101
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Mendolicchio M, Baiardi A, Fronzoni G, Stener M, Grazioli C, de Simone M, Barone V. Theory meets experiment for unravelling the C1s X-ray photoelectron spectra of pyridine, 2-fluoropyridine, and 2,6-difluoropyridine. J Chem Phys 2019; 151:124105. [DOI: 10.1063/1.5122310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | - Alberto Baiardi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Giovanna Fronzoni
- Dipartimento di Scienze Chimiche e Farmaceutiche, Universita’ di Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Mauro Stener
- Dipartimento di Scienze Chimiche e Farmaceutiche, Universita’ di Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Cesare Grazioli
- IOM- CNR Laboratorio TASC, Basovizza SS-14, km 163.5, 34149 Trieste, Italy
| | - Monica de Simone
- IOM- CNR Laboratorio TASC, Basovizza SS-14, km 163.5, 34149 Trieste, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
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102
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Wang J, Spada L, Chen J, Gao S, Alessandrini S, Feng G, Puzzarini C, Gou Q, Grabow J, Barone V. The Unexplored World of Cycloalkene–Water Complexes: Primary and Assisting Interactions Unraveled by Experimental and Computational Spectroscopy. Angew Chem Int Ed Engl 2019; 58:13935-13941. [DOI: 10.1002/anie.201906977] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/12/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Juan Wang
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
- Institut für Physikalische Chemie & ElektrochemieGottfried-Wilhelm-Leibniz-Universität Hannover Callinstr. 3A 30167 Hannover Germany
| | - Lorenzo Spada
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 I-40126 Bologna Italy
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Junhua Chen
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Shuang Gao
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | | | - Gang Feng
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 I-40126 Bologna Italy
| | - Qian Gou
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Jens‐Uwe Grabow
- Institut für Physikalische Chemie & ElektrochemieGottfried-Wilhelm-Leibniz-Universität Hannover Callinstr. 3A 30167 Hannover Germany
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
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103
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Ventura ON, Kieninger M, Salta Z, Kosmas AM, Barone V. Enthalpies of formation of the benzyloxyl, benzylperoxyl, hydroxyphenyl radicals and related species on the potential energy surface for the reaction of toluene with the hydroxyl radical. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2500-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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104
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d'Ischia M, Manini P, Moracci M, Saladino R, Ball V, Thissen H, Evans RA, Puzzarini C, Barone V. Astrochemistry and Astrobiology: Materials Sciencein Wonderland? Int J Mol Sci 2019; 20:E4079. [PMID: 31438518 PMCID: PMC6747172 DOI: 10.3390/ijms20174079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 02/04/2023] Open
Abstract
Astrochemistry and astrobiology, the fascinating disciplines that strive to unravel the origin of life, have opened unprecedented and unpredicted vistas into exotic compounds as well as extreme or complex reaction conditions of potential relevance for a broad variety of applications. Representative, and so far little explored sources of inspiration include complex organic systems, such as polycyclic aromatic hydrocarbons (PAHs) and their derivatives; hydrogen cyanide (HCN) and formamide (HCONH2) oligomers and polymers, like aminomalononitrile (AMN)-derived species; and exotic processes, such as solid-state photoreactions on mineral surfaces, phosphorylation by minerals, cold ice irradiation and proton bombardment, and thermal transformations in fumaroles. In addition, meteorites and minerals like forsterite, which dominate dust chemistry in the interstellar medium, may open new avenues for the discovery of innovative catalytic processes and unconventional methodologies. The aim of this review was to offer concise and inspiring, rather than comprehensive, examples of astrochemistry-related materials and systems that may be of relevance in areas such as surface functionalization, nanostructures, and hybrid material design, and for innovative technological solutions. The potential of computational methods to predict new properties from spectroscopic data and to assess plausible reaction pathways on both kinetic and thermodynamic grounds has also been highlighted.
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Affiliation(s)
- Marco d'Ischia
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy.
| | - Paola Manini
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100 Viterbo, Italy
| | - Vincent Ball
- Institut National de la Santé et de la RechercheMédicale, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 1 Place de l'Hôpital, 67000 Strasbourg, France
| | - Helmut Thissen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia
| | - Richard A Evans
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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105
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Wang J, Spada L, Chen J, Gao S, Alessandrini S, Feng G, Puzzarini C, Gou Q, Grabow J, Barone V. The Unexplored World of Cycloalkene–Water Complexes: Primary and Assisting Interactions Unraveled by Experimental and Computational Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Juan Wang
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
- Institut für Physikalische Chemie & ElektrochemieGottfried-Wilhelm-Leibniz-Universität Hannover Callinstr. 3A 30167 Hannover Germany
| | - Lorenzo Spada
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 I-40126 Bologna Italy
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Junhua Chen
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Shuang Gao
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | | | - Gang Feng
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 I-40126 Bologna Italy
| | - Qian Gou
- Department of ChemistrySchool of Chemistry and Chemical EngineeringChongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Jens‐Uwe Grabow
- Institut für Physikalische Chemie & ElektrochemieGottfried-Wilhelm-Leibniz-Universität Hannover Callinstr. 3A 30167 Hannover Germany
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
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106
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Zanetti-Polzi L, Biswas AD, Del Galdo S, Barone V, Daidone I. Hydration Shell of Antifreeze Proteins: Unveiling the Role of Non-Ice-Binding Surfaces. J Phys Chem B 2019; 123:6474-6480. [PMID: 31280567 DOI: 10.1021/acs.jpcb.9b06375] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Antifreeze proteins (AFPs) have the ability to inhibit ice growth by binding to ice nuclei. Their ice-binding mechanism is still unclear, yet the hydration layer is thought to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of two AFPs and two non-AFPs. The calculated shell thickness and density of the AFPs do not feature any relevant difference with respect to the non-AFPs. Moreover, the hydration shell density is always higher than the bulk density and, thus, no low-density, ice-like layer is detected at the ice-binding surface (IBS) of AFPs. Instead, we observe local water-density differences in AFPs between the IBS (lower density) and the non-IBS (higher density). The lower solvent density at the ice-binding site can pave the way to the protein binding to ice nuclei, while the higher solvent density at the non-ice-binding surfaces might provide protection against ice growth.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Akash Deep Biswas
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy.,Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy.,Institute for the Chemistry of Organometallic Compounds , Italian National Council for Research (ICCOMCNR) , Via G. Moruzzi 1 , I-6124 Pisa , Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy.,National Institute for Nuclear Physics (INFN) Pisa Section , Largo BrunoPontecorvo 3 , 56127 Pisa , Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
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107
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Paoloni L, Rampino S, Barone V. Potential-Energy Surfaces for Ring-Puckering Motions of Flexible Cyclic Molecules through Cremer-Pople Coordinates: Computation, Analysis, and Fitting. J Chem Theory Comput 2019; 15:4280-4294. [PMID: 31244128 DOI: 10.1021/acs.jctc.9b00363] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ring-puckering motion in 12 flexible cyclic molecules is investigated by calculation and analysis of two-dimensional potential-energy surfaces (PESs) using the so-called ring-puckering coordinates proposed by Cremer and Pople. The PESs are calculated by means of density-functional theory using a B2PLYP-D3BJ exchange-correlation functional with a maug-cc-pVTZ basis set, and results are compared to the available experimental and theoretical data. Special care is devoted to the aspect of symmetry in such two-dimensional PESs, which are here reported for the first time also for molecules whose planar form has symmetry lower than D5 h or C2 v. The issue of PES fitting and that of solving the nuclear dynamics using ring-puckering coordinates are also addressed. Analytical formulations of the computed PESs using suitable functional forms with a limited set of parameters are provided.
