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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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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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3
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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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4
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Giovannini T, Grazioli L, Ambrosetti M, Cappelli C. Calculation of IR Spectra with a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles. J Chem Theory Comput 2019; 15:5495-5507. [DOI: 10.1021/acs.jctc.9b00574] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Laura Grazioli
- 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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5
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Jansen TLC, Saito S, Jeon J, Cho M. Theory of coherent two-dimensional vibrational spectroscopy. J Chem Phys 2019; 150:100901. [DOI: 10.1063/1.5083966] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas la Cour Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Jonggu Jeon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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6
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Battisti A, Ambrosetti M, Ruggeri G, Cappelli C, Pucci A. A 4,4'-bis(2-benzoxazolyl)stilbene luminescent probe: assessment of aggregate formation through photophysics experiments and quantum-chemical calculations. Phys Chem Chem Phys 2018; 20:26249-26258. [PMID: 30324198 DOI: 10.1039/c8cp04450c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A combination of experimental and quantum mechanical investigations is applied to the study of the optical features of 4,4'-bis(2-benzoxazolyl)stilbene (BBS) dissolved in solution or in a poly(l-lactic acid) (PLA) thermoplastic matrix at different concentrations. The experimental analyses allow the characterization of BBS solutions and dispersions in terms of absorption and emission features, along with the collection of some key parameters such as fluorescence quantum yield, anisotropy and lifetime, while the computational approach gives a detailed description of the photophysical behavior of BBS in the different environments. For the 10-5 M BBS solution, the fluorescence spectra show the expected peaks at 425 and 455 nm of the non-interacting BBS molecules with a single fluorescence lifetime of 0.85 ns without revealing any aggregation phenomena, prevented by the short lifetime and fast diffusion rate of the monomer. Moreover, the calculated spectra are in excellent agreement with the experiments, thus showing the reliability of the computational approach. In time-resolved emission experiments (TRES) on more concentrated solutions (10-4 M) and on BBS crystals, the presence of an excimer is revealed by the appearance of a broad peak around 540 nm, followed by the disappearance of the two main peaks at 460 nm on a time scale of about 10 ns. The computational analysis attributes this behavior to the formation of aggregates of different geometries. The BBS dispersions in PLA reveal the presence of different BBS architectures depending on the fluorophore content. Even at low concentrations, BBS is mainly dispersed as a monomer in the matrix, spheroid aggregates of about 800-900 nm in diameter are also present and the relevant fluorescence spectra arise from the combination of monomer and aggregate contributions. At higher concentrations, BBS starts forming crystals of a peculiar helicoidal shape, with a diameter of about 2 μm, variable length up to several hundreds of μm and emission spectra similar to those of isolated BBS crystals.
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Affiliation(s)
- Antonella Battisti
- NEST - Scuola Normale Superiore and Istituto Nanoscienze - CNR (CNR-NANO), Piazza San Silvestro 12, I-56127 Pisa, Italy. and M3-Village, Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali - INSTM, p.zza San Silvestro 12, I-56127 Pisa, Italy
| | - Matteo Ambrosetti
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Giacomo Ruggeri
- Dipartimento di Chimica e Chimica Industriale, Universitá di Pisa, Via Moruzzi 13, I-56124 Pisa, Italy.
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Andrea Pucci
- Dipartimento di Chimica e Chimica Industriale, Universitá di Pisa, Via Moruzzi 13, I-56124 Pisa, Italy.
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7
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Giovannini T, Del Frate G, Lafiosca P, Cappelli C. Effective computational route towards vibrational optical activity spectra of chiral molecules in aqueous solution. Phys Chem Chem Phys 2018; 20:9181-9197. [DOI: 10.1039/c8cp00487k] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A polarizable QM/MM approach to accurately compute the Vibrational Optical Activity (VOA) spectra of chiral systems is proposed and applied to aqueous solutions of (l)-methyl lactate and (S)-glycidol.
