1
|
Greff da Silveira L, Livotto PR, Padula D, Vilhena JG, Prampolini G. Accurate Quantum-Mechanically Derived Force-Fields through a Fragment-Based Approach: Balancing Specificity and Transferability in the Prediction of Self-Assembly in Soft Matter. J Chem Theory Comput 2022; 18:6905-6919. [PMID: 36260420 DOI: 10.1021/acs.jctc.2c00747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The wide range of time/length scales covered by self-assembly in soft matter makes molecular dynamics (MD) the ideal candidate for simulating such a supramolecular phenomenon at an atomistic level. However, the reliability of MD outcomes heavily relies on the accuracy of the adopted force-field (FF). The spontaneous re-ordering in liquid crystalline materials stands as a clear example of such collective self-assembling processes, driven by a subtle and delicate balance between supramolecular interactions and single-molecule flexibility. General-purpose transferable FFs often dramatically fail to reproduce such complex phenomena, for example, the error on the transition temperatures being larger than 100 K. Conversely, quantum-mechanically derived force-fields (QMD-FFs), specifically tailored for the target system, were recently shown (J. Phys. Chem. Lett.2022,13, 243) to allow for the required accuracy as they not only well reproduced transition temperatures but also yielded a quantitative agreement with the experiment on a wealth of structural, dynamic, and thermodynamic properties. The main drawback of this strategy stands in the computational burden connected to the numerous quantum mechanical (QM) calculations usually required for a target-specific parameterization, which has undoubtedly hampered the routine application of QMD-FFs. In this work, we propose a fragment-based strategy to extend the applicability of QMD-FFs, in which the amount of QM calculations is significantly reduced, being a single-molecule-optimized geometry and its Hessian matrix the only QM information required. To validate this route, a new FF is assembled for a large mesogen, exploiting the parameters obtained for two smaller liquid crystalline molecules, in this and previous work. Lengthy MD simulations are carried out with the new transferred QMD-FF, observing again a spontaneous re-orientation in the correct range of temperatures, with good agreement with the available experimental measures. The present results strongly suggest that a partial transfer of QMD-FF parameters can be invoked without a significant loss of accuracy, thus paving the way to exploit the method's intrinsic predictive capabilities in the simulation of novel soft materials.
Collapse
Affiliation(s)
- Leandro Greff da Silveira
- Instituto de Química (Universidade Federal do Rio Grande do Sul), Avenida Bento Gonçalves 9500, CEP 91501-970Porto Alegre, Brazil
| | - Paolo Roberto Livotto
- Instituto de Química (Universidade Federal do Rio Grande do Sul), Avenida Bento Gonçalves 9500, CEP 91501-970Porto Alegre, Brazil
| | - Daniele Padula
- Dipartimento di Biotecnologie, Chimica e Farmacia (Università di Siena), via Aldo Moro 2, 53100Siena, SI, Italy
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada (Universidad Autónoma de Madrid), E-28049Madrid, Spain.,Condensed Matter Physics Center (IFIMAC) (Universidad Autónoma de Madrid), E-28049Madrid, Spain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124Pisa, Italy
| |
Collapse
|
2
|
Ferretti A, Prampolini G. Complexes of Alkaline and Ammonium Cations with Dopamine and Eumelanin Precursors: Dissecting the Role of Noncovalent Cation-π and Cation-Lone Pair (σ-Type) Interactions. J Phys Chem A 2022; 126:2330-2341. [PMID: 35394779 DOI: 10.1021/acs.jpca.2c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cation-π interactions and their possible competition with other noncovalent interactions (NCI) might play a key role in both dopamine- and eumelanin-based bioinspired materials. In this contribution, to unravel the delicate interplay between cation-π interactions and other possible competing forces, the configurational space of noncovalent complexes formed by dopamine or eumelanin precursors (o-benzoquinone, DHI and a semiquinone dimer) and three different cations (Na+, K+, and NH4+) is sampled by means of accurate ab initio calculations. To this end, we resort to the mp2mod method, recently validated by us for benzene-, phenol-, and catechol-cation complexes, whose computational convenience allows for an extensive exploration of the cation-molecule interaction energy surface, by sampling a total of more than 104 arrangements. The mp2mod interaction energy landscapes reveal that, besides the expected cation-π driven arrangements, for all considered molecule-cation pairs the most stable complexes are found when the cation lies within the plane containing the six-membered ring, thus maximizing the σ-type interaction with the oxygen's lone pairs. Due to the loss of aromaticity, the σ-type/cation-π strength ratio is remarkably large in o-benzoquinone, where cation-π complexes seem unlikely to be formed. The above features are shared among all considered cations but are significantly larger when considering the smaller Na+. Besides delivering a deeper insight onto the NCI network established by the considered precursors in the presence of ions, the present results can serve as a reference database to validate or refine lower level methods, as, for instance, the force fields employed in classical simulations.