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Affiliation(s)
- Lorenzo Paoloni
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| | - Sergio Rampino
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| | - Vincenzo Barone
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
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108
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Puzzarini C, Bloino J, Tasinato N, Barone V. Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy. Chem Rev 2019; 119:8131-8191. [DOI: 10.1021/acs.chemrev.9b00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- 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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109
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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110
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Giovannini T, Lafiosca P, Chandramouli B, Barone V, Cappelli C. Effective yet reliable computation of hyperfine coupling constants in solution by a QM/MM approach: Interplay between electrostatics and non-electrostatic effects. J Chem Phys 2019; 150:124102. [DOI: 10.1063/1.5080810] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Piero Lafiosca
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163 Genova, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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111
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Salta Z, Kosmas AM, Ventura ON, Barone V. Computational Evidence Suggests That 1-Chloroethanol May Be an Intermediate in the Thermal Decomposition of 2-Chloroethanol into Acetaldehyde and HCl. J Phys Chem A 2019; 123:1983-1998. [PMID: 30794424 DOI: 10.1021/acs.jpca.8b11966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dehalogenation of 2-chloroethanol (2ClEtOH) in the gas phase with and without the participation of catalytic water molecules has been investigated using methods rooted into the density functional theory. The well-known HCl elimination leading to vinyl alcohol (VA) was compared to the alternative elimination route toward oxirane and shown to be kinetically and thermodynamically more favorable. However, the isomerization of VA to acetaldehyde in the gas phase, in the absence of water, was shown to be kinetically and thermodynamically less favorable than the recombination of VA and HCl to form the isomeric 1-chloroethanol (1ClEtOH) species. At the ωB97X-D/cc-pVTZ level of calculation, this species is more stable than 2ClEtOH by about 6 kcal mol-1 at 298 K, and the reaction barrier for VA to 1ClEtOH is 23 kcal mol-1 versus 55 kcal mol-1 for the direct transformation of VA to acetaldehyde. In a successive step, 1ClEtOH can decompose directly to acetaldehyde and HCl with a lower barrier (29 kcal mol-1) than that of VA to the same products (55 kcal mol-1). The calculations were repeated using a single ancillary water molecule (W) in the complexes 2ClEtOH_W and 1ClEtOH_W. The latter adduct is now more stable than 2ClEtOH_W by about 8 kcal mol-1 at 298 K, implying that the water molecule increased the already higher stability of 1ClEtOH in the gas phase. However, this catalytic water molecule lowers dramatically the barrier for the interconversion of VA to acetaldehyde (from 55 to 7 kcal mol-1). This barrier is now smaller than the one for the conversion to 1ClEtOH (which also decreases, but not so much, from 23 to 13 kcal mol-1). Thus, it is concluded that while 1ClEtOH may be a plausible intermediate in the gas phase dehalogenation of 2ClEtOH, it is unlikely that it plays a major role in water complexes (or, by inference, aqueous solution). It is also shown that neither in the gas phase nor in the cluster with one water molecule, the oxirane path is more favorable than the VA alcohol path. Additionally, a direct conversion of 2ClEtOH to 1ClEtOH through a transition state which resembles a VA molecule in a complex with a chlorine atom and a hydrogen atom on both sides of this planar species was found. This reaction path has also lower activation energy than the conversion to oxirane but not as low as the conversion to VA.
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Affiliation(s)
- Zoi Salta
- SMART Lab , Scuola Normale Superiore di Pisa , Piazza dei Cavalieri, 7 , 56126 Pisa , Italy
| | - Agnie M Kosmas
- Physical Chemistry Sector, Department of Chemistry , University of Ioannina , PC 45110 Ioannina , Greece
| | - Oscar N Ventura
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química , Universidad de la Republica (Udelar) , Montevideo 11400 , Uruguay
| | - Vincenzo Barone
- SMART Lab , Scuola Normale Superiore di Pisa , Piazza dei Cavalieri, 7 , 56126 Pisa , Italy
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112
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Baiardi A, Stein CJ, Barone V, Reiher M. Optimization of highly excited matrix product states with an application to vibrational spectroscopy. J Chem Phys 2019; 150:094113. [DOI: 10.1063/1.5068747] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alberto Baiardi
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Christopher J. Stein
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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113
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Puzzarini C, Tasinato N, Bloino J, Spada L, Barone V. State-of-the-art computation of the rotational and IR spectra of the methyl-cyclopropyl cation: hints on its detection in space. Phys Chem Chem Phys 2019; 21:3431-3439. [PMID: 30110028 DOI: 10.1039/c8cp04629h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent measurements by the Cassini Ion Neutral Mass Spectrometer demonstrated the presence of numerous carbocations in Titan's upper atmosphere. In [Ali et al., Planet. Space Sci., 2013, 87, 96], an analysis of these measurements revealed the formation of the three-membered cyclopropenyl cation and its methyl derivatives. As a starting point of a future coordinated effort of laboratory experiments, quantum-chemical calculations, and astronomical observations, in the present work the molecular structure and spectroscopic properties of the methyl-cyclopropenyl cation have been investigated by means of state-of-the-art computational approaches in order to simulate its rotational and infrared spectra. Rotational parameters have been predicted with an expected accuracy better than 0.1% for rotational constants and on the order of 1-2% for centrifugal-distortion terms. As for the infrared spectrum, despite the challenge of a large amplitude motion, fundamental transitions have been computed to a good accuracy, i.e., the uncertainties are expected to be smaller than 5-10 wavenumbers.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, via F. Selmi 2, I-40126 Bologna, Italy.
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114
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Patti A, Pedotti S, Mazzeo G, Longhi G, Abbate S, Paoloni L, Bloino J, Rampino S, Barone V. Ferrocenes with simple chiral substituents: an in-depth theoretical and experimental VCD and ECD study. Phys Chem Chem Phys 2019; 21:9419-9432. [DOI: 10.1039/c9cp00437h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ferrocenes bearing chiral pendants are investigated through VCD and ECD. The VCD spectra are best interpreted by GVPT2-anharmonic DFT calculations. Diagnostic bands related to the absolute configuration of the title compounds are found in both kinds of spectra.
