51
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Sugden I, Adjiman CS, Pantelides CC. Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:864-874. [PMID: 27910837 PMCID: PMC5134761 DOI: 10.1107/s2052520616015122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/26/2016] [Indexed: 05/14/2023]
Abstract
The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015). J. Chem. Theory Comput. 11, 1957-1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule's conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016). Acta Cryst. B72, 439-459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions.
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Affiliation(s)
- Isaac Sugden
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
| | - Claire S. Adjiman
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
| | - Constantinos C. Pantelides
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
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52
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Cai XQ, Tian B, Zhang JN, Jin ZM. The hydrogen-bonded complex bis(tert-butylammonium) 2,6-dichlorophenolate 2,4-dichlorophenol-2,4-dichlorophenolate tetrahydrofuran disolvate containing a chiral R 53(10) hydrogen-bonded ring as a supramolecular synthon. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2016; 72:720-723. [PMID: 27703117 DOI: 10.1107/s2053229616013577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/23/2016] [Indexed: 11/10/2022]
Abstract
A fixed hydrogen-bonding motif with a high probability of occurring when appropriate functional groups are involved is described as a `supramolecular hydrogen-bonding synthon'. The identification of these synthons may enable the prediction of accurate crystal structures. The rare chiral hydrogen-bonding motif R53(10) was observed previously in a cocrystal of 2,4,6-trichlorophenol, 2,4-dichlorophenol and dicyclohexylamine. In the title solvated salt, 2C4H12N+·C6H3Cl2O-·(C6H3Cl2O-·C6H4Cl2O)·2C4H8O, five components, namely two tert-butylammonium cations, one 2,4-dichlorophenol molecule, one 2,4-dichlorophenolate anion and one 2,6-dichlorophenolate anion, are bound by N-H...O and O-H...O hydrogen bonds to form a hydrogen-bonded ring, with the graph-set motif R53(10), which is further associated with two pendant tetrahydrofuran molecules by N-H...O hydrogen bonds. The hydrogen-bonded ring has internal symmetry, with a twofold axis running through the centre of the 2,6-dichlorophenolate anion, and is isostructural with a previous and related structure formed from 2,4-dichlorophenol, dicyclohexylamine and 2,4,6-trichlorophenol. In the title crystal, helical columns are built by the alignment and twisting of the chiral hydrogen-bonded rings, along and across the c axis, and successive pairs of rings are associated with each other through C-H...π interactions. Neighbouring helical columns are inversely related and, therefore, no chirality is sustained, in contrast to the previous case.
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Affiliation(s)
- Xiao Qing Cai
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, People's Republic of China
| | - Bei Tian
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Jian Nan Zhang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhi Min Jin
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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53
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Elking DM. Torque and atomic forces for Cartesian tensor atomic multipoles with an application to crystal unit cell optimization. J Comput Chem 2016; 37:2067-80. [PMID: 27349179 DOI: 10.1002/jcc.24427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/17/2016] [Indexed: 01/31/2023]
Abstract
New equations for torque and atomic force are derived for use in flexible molecule force fields with atomic multipoles. The expressions are based on Cartesian tensors with arbitrary multipole rank. The standard method for rotating Cartesian tensor multipoles and calculating torque is to first represent the tensor with n indexes and 3(n) redundant components. In this work, new expressions for directly rotating the unique (n + 1)(n + 2)/2 Cartesian tensor multipole components Θpqr are given by introducing Cartesian tensor rotation matrix elements X(R). A polynomial expression and a recursion relation for X(R) are derived. For comparison, the analogous rotation matrix for spherical tensor multipoles are the Wigner functions D(R). The expressions for X(R) are used to derive simple equations for torque and atomic force. The torque and atomic force equations are applied to the geometry optimization of small molecule crystal unit cells. In addition, a discussion of computational efficiency as a function of increasing multipole rank is given for Cartesian tensors. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Dennis M Elking
- Openeye Scientific Software, Santa Fe, New Mexico, 87508.,Elking Scientific Modeling, Ballwin, Missouri, 63102
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54
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Heit YN, Beran GJO. How important is thermal expansion for predicting molecular crystal structures and thermochemistry at finite temperatures? ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:514-529. [PMID: 27484373 DOI: 10.1107/s2052520616005382] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/30/2016] [Indexed: 06/06/2023]
Abstract
Molecular crystals expand appreciably upon heating due to both zero-point and thermal vibrational motion, yet this expansion is often neglected in molecular crystal modeling studies. Here, a quasi-harmonic approximation is coupled with fragment-based hybrid many-body interaction calculations to predict thermal expansion and finite-temperature thermochemical properties in crystalline carbon dioxide, ice Ih, acetic acid and imidazole. Fragment-based second-order Möller-Plesset perturbation theory (MP2) and coupled cluster theory with singles, doubles and perturbative triples [CCSD(T)] predict the thermal expansion and the temperature dependence of the enthalpies, entropies and Gibbs free energies of sublimation in good agreement with experiment. The errors introduced by neglecting thermal expansion in the enthalpy and entropy cancel somewhat in the Gibbs free energy. The resulting ∼ 1-2 kJ mol(-1) errors in the free energy near room temperature are comparable to or smaller than the errors expected from the electronic structure treatment, but they may be sufficiently large to affect free-energy rankings among energetically close polymorphs.
