1
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Gómez S, Cappelli C. The Role of Hydrogen Bonding in the Raman Spectral Signals of Caffeine in Aqueous Solution. Molecules 2024; 29:3035. [PMID: 38998986 PMCID: PMC11243038 DOI: 10.3390/molecules29133035] [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: 06/06/2024] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 07/14/2024] Open
Abstract
The identification and quantification of caffeine is a common need in the food and pharmaceutical industries and lately also in the field of environmental science. For that purpose, Raman spectroscopy has been used as an analytical technique, but the interpretation of the spectra requires reliable and accurate computational protocols, especially as regards the Resonance Raman (RR) variant. Herein, caffeine solutions are sampled using Molecular Dynamics simulations. Upon quantification of the strength of the non-covalent intermolecular interactions such as hydrogen bonding between caffeine and water, UV-Vis, Raman, and RR spectra are computed. The results provide general insights into the hydrogen bonding role in mediating the Raman spectral signals of caffeine in aqueous solution. Also, by analyzing the dependence of RR enhancement on the absorption spectrum of caffeine, it is proposed that the sensitivity of the RR technique could be exploited at excitation wavelengths moderately far from 266 nm, yet achieving very low detection limits in the quantification caffeine content.
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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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2
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Gómez S, Ambrosetti M, Giovannini T, Cappelli C. Close-Up Look at Electronic Spectroscopic Signatures of Common Pharmaceuticals in Solution. J Phys Chem B 2024; 128:2432-2446. [PMID: 38416564 DOI: 10.1021/acs.jpcb.3c07795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Simulating electronic properties and spectral signals requires robust computational approaches that need tuning with the system's peculiarities. In this paper, we test implicit and fully atomistic solvation models for the calculation of UV-vis and electronic circular dichroism (ECD) spectra of two pharmaceutically relevant molecules, namely, (2S)-captopril and (S)-naproxen, dissolved in aqueous solution. Room temperature molecular dynamics simulations reveal that these two drugs establish strong contacts with the surrounding solvent molecules via hydrogen bonds. Such specific interactions, which play a major role in the spectral response and are neglected in implicit approaches, are further characterized and quantified with natural bond orbital methods. Our calculations show that simulated spectra, and especially ECD, are in good agreement with experiments solely when conformational and configurational dynamics, mutual polarization, and solute-solvent repulsion effects are considered.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Matteo Ambrosetti
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa 56126, Italy
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3
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Casoria M, Macchiagodena M, Rovero P, Andreini C, Papini AM, Cardini G, Pagliai M. Upgrading of the general AMBER force field 2 for fluorinated alcohol biosolvents: A validation for water solutions and melittin solvation. J Pept Sci 2024; 30:e3543. [PMID: 37734745 DOI: 10.1002/psc.3543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/16/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
The standard GAFF2 force field parameterization has been refined for the fluorinated alcohols 2,2,2-trifluoroethanol (TFE), 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), and 1,1,1,3,3,3-hexafluoropropan-2-one (HFA), which are commonly used to study proteins and peptides in biomimetic media. The structural and dynamic properties of both proteins and peptides are significantly influenced by the biomimetic environment created by the presence of these cosolvents in aqueous solutions. Quantum mechanical calculations on stable conformers were used to parameterize the atomic charges. Different systems, such as pure liquids, aqueous solutions, and systems formed by melittin protein and cosolvent/water solutions, have been used to validate the new models. The calculated macroscopic and structural properties are in agreement with experimental findings, supporting the validity of the newly proposed models.