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Affiliation(s)
- Angela Patti
- Institute of Biomolecular Chemistry – CNR
- 95126 Catania
- Italy
| | - Sonia Pedotti
- Institute of Biomolecular Chemistry – CNR
- 95126 Catania
- Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT)
- Università di Brescia
- 25123 Brescia
- Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT)
- Università di Brescia
- 25123 Brescia
- Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT)
- Università di Brescia
- 25123 Brescia
- Italy
| | | | - Julien Bloino
- Scuola Normale Superiore
- I-56126 Pisa
- Italy
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti OrganoMetallici (CNR-ICCOM) Area della Ricerca CNR
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115
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Chandramouli B, Del Galdo S, Fusè M, Barone V, Mancini G. Two-level stochastic search of low-energy conformers for molecular spectroscopy: implementation and validation of MM and QM models. Phys Chem Chem Phys 2019; 21:19921-19934. [DOI: 10.1039/c9cp03557e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The search for stationary points in the molecular potential energy surfaces (PES) is a problem of increasing relevance in molecular sciences especially for large, flexible systems featuring several large-amplitude internal motions.
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Affiliation(s)
| | | | | | - Vincenzo Barone
- Scuola Normale Superiore
- 56126 Pisa
- Italy
- Istituto Nazionale di Fisica Nucleare (INFN)
- Sezione di Pisa
| | - Giordano Mancini
- Scuola Normale Superiore
- 56126 Pisa
- Italy
- Istituto Nazionale di Fisica Nucleare (INFN)
- Sezione di Pisa
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116
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Gambi A, Pietropolli Charmet A, Stoppa P, Tasinato N, Ceselin G, Barone V. Molecular synthons for accurate structural determinations: the equilibrium geometry of 1-chloro-1-fluoroethene. Phys Chem Chem Phys 2019; 21:3615-3625. [DOI: 10.1039/c8cp04888f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The equilibrium structure for 1-chloro-1-fluoroethene is obtained by high-level quantum chemical calculations and the semi-experimental approach.
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Affiliation(s)
- Alberto Gambi
- Università degli Studi di Udine
- Dipartimento Politecnico di Ingegneria e Architettura
- I-33100 Udine
- Italy
| | | | - Paolo Stoppa
- Università Ca’ Foscari Venezia
- Dipartimento di Scienze Molecolari e Nanosistemi
- I-30172 Mestre (VE)
- Italy
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117
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Chandramouli B, Del Galdo S, Mancini G, Barone V. Mechanistic insights into metal ions transit through threefold ferritin channel. Biochim Biophys Acta Gen Subj 2018; 1863:472-480. [PMID: 30496786 DOI: 10.1016/j.bbagen.2018.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/26/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND The mechanism of how the hydrophilic threefold channel (C3) of ferritin nanocages facilitates diffusion of diverse metal ions into the internal cavity remains poorly explored. METHODS Computational modeling and free energy estimations were carried out on R. catesbeiana H´ ferritin. Transit features and associated energetics for Fe2+, Mg2+, Zn2+ ions through the C3 channel have been examined. RESULTS We highlight that iron conduction requires the involvement of two Fe2+ ions in the channel. In such doubly occupied configuration, as observed in X-ray structures, Fe2+ is displaced from the internal site (stabilized by D127) at lower energetic cost. Moreover, comparison of Fe2+, Mg2+ and Zn2+ transit features shows that E130 geometric constriction provides not only an electrostatic anchor to the incoming ions but also differentially influence their diffusion kinetics. CONCLUSIONS Overall, the study provides insights into Fe2+ entry mechanism and characteristic features of metal-protein interactions that influence the metal ions passage. The dynamics data suggest that E130 may act as a metal selectivity gate. This implicates an ion-specific entry mechanism through the channel with the distinct diffusion kinetics being the discriminating factor. GENERAL SIGNIFICANCE Ferritin nanocages not only act as biological iron reservoirs but also have gained importance in material science as template scaffolds for synthesizing metal nanoparticles. This study provides mechanistic understanding on the conduction of different metal ions through the channel.
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Affiliation(s)
- Balasubramanian Chandramouli
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy; Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy; Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOMCNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - 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
| | - 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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118
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Abstract
In this work, we extend the theoretical framework recently developed for the simulation of resonance Raman (RR) spectra of medium-to-large sized systems to its chiral counterpart, namely, resonance Raman optical activity (RROA). The theory is based on a time-dependent (TD) formulation, with the transition tensors obtained as half-Fourier transforms of the appropriate cross-correlation functions. The implementation has been kept as general as possible, supporting adiabatic and vertical models for the PES representation, both in Cartesian and internal coordinates, with the possible inclusion of Herzberg-Teller (HT) effects. Thanks to the integration of this TD-RROA procedure within a general-purpose quantum-chemistry program, both solvation and leading anharmonicity effects can be included in an effective way. The implementation is validated on one of the smallest chiral molecule (methyloxirane). Practical applications are illustrated with three medium-size organic molecules (naproxen-OCD3, quinidine and 2-Br-hexahelicene), whose simulated spectra are compared to the corresponding experimental data.
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Affiliation(s)
- Alberto Baiardi
- Scuola Normale Superiore , piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Julien Bloino
- 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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119
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Obenchain DA, Spada L, Alessandrini S, Rampino S, Herbers S, Tasinato N, Mendolicchio M, Kraus P, Gauss J, Puzzarini C, Grabow JU, Barone V. Unveiling the Sulfur-Sulfur Bridge: Accurate Structural and Energetic Characterization of a Homochalcogen Intermolecular Bond. Angew Chem Int Ed Engl 2018; 57:15822-15826. [PMID: 30303600 DOI: 10.1002/anie.201810637] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Indexed: 11/11/2022]
Abstract
By combining rotational spectroscopy in supersonic expansion with the capability of state-of-the-art quantum-chemical computations in accurately determining structural and energetic properties, the genuine nature of a sulfur-sulfur chalcogen bond between dimethyl sulfide and sulfur dioxide has been unveiled in a gas-jet environment free from collision, solvent and matrix perturbations. A SAPT analysis pointed out that electrostatic S⋅⋅⋅S interactions play the dominant role in determining the stability of the complex, largely overcoming dispersion and C-H⋅⋅⋅O hydrogen-bond contributions. Indeed, in agreement with the analysis of the quadrupole-coupling constants and of the methyl internal rotation barrier, the NBO and NOCV/CD approaches show a marked charge transfer between the sulfur atoms. Based on the assignment of the rotational spectra for 7 isotopologues, an accurate semi-experimental equilibrium structure for the heavy-atom backbone of the molecular complex has been determined, which is characterized by a S⋅⋅⋅S distance (2.947(3) Å) well below the sum of van der Waals radii.