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Affiliation(s)
- Yonaton N Heit
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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55
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Cruz-Cabeza AJ. Crystal structure prediction: are we there yet? ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2016; 72:437-8. [DOI: 10.1107/s2052520616011367] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 11/10/2022]
Abstract
This contribution comments on the advances of the latest Crystal Structure Prediction blind test and the challenges still lying ahead.
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56
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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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57
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Elking DM, Fusti-Molnar L, Nichols A. Crystal structure prediction of rigid molecules. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2016; 72:488-501. [DOI: 10.1107/s2052520616010118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/21/2016] [Indexed: 11/11/2022]
Abstract
A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties andab initiogas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r6dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups.
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58
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Cole JC, Groom CR, Read MG, Giangreco I, McCabe P, Reilly AM, Shields GP. Generation of crystal structures using known crystal structures as analogues. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:530-41. [PMID: 27484374 PMCID: PMC4971547 DOI: 10.1107/s2052520616006533] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/18/2016] [Indexed: 06/06/2023]
Abstract
This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes - sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach.
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Affiliation(s)
- Jason C. Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, Cambridgeshire CB2 1EZ, England
| | - Colin R. Groom
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, Cambridgeshire CB2 1EZ, England
| | - Murray G. Read
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, Cambridgeshire CB2 1EZ, England
| | - Ilenia Giangreco
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, Cambridgeshire CB2 1EZ, England
| | - Patrick McCabe
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, Cambridgeshire CB2 1EZ, England
| | - Anthony M. Reilly
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, Cambridgeshire CB2 1EZ, England
| | - Gregory P. Shields
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, Cambridgeshire CB2 1EZ, England
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59
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Schneider E, Vogt L, Tuckerman ME. Exploring polymorphism of benzene and naphthalene with free energy based enhanced molecular dynamics. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:542-550. [PMID: 27484375 DOI: 10.1107/s2052520616007873] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/13/2016] [Indexed: 06/06/2023]
Abstract
Prediction and exploration of possible polymorphism in organic crystal compounds are of great importance for industries ranging from organic electronics to pharmaceuticals to high-energy materials. Here we apply our crystal structure prediction procedure and the enhanced molecular dynamics based sampling approach called the Crystal-Adiabatic Free Energy Dynamics (Crystal-AFED) method to benzene and naphthalene. Crystal-AFED allows the free energy landscape of structures to be explored efficiently at any desired temperature and pressure. For each system, we successfully predict the most stable crystal structures at atmospheric pressure and explore the relative Gibbs free energies of predicted polymorphs at high pressures. Using Crystal-AFED sampling, we find that mixed structures, which typically cannot be discovered by standard crystal structure prediction methods, are prevalent in the solid forms of these compounds at high pressure.
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Affiliation(s)
- Elia Schneider
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Leslie Vogt
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Mark E Tuckerman
- Department of Chemistry, New York University, New York, NY 10003, USA
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60
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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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61
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Reilly AM, Cooper RI, Adjiman CS, Bhattacharya S, Boese AD, Brandenburg JG, Bygrave PJ, Bylsma R, Campbell JE, Car R, Case DH, Chadha R, Cole JC, Cosburn K, Cuppen HM, Curtis F, Day GM, DiStasio Jr RA, Dzyabchenko A, van Eijck BP, Elking DM, van den Ende JA, Facelli JC, Ferraro MB, Fusti-Molnar L, Gatsiou CA, Gee TS, de Gelder R, Ghiringhelli LM, Goto H, Grimme S, Guo R, Hofmann DWM, Hoja J, Hylton RK, Iuzzolino L, Jankiewicz W, de Jong DT, Kendrick J, de Klerk NJJ, Ko HY, Kuleshova LN, Li X, Lohani S, Leusen FJJ, Lund AM, Lv J, Ma Y, Marom N, Masunov AE, McCabe P, McMahon DP, Meekes H, Metz MP, Misquitta AJ, Mohamed S, Monserrat B, Needs RJ, Neumann MA, Nyman J, Obata S, Oberhofer H, Oganov AR, Orendt AM, Pagola GI, Pantelides CC, Pickard CJ, Podeszwa R, Price LS, Price SL, Pulido A, Read MG, Reuter K, Schneider E, Schober C, Shields GP, Singh P, Sugden IJ, Szalewicz K, Taylor CR, Tkatchenko A, Tuckerman ME, Vacarro F, Vasileiadis M, Vazquez-Mayagoitia A, Vogt L, Wang Y, Watson RE, de Wijs GA, Yang J, Zhu Q, Groom CR. Report on the sixth blind test of organic crystal structure prediction methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:439-59. [PMID: 27484368 PMCID: PMC4971545 DOI: 10.1107/s2052520616007447] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/04/2016] [Indexed: 05/05/2023]
Abstract
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.
