201
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Guerrero M, Vázquez S, Ayllón JA, Calvet T, Font-Bardia M, Pons J. Zn(II) and Cd(II) Coordination Dimers Based on Mixed Benzodioxole-Carboxylate and N-Donor Ligands: Synthesis, Characterization, Crystal Structures and Photoluminescence Properties. ChemistrySelect 2017. [DOI: 10.1002/slct.201602017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Miguel Guerrero
- Departament de Química; Universitat Autònoma de Barcelona; 08193-Bellaterra Barcelona Spain
- Departament de Física; Universitat Autònoma de Barcelona; 08193-Bellaterra Barcelona Spain
| | - Sergio Vázquez
- Departament de Química; Universitat Autònoma de Barcelona; 08193-Bellaterra Barcelona Spain
| | - José A. Ayllón
- Departament de Química; Universitat Autònoma de Barcelona; 08193-Bellaterra Barcelona Spain
| | - Teresa Calvet
- Cristal⋅lografia, Mineralogia i Dipòsits Minerals; Universitat de Barcelona, Martí i Franquès s/n; 08028- Barcelona Spain
| | - Merce Font-Bardia
- Unitat de Difracció de Raig-X; Centres Científics i Tecnològics de la Universitat de Barcelona (CCiTUB); Universitat de Barcelona; Solé i Sabarís, 1-3 08028- Barcelona Spain
| | - Josefina Pons
- Departament de Química; Universitat Autònoma de Barcelona; 08193-Bellaterra Barcelona Spain
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202
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Whittleton SR, Otero-de-la-Roza A, Johnson ER. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction. J Chem Theory Comput 2017; 13:441-450. [PMID: 27977188 DOI: 10.1021/acs.jctc.6b00679] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.
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Affiliation(s)
- Sarah R Whittleton
- Department of Chemistry, Dalhousie University , 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - A Otero-de-la-Roza
- Department of Chemistry, University of British Columbia, Okanagan , 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University , 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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203
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Tan SYS, Wylie L, Begic I, Tran D, Izgorodina EI. Application of spin-ratio scaled MP2 for the prediction of intermolecular interactions in chemical systems. Phys Chem Chem Phys 2017; 19:28936-28942. [DOI: 10.1039/c7cp04391k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Accurate prediction of intermolecular interactions plays a pivotal role in many areas of chemistry and biology including (but not limited to) the design of pharmaceuticals, solid electrolytes and food additives.
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Affiliation(s)
| | - Luke Wylie
- School of Chemistry
- Monash University
- Clayton
- Australia
| | - Ivan Begic
- School of Chemistry
- Monash University
- Clayton
- Australia
| | - Dennis Tran
- School of Chemistry
- Monash University
- Clayton
- Australia
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204
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Dudek MK, Bujacz G, Potrzebowski MJ. Experimental tests for quality validation of computationally predicted crystal structures – a case of a conformationally flexible procyanidin A-2 dihydrate. CrystEngComm 2017. [DOI: 10.1039/c7ce00618g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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205
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Nemausat R, Gervais C, Brouder C, Trcera N, Bordage A, Coelho-Diogo C, Florian P, Rakhmatullin A, Errea I, Paulatto L, Lazzeri M, Cabaret D. Temperature dependence of X-ray absorption and nuclear magnetic resonance spectra: probing quantum vibrations of light elements in oxides. Phys Chem Chem Phys 2017; 19:6246-6256. [DOI: 10.1039/c6cp08393e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Probing the quantum thermal fluctuations of nuclei in light-element oxides using XANES and NMR spectroscopies.
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Affiliation(s)
- Ruidy Nemausat
- Sorbonne Universités
- UPMC Univ Paris 06
- IMPMC
- UMR CNRS 7590
- F-75005 Paris
| | - Christel Gervais
- Sorbonne Universités
- UPMC Univ Paris 06
- LCMCP
- Collège de France
- UMR CNRS 7574
| | - Christian Brouder
- Sorbonne Universités
- UPMC Univ Paris 06
- IMPMC
- UMR CNRS 7590
- F-75005 Paris
| | - Nicolas Trcera
- Synchrotron SOLEIL
- L'Orme des Merisiers
- F-91192 Gif sur Yvette
- France
| | - Amélie Bordage
- ICMMO
- Univ Paris Sud
- Univ Paris-Saclay
- UMR CNRS 8182
- F-91405 Orsay
| | | | | | | | - Ion Errea
- Fisika Aplikatua 1 Saila
- Bilboko Ingeniaritza Eskola
- University of the Basque Country (UPV/EHU)
- 48013 Bilbao
- Spain
| | - Lorenzo Paulatto
- Sorbonne Universités
- UPMC Univ Paris 06
- IMPMC
- UMR CNRS 7590
- F-75005 Paris
| | - Michele Lazzeri
- Sorbonne Universités
- UPMC Univ Paris 06
- IMPMC
- UMR CNRS 7590
- F-75005 Paris
| | - Delphine Cabaret
- Sorbonne Universités
- UPMC Univ Paris 06
- IMPMC
- UMR CNRS 7590
- F-75005 Paris
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206
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Abstract
We analyze the processes governing the lifetimes of transient metastable polymorphs, within the context of classical nucleation theory.