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Affiliation(s)
- Michele Casoria
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Department of NeuroFarBa, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Claudia Andreini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
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4
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Di Mino C, Clancy AJ, Sella A, Howard CA, Headen TF, Seel AG, Skipper NT. Weak Interactions in Dimethyl Sulfoxide (DMSO)-Tertiary Amide Solutions: The Versatility of DMSO as a Solvent. J Phys Chem B 2023; 127:1357-1366. [PMID: 36752593 PMCID: PMC9940205 DOI: 10.1021/acs.jpcb.2c07155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The structures of equimolar mixtures of the commonly used polar aprotic solvents dimethylformamide (DMF) and dimethylacetamide (DMAc) in dimethyl sulfoxide (DMSO) have been investigated via neutron diffraction augmented by extensive hydrogen/deuterium isotopic substitution. Detailed 3-dimensional structural models of these solutions have been derived from the neutron data via Empirical Potential Structure Refinement (EPSR). The intermolecular center-of-mass (CoM) distributions show that the first coordination shell of the amides comprises ∼13-14 neighbors, of which approximately half are DMSO. In spite of this near ideal coordination shell mixing, the changes to the amide-amide structure are found to be relatively subtle when compared to the pure liquids. Analysis of specific intermolecular atom-atom correlations allows quantitative interpretation of the competition between weak interactions in the solution. We find a hierarchy of formic and methyl C-H···O hydrogen bonds forms the dominant local motifs, with peak positions in the range of 2.5-3.0 Å. We also observe a rich variety of steric and dispersion interactions, including those involving the O═C-N amide π-backbones. This detailed insight into the structural landscape of these important liquids demonstrates the versatility of DMSO as a solvent and the remarkable sensitivity of neutron diffraction, which is critical for understanding weak intermolecular interactions at the nanoscale and thereby tailoring solvent properties to specific applications.
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Affiliation(s)
- Camilla Di Mino
- Department
of Physics and Astronomy, University College
London, Gower Street, LondonWC1E
6BT, U.K.
| | - Adam J. Clancy
- Department
of Chemistry, University College London, 20 Gordon Street, LondonWC1H 0AJ, U.K.
| | - Andrea Sella
- Department
of Chemistry, University College London, 20 Gordon Street, LondonWC1H 0AJ, U.K.
| | - Christopher A. Howard
- Department
of Physics and Astronomy, University College
London, Gower Street, LondonWC1E
6BT, U.K.
| | - Thomas F. Headen
- ISIS
Neutron and Muon Source, Science and Technology
Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, DidcotOX11 0QX, U.K.
| | - Andrew G. Seel
- ISIS
Neutron and Muon Source, Science and Technology
Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, DidcotOX11 0QX, U.K.,E-mail: . Phone: +44 (0)1793 547500
| | - Neal T. Skipper
- Department
of Physics and Astronomy, University College
London, Gower Street, LondonWC1E
6BT, U.K.,E-mail: . Phone: +44 (0)207 679 3526
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5
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Macchiagodena M, Bassu G, Vettori I, Fratini E, Procacci P, Pagliai M. 2-Butanol Aqueous Solutions: A Combined Molecular Dynamics and Small/Wide-Angle X-ray Scattering Study. J Phys Chem A 2022; 126:8826-8833. [DOI: 10.1021/acs.jpca.2c05708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Marina Macchiagodena
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Gavino Bassu
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Irene Vettori
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Emiliano Fratini
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Piero Procacci
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Marco Pagliai
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
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6
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Di Grande S, Ciofini I, Adamo C, Pagliai M, Cardini G. Absorption Spectra of Flexible Fluorescent Probes by a Combined Computational Approach: Molecular Dynamics Simulations and Time-Dependent Density Functional Theory. J Phys Chem A 2022; 126:8809-8817. [DOI: 10.1021/acs.jpca.2c04637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Silvia Di Grande