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Affiliation(s)
- Anthony M. Reilly
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Richard I. Cooper
- Chemical Crystallography, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England
| | - Claire S. Adjiman
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Saswata Bhattacharya
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - A. Daniel Boese
- Department of Chemistry, Institute of Physical and Theoretical Chemistry, University of Graz, Heinrichstraße 28/IV, 8010 Graz, Austria
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Peter J. Bygrave
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Rita Bylsma
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Josh E. Campbell
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - David H. Case
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Renu Chadha
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Jason C. Cole
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Katherine Cosburn
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Physics, University of Toronto, Toronto, Canada M5S 1A7
| | - Herma M. Cuppen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Farren Curtis
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Graeme M. Day
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Robert A. DiStasio Jr
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Dennis M. Elking
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
| | - Joost A. van den Ende
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Julio C. Facelli
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
- Department of Biomedical Informatics, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Marta B. Ferraro
- Departamento de Física and Ifiba (CONICET) Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina
| | - Laszlo Fusti-Molnar
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
| | - Christina-Anna Gatsiou
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Thomas S. Gee
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - René de Gelder
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Luca M. Ghiringhelli
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Hitoshi Goto
- Educational Programs on Advanced Simulation Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
- Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Rui Guo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Detlef W. M. Hofmann
- CRS4, Parco Scientifico e Tecnologico, POLARIS, Edificio 1, 09010 PULA, Italy
- FlexCryst, Schleifweg 23, 91080 Uttenreuth, Germany
| | - Johannes Hoja
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Rebecca K. Hylton
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Luca Iuzzolino
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Wojciech Jankiewicz
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Daniël T. de Jong
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - John Kendrick
- Faculty of Life Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, England
| | - Niek J. J. de Klerk
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hsin-Yu Ko
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | - Xiayue Li
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sanjaya Lohani
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
| | - Frank J. J. Leusen
- Faculty of Life Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, England
| | - Albert M. Lund
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
- Department of Chemistry, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Jian Lv
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Yanming Ma
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Noa Marom
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Materials Science and Engineering and Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Artëm E. Masunov
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, PAV400, Orlando, FL 32826, USA
- Department of Chemistry, University of Central Florida, 4111 Libra Drive PSB225, Orlando, FL 32816, USA
- Department of Physics, University of Central Florida, 4111 Libra Drive PSB430, Orlando, FL 32816, USA
- Department of Condensed Matter Physics, National Research Nuclear University MEPhI, Kashirskoye shosse 31, Moscow 115409, Russia
| | - Patrick McCabe
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - David P. McMahon
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Hugo Meekes
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Michael P. Metz
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | - Alston J. Misquitta
- School of Physics and Astronomy, Queen Mary University of London, London E1 4NS, England
| | | | - Bartomeu Monserrat
- Cavendish Laboratory, 19, J. J. Thomson Avenue, Cambridge CB3 0HE, England
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019, USA
| | - Richard J. Needs
- Cavendish Laboratory, 19, J. J. Thomson Avenue, Cambridge CB3 0HE, England
| | | | - Jonas Nyman
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Shigeaki Obata
- Educational Programs on Advanced Simulation Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Artem R. Oganov
- Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, SUNY Stony Brook, NY 11794-2100, USA
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Centers, Bldg. 3, Moscow Region, 143026, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny City, Moscow Region 141700, Russia
- International Center for Materials Discovery, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, China
| | - Anita M. Orendt
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Gabriel I. Pagola
- Departamento de Física and Ifiba (CONICET) Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina
| | - Constantinos C. Pantelides
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Chris J. Pickard
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, England
- Department of Physics and Astronomy, University College London, Gower St., London WC1E 6BT, England
| | - Rafal Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Louise S. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Angeles Pulido
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Murray G. Read
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Elia Schneider
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Christoph Schober
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Gregory P. Shields
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Pawanpreet Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Isaac J. Sugden
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | | | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg
| | - Mark E. Tuckerman
- Department of Chemistry, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
| | - Francesca Vacarro
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Chemistry, Loyola University, New Orleans, LA 70118, USA
| | - Manolis Vasileiadis
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | | | - Leslie Vogt
