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Gómez S, Lafiosca P, Giovannini T. Modeling UV/Vis Absorption Spectra of Food Colorants in Solution: Anthocyanins and Curcumin as Case Studies. Molecules 2024; 29:4378. [PMID: 39339373 DOI: 10.3390/molecules29184378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 09/06/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
We present a comprehensive computational study of UV/Vis absorption spectra of significant food colorants, specifically anthocyanins and curcumin tautomers, dissolved in polar protic solvents, namely water and ethanol. The absorption spectra are simulated using two fully polarizable quantum mechanical (QM)/molecular mechanics (MM) models based on the fluctuating charge (FQ) and fluctuating charge and dipoles (FQFμ) force fields. To accurately capture the dynamical aspects of the solvation phenomenon, atomistic approaches are combined with configurational sampling obtained through classical molecular dynamics (MD) simulations. The calculated QM/FQ and QM/FQFμ spectra are then compared with experiments. Our findings demonstrate that a precise reproduction of the UV/Vis spectra of the studied pigments can be achieved by adequately accounting for configurational sampling, polarization effects, and hydrogen bonding interactions.
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Affiliation(s)
- Sara Gómez
- Classe di Scienze, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Piero Lafiosca
- Classe di Scienze, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Department of Physics, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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Gómez S, Cappelli C. When Tautomers Matter: UV-Vis Absorption Spectra of Hypoxanthine in Aqueous Solution from Fully Atomistic Simulations. Chemphyschem 2024; 25:e202400107. [PMID: 38747323 DOI: 10.1002/cphc.202400107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/13/2024] [Indexed: 07/03/2024]
Abstract
The UV-Vis spectrum of the solvated purine derivative Hypoxanthine (HYX) is investigated using the Quantum Mechanics/Fluctuating Charges (QM/FQ) multiscale approach combined with a sampling of configurations through atomistic Molecular Dynamics (MD) simulations. Keto 1H7H and 1H9H tautomeric forms of HYX are the most stable in aqueous solution and form different stable complexes with the surrounding water molecules, ultimately affecting the electronic absorption spectra. The final simulated spectrum resulting from the combination of the individual spectra of tautomers agrees very well with most of the characteristics in the measured spectrum. The importance of considering the effect of the solute tautomers and, in parallel, the contribution of the different solvent arrangements around the solute when modeling spectral properties, is highlighted. In addition, the high quality of the computed spectra leads to suggesting an alternative way for acquiring tautomeric populations from combined computational/experimental spectra.
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Affiliation(s)
- Sara Gómez
- 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
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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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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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Sodomaco S, Gómez S, Giovannini T, Cappelli C. Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces. J Phys Chem A 2023; 127:10282-10294. [PMID: 37993110 DOI: 10.1021/acs.jpca.3c05560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.
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Affiliation(s)
- Sveva Sodomaco
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - 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
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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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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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