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Affiliation(s)
- Daniel A Obenchain
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Lorenzo Spada
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | | | - Sergio Rampino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Sven Herbers
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | | | - Peter Kraus
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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120
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Li W, Spada L, Tasinato N, Rampino S, Evangelisti L, Gualandi A, Cozzi PG, Melandri S, Barone V, Puzzarini C. Theory Meets Experiment for Noncovalent Complexes: The Puzzling Case of Pnicogen Interactions. Angew Chem Int Ed Engl 2018; 57:13853-13857. [DOI: 10.1002/anie.201807751] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/20/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Weixing Li
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Lorenzo Spada
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Nicola Tasinato
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Sergio Rampino
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Andrea Gualandi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Pier Giorgio Cozzi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Sonia Melandri
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
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121
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Salvadori A, Fusè M, Mancini G, Rampino S, Barone V. Diving into chemical bonding: An immersive analysis of the electron charge rearrangement through virtual reality. J Comput Chem 2018; 39:2607-2617. [DOI: 10.1002/jcc.25523] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Andrea Salvadori
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
| | - Giordano Mancini
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
| | - Sergio Rampino
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
| | - Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
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122
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Li W, Spada L, Tasinato N, Rampino S, Evangelisti L, Gualandi A, Cozzi PG, Melandri S, Barone V, Puzzarini C. Theory Meets Experiment for Noncovalent Complexes: The Puzzling Case of Pnicogen Interactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Weixing Li
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Lorenzo Spada
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Nicola Tasinato
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Sergio Rampino
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Andrea Gualandi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Pier Giorgio Cozzi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Sonia Melandri
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
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123
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Zanetti-Polzi L, Del Galdo S, Daidone I, D'Abramo M, Barone V, Aschi M, Amadei A. Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory. Phys Chem Chem Phys 2018; 20:24369-24378. [PMID: 30215645 DOI: 10.1039/c8cp04190c] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for the investigation of chemical processes in complex systems, that proved to be a valuable tool for the simulation of relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations the quantum sub-part of the system, the quantum centre, is embedded into an external perturbing field providing a perturbation operator explicitly calculated up to the dipolar terms. In this paper we further develop the PMM approach, beyond the dipolar terms in the perturbation operator expansion, by including explicitly the quadrupolar terms and/or by expanding the perturbation operator on each atom of the quantum centre. These different levels of the perturbation operator expansion, providing different levels of theory, have been tested by calculating three different spectroscopic observables: the spectral signal of liquid water and aqueous benzene due to the lowest energy electronic excitation and the infrared amide I band of aqueous trans-N-methylacetamide. All the systems tested show that, even though the previous PMM level of theory is already capable of reproducing the main features of the spectral signal, the higher levels of theory improve the quantitative reproduction of the spectral details.
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Affiliation(s)
- Laura Zanetti-Polzi
- Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila, via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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124
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Fornaro T, Brucato JR, Feuillie C, Sverjensky DA, Hazen RM, Brunetto R, D'Amore M, Barone V. Binding of Nucleic Acid Components to the Serpentinite-Hosted Hydrothermal Mineral Brucite. Astrobiology 2018; 18:989-1007. [PMID: 30048146 DOI: 10.1089/ast.2017.1784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The adsorption of nucleic acid components onto the serpentinite-hosted hydrothermal mineral brucite has been investigated experimentally by determining the equilibrium adsorption isotherms in aqueous solution. Thermodynamic characterization of the adsorption data has been performed using the extended triple-layer model (ETLM) to establish a model for the stoichiometry and equilibrium constants of surface complexes. Infrared characterization of the molecule-mineral complexes has helped gain insight into the molecular functional groups directly interacting with the mineral surface. Quantum mechanical calculations have been carried out to identify the possible complexes formed on surfaces by nucleic acid components and their binding configurations on mineral surfaces, both in the presence of water molecules and in water-free conditions. The results indicate that brucite favors adsorption of nucleotides with respect to nucleosides and nucleobases from dilute aqueous environments. The surface of this mineral is able to induce well-defined orientations of the molecules through specific molecule-mineral interactions. This result suggests plausible roles of the mineral brucite in assisting prebiotic molecular self-organization. Furthermore, the detection of the infrared spectroscopic features of such building blocks of life adsorbed on brucite at very low degrees of coverage provides important support to life detection investigations.
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Affiliation(s)
- Teresa Fornaro
- 1 Geophysical Laboratory, Carnegie Institution for Science , Washington, District of Columbia, United States
- 2 INAF-Astrophysical Observatory of Arcetri , Firenze, Italy
- 3 Scuola Normale Superiore , Pisa, Italy
| | - John R Brucato
- 2 INAF-Astrophysical Observatory of Arcetri , Firenze, Italy
| | - Cécile Feuillie
- 4 Louvain Institute of Biomolecular Science and Technology, University Catholique de Louvain , Louvain-la-Neuve, Belgium
| | - Dimitri A Sverjensky
- 5 Department of Earth and Planetary Sciences, Johns Hopkins University , Baltimore, Maryland, United States
| | - Robert M Hazen
- 1 Geophysical Laboratory, Carnegie Institution for Science , Washington, District of Columbia, United States
| | - Rosario Brunetto
- 6 Institut d'Astrophysique Spatiale, UMR8617 CNRS-Univ. Paris-Sud, Université Paris-Saclay , Orsay, France
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125
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Schiavo E, Latouche C, Barone V, Crescenzi O, Muñoz-García AB, Pavone M. An ab initio study of Cu-based delafossites as an alternative to nickel oxide in photocathodes: effects of Mg-doping and surface electronic features. Phys Chem Chem Phys 2018; 20:14082-14089. [PMID: 29748688 DOI: 10.1039/c8cp00848e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
CuMO2 delafossites (M = Al, Ga, and Cr) are p-type semiconductor oxides that have been recently proposed as the electrode in p-type dye-sensitized solar cells (p-DSSC) which is an alternative to the standard, low-performing nickel oxide. To assess this potential application of delafossites, we report here a DFT-based investigation of the structural and electronic properties of CuAlO2, CuGaO2 and CuCrO2. In particular, we address the role of Mg doping to obtain the p-type semiconducting character: the substitution of an M3+ cation with Mg2+ is easier with Ga than with Al and Cr, and, in all cases, the hole introduced by Mg2+ leads to the formation of Cu2+ species. Moreover, we address surface electronic features in order to characterize the most exposed delafossite surface termination and, more importantly, to predict the valence band maximum energy value, which determines the p-DSSC open circuit potential. From analysis of all our results, CuGaO2 emerges as the most promising system that can boost the development of new photocathodes for p-DSSCs.
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Affiliation(s)
- Eduardo Schiavo
- Department of Chemical Sciences, University of Naples Federico II, Comp. Univ. Monte Sant'Angelo Via Cintia 21, 80126 Naples, Italy.