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Yanchao Wang
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Rona E. Watson
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Gilles A. de Wijs
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jack Yang
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Qiang Zhu
- Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, SUNY Stony Brook, NY 11794-2100, USA
| | - Colin R. Groom
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
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62
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Day GM, Görbitz CH. Introduction to the special issue on crystal structure prediction. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:435-436. [PMID: 27484366 DOI: 10.1107/s2052520616012348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Graeme M Day
- Department of Chemistry, University of Southampton, Highfield Campus, Southampton, Hampshire SO17 1BJ, England
| | - Carl Henrik Görbitz
- Department of Chemistry, University of Oslo, PO Box 1033 Blindern, N-0315 Oslo, Norway
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63
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Dybeck EC, Schieber NP, Shirts MR. Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials. J Chem Theory Comput 2016; 12:3491-505. [DOI: 10.1021/acs.jctc.6b00397] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric C. Dybeck
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Natalie P. Schieber
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Michael R. Shirts
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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64
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Broo A, Nilsson Lill SO. Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2016; 72:460-76. [DOI: 10.1107/s2052520616006831] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/22/2016] [Indexed: 11/10/2022]
Abstract
A new force field, here called AZ-FF, aimed at being used for crystal structure predictions, has been developed. The force field is transferable to a new type of chemistry without additional training or modifications. This makes the force field very useful in the prediction of crystal structures of new drug molecules since the time-consuming step of developing a new force field for each new molecule is circumvented. The accuracy of the force field was tested on a set of 40 drug-like molecules and found to be very good where observed crystal structures are found at the top of the ranked list of tentative crystal structures. Re-ranking with dispersion-corrected density functional theory (DFT-D) methods further improves the scoring. After DFT-D geometry optimization the observed crystal structure is found at the leading top of the ranking list. DFT-D methods and force field methods have been evaluated for use in predicting properties such as phase transitions upon heating, mechanical properties or intrinsic crystalline solubility. The utility of using crystal structure predictions and the associated material properties in risk assessment in connection with form selection in the drug development process is discussed.
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65
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Mohamed S, Karothu DP, Naumov P. Using crystal structure prediction to rationalize the hydration propensities of substituted adamantane hydrochloride salts. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2016; 72:551-61. [DOI: 10.1107/s2052520616006326] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/14/2016] [Indexed: 12/31/2022]
Abstract
The crystal energy landscapes of the salts of two rigid pharmaceutically active molecules reveal that the experimental structure of amantadine hydrochloride is the most stable structure with the majority of low-energy structures adopting a chain hydrogen-bond motif and packings that do not have solvent accessible voids. By contrast, memantine hydrochloride which differs in the substitution of two methyl groups on the adamantane ring has a crystal energy landscape where all structures within 10 kJ mol−1of the global minimum have solvent-accessible voids ranging from 3 to 14% of the unit-cell volume including the lattice energy minimum that was calculated after removing water from the hydrated memantine hydrochloride salt structure. The success in using crystal structure prediction (CSP) to rationalize the different hydration propensities of these substituted adamantane hydrochloride salts allowed us to extend the model to predict under blind test conditions the experimental crystal structures of the previously uncharacterized 1-(methylamino)adamantane base and its corresponding hydrochloride salt. Although the crystal structure of 1-(methylamino)adamantane was correctly predicted as the second ranked structure on the static lattice energy landscape, the crystallization of aZ′ = 3 structure of 1-(methylamino)adamantane hydrochloride reveals the limits of applying CSP when the contents of the crystallographic asymmetric unit are unknown.
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66
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Zurek E. Discovering New Materials via A PrioriCrystal Structure Prediction. REVIEWS IN COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1002/9781119148739.ch5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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67
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Ashbrook SE, McKay D. Combining solid-state NMR spectroscopy with first-principles calculations - a guide to NMR crystallography. Chem Commun (Camb) 2016; 52:7186-204. [PMID: 27117884 DOI: 10.1039/c6cc02542k] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent advances in the application of first-principles calculations of NMR parameters to periodic systems have resulted in widespread interest in their use to support experimental measurement. Such calculations often play an important role in the emerging field of "NMR crystallography", where NMR spectroscopy is combined with techniques such as diffraction, to aid structure determination. Here, we discuss the current state-of-the-art for combining experiment and calculation in NMR spectroscopy, considering the basic theory behind the computational approaches and their practical application. We consider the issues associated with geometry optimisation and how the effects of temperature may be included in the calculation. The automated prediction of structural candidates and the treatment of disordered and dynamic solids are discussed. Finally, we consider the areas where further development is needed in this field and its potential future impact.
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Affiliation(s)
- Sharon E Ashbrook
- School of Chemistry, EaStCHEM and Centre of Magnetic Resonance, University of St Andrews, St Andrews, KY16 9ST, UK.
