publication . Other literature type . Article . Preprint . 2019

fromage: A library for the study of molecular crystal excited states at the aggregate scale

Rivera, Miguel; Dommett, Michael; Sidat, Amir; Rahim, Warda; Crespo‐Otero, Rachel;
Open Access English
  • Published: 10 Sep 2019
Abstract
Abstract The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in‐house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we prese...
Subjects
free text keywords: Computational Chemistry and Modeling, Theory - Computational, excited states, dimers, molecular crystals, electrostatic embedding, ONIOM, Software News and Updates, molecular aggregate, photochemistry, Python library, General Chemistry, Computational Mathematics, Exciton, Chemistry, Excited state, Computational chemistry, Chemical physics
Funded by
RCUK| MATERIALS CHEMISTRY HIGH END COMPUTING CONSORTIUM
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: EP/L000202/1
  • Funding stream: EPSRC
,
RCUK| Towards the Computational Design of Highly Emissive Organic-Single Crystals
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: EP/R029385/1
  • Funding stream: EPSRC
,
RCUK| Tier 2 Hub in Materials and Molecular Modelling
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: EP/P020194/1
  • Funding stream: EPSRC
68 references, page 1 of 5

1 J.Aragó, A.Troisi, Phys. Rev. Lett.2015, 114, 026402.25635554 [PubMed]

2 R.Dovesi, A.Erba, R.Orlando, C. M.Zicovich‐Wilson, B.Civalleri, L.Maschio, M.Rérat, S.Casassa, J.Baima, S.Salustro, B.Kirtman, Wiley Interdiscip. Rev. Comput. Mol. Sci.2018, 8, e1360.

3 C. R.Groom, I. J.Bruno, M. P.Lightfoot, S. C.Ward, Acta Crystallogr. Sect. B 2016, 72, 171.

4 A.Hjorth Larsen, J.Jørgen Mortensen, J.Blomqvist, I. E.Castelli, R.Christensen, M.Du lak, J.Friis, M. N.Groves, B.Hammer, C.Hargus, E. D.Hermes, P. C.Jennings, P.Bjerre Jensen, J.Kermode, J. R.Kitchin, E.Leonhard Kolsbjerg, J.Kubal, K.Kaasbjerg, S.Lysgaard, J.Bergmann Maronsson, T.Maxson, T.Olsen, L.Pastewka, A.Peterson, C.Rostgaard, J.Schiøtz, O.Schütt, M.Strange, K. S.Thygesen, T.Vegge, L.Vilhelmsen, M.Walter, Z.Zeng, K. W.Jacobsen, J. Phys. Condens. Matter 2017, 273002, 29.

5 RDKit : Open‐Source Cheminformatics, http://www.rdkit.org (accessed 1st of January 2020).

6 Y.Lu, M. R.Farrow, P.Fayon, A. J.Logsdail, A. A.Sokol, C. R. A.Catlow, P.Sherwood, T. W.Keal, J. Chem. Theory Comput.2019, 15, 1317.30511845 [PubMed]

7 A. V.Akimov, J. Comput. Chem.2016, 37, 1626.27016373 [PubMed]

8 B.Aradi, B.Hourahine, T.Frauenheim, J. Phys. Chem. A 2007, 111, 5678.17567110 [PubMed]

9 M. J.Frisch, G. W.Trucks, H. B.Schlegel, G. E.Scuseria, M. A.Robb, J. R.Cheeseman, G.Scalmani, V.Barone, G. A.Petersson, H.Nakatsuji, X.Li, M.Caricato, A. V.Marenich, J.Bloino, B. G.Janesko, R.Gomperts, B.Mennucci, H. P.Hratchian, J. V.Ortiz, A. F.Izmaylov, J. L.Sonnenberg, D.Williams‐Young, F.Ding, F.Lipparini, F.Egidi, J.Goings, B.Peng, A.Petrone, T.Henderson, D.Ranasinghe, V. G.Zakrzewski, J.Gao, N.Rega, G.Zheng, W.Liang, M.Hada, M.Ehara, K.Toyota, R.Fukuda, J.Hasegawa, M.Ishida, T.Nakajima, Y.Honda, O.Kitao, H.Nakai, T.Vreven, K.Throssell, J. A.Montgomery Jr., J. E.Peralta, F.Ogliaro, M. J.Bearpark, J. J.Heyd, E. N.Brothers, K. N.Kudin, V. N.Staroverov, T. A.Keith, R.Kobayashi, J.Normand, K.Raghavachari, A. P.Rendell, J. C.Burant, S. S.Iyengar, J.Tomasi, M.Cossi, J. M.Millam, M.Klene, C.Adamo, R.Cammi, J. W.Ochterski, R. L.Martin, K.Morokuma, O.Farkas, J. B.Foresman, D. J.Fox, Gaussian 16 Revision B.01, Gaussian Inc., Wallingford, CT 2016.

