1
|
Headen TF, Di Mino C, Youngs TG, Clancy AJ. The structure of liquid thiophene from total neutron scattering. Phys Chem Chem Phys 2023; 25:25157-25165. [PMID: 37712384 DOI: 10.1039/d3cp03932c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
The structure of pure liquid thiophene is revealed by using a combination of total neutron scattering experiments with isotopic substitution and molecular simulations via the next generation empirical potential refinement software, Dissolve. In the liquid, thiophene presents three principle local structural motifs within the first solvation shell, in plane and out of the plane of the thiophene ring. Firstly, above/below the ring plane thiophenes present a single H towards the π cloud, due to a combination of electrostatic and dispersion interactions. Secondly, around the ring plane, perpendicular thiophene molecules find 5 preferred sites driven by bifurcated C-H⋯S interactions, showing that hydrogen-sulfur bonding prevails over the charge asymmetry created by the heteroatom. Finally, parallel thiophenes sit above and below the ring, excluded from directly above the ring center and above the sulfur.
Collapse
Affiliation(s)
- Thomas F Headen
- ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK.
| | - Camilla Di Mino
- Department of Materials, University of Oxford, 21 Banbury Rd, Oxford, OX2 6NN, UK
- Department of Physics & Astronomy, University College London, Gower St, London WC1E 6BT, UK
| | - Tristan Ga Youngs
- ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK.
| | - Adam J Clancy
- Department of Chemistry, University College London, 20 Gordon St, London, WC1H 0AJ, UK.
| |
Collapse
|
5
|
Greff da Silveira L, Jacobs M, Prampolini G, Livotto PR, Cacelli I. Development and Validation of Quantum Mechanically Derived Force-Fields: Thermodynamic, Structural, and Vibrational Properties of Aromatic Heterocycles. J Chem Theory Comput 2018; 14:4884-4900. [PMID: 30040902 DOI: 10.1021/acs.jctc.8b00218] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A selection of several aromatic molecules, representative of the important class of heterocyclic compounds, has been considered for testing and validating an automated Force Field (FF) parametrization protocol, based only on Quantum Mechanical data. The parametrization is carried out separately for the intra- and intermolecular contributions, employing respectively the Joyce and Picky software packages, previously implemented and refined in our research group. The whole approach is here automated and integrated with a computationally effective yet accurate method, devised very recently ( J. Chem. THEORY Comput., 2018, 14, 543-556) to evaluate a large number of dimer interaction energies. The resulting quantum mechanically derived FFs are then used in extensive molecular dynamics simulations, in order to evaluate a number of thermodynamic, structural, and dynamic properties of the heterocycle's gas and liquid phases. The comparison with the available experimental data is good and furnishes a validation of the presented approach, which can be confidently exploited for the design of novel and more complex materials.
Collapse
Affiliation(s)
- Leandro Greff da Silveira
- Instituto de Química , Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves 9500 , CEP 91501-970 Porto , Alegre , Brazil
| | - Matheus Jacobs
- Instituto de Química , Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves 9500 , CEP 91501-970 Porto , Alegre , Brazil.,Institut für Physik , Humboldt-Universität zu Berlin , Newtonstrasse 15 , 12489 , Berlin , Germany.,IRIS Adelrshof , Humboldt-Universität zu Berlin , Zum Großen Windkanal 6 , 12489 , Berlin , Germany
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy
| | - Paolo Roberto Livotto
- Instituto de Química , Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves 9500 , CEP 91501-970 Porto , Alegre , Brazil
| | - Ivo Cacelli
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy.,Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , I-56124 Pisa , Italy
| |
Collapse
|
7
|
Cacelli I, Prampolini G. Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations. J Chem Theory Comput 2015; 3:1803-17. [PMID: 26627623 DOI: 10.1021/ct700113h] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The energy and its first and second geometrical derivatives obtained by DFT calculations for a number of conformations of a single molecule are used to parametrize intramolecular force fields, suitable for computer simulations. A systematic procedure is proposed to adequately treat either fully atomistic or more simplified force fields, as within the united atom approach or other coarse grained models. The proposed method is tested and validated by performing molecular dynamics simulations on several different molecules, comparing the results with literature force fields and relevant experimental data. Particular emphasis is given to the united atom approach for flexible molecules characterized by "soft" torsional potentials which are known to retain a high degree of chemical specificity.