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68
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Dybeck EC, König G, Brooks BR, Shirts MR. Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials. J Chem Theory Comput 2016; 12:1466-80. [PMID: 26928941 PMCID: PMC6497519 DOI: 10.1021/acs.jctc.5b01188] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We examine methods to reweight classical molecular mechanics solvation calculations to more expensive QM/MM energy functions. We first consider the solvation free energy difference between ethane and methanol in a QM/MM Hamiltonian from configurations generated in a cheaper MM potential. The solute molecules in the QM/MM Hamiltonian are treated with B3LYP/6-31G*, and the solvent water molecules are treated classically. The free energy difference in the QM/MM Hamiltonian is estimated using Boltzmann reweighting with both the non-Boltzmann Bennett method (NBB) and the multistate Bennett acceptance ratio (MBAR), and the variance of each method is directly compared for an identical data set. For this system, MBAR-derived methods are found to produce smaller overall uncertainties than NBB-based methods. Additionally, we show that to reduce the variance in the overall free energy difference estimate in this system for a fixed amount of QM/MM calculations, the energy re-evaluations in the Boltzmann reweighting step should be concentrated on the physical MM states with the highest overlap to the QM/MM states, rather than allocated equally over all sampled MM states. We also show that reallocating the QM/MM re-evaluations can be used to diagnose poor overlap between the sampled and target state. The solvation free energies for molecules in the SAMPL4 solvation data set are also calculated in the QM/MM Hamiltonian with NBB and MBAR, and the variances are marginally smaller for MBAR. Overall, NBB and MBAR produce similar variances for systems with poor sampling efficiency, and MBAR provides smaller variances than NBB in systems with high sampling efficiency. Both NBB and MBAR converge to identical solvation free energy estimates in the QM/MM Hamiltonian, and the RMSD to experimental values for molecules in the SAMPL4 solvation data set decreases by approximately 28% when switching from the MM Hamiltonian to the QM/MM Hamiltonian.
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Affiliation(s)
- Eric C Dybeck
- Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States
| | - Gerhard König
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Michael R Shirts
- Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States
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69
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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70
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Tang X, Liu X, Shen W, Hu W, He R, Li M. Theoretical investigations of the small molecular acceptor materials based on oligothiophene – naphthalene diimide in organic solar cells. RSC Adv 2016. [DOI: 10.1039/c6ra20619k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The electronic transmission paths of NDI-T3DCRD with the centroid distance from core molecule to ambient molecules marked.
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Affiliation(s)
- Xiaoqin Tang
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Xiaorui Liu
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Wei Shen
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Weixia Hu
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Rongxing He
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
| | - Ming Li
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
- China
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71
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Heit YN, Nanda KD, Beran GJO. Predicting finite-temperature properties of crystalline carbon dioxide from first principles with quantitative accuracy. Chem Sci 2015; 7:246-255. [PMID: 29861980 PMCID: PMC5952317 DOI: 10.1039/c5sc03014e] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/28/2015] [Indexed: 11/21/2022] Open
Abstract
The temperature-dependence of the crystalline carbon dioxide (phase I) structure, thermodynamics, and mechanical properties are predicted in excellent agreement with experiment over a 200 K temperature range using high-level electronic structure calculations.
Molecular crystal structures, thermodynamics, and mechanical properties can vary substantially with temperature, and predicting these temperature-dependencies correctly is important for many practical applications in the pharmaceutical industry and other fields. However, most electronic structure predictions of molecular crystal properties neglect temperature and/or thermal expansion, leading to potentially erroneous results. Here, we demonstrate that by combining large basis set second-order Møller–Plesset (MP2) or even coupled cluster singles, doubles, and perturbative triples (CCSD(T)) electronic structure calculations with a quasiharmonic treatment of thermal expansion, experimentally observable properties such as the unit cell volume, heat capacity, enthalpy, entropy, sublimation point and bulk modulus of phase I crystalline carbon dioxide can be predicted in excellent agreement with experiment over a broad range of temperatures. These results point toward a promising future for ab initio prediction of molecular crystal properties at real-world temperatures and pressures.
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Affiliation(s)
- Yonaton N Heit
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
| | - Kaushik D Nanda
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
| | - Gregory J O Beran
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
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72
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Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening. Nat Commun 2015. [PMID: 26198974 PMCID: PMC4525153 DOI: 10.1038/ncomms8793] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. Crystal polymorphism can lead to substances with vastly differing physicochemical properties, which has serious implications in the pharmaceutical industry. Here, the authors use in silico polymorph screening to accurately predict the resulting structures under set crystallisation environments.