10 F.Aquilante, J.Autschbach, R. K.Carlson, L. F.Chibotaru, M. G.Delcey, L.De Vico, I. F.Galván, N.Ferré, L. M.Frutos, L.Gagliardi, M.Garavelli, A.Giussani, C. E.Hoyer, G. L.Manni, H.Lischka, D.Ma, P. Å.Malmqvist, T.Müller, A.Nenov, M.Olivucci, T. B.Pedersen, D.Peng, F.Plasser, B.Pritchard, M.Reiher, I.Rivalta, I.Schapiro, J.Segarra‐Mart'ı, M.Stenrup, D. G.Truhlar, L.Ungur, A.Valentini, S.Vancoillie, V.Veryazov, V. P.Vysotskiy, O.Weingart, F.Zapata, R.Lindh, J. Comput. Chem.2016, 37, 506.26561362 [OpenAIRE] [PubMed]

11 TURBOMOLE V6.2 2010, A Development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989–2007, TURBOMOLE GmbH, Since 2007. http://www.turbomole.com (accessed 1st of January 2020).

12 M.Rivera, M.Dommett, R.Crespo‐Otero, J.Chem, Theory Comput.2019, 15, 2504.

13 L.Stojanović, R.Crespo‐Otero, ChemPhotoChem 2019, 3, 907 10.1002/cptc.201900075 [OpenAIRE] [DOI]

14 M.Dommett, M.Rivera, M. T. H.Smith, R.Crespo‐Otero, Chemrxiv 2019 10.26434/chemrxiv.8283710.v1 [OpenAIRE] [DOI]

15 T.Oliphant, NumPy: A Guide to NumPy, Trelgol Publishing, Spanish Fork, UT 2006 http://www.numpy.org/.

68 references, page 1 of 5
Abstract
Abstract The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in‐house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we prese...
Subjects
free text keywords: Computational Chemistry and Modeling, Theory - Computational, excited states, dimers, molecular crystals, electrostatic embedding, ONIOM, Software News and Updates, molecular aggregate, photochemistry, Python library, General Chemistry, Computational Mathematics, Exciton, Chemistry, Excited state, Computational chemistry, Chemical physics
Funded by
RCUK| MATERIALS CHEMISTRY HIGH END COMPUTING CONSORTIUM
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: EP/L000202/1
  • Funding stream: EPSRC
,
RCUK| Towards the Computational Design of Highly Emissive Organic-Single Crystals
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: EP/R029385/1
  • Funding stream: EPSRC
,
RCUK| Tier 2 Hub in Materials and Molecular Modelling
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: EP/P020194/1
  • Funding stream: EPSRC
68 references, page 1 of 5

1 J.Aragó, A.Troisi, Phys. Rev. Lett.2015, 114, 026402.25635554 [PubMed]

2 R.Dovesi, A.Erba, R.Orlando, C. M.Zicovich‐Wilson, B.Civalleri, L.Maschio, M.Rérat, S.Casassa, J.Baima, S.Salustro, B.Kirtman, Wiley Interdiscip. Rev. Comput. Mol. Sci.2018, 8, e1360.

3 C. R.Groom, I. J.Bruno, M. P.Lightfoot, S. C.Ward, Acta Crystallogr. Sect. B 2016, 72, 171.

4 A.Hjorth Larsen, J.Jørgen Mortensen, J.Blomqvist, I. E.Castelli, R.Christensen, M.Du lak, J.Friis, M. N.Groves, B.Hammer, C.Hargus, E. D.Hermes, P. C.Jennings, P.Bjerre Jensen, J.Kermode, J. R.Kitchin, E.Leonhard Kolsbjerg, J.Kubal, K.Kaasbjerg, S.Lysgaard, J.Bergmann Maronsson, T.Maxson, T.Olsen, L.Pastewka, A.Peterson, C.Rostgaard, J.Schiøtz, O.Schütt, M.Strange, K. S.Thygesen, T.Vegge, L.Vilhelmsen, M.Walter, Z.Zeng, K. W.Jacobsen, J. Phys. Condens. Matter 2017, 273002, 29.

