposes and transferable explicit embeddings. The main objective to achieve here is to design a more physically grounded multiscale approach. To do so, one should apply advanced new generation classical models to account for refined induction effects that are able to (i) improve the quality of QM/MM interaction energies; (ii) enhance transferability by avoiding the compulsory partial (or total) reparameterization of the classical model. Moreover, the extension of recent developments originating from the field of advanced classical molecular dynamics (MD) to the realm of QM/APE methods is a key direction to improve both speed and efficiency for the phase space exploration of systems of growing size and complexity.Lastly, we point out specific research topics where an advanced QM/APE dynamics can certainly shed some light. For example, we discuss chemical reactions in "harsh" environments and the case of spectroscopic theoretical modeling where the inclusion of refined environment effects is often mandatory.
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Affiliation(s)
- Daniele Loco
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
- Intitut
Parisien de Chimie Physique et Théorique, Sorbonne Université, FR 2622 CNRS, 75005 Paris, France
| | - Olivier Adjoua
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
- Institut
Universitaire de France, F-75005 Paris, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
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13
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Fu M, Wesolowski TA. The Challenge of Accurate Computation of Two-Photon Absorption Properties of Organic Chromophores in the Condensed Phase. J Chem Theory Comput 2021; 17:3652-3665. [PMID: 33944563 DOI: 10.1021/acs.jctc.1c00204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two strategies are applied to evaluate the effect of the environment on the two-photon absorption (TPA) cross sections for two characteristic excited states of C2H4 upon complexation with H2O. The supermolecular strategy provides the reference complexation-induced shifts and uses either the EOM-CCSD or ADC(2) method. The embedding strategy is based on frozen-density-embedding theory (FDET) and uses only fundamental constants. The TPA cross sections from high-level supermolecular calculations are extremely basis-set-sensitive. Literature data and the present study indicate that accuracy of the absolute TPA cross sections below 100 atomic units and their shifts below 10 atomic units remains a challenge. The obtained FDET results show a similar basis-set behavior. For the largest basis set (d-aug-cc-pVQZ), TPA cross sections obtained from these two strategies are in excellent agreement. The complexation-induced shifts have the correct sign of the effect and a small (12-33%) relative error in magnitude. The deviations of the FDET-derived shifts from the reference are of similar magnitude as the reliability threshold of the reference shifts.
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Affiliation(s)
- Mingxue Fu
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Tomasz A Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
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14
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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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15
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Skoko S, Ambrosetti M, Giovannini T, Cappelli C. Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study. Molecules 2020; 25:E5853. [PMID: 33322361 PMCID: PMC7764712 DOI: 10.3390/molecules25245853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022] Open
Abstract
We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.
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Affiliation(s)
- Sulejman Skoko
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy; (S.S.); (M.A.)
| | - Matteo Ambrosetti
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy; (S.S.); (M.A.)
| | - Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway;
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy; (S.S.); (M.A.)
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16
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Marrazzini G, Giovannini T, Egidi F, Cappelli C. Calculation of Linear and Non-linear Electric Response Properties of Systems in Aqueous Solution: A Polarizable Quantum/Classical Approach with Quantum Repulsion Effects. J Chem Theory Comput 2020; 16:6993-7004. [PMID: 33058671 PMCID: PMC8015238 DOI: 10.1021/acs.jctc.0c00674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Indexed: 01/10/2023]
Abstract
We present a computational study of polarizabilities and hyperpolarizabilities of organic molecules in aqueous solutions, focusing on solute-water interactions and the way they affect a molecule's linear and non-linear electric response properties. We employ a polarizable quantum mechanics/molecular mechanics (QM/MM) computational model that treats the solute at the QM level while the solvent is treated classically using a force field that includes polarizable charges and dipoles, which dynamically respond to the solute's quantum-mechanical electron density. Quantum confinement effects are also treated by means of a recently implemented method that endows solvent molecules with a parametric electron density, which exerts Pauli repulsion forces upon the solute. By applying the method to a set of aromatic molecules in solution we show that, for both polarizabilities and first hyperpolarizabilities, observed solution values are the result of a delicate balance between electrostatics, hydrogen-bonding, and non-electrostatic solute solvent interactions.