- Scuola Superiore Meridionale,Largo San Marcellino 10, I-80138Napoli, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126Napoli, Italy
| | - Ilaria Ciofini
- PSL University, Chimie ParisTech-PSL, CNRS, Institute of Chemistry for Health and Life Sciences (iCLeHS UMR8060), F-75005Paris, France
| | - Carlo Adamo
- PSL University, Chimie ParisTech-PSL, CNRS, Institute of Chemistry for Health and Life Sciences (iCLeHS UMR8060), F-75005Paris, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005Paris, France
| | - Marco Pagliai
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, Sesto FiorentinoI-50019, Italy
| | - Gianni Cardini
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, Sesto FiorentinoI-50019, Italy
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7
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Falbo E, Fusè M, Lazzari F, Mancini G, Barone V. Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents. J Chem Theory Comput 2022; 18:6203-6216. [PMID: 36166322 PMCID: PMC9558374 DOI: 10.1021/acs.jctc.2c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 11/30/2022]
Abstract
The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromophores in condensed phases. In this context we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper we report our latest developments with specific reference to unsupervised atomistic simulations employing non periodic boundary conditions (NPBC) followed by clustering of the trajectories employing optimized feature spaces. Next accurate variational computations are performed for a representative point of each cluster, whereas intracluster fluctuations are taken into account by a cheap yet reliable perturbative approach. A number of methodological improvements have been introduced including, e.g., more realistic reaction field effects at the outer boundary of the simulation sphere, automatic definition of the feature space by continuous perception of solute-solvent interactions, full account of polarization and charge transfer in the first solvation shell, and inclusion of vibronic contributions. After its validation, this new approach has been applied to the challenging case of solvatochromic effects on the UV-vis spectra of a prototypical nitroxide radical (TEMPO) in different solvents. The reliability, effectiveness, and robustness of the new platform is demonstrated by the remarkable agreement with experiment of the results obtained through an unsupervised approach characterized by a strongly reduced computational cost as compared to that of conventional quantum mechanics and molecular mechanics models without any accuracy reduction.
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Affiliation(s)
- Emanuele Falbo
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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8
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9
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Yasoshima N, Ishiyama T, Gemmei-Ide M, Matubayasi N. Molecular Structure and Vibrational Spectra of Water Molecules Sorbed in Poly(2-methoxyethylacrylate) Revealed by Molecular Dynamics Simulation. J Phys Chem B 2021; 125:12095-12103. [PMID: 34677976 DOI: 10.1021/acs.jpcb.1c07342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular dynamics (MD) simulations of water sorption in poly(2-methoxyethylacrylate) (PMEA) are carried out to elucidate the hydrogen bonding (H-bonding) structures of the water molecules and the side chains of PMEA. A PMEA model incorporating lone-pair virtual sites on the carbonyl and methoxy oxygens of the side chain of PMEA, which are the key interaction sites in a biocompatible polymer, is newly developed. The PMEA model well reproduces the experimentally observed features in the infrared spectra of the hydrated polymer, as well as the radial distribution function of the water molecules in contact with the polymer, as calculated by ab initio MD simulations. The MD simulation results reveal that water molecules tend to form H-bonds with the carbonyl oxygen and the methoxy oxygen of the side chain of PMEA simultaneously, which enhance the "head-to-tail" stacking structure of the side chains at a low concentration range of water. Further penetration of water into the PMEA structure gradually increases the water-water H-bonding state and promotes the formation of water clusters even below the equilibrium water content.