Collapse
Affiliation(s)
- Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| |
Collapse
|
3
|
Ferretti A, Prampolini G, d’Ischia M. Noncovalent interactions in catechol/ammonium-rich adhesive motifs: Reassessing the role of cation-π complexes? Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
4
|
Vilhena JG, Greff da Silveira L, Livotto PR, Cacelli I, Prampolini G. Automated Parameterization of Quantum Mechanically Derived Force Fields for Soft Materials and Complex Fluids: Development and Validation. J Chem Theory Comput 2021; 17:4449-4464. [PMID: 34185536 DOI: 10.1021/acs.jctc.1c00213] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The reliability of molecular dynamics (MD) simulations in predicting macroscopic properties of complex fluids and soft materials, such as liquid crystals, colloidal suspensions, or polymers, relies on the accuracy of the adopted force field (FF). We present an automated protocol to derive specific and accurate FFs, fully based on ab initio quantum mechanical (QM) data. The integration of the Joyce and Picky procedures, recently proposed by our group to provide an accurate description of simple liquids, is here extended to larger molecules, capable of exhibiting more complex fluid phases. While the standard Joyce protocol is employed to parameterize the intramolecular FF term, a new automated procedure is here proposed to handle the computational cost of the QM calculations required for the parameterization of the intermolecular FF term. The latter is thus obtained by integrating the old Picky procedure with a fragmentation reconstruction method (FRM) that allows for a reliable, yet computationally feasible sampling of the intermolecular energy surface at the QM level. The whole FF parameterization protocol is tested on a benchmark liquid crystal, and the performances of the resulting quantum mechanically derived (QMD) FF were compared with those delivered by a general-purpose, transferable one, and by the third, "hybrid" FF, where only the bonded terms were refined against QM data. Lengthy atomistic MD simulations are carried out with each FF on extended 5CB systems in both isotropic and nematic phases, eventually validating the proposed protocol by comparing the resulting macroscopic properties with other computational models and with experiments. The QMD-FF yields the best performances, reproducing both phases in the correct range of temperatures and well describing their structure, dynamics, and thermodynamic properties, thus providing a clear protocol that may be explored to predict such properties on other complex fluids or soft materials.
Collapse
Affiliation(s)
- J G Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Leandro Greff da Silveira
- Instituto de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - 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
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM-CNR, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| |
Collapse
|
5
|
Prampolini G, d'Ischia M, Ferretti A. The phenoxyl group-modulated interplay of cation-π and σ-type interactions in the alkali metal series. Phys Chem Chem Phys 2020; 22:27105-27120. [PMID: 33225336 DOI: 10.1039/d0cp03707a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The interaction potential energy surfaces (IPESs) of four alkaline metal cations (Na+, K+, Rb+ and Cs+) complexed with phenol and catechol were explored by accurate ab initio calculations to investigate the interplay of different noncovalent interactions and their behavior along the alkali metal series and upon -OH substitution. Selected one-dimensional interaction energy curves revealed two different minimum energy configurations for all phenol- and catechol-metal complexes, characterized either by cation-π or σ-type interactions. For each investigated complex several two-dimensional IPES maps were also computed, exploiting the computational advantages of the MP2mod approach. The size of the alkali cation was found to play a similar role in modulating both kinds of complexes, as the interaction strength always decreases along the metal series, from Na+ to Cs+. Conversely, the number of hydroxyl substituents markedly affected cation-π complexes vs. σ-type ones. As a most relevant finding, in catechol-metal complexes the strength of cation-π interactions is around half that of the σ-type ones. It is argued that the combined effect of cation dimensions and hydroxyl substitution in catechol-Na+ complexes makes σ-type configurations remarkably more stable and easily accessible than cation-π ones. Besides shedding new light on the origin of biological phenomena connected with underwater adhesion, the quantum mechanical interaction energy database provided herein may offer a useful reference for tuning accurate force fields, suitable for molecular dynamics simulations, where environmental effects might be also taken into account.