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73
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Abstract
Nearly twenty years ago, Dunitz and Bernstein described a selection of intriguing cases of polymorphs that disappear. The inability to obtain a crystal form that has previously been prepared is indeed a frustrating and potentially serious problem for solid-state scientists. This Review discusses recent occurrences and examples of disappearing polymorphs (as well as the emergence of elusive crystal forms) to demonstrate the enduring relevance of this troublesome, but always captivating, phenomenon in solid-state research. A number of these instances have been central issues in patent litigations. This Review, therefore, also highlights the complex relationship between crystal chemistry and the law.
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Affiliation(s)
- Dejan-Krešimir Bučar
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom).
| | - Robert W Lancaster
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom).
| | - Joel Bernstein
- Faculty of Natural Sciences, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi (United Arab Emirates). ,
- New York University Shanghai, Pudong New Area, Shanghai 200122 (China). ,
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84120 (Israel). ,
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74
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Bučar DK, Lancaster RW, Bernstein J. Verschwundene Polymorphe: eine Neubetrachtung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410356] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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75
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Lund AM, Pagola GI, Orendt AM, Ferraro MB, Facelli JC. Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine. Chem Phys Lett 2015; 626:20-24. [PMID: 25843964 DOI: 10.1016/j.cplett.2015.03.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.
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Affiliation(s)
- Albert M Lund
- Department of Chemistry, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, US ; Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, US
| | - Gabriel I Pagola
- Departamento de Física, and Ifiba (CONICET) Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina
| | - Anita M Orendt
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, US
| | - Marta B Ferraro
- Departamento de Física, and Ifiba (CONICET) Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina
| | - Julio C Facelli
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, US ; Department of Biomedical Informatics, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, US
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76
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Graiff C, Pontiroli D, Bergamonti L, Cavallari C, Lottici PP, Predieri G. Structural investigation ofN,N′-methylenebisacrylamideviaX-ray diffraction assisted by crystal structure prediction. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715004161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The crystal structure ofN,N′-methylenebisacrylamide was determined through the geometry optimization of the molecular unit with density functional theory and conformational analysis, and then through the calculation of the packingviaa crystal structure prediction protocol, based on lattice energy minimization. All the calculated structures were ranked, comparing their powder pattern with the laboratory low-quality X-ray diffraction data. Rietveld refinement of the best three proposed structures allowed the most probable crystal arrangement of the molecules to be obtained. This approach was essential for disentangling the twinning problems affecting the single-crystal X-ray diffraction data, collected on samples obtainedviarecrystallization of powder, which definitely confirmed the predicted model. It was found thatN,N′-methylenebisacrylamide shows a monoclinic structure in the space groupC2/c, with lattice parametersa= 17.822 (12),b= 4.850 (3),c= 19.783 (14) Å, β = 102.370 (9)°,V= 1670 (2) Å3. Two strong interactions between the amide protons and the carbonyl groups of neighbouring molecules were found along thebaxis, determining the crystal growth in the form of wires in this direction. This work provides a further example of how computational methods may help to investigate low-quality molecular crystals with standard diffraction techniques.
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77
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Habgood M, Sugden IJ, Kazantsev AV, Adjiman CS, Pantelides CC. Efficient Handling of Molecular Flexibility in Ab Initio Generation of Crystal Structures. J Chem Theory Comput 2015; 11:1957-69. [DOI: 10.1021/ct500621v] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Matthew Habgood
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Isaac J. Sugden
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrei V. Kazantsev
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claire S. Adjiman
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Constantinos C. Pantelides
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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78
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Vasileiadis M, Pantelides CC, Adjiman CS. Prediction of the crystal structures of axitinib, a polymorphic pharmaceutical molecule. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.08.058] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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79
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Wicker JGP, Cooper RI. Will it crystallise? Predicting crystallinity of molecular materials. CrystEngComm 2015. [DOI: 10.1039/c4ce01912a] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Machine learning algorithms can be used to create models which separate molecular materials which will form good-quality crystals from those that will not, and predict how synthetic modifications will change the crystallinity.
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80
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Saha S, Rajput L, Joseph S, Mishra MK, Ganguly S, Desiraju GR. IR spectroscopy as a probe for C–H⋯X hydrogen bonded supramolecular synthons. CrystEngComm 2015. [DOI: 10.1039/c4ce02034k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We describe a five step IR spectroscopic method that identifies supramolecular synthons in weak hydrogen bonded dimer assemblies, bifurcated systems, and π-electron mediated synthons.
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Affiliation(s)
- Subhankar Saha
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
| | - Lalit Rajput
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
| | - Sumy Joseph
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
| | - Manish Kumar Mishra
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
| | - Somnath Ganguly
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
| | - Gautam R. Desiraju
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
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81
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Mörschel P, Schmidt MU. Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2014; 71:26-35. [PMID: 25537386 DOI: 10.1107/s2053273314018907] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 08/20/2014] [Indexed: 11/10/2022]
Abstract
A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.