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Affiliation(s)
- Nobuhiro Yasoshima
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Makoto Gemmei-Ide
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
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10
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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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11
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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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12
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Jindal A, Vasudevan S. Molecular Conformation and Hydrogen Bond Formation in Liquid Ethylene Glycol. J Phys Chem B 2020; 124:9136-9143. [PMID: 32945675 DOI: 10.1021/acs.jpcb.0c06324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ethylene glycol (EG) molecule, HOCH2CH2OH, adopts a conformation where the central OCCO dihedral is exclusively gauche in the gaseous and crystalline states, but in the liquid state, for close to 20% of the molecules, the central OCCO adopts the energetically unfavorable trans conformation. Here we report calculations, based on ab initio molecular dynamics simulations, on the thermodynamics associated with hydrogen bond formation in the liquid state of EG between donor-acceptor pairs with different molecular conformations. We establish an operational, geometric definition of hydrogen bonds in liquid EG from an analysis of the proton NMR data and show that the key feature, irrespective of the conformation, is marked directionality with almost linear ∠HO···O angles. The free energy for hydrogen bond formation estimated as the potential of mean force for the reversible work associated with the passage from a hypothetical state where hydrogen bonding is absent and donor-acceptor pairs are randomly oriented to the hydrogen-bonded state where the pairs are oriented showed comparable magnitudes irrespective of the molecular conformation of either the donor or acceptor. The results suggest that the presence of the trans conformer in liquid EG would require an understanding of its role in the extended hydrogen-bonded network of the liquid.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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13
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Spinn A, Handle PH, Kraml J, Hofer TS, Liedl KR. Charge Anisotropy of Nitrogen: Where Chemical Intuition Fails. J Chem Theory Comput 2020; 16:4443-4453. [PMID: 32427474 PMCID: PMC7365557 DOI: 10.1021/acs.jctc.0c00204] [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: 03/02/2020] [Indexed: 01/03/2023]
Abstract
For more than half a century computer simulations were developed and employed to study ensemble properties of a wide variety of atomic and molecular systems with tremendous success. Nowadays, a selection of force-fields is available that describe the interactions in such systems. A key feature of force-fields is an adequate description of the electrostatic potential (ESP). Several force-fields model the ESP via point charges positioned at the atom centers. A major shortcoming of this approach, its inability to model anisotropies in the ESP, can be mitigated using additional charge sites. It has been shown that nitrogen is the most problematic element abundant in many polymers as well as large molecules of biological origin. To tackle this issue, small organic molecules containing a single nitrogen atom were studied. In performing rigorous scans of the surroundings of these nitrogen atoms, positions where a single extra charge can enhance the ESP description the most were identified. Significant improvements are found for ammonia, amines, and amides. Interestingly, the optimal location for the extra charge does not correlate with the chemically intuitive position of the nitrogen lone pair. In fact, the placement of an extra charge in the lone-pair location does not lead to significant improvements in most cases.
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Affiliation(s)
| | | | - Johannes Kraml
- Institute of General, Inorganic
and Theoretical Chemistry, University of
Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Institute of General, Inorganic
and Theoretical Chemistry, University of
Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic
and Theoretical Chemistry, University of
Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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14
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Del Galdo S, Fusè M, Barone V. CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach. Front Chem 2020; 8:584. [PMID: 32733856 PMCID: PMC7358700 DOI: 10.3389/fchem.2020.00584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/05/2020] [Indexed: 11/16/2022] Open
Abstract
We extend a recently proposed computational strategy for the simulation of absorption spectra of semi-rigid molecular systems in condensed phases to the emission spectra of flexible chromophores. As a case study, we have chosen the CPL spectrum of camphor in methanol solution, which shows a well-defined bisignate shape. The first step of our approach is the quantum mechanical computation of reference spectra including vibrational averaging effects and taking bulk solvent effects into account by means of the polarizable continuum model. In the present case, the large amplitude inversion mode is explicitly treated by a numerical approach, whereas the other small-amplitude vibrational modes are taken into account within the harmonic approximation. Next, the snapshots of classical molecular dynamics computations are clusterized and one representative configuration from each cluster is used to compute a reference spectrum. In the present case, different clusters correspond to the two stable conformers of camphor in the S1 excited electronic state and, for each of them, to different numbers of strong solute-solvent hydrogen bonds. Finally, local fluctuation effects within each cluster are taken into account by means of the perturbed matrix model. The overall procedure leads to good agreement with experiment for absorption and emission spectra together with their chiral counterparts, thus allowing to analyze the role of different effects (stereo-electronic, vibrational, environmental) in tuning the overall experimental spectra.
