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Del Frate G, Macchiagodena M, Akhunzada MJ, D'Autilia F, Catte A, Bhattacharjee N, Barone V, Cardarelli F, Brancato G. Probing Liquid-Ordered and Disordered Phases in Lipid Model Membranes: A Combined Theoretical and Spectroscopic Study of a Fluorescent Molecular Rotor. J Phys Chem B 2022; 126:480-491. [PMID: 35001625 PMCID: PMC8785181 DOI: 10.1021/acs.jpcb.1c08324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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An integrated theoretical/experimental
strategy has been applied
to the study of environmental effects on the spectroscopic parameters
of 4-(diphenylamino)phtalonitrile (DPAP), a fluorescent molecular
rotor. The computational part starts from the development of an effective
force field for the first excited electronic state of DPAP and proceeds
through molecular dynamics simulations in solvents of different polarities
toward the evaluation of Stokes shifts by quantum mechanics/molecular
mechanics (QM/MM) approaches. The trends of the computed results closely
parallel the available experimental results thus giving confidence
to the interpretation of new experimental studies of the photophysics
of DPAP in lipid bilayers. In this context, results show unambiguously
that both flexible dihedral angles and global rotations are significantly
retarded in a cholesterol/DPPC lipid matrix with respect to the DOPC
matrix, thus confirming the sensitivity of DPAP to probe different
environments and, therefore, its applicability as a probe for detecting
different structures and levels of plasma membrane organization.
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Affiliation(s)
| | | | | | - Francesca D'Autilia
- Center for Nanotechnology Innovation@NEST (CNI@NEST), Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Andrea Catte
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare(INFN), Largo Pontecorvo 3, I-56 127 Pisa, Italy.,Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, I-50 019 Sesto Fiorentino, Florence, Italy
| | | | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare(INFN), Largo Pontecorvo 3, I-56 127 Pisa, Italy.,Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, I-50 019 Sesto Fiorentino, Florence, Italy
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Nikitin A, Del Frate G. Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction. J Comput Chem 2019; 40:2464-2472. [PMID: 31301182 DOI: 10.1002/jcc.26021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/14/2019] [Accepted: 06/06/2019] [Indexed: 12/24/2022]
Abstract
The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12-6 Lennard-Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges. The electronic continuum correction (ECC) can fix this problem through a simple inclusion of solvent polarization effects via ionic charge rescaling. In this work, the development of novel nonbonded models for mono, divalent, and highly charged metal ions is presented. For each metal species, the ionic charge has been scaled, according to the ECC. Lennard-Jones parameters have been optimized using experimental structural and thermodynamic properties as target quantities. Performances of the proposed models are discussed and compared with the literature data, while transferability attitudes among different and well-known water models are evaluated. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexei Nikitin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Gianluca Del Frate
- IMT School for Advanced Studies Lucca, Piazza S. Francesco 19, I-55100, Lucca, Italy
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Egidi F, Giovannini T, Del Frate G, Lemler PM, Vaccaro PH, Cappelli C. A combined experimental and theoretical study of optical rotatory dispersion for (R)-glycidyl methyl ether in aqueous solution. Phys Chem Chem Phys 2019; 21:3644-3655. [PMID: 30383044 DOI: 10.1039/c8cp04445g] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The dispersive optical activity for aqueous solutions of non-rigid (R)-glycidyl methyl ether (R-GME) has been explored synergistically from experimental and theoretical perspectives. Density functional theory analyses performed with the polarizable continuum model for implicit solvation identified nine low-lying stable conformers that are interconverted by rotation about two large-amplitude torsional coordinates. The antagonistic chiroptical signatures predicted for these structural isomers were averaged under a Boltzmann-weighting ansatz to estimate the behavior expected for a thermally equilibrated ensemble. This led to optical rotatory dispersion profiles that reproduced the overall shape of observations but failed to achieve uniform agreement with measured specific-rotation values even when anharmonic vibrational corrections were applied. A mixed QM/FQ paradigm, whereby quantum-mechanical (QM) calculations of optical activity were combined with classical molecular dynamics simulations of explicit solvation that included mutual-polarization effects by means of fluctuating charges (FQ), was enlisted to elucidate the microsolvation environment and gauge its impact upon conformer distributions and response properties. Although quantitative accord with experiments remained elusive, this approach revealed strong variations in the magnitude and sign of rotatory powers for R-GME as the configuration of surrounding water molecules evolved, thereby highlighting the inherently dynamical nature of the solvated chiroptical response, calling into question the validity of "static" descriptions based on the presumption of distinct energy minima, and giving insight into the inherent complexity posed by the modeling of such properties for solvated systems.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, Italy
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Macchiagodena M, Del Frate G, Brancato G, Chandramouli B, Mancini G, Barone V. Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations. Phys Chem Chem Phys 2018; 19:30590-30602. [PMID: 29115317 DOI: 10.1039/c7cp04688j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fluorescent molecular rotors (FMRs) belong to an important class of environment-sensitive dyes capable of acting as nanoprobes in the measurement of viscosity and polarity of their micro-environment. FMRs have found widespread applications in various research fields, ranging from analytical to biochemical sciences, for example in intracellular imaging studies or in volatile organic compound detection. Here, a computational investigation of a recently proposed FMR, namely 4-(diphenylamino)phthalonitrile (DPAP), in various chemical environments is presented. A purposely developed molecular mechanics force field is proposed and then applied to simulate the rotor in a high- and low-polar solvent (i.e., acetonitrile, tetrahydrofuran, o-xylene and cyclohexane), a polymer matrix and a lipid membrane. Subtle effects of the molecular interactions with the embedding medium, the structural fluctuations of the rotor and its rotational dynamics are analyzed in some detail. The results correlate with a previous work, thus supporting the reliability of the model, and provide further insights into the environment-specific properties of the dye. In particular, it is shown how molecular diffusion and rotational correlation times of the FMR are affected by the surrounding medium and how the molecular orientation of the dye becomes anisotropic once immersed in the lipid bilayer. Moreover, a qualitative correlation between the FMR rotational dynamics and the fluorescence lifetime is detected, a result in line with the observed viscosity dependence of its emission. Finally, optical absorption spectra are computed and successfully compared with their experimental counterparts.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
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A novel
statistical procedure has been developed to optimize the parameters
of nonbonded force fields of metal ions in soft matter. The criterion
for the optimization is the minimization of the deviations from ab initio forces and energies calculated for model systems.