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Affiliation(s)
- Philipp Mörschel
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Martin U Schmidt
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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82
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Hursthouse M. Chemistry Central Journal themed issue: Current Topics in Chemical Crystallography. Chem Cent J 2014; 8:69. [PMID: 25512762 PMCID: PMC4266190 DOI: 10.1186/s13065-014-0069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/30/2014] [Indexed: 11/10/2022] Open
Abstract
No abstract
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Affiliation(s)
- Mike Hursthouse
- Chemistry, Faculty of Natural and Life Sciences, University of Southampton, Southampton, SO17 1BJ UK
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21588 Saudi Arabia
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83
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Abstract
The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.
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Affiliation(s)
- Tejender S Thakur
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226 031, India
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84
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Zhu Q, Sharma V, Oganov AR, Ramprasad R. Predicting polymeric crystal structures by evolutionary algorithms. J Chem Phys 2014; 141:154102. [DOI: 10.1063/1.4897337] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Qiang Zhu
- Department of Geosciences, Stony Brook University, Center for Materials by Design, Institute for Advanced Computational Science, Stony Brook, New York 11794, USA
| | - Vinit Sharma
- Materials Science and Engineering, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06626, USA
| | - Artem R. Oganov
- Department of Geosciences, Stony Brook University, Center for Materials by Design, Institute for Advanced Computational Science, Stony Brook, New York 11794, USA
- Department of Problems of Physics and Energetics, Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny City, Moscow Region 141700, Russia
- Department of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Ramamurthy Ramprasad
- Materials Science and Engineering, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06626, USA
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85
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Song HJ, Zhang YG, Li H, Zhou T, Huang FL. All-atom, non-empirical, and tailor-made force field for α-RDX from first principles. RSC Adv 2014. [DOI: 10.1039/c4ra07195f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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86
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Groom CR, Reilly AM. Sixth blind test of organic crystal-structure prediction methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2014; 70:776-777. [PMID: 25080257 DOI: 10.1107/s2052520614015923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 07/08/2014] [Indexed: 06/03/2023]
Abstract
Over the past 15 years progress in predicting crystal structures of small organic molecules has been charted by a series of blind tests hosted by the Cambridge Crystallographic Data Centre. This letter announces a sixth blind test to take place between September 2014 and August 2015, giving details of the target systems and the revised procedure. We hope that as many methods as possible will be assessed and benchmarked in this new blind test.
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Affiliation(s)
- Colin R Groom
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Anthony M Reilly
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
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87
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Presti D, Pedone A, Menziani MC. Unraveling the Polymorphism of [(p-cymene)Ru(κN-INA)Cl2] through Dispersion-Corrected DFT and NMR GIPAW Calculations. Inorg Chem 2014; 53:7926-35. [DOI: 10.1021/ic5006743] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Davide Presti
- Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio-Emilia, 183 via G. Campi, I-41125 Modena, Italy
| | - Alfonso Pedone
- Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio-Emilia, 183 via G. Campi, I-41125 Modena, Italy
| | - Maria Cristina Menziani
- Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio-Emilia, 183 via G. Campi, I-41125 Modena, Italy
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88
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Habermehl S, Mörschel P, Eisenbrandt P, Hammer SM, Schmidt MU. Structure determination from powder data without prior indexing, using a similarity measure based on cross-correlation functions. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2014; 70:347-59. [DOI: 10.1107/s2052520613033994] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/17/2013] [Indexed: 11/10/2022]
Abstract
A method to refine organic crystal structures from powder diffraction data with incorrect lattice parameters has been developed. The method is based on the similarity measure developed by de Gelderet al.[J. Comput. Chem.(2001),22, 273–289], using the cross- and auto-correlation functions of a simulated and an experimental powder pattern. The lattice parameters, molecular position, molecular orientation and selected intramolecular degrees of freedom are optimized until the similarity measure reaches a maximum; subsequently, a Rietveld refinement is carried out. The programFIDEL(FIt with DEviating Lattice parameters) implements this method. The procedure is also suitable for unindexed powder data, powder diagrams of very low quality and powder diagrams of non-phase-pure samples. Various applications are shown, including structure determinations from powder data using crystal structure predictions by standard force-field methods. Other useful applications include the automatic structure determination from powder data starting from the crystal structures of isostructural compounds (e.g.a solvate, hydrate or chemical derivative), or from crystal data measured at a different temperature or pressure.
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89
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A review of the effect of multiple conformers on crystallization from solution and strategies for crystallizing slow inter-converting conformers. Chem Eng Sci 2014. [DOI: 10.1016/j.ces.2013.11.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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90
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Thompson HPG, Day GM. Which conformations make stable crystal structures? Mapping crystalline molecular geometries to the conformational energy landscape. Chem Sci 2014. [DOI: 10.1039/c4sc01132e] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Flexible organic molecules often do not adopt their lowest energy conformer in crystal structures. We find that there is a preference for molecules to crystallise with high surface area conformers.