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Affiliation(s)
- Wenhao Sun
- Department of Materials Science and Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Materials Sciences Division
| | - Gerbrand Ceder
- Department of Materials Science and Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Materials Sciences Division
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207
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da Silva MB, Da Cunha AM, Santos RCR, Valentini A, Caetano EWS, Freire VN. Changing the gap type of solid state boric acid by heating: a dispersion-corrected density functional study of α-, β-, and γ-metaboric acid polymorphs. NEW J CHEM 2017. [DOI: 10.1039/c7nj02945d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The gap type of solid state metaboric acid can be changed by temperature changes near 100 °C according to DFT calculations.
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Affiliation(s)
- M. Bezerra da Silva
- Departamento de Física
- Universidade Federal do Ceará
- Caixa Postal 6030
- Fortaleza-CE
- Brazil
| | - A. M. Da Cunha
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
| | - R. C. R. Santos
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
| | - A. Valentini
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
| | - E. W. S. Caetano
- Instituto Federal de Educação
- Ciência e Tecnologia do Ceará
- DEMEL
- Campus Fortaleza
- Fortaleza-CE
| | - V. N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Caixa Postal 6030
- Fortaleza-CE
- Brazil
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208
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Ruggiero MT, Axel Zeitler J, Korter TM. Concomitant polymorphism and the martensitic-like transformation of an organic crystal. Phys Chem Chem Phys 2017; 19:28502-28506. [DOI: 10.1039/c7cp04666a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Terahertz vibrational spectroscopy and solid-state density functional theory together reveal the true nature of a pseudo-continuous crystalline polymorphic phase transition.
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Affiliation(s)
- Michael T. Ruggiero
- Department of Chemistry
- Syracuse University
- Syracuse
- USA
- Department of Chemical Engineering and Biotechnology, University of Cambridge
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge
- Cambridge
- UK
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209
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Ruggiero MT, Zeitler JA, Erba A. Intermolecular anharmonicity in molecular crystals: interplay between experimental low-frequency dynamics and quantum quasi-harmonic simulations of solid purine. Chem Commun (Camb) 2017; 53:3781-3784. [DOI: 10.1039/c7cc00509a] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined experimental spectroscopic and theoretical quasi-harmonic investigation of intermolecular anharmonicity in crystalline purine.
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Affiliation(s)
- Michael T. Ruggiero
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge
- UK
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge
- UK
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210
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Hoja J, Reilly AM, Tkatchenko A. First-principles modeling of molecular crystals: structures and stabilities, temperature and pressure. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1294] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Johannes Hoja
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Berlin Germany
- Physics and Materials Science Research Unit; University of Luxembourg; Luxembourg City Luxembourg
| | | | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Berlin Germany
- Physics and Materials Science Research Unit; University of Luxembourg; Luxembourg City Luxembourg
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211
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Cutini M, Corno M, Ugliengo P. Method Dependence of Proline Ring Flexibility in the Poly-l-Proline Type II Polymer. J Chem Theory Comput 2016; 13:370-379. [PMID: 27976574 DOI: 10.1021/acs.jctc.6b01045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We studied the sensitivity of the energetic and geometrical features of the proline ring (pyrrolidine) to the quantum mechanical computational approach by adopting the proline monomer, trimer, and polymer, as simplified collagen protein models. Within the Density Functional Theory (DFT) approach, we tested the ability of different functionals (GGA PBE and the hybrid B3LYP), added with a posteriori empirical dispersion corrections (D), to predict the conformational potential energy surface of the five-membered heterocycle pyrrolidine ring for the above models, dictating the collagen main features. We also compared the DFT-D results with those from the recently proposed cost-effective HF-3c method and our variant HF-3c-027, both based on Hartree-Fock Hamiltonian and Gaussian minimal basis set properly corrected for basis set superposition error, structure deficiencies, and dispersion interactions. We found that dispersion interactions are essential to destabilize specific conformers. While the HF-3c and its HF-3c-027 variant are unreliable to predict accurately the energy of the ring conformers, structures are accurate. Indeed, the cost-effective DFT-D//HF-3c-027 approach in which the energetic is from the accurate DFT-D method on HF-3c-027 structures provides energetic in line with that derived by the costly DFT-D//DFT-D approach, paving the way to simulate more realistic collagen models of much larger size. The adoption of either PBE or B3LYP functional for the electronic part of the DFT-D method gives very similar results, recommending the first as the most cost-effective method for simulating large collagen models. The predicted most stable conformation computed for the periodic poly proline (type II) model allows for a higher flexibility, in agreement with experimental studies on collagen protein. The present results open the way to large-scale calculations of the collagen/hydroxyapatite system, crucial for understanding the atomistic details in bones and teeth.