Collapse
Affiliation(s)
- Ivo Cacelli
- Dipartimento di Chimica e Chimica Industriale, Universita di Pisa, via Risorgimento 35, I-56126 Pisa, Italy
| | - Giacomo Prampolini
- Dipartimento di Chimica e Chimica Industriale, Universita di Pisa, via Risorgimento 35, I-56126 Pisa, Italy
| |
Collapse
|
8
|
Barone V, Cacelli I, De Mitri N, Licari D, Monti S, Prampolini G. Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data. Phys Chem Chem Phys 2013; 15:3736-51. [PMID: 23389748 DOI: 10.1039/c3cp44179b] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.
Collapse
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | | | | | | | | |
Collapse
|
10
|
Gontrani L, Russina O, Lo Celso F, Caminiti R, Annat G, Triolo A. Liquid Structure of Trihexyltetradecylphosphonium Chloride at Ambient Temperature: An X-ray Scattering and Simulation Study. J Phys Chem B 2009; 113:9235-40. [DOI: 10.1021/jp808333a] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lorenzo Gontrani
- Dipartimento di Chimica, Università degli Studi di Cagliari, Cittadella universitaria di Monserrato 09042 Monserrato, CA, Italy, Dipartimento di Chimica, Università di Roma “Sapienza”, P. le A. Moro, 5—00185 Roma, Italy, Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Salita Sperone, C. da Papardo, 98158 Faro Superiore, Messina, Italy, Dipartimento di Chimica-Fisica, Università di Palermo, Italy, School of Chemistry, Monash University, Australia, and Helmholtz Zentrum Berlin
| | - Olga Russina
- Dipartimento di Chimica, Università degli Studi di Cagliari, Cittadella universitaria di Monserrato 09042 Monserrato, CA, Italy, Dipartimento di Chimica, Università di Roma “Sapienza”, P. le A. Moro, 5—00185 Roma, Italy, Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Salita Sperone, C. da Papardo, 98158 Faro Superiore, Messina, Italy, Dipartimento di Chimica-Fisica, Università di Palermo, Italy, School of Chemistry, Monash University, Australia, and Helmholtz Zentrum Berlin
| | - Fabrizio Lo Celso
- Dipartimento di Chimica, Università degli Studi di Cagliari, Cittadella universitaria di Monserrato 09042 Monserrato, CA, Italy, Dipartimento di Chimica, Università di Roma “Sapienza”, P. le A. Moro, 5—00185 Roma, Italy, Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Salita Sperone, C. da Papardo, 98158 Faro Superiore, Messina, Italy, Dipartimento di Chimica-Fisica, Università di Palermo, Italy, School of Chemistry, Monash University, Australia, and Helmholtz Zentrum Berlin
| | - Ruggero Caminiti
- Dipartimento di Chimica, Università degli Studi di Cagliari, Cittadella universitaria di Monserrato 09042 Monserrato, CA, Italy, Dipartimento di Chimica, Università di Roma “Sapienza”, P. le A. Moro, 5—00185 Roma, Italy, Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Salita Sperone, C. da Papardo, 98158 Faro Superiore, Messina, Italy, Dipartimento di Chimica-Fisica, Università di Palermo, Italy, School of Chemistry, Monash University, Australia, and Helmholtz Zentrum Berlin
| | - Gary Annat
- Dipartimento di Chimica, Università degli Studi di Cagliari, Cittadella universitaria di Monserrato 09042 Monserrato, CA, Italy, Dipartimento di Chimica, Università di Roma “Sapienza”, P. le A. Moro, 5—00185 Roma, Italy, Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Salita Sperone, C. da Papardo, 98158 Faro Superiore, Messina, Italy, Dipartimento di Chimica-Fisica, Università di Palermo, Italy, School of Chemistry, Monash University, Australia, and Helmholtz Zentrum Berlin
| | - Alessandro Triolo
- Dipartimento di Chimica, Università degli Studi di Cagliari, Cittadella universitaria di Monserrato 09042 Monserrato, CA, Italy, Dipartimento di Chimica, Università di Roma “Sapienza”, P. le A. Moro, 5—00185 Roma, Italy, Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Salita Sperone, C. da Papardo, 98158 Faro Superiore, Messina, Italy, Dipartimento di Chimica-Fisica, Università di Palermo, Italy, School of Chemistry, Monash University, Australia, and Helmholtz Zentrum Berlin
| |
Collapse
|