The method exploits the combination of the linear ridge regression
and the cross-validation techniques with the differential evolution
algorithm. Wide freedom in the choice of the functional form of the
force fields is allowed since both linear and nonlinear parameters
can be optimized. In order to maximize the information content of
the data employed in the fitting procedure, the composition of the
training set is entrusted to a combinatorial optimization algorithm
which maximizes the dissimilarity of the included instances. The methodology
has been validated using the force field parametrization of five metal
ions (Zn2+, Ni2+, Mg2+, Ca2+, and Na+) in water as test cases.
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Affiliation(s)
| | | | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa , Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - Walter Rocchia
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , 16163 Genova, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa , Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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Macchiagodena M, Mancini G, Pagliai M, Del Frate G, Barone V. Fine-tuning of atomic point charges: Classical simulations of pyridine in different environments. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Salvadori A, Del Frate G, Pagliai M, Mancini G, Barone V. Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data. Int J Quantum Chem 2016; 116:1731-1746. [PMID: 27867214 PMCID: PMC5101850 DOI: 10.1002/qua.25207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 05/31/2023]
Abstract
The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.
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Affiliation(s)
- Andrea Salvadori
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | | | - Marco Pagliai
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
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Del Frate G, Bellina F, Mancini G, Marianetti G, Minei P, Pucci A, Barone V. Tuning of dye optical properties by environmental effects: a QM/MM and experimental study. Phys Chem Chem Phys 2016; 18:9724-33. [PMID: 27001346 PMCID: PMC5123643 DOI: 10.1039/c6cp00841k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The present work is aimed at a deeper investigation of two recently synthesized heteroaromatic fluorophores by means of a computational multilayer approach, integrating quantum mechanics (QM) and molecular mechanics (MM).
The present work is aimed at a deeper investigation of two recently synthesized heteroaromatic fluorophores by means of a computational multilayer approach, integrating quantum mechanics (QM) and molecular mechanics (MM). In particular, dispersion of the title dyes in a polymer matrix is studied in connection with potential applications as photoactive species in luminescent solar concentrators (LSCs). Molecular dynamics simulations, based on accurate QM-derived force fields, reveal increased stiffness of these organic dyes when going from CHCl3 solution to the polymer matrix. QM/MM computations of UV spectra for snapshots extracted from MD simulations show that this different flexibility permits explaining the different spectral shapes obtained experimentally for the two different environments. Moreover, the general spectroscopic trends are reproduced well by static computations employing a polarizable continuum description of environmental effects.
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Granchi C, Capecchi A, Del Frate G, Martinelli A, Macchia M, Minutolo F, Tuccinardi T. Development and validation of a docking-based virtual screening platform for the identification of new lactate dehydrogenase inhibitors. Molecules 2015; 20:8772-90. [PMID: 25988609 PMCID: PMC6272605 DOI: 10.3390/molecules20058772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/06/2015] [Accepted: 05/11/2015] [Indexed: 12/11/2022] Open
Abstract
The human muscle isoform of lactate dehydrogenase (hLDH5) is one of the key enzymes of the glycolytic process. It is overexpressed in metastatic cancer cells and is linked to the vitality of tumors in hypoxic conditions. With the aim of identifying new hLDH5 inhibitors, a fully automated docking-based virtual screening platform was developed by considering different protein conformations and the consensus docking strategy. In order to verify the reliability of the reported platform, a small database of about 10,000 compounds was filtered by using this method, and the top-ranked compounds were tested for their hLDH5 inhibition activity. Enzymatic assays revealed that, among the ten selected compounds, two proved to efficiently inhibit enzyme activity with IC50 values in the micromolar range. These results demonstrate the validity of the methodologies we followed, encouraging the application of larger virtual screening studies and further refinements of the platform. Furthermore, the two active compounds herein described may be considered as interesting leads for the development of new and more efficient LDH inhibitors.
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Affiliation(s)
| | - Alice Capecchi
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy.
| | | | | | - Marco Macchia
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy.
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