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Affiliation(s)
| | - Graeme M. Day
- School of Chemistry
- University of Southampton
- Southampton, UK
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91
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Pyzer-Knapp EO, Thompson HPG, Schiffmann F, Jelfs KE, Chong SY, Little MA, Cooper AI, Day GM. Predicted crystal energy landscapes of porous organic cages. Chem Sci 2014. [DOI: 10.1039/c4sc00095a] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Computational methods predict the crystal packing of porous organic cage molecules, allowing crystal structure and porosity to be predicted starting from the chemical diagram alone.
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Affiliation(s)
| | | | | | - Kim E. Jelfs
- Department of Chemistry
- Imperial College London
- London, UK
| | - Samantha Y. Chong
- Department of Chemistry and Centre for Materials Discovery
- University of Liverpool
- Liverpool, UK
| | - Marc A. Little
- Department of Chemistry and Centre for Materials Discovery
- University of Liverpool
- Liverpool, UK
| | - Andrew I. Cooper
- Department of Chemistry and Centre for Materials Discovery
- University of Liverpool
- Liverpool, UK
| | - Graeme M. Day
- School of Chemistry
- University of Southampton
- Southampton, UK
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92
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Pantelides CC, Adjiman CS, Kazantsev AV. General Computational Algorithms for Ab Initio Crystal Structure Prediction for Organic Molecules. Top Curr Chem (Cham) 2014; 345:25-58. [DOI: 10.1007/128_2013_497] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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93
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Saha S, Ganguly S, Desiraju GR. Graded IR Filters: Distinguishing Between Single and Multipoint NO2···I Halogen Bonded Supramolecular Synthons (P, Q, and R Synthons). Aust J Chem 2014. [DOI: 10.1071/ch14361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The NO2···I supramolecular synthon is a halogen bonded recognition pattern that is present in the crystal structures of many compounds that contain these functional groups. These synthons have been previously distinguished as P, Q, and R types using topological and geometrical criteria. A five step IR spectroscopic sequence is proposed here to distinguish between these synthon types in solid samples. Sets of known compounds that contain the P, Q, and R synthons are first taken to develop IR spectroscopic identifiers for them. The identifiers are then used to create graded IR filters that sieve the synthons. These filters contain signatures of the individual NO2···I synthons and may be applied to distinguish between P, Q, and R synthon varieties. They are also useful to identify synthons that are of a borderline character, synthons in disordered structures wherein the crystal structure in itself is not sufficient to distinguish synthon types, and in the identification of the NO2···I synthons in compounds with unknown crystal structures. This study establishes clear differences for the three different geometries P, Q, and R and in the chemical differences in the intermolecular interactions contained in the synthons. Our IR method can be conveniently employed when single crystals are not readily available also in high throughput analysis. It is possible that such identification may also be adopted as an input for crystal structure prediction analysis of compounds with unknown crystal structures.
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94
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Crystal Structure Prediction and Its Application in Earth and Materials Sciences. Top Curr Chem (Cham) 2014; 345:223-56. [DOI: 10.1007/128_2013_508] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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95
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96
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Yuan Y, Mills MJL, Popelier PLA. Multipolar electrostatics for proteins: Atom-atom electrostatic energies in crambin. J Comput Chem 2013; 35:343-59. [DOI: 10.1002/jcc.23469] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/04/2013] [Accepted: 09/29/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Yongna Yuan
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN United Kingdom
- School of Chemistry, University of Manchester; Oxford Road Manchester M13 9PL United Kingdom
| | - Matthew J. L. Mills
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN United Kingdom
- School of Chemistry, University of Manchester; Oxford Road Manchester M13 9PL United Kingdom
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN United Kingdom
- School of Chemistry, University of Manchester; Oxford Road Manchester M13 9PL United Kingdom
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97
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Ananyev IV, Nefedov SE, Lyssenko KA. From Coordination Polyhedra to Molecular Environment and Back - Interplay between Coordinate and Hydrogen Bonds in Two Polymorphs of a Cobalt Complex. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201201363] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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98
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Zhang Y, Maginn EJ. Toward Fully in Silico Melting Point Prediction Using Molecular Simulations. J Chem Theory Comput 2013; 9:1592-9. [DOI: 10.1021/ct301095j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Edward J. Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556,
United States
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99
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Brog JP, Chanez CL, Crochet A, Fromm KM. Polymorphism, what it is and how to identify it: a systematic review. RSC Adv 2013. [DOI: 10.1039/c3ra41559g] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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100
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Harper JK, Iuliucci R, Gruber M, Kalakewich K. Refining crystal structures with experimental 13C NMR shift tensors and lattice-including electronic structure methods. CrystEngComm 2013. [DOI: 10.1039/c3ce40108a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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