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Affiliation(s)
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore, Pisa, Italy
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15
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Del Galdo S, Fusè M, Barone V. The ONIOM/PMM Model for Effective Yet Accurate Simulation of Optical and Chiroptical Spectra in Solution: Camphorquinone in Methanol as a Case Study. J Chem Theory Comput 2020; 16:3294-3306. [PMID: 32250614 PMCID: PMC7222099 DOI: 10.1021/acs.jctc.0c00124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
This paper deals
with the development and first validation of a
composite approach for the simulation of chiroptical spectra in solution
aimed to strongly reduce the number of full QM computations without
any significant accuracy loss. The approach starts from the quantum
mechanical computation of reference spectra including vibrational
averaging effects and taking average solvent effects into account
by means of the polarizable continuum model. Next, the snapshots of
classical molecular dynamics computations are clusterized and one
reference configuration from each cluster is used to compute a reference
spectrum. Local fluctuation effects within each cluster are then taken
into account by means of the perturbed matrix model. The performance
of the proposed approach is tested on the challenging case of the
optical and chiroptical spectra
of camphorquinone in methanol solution. Although further validations
are surely needed, the results of this first study are quite promising
also taking into account that agreement with experimental data is
reached by just a couple of full quantum mechanical geometry optimizations
and frequency computations.
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Affiliation(s)
- Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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16
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Lazzari F, Salvadori A, Mancini G, Barone V. Molecular Perception for Visualization and Computation: The Proxima Library. J Chem Inf Model 2020; 60:2668-2672. [PMID: 32271572 PMCID: PMC7997373 DOI: 10.1021/acs.jcim.0c00076] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proxima is a molecular perception library designed with a double purpose: to be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies. The current version of Proxima is available for evaluation purposes at https://bitbucket.org/sns-smartlab/proxima/src/master/.
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Affiliation(s)
- Federico Lazzari
- Scuola Normale Superiore, Piazza dei Cavalieri, 7-56126 Pisa, Italy
| | - Andrea Salvadori
- Scuola Normale Superiore, Piazza dei Cavalieri, 7-56126 Pisa, Italy
| | - Giordano Mancini
- 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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17
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Shin HK. Inter- and Intramolecular Vibrational Energy Flow in a Formamide–Water Complex. J Phys Chem A 2020; 124:3031-3037. [PMID: 32227959 DOI: 10.1021/acs.jpca.0c00584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- H. K. Shin
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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18
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Carmona-Espíndola J, Núñez-Rojas E, García-Melgarejo V, Gázquez JL, Alejandre J. Constrained dipole moment density functional theory for charge distributions in force fields for the study of molecular fluids. J Chem Phys 2020; 152:124116. [PMID: 32241143 DOI: 10.1063/5.0002050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A new procedure, based on electronic structure calculations that only requires a dipole moment value for a given molecule as input and, from which the charges for all the atoms in it are uniquely determined, is developed and applied to the study of molecular fluids with classical dynamics. The dipole moment value considered for the isolated molecule is the one that reproduces the dielectric constant of its corresponding fluid. Following previous work, the Lennard-Jones parameters are determined to reproduce the liquid density and the surface tension at the liquid-vapor interface. The force field thus obtained leads to a reasonable description of several properties such as heats of vaporization, self-diffusion coefficients, shear viscosities, isothermal compressibilities, and volumetric expansion coefficients of pure substances.
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Affiliation(s)
- Javier Carmona-Espíndola
- Departamento de Química, CONACYT-Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - Edgar Núñez-Rojas
- Departamento de Química, CONACYT-Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - Valeria García-Melgarejo
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - José L Gázquez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - José Alejandre
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de México 09340, Mexico
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19
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Del Galdo S, Chandramouli B, Mancini G, Barone V. Assessment of Multi-Scale Approaches for Computing UV–Vis Spectra in Condensed Phases: Toward an Effective yet Reliable Integration of Variational and Perturbative QM/MM Approaches. J Chem Theory Comput 2019; 15:3170-3184. [DOI: 10.1021/acs.jctc.9b00120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sara Del Galdo
- Istituto di Chimica dei Composti OrganoMetallici (ICCOMCNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, 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
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, 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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20
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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] [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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21
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Horton JT, Allen AEA, Dodda LS, Cole DJ. QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics. J Chem Inf Model 2019; 59:1366-1381. [DOI: 10.1021/acs.jcim.8b00767] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joshua T. Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Alice E. A. Allen
- TCM Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Leela S. Dodda
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Daniel J. Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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22
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Puglisi A, Giovannini T, Antonov L, Cappelli C. Interplay between conformational and solvent effects in UV-visible absorption spectra: curcumin tautomers as a case study. Phys Chem Chem Phys 2019; 21:15504-15514. [PMID: 31259324 DOI: 10.1039/c9cp00907h] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a combined theoretical and experimental study on the UV-vis spectra of enol-keto (EK) and keto-keto (KK) tautomeric forms of curcumin dissolved in aqueous solution. Solvent effects have been investigated by resorting to the implicit polarizable continuum model (QM/PCM) and non-polarizable and fully polarizable QM/MM approaches, the latter based on the fluctuating charges (FQ) force-field. In particular, all methods are challenged to rationalize the contribution of conformational, electrostatic and polarization effects in the calculation of the vertical excitation spectra of curcumin tautomers. The obtained results highlight that for both tautomers specific solute-solvent hydrogen-bond interactions play a minor role with respect to conformational and electrostatic effects.