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Affiliation(s)
- Gioia Marrazzini
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Tommaso Giovannini
- Department
of Chemistry, Norwegian University of Science
and Technology, Trondheim 7491, Norway
| | - Franco Egidi
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Chiara Cappelli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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17
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Giovannini T, Egidi F, Cappelli C. Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems. Phys Chem Chem Phys 2020; 22:22864-22879. [PMID: 33043930 DOI: 10.1039/d0cp04027d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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18
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Giovannini T, Egidi F, Cappelli C. Molecular spectroscopy of aqueous solutions: a theoretical perspective. Chem Soc Rev 2020; 49:5664-5677. [PMID: 32744278 DOI: 10.1039/c9cs00464e] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Computational spectroscopy is an invaluable tool to both accurately reproduce the spectra of molecular systems and provide a rationalization for the underlying physics. However, the inherent difficulty to accurately model systems in aqueous solutions, owing to water's high polarity and ability to form hydrogen bonds, has severely hampered the development of the field. In this tutorial review we present a technique developed and tested in recent years based on a fully atomistic and polarizable classical modeling of water coupled with a quantum mechanical description of the solute. Thanks to its unparalleled accuracy and versatility, this method can change the perspective of computational and experimental chemists alike.
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Affiliation(s)
| | - Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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19
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Folkestad SD, Kjønstad EF, Myhre RH, Andersen JH, Balbi A, Coriani S, Giovannini T, Goletto L, Haugland TS, Hutcheson A, Høyvik IM, Moitra T, Paul AC, Scavino M, Skeidsvoll AS, Tveten ÅH, Koch H. e T 1.0: An open source electronic structure program with emphasis on coupled cluster and multilevel methods. J Chem Phys 2020; 152:184103. [PMID: 32414265 DOI: 10.1063/5.0004713] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The eT program is an open source electronic structure package with emphasis on coupled cluster and multilevel methods. It includes efficient spin adapted implementations of ground and excited singlet states, as well as equation of motion oscillator strengths, for CCS, CC2, CCSD, and CC3. Furthermore, eT provides unique capabilities such as multilevel Hartree-Fock and multilevel CC2, real-time propagation for CCS and CCSD, and efficient CC3 oscillator strengths. With a coupled cluster code based on an efficient Cholesky decomposition algorithm for the electronic repulsion integrals, eT has similar advantages as codes using density fitting, but with strict error control. Here, we present the main features of the program and demonstrate its performance through example calculations. Because of its availability, performance, and unique capabilities, we expect eT to become a valuable resource to the electronic structure community.
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Affiliation(s)
- Sarai D Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Eirik F Kjønstad
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Rolf H Myhre
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Josefine H Andersen
- DTU Chemistry-Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Alice Balbi
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, IT-56126 Pisa, PI, Italy
| | - Sonia Coriani
- DTU Chemistry-Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Linda Goletto
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Tor S Haugland
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Anders Hutcheson
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Ida-Marie Høyvik
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Torsha Moitra
- DTU Chemistry-Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Alexander C Paul
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Marco Scavino
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, IT-56126 Pisa, PI, Italy
| | - Andreas S Skeidsvoll
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Åsmund H Tveten
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
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20
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Gómez S, Giovannini T, Cappelli C. Absorption spectra of xanthines in aqueous solution: a computational study. Phys Chem Chem Phys 2020; 22:5929-5941. [PMID: 32115599 DOI: 10.1039/c9cp05420k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a detailed computational analysis of the UV/Vis spectra of caffeine, paraxanthine and theophylline in aqueous solution. A hierarchy of solvation approaches for modeling the aqueous environment have been tested, ranging from the continuum model to the non-polarizable and polarizable quantum mechanical (QM)/molecular mechanics (MM) models, with and without the explicit inclusion of water molecules in the QM portion. The computed results are directly compared with the experimental data, thus highlighting the role of electrostatic, polarization and hydrogen boding solute-solvent interactions.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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21
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Giovannini T, Riso RR, Ambrosetti M, Puglisi A, Cappelli C. Electronic transitions for a fully polarizable QM/MM approach based on fluctuating charges and fluctuating dipoles: Linear and corrected linear response regimes. J Chem Phys 2019; 151:174104. [PMID: 31703497 DOI: 10.1063/1.5121396] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The fully polarizable Quantum Mechanics/Molecular Mechanics (QM/MM) approach based on fluctuating charges and fluctuating dipoles, named QM/FQFμ [T. Giovannini et al., J. Chem. Theory Comput. 15, 2233 (2019)], is extended to the calculation of vertical excitation energies of solvated molecular systems. Excitation energies are defined within two different solvation regimes, i.e., linear response (LR), where the response of the MM portion is adjusted to the QM transition density, and corrected-Linear Response (cLR) in which the MM response is adjusted to the relaxed QM density, thus being able to account for charge equilibration in the excited state. The model, which is specified in terms of three physical parameters (electronegativity, chemical hardness, and polarizability) is applied to vacuo-to-water solvatochromic shifts of aqueous solutions of para-nitroaniline, pyridine, and pyrimidine. The results show a good agreement with their experimental counterparts, thus highlighting the potentialities of this approach.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | | | | | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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