Collapse
Affiliation(s)
- Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | | | | |
Collapse
|
6
|
Tao E, Inoue M, Jeong T, Kim IS, Yoshimitsu T. Total Synthesis of (±)-Liphagal via Organic-Redox-Driven Palladium-Catalyzed Hydroxybenzofuran Formation. J Org Chem 2020; 85:9064-9070. [PMID: 32597646 DOI: 10.1021/acs.joc.0c00965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A synthetic route to liphagal, a natural PI3Kα inhibitor isolated from Aka coralliphaga, was established. The present route features an organic redox process where an alkynylquinone undergoes reductive cyclization in the presence of a hydroquinone derivative such as hydroxyquinol (1,2,4-benzenetriol) and catalytic PdCl2 to provide a substituted benzofuran suitable for accessing the natural product. The benzofuran formation takes place via the redox transformation between the alkynylquinone and the electron-rich hydroquinones followed by the concomitant Pd(II)-catalyzed oxycyclization of the resultant alkynylhydroquinone.
Collapse
Affiliation(s)
- Eriko Tao
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Masaki Inoue
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Taejoo Jeong
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.,School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - In Su Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Takehiko Yoshimitsu
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| |
Collapse
|
7
|
McKay G. Emerging investigator series: critical review of photophysical models for the optical and photochemical properties of dissolved organic matter. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:1139-1165. [PMID: 32270849 DOI: 10.1039/d0em00056f] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Optical measurements (absorbance and fluorescence) are widely used to track dissolved organic matter (DOM) quantity and quality in natural and engineered systems. Despite many decades of research on the optical properties of DOM, there is a lack of understanding with regards to the underlying photophysical model that is the basis for these optical properties. This review both summarizes advances to date on the photophysical properties of DOM and seeks to critically evaluate the photophysical models for DOM optical properties. Recent studies have refined the quantitative understanding of DOM photophysical properties such as excited state lifetimes and energies, rates of different photophysical processes, and quantum yields. Considering fundamental models, more clarity is needed on whether DOM photophysical processes are due to a superposition of non-interacting components (superposition model), or whether a portion of optical signals can be ascribed to electronically interacting moieties, for example in the form of electron donor-acceptor complexes (charge transfer model). Multiple studies over more than two decades have provided evidence for the charge transfer model. Questions have been raised, however, about the broad applicability of the charge transfer model. The charge transfer and superposition model are critically reviewed in light of this current research. Recommendations are given for future studies to help clarify the accuracy of these competing photophysical models.
Collapse
Affiliation(s)
- Garrett McKay
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
8
|
Ferretti A, d’Ischia M, Prampolini G. Benchmarking Cation−π Interactions: Assessment of Density Functional Theory and Möller–Plesset Second-Order Perturbation Theory Calculations with Optimized Basis Sets (mp2mod) for Complexes of Benzene, Phenol, and Catechol with Na+, K+, Rb+, and Cs+. J Phys Chem A 2020; 124:3445-3459. [DOI: 10.1021/acs.jpca.0c02090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Marco d’Ischia
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, I-80126 Napoli, Italy
| | | |
Collapse
|
9
|
Wild U, Hübner O, Himmel H. Redox-Active Guanidines in Proton-Coupled Electron-Transfer Reactions: Real Alternatives to Benzoquinones? Chemistry 2019; 25:15988-15992. [PMID: 31535741 PMCID: PMC7065378 DOI: 10.1002/chem.201903438] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Indexed: 01/24/2023]
Abstract
Guanidino-functionalized aromatics (GFAs) are readily available, stable organic redox-active compounds. In this work we apply one particular GFA compound, 1,2,4,5-tetrakis(tetramethylguanidino)benzene, in its oxidized form in a variety of oxidation/oxidative coupling reactions to demonstrate the scope of its proton-coupled electron transfer (PCET) reactivity. Addition of an excess of acid boosts its oxidation power, enabling the oxidative coupling of substrates with redox potentials of at least +0.77 V vs. Fc+ /Fc. The green recyclability by catalytic re-oxidation with dioxygen is also shown. Finally, a direct comparison indicates that GFAs are real alternatives to toxic halo- or cyano-substituted benzoquinones.