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Affiliation(s)
| | | | - Liudmil Antonov
- Bulgarian Academy of Sciences, Institute of Organic Chemistry with Centre of Phytochemistry, Acad. G. Bonchev str., Bldg. 9, Sofia 1113, Bulgaria
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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23
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Pérez de la Luz A, Aguilar-Pineda JA, Méndez-Bermúdez JG, Alejandre J. Force Field Parametrization from the Hirshfeld Molecular Electronic Density. J Chem Theory Comput 2018; 14:5949-5958. [DOI: 10.1021/acs.jctc.8b00554] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander Pérez de la Luz
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa. Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, México
| | - Jorge Alberto Aguilar-Pineda
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa. Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, México
| | - José Guillermo Méndez-Bermúdez
- Centro Universitario de los Valles, Universidad de Guadalajara, Carretera Guadalajara-Ameca km. 45.4, Ameca, Jalisco 46600, México
| | - José Alejandre
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa. Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, México
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24
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Greff da Silveira L, Jacobs M, Prampolini G, Livotto PR, Cacelli I. Development and Validation of Quantum Mechanically Derived Force-Fields: Thermodynamic, Structural, and Vibrational Properties of Aromatic Heterocycles. J Chem Theory Comput 2018; 14:4884-4900. [PMID: 30040902 DOI: 10.1021/acs.jctc.8b00218] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A selection of several aromatic molecules, representative of the important class of heterocyclic compounds, has been considered for testing and validating an automated Force Field (FF) parametrization protocol, based only on Quantum Mechanical data. The parametrization is carried out separately for the intra- and intermolecular contributions, employing respectively the Joyce and Picky software packages, previously implemented and refined in our research group. The whole approach is here automated and integrated with a computationally effective yet accurate method, devised very recently ( J. Chem. THEORY Comput., 2018, 14, 543-556) to evaluate a large number of dimer interaction energies. The resulting quantum mechanically derived FFs are then used in extensive molecular dynamics simulations, in order to evaluate a number of thermodynamic, structural, and dynamic properties of the heterocycle's gas and liquid phases. The comparison with the available experimental data is good and furnishes a validation of the presented approach, which can be confidently exploited for the design of novel and more complex materials.