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126
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Del Galdo S, Mancini G, Daidone I, Zanetti Polzi L, Amadei A, Barone V. Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties. J Comput Chem 2018; 39:1747-1756. [DOI: 10.1002/jcc.25351] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa 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; Pisa 56127 Italy
| | - Isabella Daidone
- Dipartimento di Scienze Fisiche e Chimiche; Università di L'Aquila, Via Vetoio s.n.c.67100; L'Aquila Italy
| | - Laura Zanetti Polzi
- Dipartimento di Scienze Fisiche e Chimiche; Università di L'Aquila, Via Vetoio s.n.c.67100; L'Aquila Italy
| | - Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma Tor Vergata, Via Della Ricerca Scientifica; Roma 00100 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; Pisa 56127 Italy
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127
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Egidi F, Fusè M, Baiardi A, Bloino J, Li X, Barone V. Computational simulation of vibrationally resolved spectra for spin-forbidden transitions. Chirality 2018; 30:850-865. [PMID: 29727500 DOI: 10.1002/chir.22864] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/25/2022]
Abstract
In this computational study, we illustrate a method for computing phosphorescence and circularly polarized phosphorescence spectra of molecular systems, which takes into account vibronic effects including both Franck-Condon and Herzberg-Teller contributions. The singlet and triplet states involved in the phosphorescent emission are described within the harmonic approximation, and the method fully takes mode-mixing effects into account when evaluating Franck-Condon integrals. Spin-orbit couplings, which are responsible for these otherwise forbidden phenomena, are accounted for by means of a relativistic two-component time-dependent density functional theory method. The model is applied to two types of chiral systems: camphorquinone, a rigid organic system that allows for an extensive benchmark, and some members of a class of iridium complexes. The merits and shortcomings of the methods are discussed, and some perspectives for future developments are offered.
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Affiliation(s)
| | | | | | - Julien Bloino
- Institute of Chemistry of Organometallic Compounds, National Research Council of Italy, Pisa, Italy
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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128
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Manini P, Bietti M, Galeotti M, Salamone M, Lanzalunga O, Cecchini MM, Reale S, Crescenzi O, Napolitano A, De Angelis F, Barone V, d’Ischia M. Characterization and Fate of Hydrogen-Bonded Free-Radical Intermediates and Their Coupling Products from the Hydrogen Atom Transfer Agent 1,8-Naphthalenediol. ACS Omega 2018; 3:3918-3927. [PMID: 31458630 PMCID: PMC6641764 DOI: 10.1021/acsomega.8b00155] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/26/2018] [Indexed: 06/03/2023]
Abstract
1,8-Naphthalenediol (dihydroxynaphthalene, 1,8-DHN) has been shown to be a potent hydrogen atom transfer (HAT) antioxidant compound because of the strong stabilization of the resulting free radical by intramolecular hydrogen bonding. However, the properties, reactivity, and fate of the 1,8-DHN phenoxyl radical have remained so far uncharted. Herein, we report an integrated experimental and computational characterization of the early intermediates and dimer products that arise by the oxidation of 1,8-DHN. Laser flash photolysis (LFP) studies of HAT from 1,8-DHN to the cumyloxyl and aminoxyl radicals showed the generation of a transient species absorbing at 350, 400, and >600 nm attributable to the 1,8-DHN phenoxyl radical. Peroxidase/H2O2 oxidation of 1,8-DHN was found to proceed via an intense blue intermediate (λmax 654 nm) preceding precipitation of a black melanin-like polymer. By halting the reaction in the early stages, three main dimers featuring 2,2'-, 2,4'-, and 4,4'-bondings could be isolated and characterized in pure form. Density functional theory calculations supported the generation of the 1,8-DHN phenoxyl radical and its subsequent coupling via the 2- and 4-positions giving extended quinone dimers with intense transitions in the visible range, consistent with UV-vis and LFP data. Overall, these results allowed to elucidate the mechanism of oxidative polymerization of 1,8-DHN of possible relevance to melanogenesis in fungi and other processes of environmental and astrochemical relevance.
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Affiliation(s)
- Paola Manini
- Dipartimento
di Scienze Chimiche, Università di
Napoli Federico II, Via
Cintia 4, I-80126 Napoli, Italy
| | - Massimo Bietti
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Marco Galeotti
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Michela Salamone
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Osvaldo Lanzalunga
- Dipartimento
di Chimica e Istituto CNR di Metodologie Chimiche (IMC-CNR), Sezione
Meccanismi di Reazione, Università
di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Roma, Italy
| | - Martina M. Cecchini
- Dipartimento
di Scienze Fisiche e Chimiche, Università
dell’Aquila, Via
Vetoio, L’Aquila I-67100, Coppito, Italy
| | - Samantha Reale
- Dipartimento
di Scienze Fisiche e Chimiche, Università
dell’Aquila, Via
Vetoio, L’Aquila I-67100, Coppito, Italy
| | - Orlando Crescenzi
- Dipartimento
di Scienze Chimiche, Università di
Napoli Federico II, Via
Cintia 4, I-80126 Napoli, Italy
| | - Alessandra Napolitano
- Dipartimento
di Scienze Chimiche, Università di
Napoli Federico II, Via
Cintia 4, I-80126 Napoli, Italy
| | - Francesco De Angelis
- Dipartimento
di Scienze Fisiche e Chimiche, Università
dell’Aquila, Via
Vetoio, L’Aquila I-67100, Coppito, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Marco d’Ischia
- Dipartimento
di Scienze Chimiche, Università di
Napoli Federico II, Via
Cintia 4, I-80126 Napoli, Italy
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129
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Abstract
The aim of this short communication is to present an extremely uncommon case of penile metastases from rectal adenocarcinoma treated with an external beam radiotherapy technique. A 76-year-old man affected by very painful priapism from penile metastases was treated with radiotherapy (30 Gy) for symptom relief. In the course of the radiotherapy treatment the patient reported gradual and continuous pain reduction. One month after the end of radiotherapy both the priapism and the pain had disappeared. Although the long-term prognosis remains poor, good quality of life was achieved in this patient.
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Affiliation(s)
- Vincenzo Barone
- Department of Oncological Radiotherapy, Azienda Ospedaliera per l'Emergenza di II Livello, Ospedali Civile e Maria Paternò Arezzo, Ragusa, Italy.