Collapse
Affiliation(s)
- Ute Wild
- Anorganisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Olaf Hübner
- Anorganisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Hans‐Jörg Himmel
- Anorganisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| |
Collapse
|
10
|
Cacelli I, Lipparini F, Greff da Silveira L, Jacobs M, Livotto PR, Prampolini G. Accurate interaction energies by spin component scaled Möller-Plesset second order perturbation theory calculations with optimized basis sets (SCS-MP2mod): Development and application to aromatic heterocycles. J Chem Phys 2019; 150:234113. [DOI: 10.1063/1.5094288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Ivo Cacelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - 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
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany
- IRIS Adelrshof, Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin, Germany
| | - Paolo Roberto Livotto
- Instituto de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| |
Collapse
|
11
|
Zhang G, Chen L, Fu X, Wang H. Cellulose Microfiber-Supported TiO2@Ag Nanocomposites: A Dual-Functional Platform for Photocatalysis and in Situ Reaction Monitoring. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b00006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guolin Zhang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Long Chen
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaoqi Fu
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Hui Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| |
Collapse
|
12
|
Tong L, Chen Q, Wong AA, Gómez-Bombarelli R, Aspuru-Guzik A, Gordon RG, Aziz MJ. UV-Vis spectrophotometry of quinone flow battery electrolyte for in situ monitoring and improved electrochemical modeling of potential and quinhydrone formation. Phys Chem Chem Phys 2018; 19:31684-31691. [PMID: 29165500 DOI: 10.1039/c7cp05881k] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quinone-based aqueous flow batteries provide a potential opportunity for large-scale, low-cost energy storage due to their composition from earth abundant elements, high aqueous solubility, reversible redox kinetics and their chemical tunability such as reduction potential. In an operating flow battery utilizing 9,10-anthraquinone-2,7-disulfonic acid, the aggregation of an oxidized quinone and a reduced hydroquinone to form a quinhydrone dimer causes significant variations from ideal solution behavior and of optical absorption from the Beer-Lambert law. We utilize in situ UV-Vis spectrophotometry to establish (a), quinone, hydroquinone and quinhydrone molar attenuation profiles and (b), an equilibrium constant for formation of the quinhydrone dimer (KQHQ) ∼ 80 M-1. We use the molar optical attenuation profiles to identify the total molecular concentration and state of charge at arbitrary mixtures of quinone and hydroquinone. We report density functional theory calculations to support the quinhydrone UV-Vis measurements and to provide insight into the dimerization conformations. We instrument a quinone-bromine flow battery with a Pd-H reference electrode in order to demonstrate how complexation in both the negative (quinone) and positive (bromine) electrolytes directly impacts measured half-cell and full-cell voltages. This work shows how accounting for electrolyte complexation improves the accuracy of electrochemical modeling of flow battery electrolytes.
Collapse
Affiliation(s)
- Liuchuan Tong
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | | | | | | | | | | | | |
Collapse
|
13
|
Jacobs M, Greff Da Silveira L, Prampolini G, Livotto PR, Cacelli I. Interaction Energy Landscapes of Aromatic Heterocycles through a Reliable yet Affordable Computational Approach. J Chem Theory Comput 2018; 14:543-556. [DOI: 10.1021/acs.jctc.7b00602] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Matheus Jacobs
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Leandro Greff Da Silveira
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
- Departamento
de Ciências Exatas e da Terra, Universidade Regional Integrada do Alto Uruguay e da Missões (URI), Avenida Assis Brasil 709, CEP 98400-00 Frederico Westphalen, Brazil
| | - 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
3, I-56124 Pisa, Italy
| |
Collapse
|
14
|
Kobayashi Y, Hoshi T, Yamamoto S, Kimura M, Kobayashi N. Deep Axial Inclusion of Two Aromatic Molecules by Dimethyl-β-Cyclodextrin and β-Cyclodextrin. ChemistrySelect 2017. [DOI: 10.1002/slct.201702089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yayoi Kobayashi
- Institute for Excellence in Higher Education; Tohoku University; Sendai 980-8576 Japan
| | - Tomonori Hoshi
- Clinical Research, Innovation and Education Center; Tohoku University Hospital; Sendai 980-8574 Japan
| | - Satoshi Yamamoto
- Center for Intelligent Materials and Systems, Department of Mechanical engineering; University of Washington; Box 353600 Seattle WA 98195 USA
| | - Mutsumi Kimura
- Faculty of Textile Science and Technology; Shinshu University; Ueda 386-8567 Japan
| | - Nagao Kobayashi
- Faculty of Textile Science and Technology; Shinshu University; Ueda 386-8567 Japan
| |
Collapse
|
15
|
Barone V, Cacelli I, Ferretti A, Prampolini G. Noncovalent Interactions in the Catechol Dimer. Biomimetics (Basel) 2017; 2:E18. [PMID: 31105180 PMCID: PMC6352673 DOI: 10.3390/biomimetics2030018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/02/2022] Open
Abstract
Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller⁻Plesset (MP2) calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T))/CBS) method.