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8
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Giovannini T, Olszòwka M, Cappelli C. Effective Fully Polarizable QM/MM Approach To Model Vibrational Circular Dichroism Spectra of Systems in Aqueous Solution. J Chem Theory Comput 2016; 12:5483-5492. [PMID: 27704812 DOI: 10.1021/acs.jctc.6b00768] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a methodology, based on the combination of classical Molecular Dynamics (MD) simulations with a fully polarizable Quantum Mechanical (QM)/Molecular Mechanics (MM)/Polarizable Continuum Model (PCM) Hamiltonian, to calculate Vibrational Circular Dichroism (VCD) spectra of chiral systems in aqueous solution. Polarization effects are included in the MM force field by exploiting an approach based on Fluctuating Charges (FQ). By performing the MD, the description of the solvating environment is enriched by taking into account the dynamical aspects of the solute-solvent interactions. On the other hand, the QM/FQ/PCM calculation of the VCD spectrum ensures an accurate description of the electronic density of the solute and a proper account for the specific interactions in solution. The application of our approach to (R)-methyloxirane and (l)-alanine in aqueous solution gives calculated spectra in remarkable agreement with their experimental counterparts and a substantial improvement with respect to the same spectra calculated with the PCM.
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Affiliation(s)
| | - Marta Olszòwka
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via Moruzzi 13, 56124 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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9
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Kalinowska B, Banach M, Konieczny L, Marchewka D, Roterman I. Intrinsically disordered proteins--relation to general model expressing the active role of the water environment. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:315-46. [PMID: 24629190 DOI: 10.1016/b978-0-12-800168-4.00008-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This work discusses the role of unstructured polypeptide chain fragments in shaping the protein's hydrophobic core. Based on the "fuzzy oil drop" model, which assumes an idealized distribution of hydrophobicity density described by the 3D Gaussian, we can determine which fragments make up the core and pinpoint residues whose location conflicts with theoretical predictions. We show that the structural influence of the water environment determines the positions of disordered fragments, leading to the formation of a hydrophobic core overlaid by a hydrophilic mantle. This phenomenon is further described by studying selected proteins which are known to be unstable and contain intrinsically disordered fragments. Their properties are established quantitatively, explaining the causative relation between the protein's structure and function and facilitating further comparative analyses of various structural models.
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Affiliation(s)
- Barbara Kalinowska
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Medical College, Jagiellonian University, Krakow, Poland
| | - Damian Marchewka
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland.
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Biancardi A, Biver T, Secco F, Mennucci B. An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools. Phys Chem Chem Phys 2013; 15:4596-603. [PMID: 23423468 DOI: 10.1039/c3cp44058c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being possible, and to specifically change its photophysical properties according to the different environments. To investigate this behavior, quantum-mechanical calculations using time-dependent density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models, were performed in combination with spectroscopic measurements of the probe in the different environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of double stranded nucleic acids. According to our simulation, the electronic transition involves a displacement of the electron charge towards the external amidine groups and this feature makes the absorption energies very environment-sensitive while a much smaller sensitivity is seen in the fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA pocket and a reduced polarization due to the very "apolar" microenvironment. All these effects can be used to better understand the observed enhancement of the fluorescence, which makes it an excellent marker for DNA.
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Affiliation(s)
- Alessandro Biancardi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento, 35-56126 Pisa, Italy.
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11
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Fidder H, Yang M, Nibbering ETJ, Elsaesser T, Röttger K, Temps F. N–H Stretching Vibrations of Guanosine–Cytidine Base Pairs in Solution: Ultrafast Dynamics, Couplings, and Line Shapes. J Phys Chem A 2013; 117:845-54. [DOI: 10.1021/jp309237u] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Henk Fidder
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, 12489 Berlin, Germany
| | - Ming Yang
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, 12489 Berlin, Germany
| | - Erik T. J. Nibbering
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, 12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, 12489 Berlin, Germany
| | - Katharina Röttger
- Institut für Physikalische
Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
| | - Friedrich Temps
- Institut für Physikalische
Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
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12
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Studying Biomacromolecules with Two-Dimensional Infrared Spectroscopy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:1-36. [DOI: 10.1016/b978-0-12-416596-0.00001-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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13
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Lipparini F, Cappelli C, Scalmani G, De Mitri N, Barone V. Analytical First and Second Derivatives for a Fully Polarizable QM/Classical Hamiltonian. J Chem Theory Comput 2012; 8:4270-8. [DOI: 10.1021/ct300635c] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento di Chimica e Chimica
Industriale, Università di Pisa, Via Risorgimento 35, 56126
Pisa, Italy
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac
Street Building 40, Wallingford, Connecticut 06492, United States
| | - Nicola De Mitri
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, 56126 Pisa, Italy
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