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Affiliation(s)
- Leandro Greff da Silveira
- Instituto de Química , Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves 9500 , CEP 91501-970 Porto , Alegre , Brazil
| | - Matheus Jacobs
- Instituto de Química , Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves 9500 , CEP 91501-970 Porto , Alegre , Brazil.,Institut für Physik , Humboldt-Universität zu Berlin , Newtonstrasse 15 , 12489 , Berlin , Germany.,IRIS Adelrshof , Humboldt-Universität zu Berlin , Zum Großen Windkanal 6 , 12489 , Berlin , Germany
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy
| | - Paolo Roberto Livotto
- Instituto de Química , Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves 9500 , CEP 91501-970 Porto , Alegre , Brazil
| | - Ivo Cacelli
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy.,Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , I-56124 Pisa , Italy
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25
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On the nature of charge-transfer excitations for molecules in aqueous solution: a polarizable QM/MM study. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2259-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Cerezo J, Prampolini G, Cacelli I. Developing accurate intramolecular force fields for conjugated systems through explicit coupling terms. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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A polarizable embedding approach to second harmonic generation (SHG) of molecular systems in aqueous solutions. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2247-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Chandramouli B, Del Galdo S, Mancini G, Tasinato N, Barone V. Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches. Biopolymers 2018. [DOI: 10.1002/bip.23109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Compunet, Istituto Italiano di Tecnologia, via Morego 30; Genova Italy
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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29
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Fracchia F, Del Frate G, Mancini G, Rocchia W, Barone V. Force Field Parametrization of Metal Ions from Statistical Learning Techniques. J Chem Theory Comput 2017; 14:255-273. [PMID: 29112432 PMCID: PMC5763284 DOI: 10.1021/acs.jctc.7b00779] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
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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30
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Chand A, Chowdhuri S. A comparative study of hydrogen bonding structure and dynamics in aqueous urea solution of amides with varying hydrophobicity: Effect of addition of trimethylamine N -oxide (TMAO). J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Kiss B, Fábián B, Idrissi A, Szőri M, Jedlovszky P. Miscibility and Thermodynamics of Mixing of Different Models of Formamide and Water in Computer Simulation. J Phys Chem B 2017; 121:7147-7155. [PMID: 28657740 DOI: 10.1021/acs.jpcb.7b04965] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The thermodynamic changes that occur upon mixing five models of formamide and three models of water, including the miscibility of these model combinations itself, is studied by performing Monte Carlo computer simulations using an appropriately chosen thermodynamic cycle and the method of thermodynamic integration. The results show that the mixing of these two components is close to the ideal mixing, as both the energy and entropy of mixing turn out to be rather close to the ideal term in the entire composition range. Concerning the energy of mixing, the OPLS/AA_mod model of formamide behaves in a qualitatively different way than the other models considered. Thus, this model results in negative, while the other ones in positive energy of mixing values in combination with all three water models considered. Experimental data supports this latter behavior. Although the Helmholtz free energy of mixing always turns out to be negative in the entire composition range, the majority of the model combinations tested either show limited miscibility, or, at least, approach the miscibility limit very closely in certain compositions. Concerning both the miscibility and the energy of mixing of these model combinations, we recommend the use of the combination of the CHARMM formamide and TIP4P water models in simulations of water-formamide mixtures.
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Affiliation(s)
- Bálint Kiss
- Institute of Chemistry, University of Miskolc , Egyetemváros A/2, H-3515 Miskolc, Hungary.,Laboratoire de Spectrochimie Infrarouge et Raman (UMR CNRS 8516), University of Lille Nord de France , 59655 Villeneuve d'Ascq Cedex, France
| | - Balázs Fábián
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Szt. Gellért tér 4, H-1111 Budapest, Hungary.,Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche-Comté , 16 route de Gray, F-25030 Besançon, France
| | - Abdenacer Idrissi
- Laboratoire de Spectrochimie Infrarouge et Raman (UMR CNRS 8516), University of Lille Nord de France , 59655 Villeneuve d'Ascq Cedex, France
| | - Milán Szőri
- Institute of Chemistry, University of Miskolc , Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly University , Leányka utca 6, H-3300 Eger, Hungary
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32
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Pagliai M, Mancini G, Carnimeo I, De Mitri N, Barone V. Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach. J Comput Chem 2017; 38:319-335. [PMID: 27910109 PMCID: PMC6680224 DOI: 10.1002/jcc.24683] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 01/06/2023]
Abstract
The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Marco Pagliai
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
| | | | - Ivan Carnimeo
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
- Compunet, Istituto Italiano di Tecnologia (IIT)via Morego 30GenovaI‐16163Italy
| | - Nicola De Mitri
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
- Present address:
Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWU.K.
| | - Vincenzo Barone
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
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