Collapse
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri, I-56126 Pisa, Italy.
| | - Ivo Cacelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy.
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy.
| |
Collapse
|
16
|
Micillo R, Panzella L, Iacomino M, Prampolini G, Cacelli I, Ferretti A, Crescenzi O, Koike K, Napolitano A, d'Ischia M. Eumelanin broadband absorption develops from aggregation-modulated chromophore interactions under structural and redox control. Sci Rep 2017; 7:41532. [PMID: 28150707 PMCID: PMC5288692 DOI: 10.1038/srep41532] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022] Open
Abstract
Eumelanins, the chief photoprotective pigments in man and mammals, owe their black color to an unusual broadband absorption spectrum whose origin is still a conundrum. Excitonic effects from the interplay of geometric order and disorder in 5,6-dihydroxyindole (DHI)-based oligomeric/polymeric structures play a central role, however the contributions of structural (scaffold-controlled) and redox (π-electron-controlled) disorder have remained uncharted. Herein, we report an integrated experimental-theoretical entry to eumelanin chromophore dynamics based on poly(vinyl alcohol)-controlled polymerization of a large set of 5,6-dihydroxyindoles and related dimers. The results a) uncover the impact of the structural scaffold on eumelanin optical properties, disproving the widespread assumption of a universal monotonic chromophore; b) delineate eumelanin chromophore buildup as a three-step dynamic process involving the rapid generation of oxidized oligomers, termed melanochromes (phase I), followed by a slow oxidant-independent band broadening (phase II) leading eventually to scattering (phase III); c) point to a slow reorganization-stabilization of melanochromes via intermolecular redox interactions as the main determinant of visible broadband absorption.
Collapse
Affiliation(s)
- Raffaella Micillo
- Department of Clinical Medicine and Surgery, University of Naples Federico II, I-80131 Naples, Italy
| | - Lucia Panzella
- Department of Chemical Sciences, University of Naples Federico II, I-80126 Naples, Italy
| | - Mariagrazia Iacomino
- Department of Chemical Sciences, University of Naples Federico II, I-80126 Naples, Italy
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca, I-56124 Pisa, Italy
| | - Ivo Cacelli
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca, I-56124 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, I-56124 Pisa, Italy
| | - Alessandro Ferretti
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca, I-56124 Pisa, Italy
| | - Orlando Crescenzi
- Department of Chemical Sciences, University of Naples Federico II, I-80126 Naples, Italy
| | - Kenzo Koike
- Hair care Products Research Laboratories, Kao Corporation, Tokyo 131-8501, Japan
| | - Alessandra Napolitano
- Department of Chemical Sciences, University of Naples Federico II, I-80126 Naples, Italy
| | - Marco d'Ischia
- Department of Chemical Sciences, University of Naples Federico II, I-80126 Naples, Italy
| |
Collapse
|
17
|
Samiee F, Pedron FN, Estrin DA, Trevani L. Experimental and Theoretical Study of the High-Temperature UV-Visible Spectra of Aqueous Hydroquinone and 1,4-Benzoquinone. J Phys Chem B 2016; 120:10547-10552. [PMID: 27627463 DOI: 10.1021/acs.jpcb.6b07893] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
UV-visible spectroscopic studies of aqueous hydroquinone (HQ) and 1,4-benzoquinone (BQ) have been carried out along with classical molecular dynamics (MD) and quantum calculations. The experimental results confirmed that HQ is stable in hot compressed water up to at least 523 K at 70 bar, but BQ decomposes at temperatures lower than 373 K, leading to the formation of HQ and other nonabsorbing products. Even though benzoquinone is not stable, our study significantly extended the temperature range of other spectroscopic studies, and the spectra of HQ up to 523 K can still be useful for other studies, particularly those related to organic species in deep ocean hydrothermal vents. Classical MD simulations at high temperatures show, as expected, a weakening of the solute-solvent H-bonding interactions. The dependence of the maximum absorption of BQ on temperature was also analyzed, although a significant degree of decomposition was observed in the time frame of our experiments. The shift of the maximum absorption peak of BQ with temperature was consistent with time-dependent density functional theory calculations.