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130
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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131
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Abstract
The prediction and interpretation of structural properties are the starting points for a deep understanding of thermochemistry, kinetics, and spectroscopic signatures of molecular systems. To give an example, detailed knowledge of the conformational behavior of the main building blocks of biomolecules in the gas phase (i.e., without the perturbing effect of the environment) is a mandatory prerequisite toward the understanding of the role played by different interactions in determining the biological activity in terms of structure-activity relationships. The first step to take is an unambiguous definition of molecular structure. We address the so-called Born-Oppenheimer equilibrium structure, which is defined in a rigorous manner and isotopically independent, and the target accuracy. For the latter, we aim at so-called "spectroscopic" accuracy, which implies uncertainties of a few milliangstroms for bond lengths and smaller than a tenth of degree for angles. If on one side the continuous enhancements of the experimental techniques give access to new and unprecedented spectroscopic determinations, on the other side they require increasing efforts for an unbiased interpretation and analysis. Among the pieces of information, accurate molecular structures play a particularly important role. Indeed, there is a strong relationship between the experimental outcome and the electronic structure of the system. Spectroscopic techniques, in particular those exploited in the gas phase, are therefore accurate and reliable sources for structural information. However, it is seldom straightforward to derive molecular structures directly from the experimental information. Indeed, even in the favorable case of investigations in the gas phase, vibrational effects are always present, and disentangling their contributions requires collection of information for all vibrational modes, a nearly impossible task. To overcome these limitations, joint theory-spectroscopy strategies can be identified, which are referred to as "top-down" and "bottom-up". The first approach, denoted as the semiexperimental approach, relies on extracting from experimental outcomes the equilibrium structure by using quantum-chemical computations to recover vibrational effects. The bottom-up approach consists in verifying the computed equilibrium geometry by means of a comparison between calculated and experimental spectroscopic parameters that probe structural characteristics. In this contribution, we try to review the most important challenges in accurate molecular structure determinations, with particular emphasis on the "solution" provided by a joint theoretical-experimental approach and on the current state of the art. Starting from the illustration of different strategies, we proceed by addressing the increasing complexity in the derivation of equilibrium geometries: we start from the construction of a database of accurate structures, we then face the problem of extending the dimension of the systems amenable to accurate structural determinations, and finally we move to the challenge of understanding the nature of intermolecular interactions.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di
Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei
Cavalieri 7, I-56126 Pisa, Italy
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132
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Grubišić S, Chandramouli B, Barone V, Brancato G. Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides. Phys Chem Chem Phys 2018; 18:20389-98. [PMID: 27402118 DOI: 10.1039/c6cp01120a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 310- and/or α-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i → i + 3 and i → i + 4 hydrogen bonds characterizing 310 and α-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides.
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Affiliation(s)
- Sonja Grubišić
- Center for Chemistry, IHTM, University of Belgrade, Njegoševa 12, P.O. Box 815, 11001 Belgrade, Serbia.
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
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133
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Macchiagodena M, Del Frate G, Brancato G, Chandramouli B, Mancini G, Barone V. Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations. Phys Chem Chem Phys 2018; 19:30590-30602. [PMID: 29115317 DOI: 10.1039/c7cp04688j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fluorescent molecular rotors (FMRs) belong to an important class of environment-sensitive dyes capable of acting as nanoprobes in the measurement of viscosity and polarity of their micro-environment. FMRs have found widespread applications in various research fields, ranging from analytical to biochemical sciences, for example in intracellular imaging studies or in volatile organic compound detection. Here, a computational investigation of a recently proposed FMR, namely 4-(diphenylamino)phthalonitrile (DPAP), in various chemical environments is presented. A purposely developed molecular mechanics force field is proposed and then applied to simulate the rotor in a high- and low-polar solvent (i.e., acetonitrile, tetrahydrofuran, o-xylene and cyclohexane), a polymer matrix and a lipid membrane. Subtle effects of the molecular interactions with the embedding medium, the structural fluctuations of the rotor and its rotational dynamics are analyzed in some detail. The results correlate with a previous work, thus supporting the reliability of the model, and provide further insights into the environment-specific properties of the dye. In particular, it is shown how molecular diffusion and rotational correlation times of the FMR are affected by the surrounding medium and how the molecular orientation of the dye becomes anisotropic once immersed in the lipid bilayer. Moreover, a qualitative correlation between the FMR rotational dynamics and the fluorescence lifetime is detected, a result in line with the observed viscosity dependence of its emission. Finally, optical absorption spectra are computed and successfully compared with their experimental counterparts.
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134
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Schiavo E, Muñoz-García AB, Barone V, Vittadini A, Casarin M, Forrer D, Pavone M. Tuning dispersion correction in DFT-D2 for metal-molecule interactions: A tailored reparameterization strategy for the adsorption of aromatic systems on Ag(1 1 1). Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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135
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Macchiagodena M, Mancini G, Pagliai M, Barone V. Accurate prediction of bulk properties in hydrogen bonded liquids: amides as case studies. Phys Chem Chem Phys 2018; 18:25342-25354. [PMID: 27711662 DOI: 10.1039/c6cp04666e] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In this contribution we show that it is possible to build accurate force fields for small organic molecules allowing the reliable reproduction of a large panel of bulk properties, which are seldom addressed in the same context. Starting from the results obtained in recent studies, we developed a protocol for charge estimation and virtual site generation for the amide class of molecules. The parametrization of electrostatic properties is based on population analysis and orbital localization of quantum mechanical computations rooted in density functional theory and the polarizable continuum model, without any additional external information. The new protocol, coupled to other recent studies in our group targeted at an accurate fitting of internal degrees of freedom, makes available a method for building force fields from scratch (excluding for the moment intermolecular van der Waals interactions) with focus on reproducing the structure and dynamics of hydrogen bonded liquids, yielding results that are in line or better than those delivered by current general force fields. The approach is tested on the demanding series formed by formamide and its two N-methyl derivatives, N-methylformamide and N,N-dimethylformamide. We show that the atomistic structure of the liquids arising from classical molecular dynamics (MD) simulations employing the new force field is in full agreement with X-ray and neutron diffraction experiments and the corresponding spatial distribution functions are in remarkable agreement with the results of ab initio MD simulations. It is noteworthy that the latter result has never been obtained before without using ad hoc (and system dependent) scale factors and that, in addition, our parameter-free procedure is able to reproduce static dielectric constants over a wide range of values without sacrificing the force field accuracy with respect to other observables. Finally, we are able to explain the trend of static dielectric constants followed by the three amides in terms of properties obtained from the simulations, namely hydrogen bond patterns and reorientational lifetimes.
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Affiliation(s)
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy. and Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Marco Pagliai
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy. and Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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136
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Licari D, Fusè M, Salvadori A, Tasinato N, Mendolicchio M, Mancini G, Barone V. Towards the SMART workflow system for computational spectroscopy. Phys Chem Chem Phys 2018; 20:26034-26052. [DOI: 10.1039/c8cp03417f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Is it possible to convert highly specialized research in the field of computational spectroscopy into robust and user-friendly aids to experiments and industrial applications?