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Affiliation(s)
- Michele Cutini
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Torino , Via P. Giuria 7, 10125 Turin, Italy
| | - Marta Corno
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Torino , Via P. Giuria 7, 10125 Turin, Italy
| | - Piero Ugliengo
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Torino , Via P. Giuria 7, 10125 Turin, Italy
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212
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Vela S, Souto M, Ratera I, Rovira C, Veciana J. Understanding the Influence of the Electronic Structure on the Crystal Structure of a TTF-PTM Radical Dyad. J Phys Chem A 2016; 120:10297-10303. [DOI: 10.1021/acs.jpca.6b11107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergi Vela
- Laboratoire
de Chimie Quantique, UMR-7177, CNRS-Université de Strasbourg, 4 rue
Blaise Pascal, F-67000 Strasbourg, France
| | - Manuel Souto
- Institut de Ciència
de Materials de Barcelona (ICMAB-CSIC)/CIBER-BBN, Campus de la UAB, 08193, Bellaterra, Spain
| | - Imma Ratera
- Institut de Ciència
de Materials de Barcelona (ICMAB-CSIC)/CIBER-BBN, Campus de la UAB, 08193, Bellaterra, Spain
| | - Concepció Rovira
- Institut de Ciència
de Materials de Barcelona (ICMAB-CSIC)/CIBER-BBN, Campus de la UAB, 08193, Bellaterra, Spain
| | - Jaume Veciana
- Institut de Ciència
de Materials de Barcelona (ICMAB-CSIC)/CIBER-BBN, Campus de la UAB, 08193, Bellaterra, Spain
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213
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The plane-wave DFT investigations into the structure and the 11B solid-state NMR parameters of lithium fluorooxoborates. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.10.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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214
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Kapoor S, Yaduvanshi N, Singh S. Study of phase transformation and elastic properties of ThX (X = N, P, As and Sb) under high-pressure. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1250964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shilpa Kapoor
- High Pressure Research Lab, Department of Physics, Barkatullah University, Bhopal, India
| | - Namrata Yaduvanshi
- High Pressure Research Lab, Department of Physics, Barkatullah University, Bhopal, India
| | - Sadhna Singh
- High Pressure Research Lab, Department of Physics, Barkatullah University, Bhopal, India
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215
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Beran GJO, Hartman JD, Heit YN. Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography. Acc Chem Res 2016; 49:2501-2508. [PMID: 27754668 DOI: 10.1021/acs.accounts.6b00404] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic errors in the enthalpy and entropy cancel somewhat. Second, because solid state nuclear magnetic resonance (NMR) plays an increasingly important role in molecular crystal studies, this Account discusses how fragment methods can be used to achieve higher-accuracy chemical shifts in molecular crystals. Whereas widely used plane wave density functional theory models are largely restricted to generalized gradient approximation (GGA) functionals like PBE in practice, fragment methods allow the routine use of hybrid density functionals with only modest increases in computational cost. In extensive molecular crystal benchmarks, hybrid functionals like PBE0 predict chemical shifts with 20-30% higher accuracy than GGAs, particularly for 1H, 13C, and 15N nuclei. Due to their higher sensitivity to polarization effects, 17O chemical shifts prove slightly harder to predict with fragment methods. Nevertheless, the fragment model results are still competitive with those from GIPAW. The improved accuracy achievable with fragment approaches and hybrid density functionals increases discrimination between different potential assignments of individual shifts or crystal structures, which is critical in NMR crystallography applications. This higher accuracy and greater discrimination are highlighted in application to the solid state NMR of different acetaminophen and testosterone crystal forms.
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Affiliation(s)
- Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joshua D. Hartman
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yonaton N. Heit
- Department of Chemistry, University of California, Riverside, California 92521, United States
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216
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Hartman J, Day GM, Beran GJO. Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions. CRYSTAL GROWTH & DESIGN 2016; 16:6479-6493. [PMID: 27829821 PMCID: PMC5095663 DOI: 10.1021/acs.cgd.6b01157] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/09/2016] [Indexed: 05/10/2023]
Abstract
Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.