Collapse
Affiliation(s)
- Fereshteh Samiee
- Faculty of Science, University of Ontario Institute of Technology , 2000 Simcoe Street North, Oshawa L1H 7K4, Ontario, Canada
| | - Federico N Pedron
- Departamento de Química Inorgánica, Analítica y Química Física, and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pab. 2, C1428EHA CABA, Argentina
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pab. 2, C1428EHA CABA, Argentina
| | - Liliana Trevani
- Faculty of Science, University of Ontario Institute of Technology , 2000 Simcoe Street North, Oshawa L1H 7K4, Ontario, Canada
| |
Collapse
|
18
|
Wild U, Federle S, Wagner A, Kaifer E, Himmel HJ. Dehydrogenative Coupling Reactions with Oxidized Guanidino-Functionalized Aromatic Compounds: Novel Options for σ-Bond Activation. Chemistry 2016; 22:11971-6. [DOI: 10.1002/chem.201602236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Ute Wild
- Anorganisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Stefanie Federle
- Anorganisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Arne Wagner
- Anorganisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Elisabeth Kaifer
- Anorganisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Hans-Jörg Himmel
- Anorganisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| |
Collapse
|
19
|
Prampolini G, Livotto PR, Cacelli I. Accuracy of Quantum Mechanically Derived Force-Fields Parameterized from Dispersion-Corrected DFT Data: The Benzene Dimer as a Prototype for Aromatic Interactions. J Chem Theory Comput 2015; 11:5182-96. [DOI: 10.1021/acs.jctc.5b00642] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- 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, Rio Grande do Sul, 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, Universitá di Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| |
Collapse
|
20
|
Rury AS, Sorenson S, Driscoll E, Dawlaty JM. Electronic State-Resolved Electron-Phonon Coupling in an Organic Charge Transfer Material from Broadband Quantum Beat Spectroscopy. J Phys Chem Lett 2015; 6:3560-3564. [PMID: 26722724 DOI: 10.1021/acs.jpclett.5b01706] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The coupling of electron and lattice phonon motion plays a fundamental role in the properties of functional organic charge-transfer materials. In this Letter we extend the use of ultrafast vibrational quantum beat spectroscopy to directly elucidate electron-phonon coupling in an organic charge-transfer material. As a case study, we compare the oscillatory components of the transient reflection (TR) of a broadband probe pulse from single crystals of quinhydrone, a 1:1 cocrystal of hydroquinone and p-benzoquinone, after exciting nonresonant impulsive stimulated Raman scattering and resonant electronic transitions using ultrafast pulses. Spontaneous resonance Raman spectra confirm the assignment of these oscillations as coherent lattice phonon excitations. Fourier transforms of the vibrational quantum beats in our broadband TR measurements allow construction of spectra that we show report the ability of these phonons to directly modulate the electronic structure of quinhydrone. These results demonstrate how coherent ultrafast processes can characterize the complex interplay of charge transfer and lattice motion in materials of fundamental relevance to chemistry, materials sciences, and condensed matter physics.
Collapse
Affiliation(s)
- Aaron S Rury
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Shayne Sorenson
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Eric Driscoll
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Jahan M Dawlaty
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| |
Collapse
|
21
|
Prampolini G, Cacelli I, Ferretti A. Intermolecular interactions in eumelanins: a computational bottom-up approach. I. small building blocks. RSC Adv 2015. [DOI: 10.1039/c5ra03773e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Building eumelanin: from basic units to spectral properties.
Collapse
Affiliation(s)
- Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)
- Area della Ricerca
- I-56124 Pisa
- Italy
| | - Ivo Cacelli
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)
- Area della Ricerca
- I-56124 Pisa
- Italy
- Dipartimento di Chimica e Chimica Industriale
| | - Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)
- Area della Ricerca
- I-56124 Pisa
- Italy
| |
Collapse
|
22
|
Barone V, Cacelli I, Ferretti A, Prampolini G, Villani G. Proton and Electron Transfer Mechanisms in the Formation of Neutral and Charged Quinhydrone-Like Complexes: A Multilayered Computational Study. J Chem Theory Comput 2014; 10:4883-95. [DOI: 10.1021/ct500778u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Ivo Cacelli
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento
35, I-56126 Pisa, Italy
| | - Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| |
Collapse
|