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Affiliation(s)
- Daniele Licari
- Scuola Normale Superiore
- 56126 Pisa
- Italy
- Istituto Italiano di Tecnologia
- 16163 Genova
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137
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Melosso M, Melli A, Puzzarini C, Codella C, Spada L, Dore L, Degli Esposti C, Lefloch B, Bachiller R, Ceccarelli C, Cernicharo J, Barone V. Laboratory measurements and astronomical search for cyanomethanimine. Astron Astrophys 2018; 609:A121. [PMID: 30078846 PMCID: PMC6071866 DOI: 10.1051/0004-6361/201731972] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
CONTEXT C-cyanomethanimine (HNCHCN), existing in the two Z and E isomeric forms, is a key prebiotic molecule, but, so far, only the E isomer has been detected toward the massive star-forming region. Sagittarius B2(N) using transitions in the radio wavelength domain. AIMS With the aim of detecting HNCHCN in Sun-like-star forming regions, the laboratory investigation of its rotational spectrum has been extended to the millimeter-/submillimeter-wave (mm-/submm-) spectral window in which several unbiased spectral surveys have been already carried out. METHODS High-resolution laboratory measurements of the rotational spectrum of C-cyanomethanimine were carried out in the 100-420 GHz range using a frequency-modulation absorption spectrometer. We then searched for the C-cyanomethanimine spectral features in the mm-wave range using the high-sensitivity and unbiased spectral surveys obtained with the IRAM 30-m antenna in the ASAI context, the earliest stages of star formation from starless to evolved Class I objects being sampled. RESULTS For both the Z and E isomers, the spectroscopic work has led to an improved and extended knowledge of the spectroscopic parameters, thus providing accurate predictions of the rotational signatures up to ~700 GHz. So far, no C-cyanomethanimine emission has been detected toward the ASAI targets, and upper limits of the column density of ~ 1011-1012 cm-2 could only be derived. Consequently, the C-cyanomethanimine abundances have to be less than a few 10-10 for starless and hot-corinos. A less stringent constraint, ≤ 10-9, is obtained for shocks sites. CONCLUSIONS The combination of the upper limits of the abundances of C-cyanomethanimine together with accurate laboratory frequencies up to ~ 700 GHz poses the basis for future higher sensitivity searches around Sun-like-star forming regions. For compact (typically less than 1″) and chemically enriched sources such as hot-corinos, the use of interferometers as NOEMA and ALMA in their extended configurations are clearly needed.
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Affiliation(s)
- M. Melosso
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - A. Melli
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - C. Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
- INAF, Osservatorio Astonomico di Arcetri, Largo E. Fermi 5, 50125, Firenze, Italy
| | - C. Codella
- INAF, Osservatorio Astonomico di Arcetri, Largo E. Fermi 5, 50125, Firenze, Italy
| | - L. Spada
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - L. Dore
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - C. Degli Esposti
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - B. Lefloch
- Univ. Grenoble Alpes, CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), 38000 Grenoble, France
| | - R. Bachiller
- IGN, Observatorio Astronómico Nacional, Calle Alfonso XII, 28004 Madrid, Spain
| | - C. Ceccarelli
- INAF, Osservatorio Astonomico di Arcetri, Largo E. Fermi 5, 50125, Firenze, Italy
- Univ. Grenoble Alpes, CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), 38000 Grenoble, France
| | - J. Cernicharo
- Grupo de Astrofísica Molecular. Instituto de CC. de Materiales de Madrid (ICMM-CSIC). Sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, Spain
| | - V. Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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138
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Fusè M, Rimoldi I, Facchetti G, Rampino S, Barone V. Exploiting coordination geometry to selectively predict the σ-donor and π-acceptor abilities of ligands: a back-and-forth journey between electronic properties and spectroscopy. Chem Commun (Camb) 2018; 54:2397-2400. [DOI: 10.1039/c7cc09627e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coordination geometry switches the carbonyl stretching frequency into a selective probe of the σ-donor and π-acceptor abilities of ligands.
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Affiliation(s)
| | - Isabella Rimoldi
- Dipartimento di Scienze Farmaceutiche
- Università di Milano
- 20133 Milano
- Italy
| | - Giorgio Facchetti
- Dipartimento di Scienze Farmaceutiche
- Università di Milano
- 20133 Milano
- Italy
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139
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Cimino P, Troiani A, Pepi F, Garzoli S, Salvitti C, Di Rienzo B, Barone V, Ricci A. From ascorbic acid to furan derivatives: the gas phase acid catalyzed degradation of vitamin C. Phys Chem Chem Phys 2018; 20:17132-17140. [DOI: 10.1039/c8cp01893f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Furan derivatives, potentially carcinogenic to humans, can be formed, in addition to carbohydrates and other sources, from the degradation of ascorbic acid (AA).
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Affiliation(s)
- Paola Cimino
- Department of Pharmaceutical Science
- University of Salerno
- Via Giovanni Paolo II
- Fisciano (SA)
- Italy
| | - Anna Troiani
- Department of Chemistry and Drug Technologies
- ‘Sapienza’ University of Rome
- Rome 00185
- Italy
| | - Federico Pepi
- Department of Chemistry and Drug Technologies
- ‘Sapienza’ University of Rome
- Rome 00185
- Italy
| | - Stefania Garzoli
- Department of Chemistry and Drug Technologies
- ‘Sapienza’ University of Rome
- Rome 00185
- Italy
| | - Chiara Salvitti
- Department of Chemistry and Drug Technologies
- ‘Sapienza’ University of Rome
- Rome 00185
- Italy
| | - Brunella Di Rienzo
- Department of Math and Phys
- Campania University
- L. Vanvitelli, yet second University of Naples
- Caserta 81100
- Italy
| | | | - Andreina Ricci
- Department of Math and Phys
- Campania University
- L. Vanvitelli, yet second University of Naples
- Caserta 81100
- Italy
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140
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Barone V, Cacelli I, Ferretti A. The role of the multiconfigurational character of nitronyl-nitroxide in the singlet–triplet energy gap of its diradicals. Phys Chem Chem Phys 2018; 20:18547-18555. [DOI: 10.1039/c8cp02165a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
CAS(2,2) reference may not be sufficient for the computation of singlet–triplet energy gap by DDCI.
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Affiliation(s)
| | - Ivo Cacelli
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- Pisa
- Italy
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)
| | - Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)
- Area della Ricerca
- I-56124 Pisa
- Italy
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141
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Piserchia A, Banerjee S, Barone V. General Approach to Coupled Reactive Smoluchowski Equations: Integration and Application of Discrete Variable Representation and Generalized Coordinate Methods to Diffusive Problems. J Chem Theory Comput 2017; 13:5900-5910. [PMID: 29091430 DOI: 10.1021/acs.jctc.7b00685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A new and more general approach to diffusion problems with the inclusion of reactivity among different coupled diffusional states is rationalized and presented. The integration of our previous developments in such a field [Phys. Chem. Chem. Phys., 2015, 17, 17362-17374; J. Chem. Theory Comput., 2016, 12, 3482-3490] are implemented in a software package tool allowing the generic user to set up and run diffusional calculations with very low efforts. We show the applicability of the whole framework to a generic diffusional case of chemical interest that is the study case of (N,N-dimethylamino)benzonitrile (DMABN) fluorescence, whose excited state undergoes twisted intramolecular charge transfer (TICT) relaxation. The population dynamics of the excited state coupled to the ground state is followed, and a fluorescence decay spectrum is calculated. The theoretical and numerical background here presented is robust and general enough to complement a wide number of diffusional problems of current interest.
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Affiliation(s)
- Andrea Piserchia
- 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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142
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Abstract
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A novel
statistical procedure has been developed to optimize the parameters
of nonbonded force fields of metal ions in soft matter. The criterion
for the optimization is the minimization of the deviations from ab initio forces and energies calculated for model systems.