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Affiliation(s)
- Joshua
D. Hartman
- Department
of Chemistry, University of California, Riverside, California 92521 United States
| | - Graeme M. Day
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Gregory J. O. Beran
- Department
of Chemistry, University of California, Riverside, California 92521 United States
- E-mail:
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217
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Klimeš J. Lattice energies of molecular solids from the random phase approximation with singles corrections. J Chem Phys 2016; 145:094506. [DOI: 10.1063/1.4962188] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jiří Klimeš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-18223 Prague 8, Czech Republic and Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, CZ-12116 Prague 2, Czech Republic
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218
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Curtis F, Wang X, Marom N. Effect of packing motifs on the energy ranking and electronic properties of putative crystal structures of tricyano-1,4-dithiino[c]-isothiazole. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:562-570. [PMID: 27484377 DOI: 10.1107/s2052520616009227] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/07/2016] [Indexed: 06/06/2023]
Abstract
We present an analysis of putative structures of tricyano-1,4-dithiino[c]-isothiazole (TCS3), generated within the sixth crystal structure prediction blind test. Typical packing motifs are identified and characterized in terms of distinct patterns of close contacts and regions of electrostatic and dispersion interactions. We find that different dispersion-inclusive density functional theory (DFT) methods systematically favor specific packing motifs, which may affect the outcome of crystal structure prediction efforts. The effect of crystal packing on the electronic and optical properties of TCS3 is investigated using many-body perturbation theory within the GW approximation and the Bethe-Salpeter equation (BSE). We find that a structure with Pna21 symmetry and a bilayer packing motif exhibits intermolecular bonding patterns reminiscent of π-π stacking and has markedly different electronic and optical properties than the experimentally observed P21/n structure with a cyclic dimer motif, including a narrower band gap, enhanced band dispersion and broader optical absorption. The Pna21 bilayer structure is close in energy to the observed structure and may be feasible to grow.
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Affiliation(s)
- Farren Curtis
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xiaopeng Wang
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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219
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Brandenburg JG, Grimme S. Organic crystal polymorphism: a benchmark for dispersion-corrected mean-field electronic structure methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:502-513. [PMID: 27484372 DOI: 10.1107/s2052520616007885] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/13/2016] [Indexed: 06/06/2023]
Abstract
We analyze the energy landscape of the sixth crystal structure prediction blind test targets with various first principles and semi-empirical quantum chemical methodologies. A new benchmark set of 59 crystal structures (termed POLY59) for testing quantum chemical methods based on the blind test target crystals is presented. We focus on different means to include London dispersion interactions within the density functional theory (DFT) framework. We show the impact of pairwise dispersion corrections like the semi-empirical D2 scheme, the Tkatchenko-Scheffler (TS) method, and the density-dependent dispersion correction dDsC. Recent methodological progress includes higher-order contributions in both the many-body and multipole expansions. We use the D3 correction with Axilrod-Teller-Muto type three-body contribution, the TS based many-body dispersion (MBD), and the nonlocal van der Waals density functional (vdW-DF2). The density functionals with D3 and MBD correction provide an energy ranking of the blind test polymorphs in excellent agreement with the experimentally found structures. As a computationally less demanding method, we test our recently presented minimal basis Hartree-Fock method (HF-3c) and a density functional tight-binding Hamiltonian (DFTB). Considering the speed-up of three to four orders of magnitudes, the energy ranking provided by the low-cost methods is very reasonable. We compare the computed geometries with the corresponding X-ray data where TPSS-D3 performs best. The importance of zero-point vibrational energy and thermal effects on crystal densities is highlighted.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4-6, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4-6, 53115 Bonn, Germany
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220
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Hartman JD, Kudla RA, Day GM, Mueller LJ, Beran GJO. Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals. Phys Chem Chem Phys 2016; 18:21686-709. [PMID: 27431490 DOI: 10.1039/c6cp01831a] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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Price SL, Braun DE, Reutzel-Edens SM. Can computed crystal energy landscapes help understand pharmaceutical solids? Chem Commun (Camb) 2016; 52:7065-77. [PMID: 27067116 PMCID: PMC5486446 DOI: 10.1039/c6cc00721j] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Computational crystal structure prediction (CSP) methods can now be applied to the smaller pharmaceutical molecules currently in drug development. We review the recent uses of computed crystal energy landscapes for pharmaceuticals, concentrating on examples where they have been used in collaboration with industrial-style experimental solid form screening. There is a strong complementarity in aiding experiment to find and characterise practically important solid forms and understanding the nature of the solid form landscape.
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Affiliation(s)
- Sarah L Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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222
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Affiliation(s)
- Matúš Dubecký
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lubos Mitas
- Department
of Physics and CHiPS, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
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