5 RDKit : Open‐Source Cheminformatics, http://www.rdkit.org (accessed 1st of January 2020).

6 Y.Lu, M. R.Farrow, P.Fayon, A. J.Logsdail, A. A.Sokol, C. R. A.Catlow, P.Sherwood, T. W.Keal, J. Chem. Theory Comput.2019, 15, 1317.30511845 [PubMed]

7 A. V.Akimov, J. Comput. Chem.2016, 37, 1626.27016373 [PubMed]

8 B.Aradi, B.Hourahine, T.Frauenheim, J. Phys. Chem. A 2007, 111, 5678.17567110 [PubMed]

9 M. J.Frisch, G. W.Trucks, H. B.Schlegel, G. E.Scuseria, M. A.Robb, J. R.Cheeseman, G.Scalmani, V.Barone, G. A.Petersson, H.Nakatsuji, X.Li, M.Caricato, A. V.Marenich, J.Bloino, B. G.Janesko, R.Gomperts, B.Mennucci, H. P.Hratchian, J. V.Ortiz, A. F.Izmaylov, J. L.Sonnenberg, D.Williams‐Young, F.Ding, F.Lipparini, F.Egidi, J.Goings, B.Peng, A.Petrone, T.Henderson, D.Ranasinghe, V. G.Zakrzewski, J.Gao, N.Rega, G.Zheng, W.Liang, M.Hada, M.Ehara, K.Toyota, R.Fukuda, J.Hasegawa, M.Ishida, T.Nakajima, Y.Honda, O.Kitao, H.Nakai, T.Vreven, K.Throssell, J. A.Montgomery Jr., J. E.Peralta, F.Ogliaro, M. J.Bearpark, J. J.Heyd, E. N.Brothers, K. N.Kudin, V. N.Staroverov, T. A.Keith, R.Kobayashi, J.Normand, K.Raghavachari, A. P.Rendell, J. C.Burant, S. S.Iyengar, J.Tomasi, M.Cossi, J. M.Millam, M.Klene, C.Adamo, R.Cammi, J. W.Ochterski, R. L.Martin, K.Morokuma, O.Farkas, J. B.Foresman, D. J.Fox, Gaussian 16 Revision B.01, Gaussian Inc., Wallingford, CT 2016.

10 F.Aquilante, J.Autschbach, R. K.Carlson, L. F.Chibotaru, M. G.Delcey, L.De Vico, I. F.Galván, N.Ferré, L. M.Frutos, L.Gagliardi, M.Garavelli, A.Giussani, C. E.Hoyer, G. L.Manni, H.Lischka, D.Ma, P. Å.Malmqvist, T.Müller, A.Nenov, M.Olivucci, T. B.Pedersen, D.Peng, F.Plasser, B.Pritchard, M.Reiher, I.Rivalta, I.Schapiro, J.Segarra‐Mart'ı, M.Stenrup, D. G.Truhlar, L.Ungur, A.Valentini, S.Vancoillie, V.Veryazov, V. P.Vysotskiy, O.Weingart, F.Zapata, R.Lindh, J. Comput. Chem.2016, 37, 506.26561362 [OpenAIRE] [PubMed]

11 TURBOMOLE V6.2 2010, A Development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989–2007, TURBOMOLE GmbH, Since 2007. http://www.turbomole.com (accessed 1st of January 2020).

12 M.Rivera, M.Dommett, R.Crespo‐Otero, J.Chem, Theory Comput.2019, 15, 2504.

13 L.Stojanović, R.Crespo‐Otero, ChemPhotoChem 2019, 3, 907 10.1002/cptc.201900075 [OpenAIRE] [DOI]

14 M.Dommett, M.Rivera, M. T. H.Smith, R.Crespo‐Otero, Chemrxiv 2019 10.26434/chemrxiv.8283710.v1 [OpenAIRE] [DOI]

15 T.Oliphant, NumPy: A Guide to NumPy, Trelgol Publishing, Spanish Fork, UT 2006 http://www.numpy.org/.

68 references, page 1 of 5
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