The method exploits the combination of the linear ridge regression
and the cross-validation techniques with the differential evolution
algorithm. Wide freedom in the choice of the functional form of the
force fields is allowed since both linear and nonlinear parameters
can be optimized. In order to maximize the information content of
the data employed in the fitting procedure, the composition of the
training set is entrusted to a combinatorial optimization algorithm
which maximizes the dissimilarity of the included instances. The methodology
has been validated using the force field parametrization of five metal
ions (Zn2+, Ni2+, Mg2+, Ca2+, and Na+) in water as test cases.
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Affiliation(s)
| | | | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa , Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - Walter Rocchia
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , 16163 Genova, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa , Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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143
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Latouche C, Liao JH, Li YJ, Shiu RY, Barone V, Kahlal S, Liu CW, Saillard JY. Encapsulating Iodine and Copper into Copper(I) Clusters Stabilized by Dichalcogenolate Ligands: Stability, Structure, and Optical Properties. Inorg Chem 2017; 56:14135-14146. [DOI: 10.1021/acs.inorgchem.7b02269] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Camille Latouche
- Institut des Matériaux
Jean Rouxel, Université de Nantes, CNRS, 2 rue de la Houssinière,
BP 32229, 44322 Nantes cedex 3, France
| | - Jian-Hong Liao
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Road, Shoufeng, Hualien 97401, Taiwan, Republic of China
| | - Yi-Juan Li
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Road, Shoufeng, Hualien 97401, Taiwan, Republic of China
| | - Ruei-Yi Shiu
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Road, Shoufeng, Hualien 97401, Taiwan, Republic of China
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Samia Kahlal
- Institut des Sciences Chimiques de Rennes, UMR CNRS 6226, Campus
de Beaulieu, 263 av. Général Leclerc, 35042 Rennes, France
| | - C. W. Liu
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Road, Shoufeng, Hualien 97401, Taiwan, Republic of China
| | - Jean-Yves Saillard
- Institut des Sciences Chimiques de Rennes, UMR CNRS 6226, Campus
de Beaulieu, 263 av. Général Leclerc, 35042 Rennes, France
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144
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Tasinato N, Puzzarini C, Barone V. Correct Modeling of Cisplatin: a Paradigmatic Case. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicola Tasinato
- Scuola Normale Superiore; Piazza dei Cavalieri, 7 56126 Pisa Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”; Università di Bologna; Italy
| | - Vincenzo Barone
- Scuola Normale Superiore; Piazza dei Cavalieri, 7 56126 Pisa Italy
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Carrillo-Parramon O, Del Galdo S, Aschi M, Mancini G, Amadei A, Barone V. Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code. J Chem Theory Comput 2017; 13:5506-5514. [DOI: 10.1021/acs.jctc.7b00341] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
| | - Massimiliano Aschi
- Dipartimento
di Scienze Fisiche e Chimiche, Universitá di L’Aquila, Via
Vetoio s.n.c.67100, L’Aquila, 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, 56127 Pisa, Italy
| | - Andrea Amadei
- Dipartimento
di Scienze e Tecnologie Chimiche, Universitá di Roma ’Tor Vergata’, Via Della Ricerca Scientifica, 00100 Roma, 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, 56127 Pisa, Italy
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146
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Abstract
Quantum chemistry is a useful tool in modern approaches to drug and material design, but only when the adopted model reflects a correct physical picture. Paradigmatic is the case of cis‐diaminodichloroplatinum(II), cis‐[Pt(NH3)2Cl2], for which the correct simulation of the structural and vibrational properties measured experimentally still remains an open question. By using this molecule as a proof of concept, it is shown that state‐of‐the‐art quantum chemical calculations and a simple model, capturing the basic physical flavors, a cis‐[Pt(NH3)2Cl2] dimer, can provide the accuracy required for interpretative purposes. The present outcomes have fundamental implications for benchmark studies aiming at assessing the accuracy of a given computational protocol.
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Affiliation(s)
- Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, 56126, Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, 56126, Pisa, Italy
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147
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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148
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Licari D, Tasinato N, Spada L, Puzzarini C, Barone V. VMS-ROT: A New Module of the Virtual Multifrequency Spectrometer for Simulation, Interpretation, and Fitting of Rotational Spectra. J Chem Theory Comput 2017; 13:4382-4396. [PMID: 28742339 PMCID: PMC5636176 DOI: 10.1021/acs.jctc.7b00533] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Virtual Multifrequency Spectrometer (VMS) is a tool that aims at integrating a wide range of computational and experimental spectroscopic techniques with the final goal of disclosing the static and dynamic physical-chemical properties "hidden" in molecular spectra. VMS is composed of two parts, namely, VMS-Comp, which provides access to the latest developments in the field of computational spectroscopy, and VMS-Draw, which provides a powerful graphical user interface (GUI) for an intuitive interpretation of theoretical outcomes and a direct comparison to experiment. In the present work, we introduce VMS-ROT, a new module of VMS that has been specifically designed to deal with rotational spectroscopy. This module offers an integrated environment for the analysis of rotational spectra: from the assignment of spectral transitions to the refinement of spectroscopic parameters and the simulation of the spectrum. While bridging theoretical and experimental rotational spectroscopy, VMS-ROT is strongly integrated with quantum-chemical calculations, and it is composed of four independent, yet interacting units: (1) the computational engine for the calculation of the spectroscopic parameters that are employed as a starting point for guiding experiments and for the spectral interpretation, (2) the fitting-prediction engine for the refinement of the molecular parameters on the basis of the assigned transitions and the prediction of the rotational spectrum of the target molecule, (3) the GUI module that offers a powerful set of tools for a vis-à-vis comparison between experimental and simulated spectra, and (4) the new assignment tool for the assignment of experimental transitions in terms of quantum numbers upon comparison with the simulated ones. The implementation and the main features of VMS-ROT are presented, and the software is validated by means of selected test cases ranging from isolated molecules of different sizes to molecular complexes. VMS-ROT therefore offers an integrated environment for the analysis of the rotational spectra, with the innovative perspective of an intimate connection to quantum-chemical calculations that can be exploited at different levels of refinement, as an invaluable support and complement for experimental studies.
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Affiliation(s)
- Daniele Licari
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Lorenzo Spada
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna , Via Selmi 2, I-40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna , Via Selmi 2, I-40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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149
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Affiliation(s)
- Alberto Baiardi
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Christopher J. Stein
- Laboratorium
für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Vincenzo Barone
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Markus Reiher
- Laboratorium
für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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150
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Banerjee S, Skouteris D, Barone V. A diabatic electronic state system to describe the internal conversion of azulene. Comput Sci Appl 2017; 10408:328-337. [PMID: 31032486 PMCID: PMC6485616 DOI: 10.1007/978-3-319-62404-4_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A diabatic system of two electronic potential energy surfaces as well as the coupling between them is presented. The system is to be used to study the dynamics of the S1 → S0 internal conversion of azulene and is based on single point calculations of the minima of the two surfaces and a dipole-quadrupole (DQ) diabatization. Based on this, a couple of harmonic diabatic surfaces together with a linear coupling surface have been devised. Some preliminary dynamics results are shown.
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