1
|
Banerjee A, Jasrasaria D, Niblett SP, Wales DJ. Crystal Structure Prediction for Benzene Using Basin-Hopping Global Optimization. J Phys Chem A 2021; 125:3776-3784. [PMID: 33881850 PMCID: PMC8279651 DOI: 10.1021/acs.jpca.1c00903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/07/2021] [Indexed: 11/29/2022]
Abstract
Organic molecules can be stable in distinct crystalline forms, known as polymorphs, which have significant consequences for industrial applications. Here, we predict the polymorphs of crystalline benzene computationally for an accurate anisotropic model parametrized to reproduce electronic structure calculations. We adapt the basin-hopping global optimization procedure to the case of crystalline unit cells, simultaneously optimizing the molecular coordinates and unit cell parameters to locate multiple low-energy structures from a variety of crystal space groups. We rapidly locate all the well-established experimental polymorphs of benzene, each of which corresponds to a single local energy minimum of the model. Our results show that basin-hopping can be both an efficient and effective tool for polymorphic crystal structure prediction, requiring no a priori experimental knowledge of cell parameters or symmetry.
Collapse
Affiliation(s)
- Atreyee Banerjee
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Max
Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Dipti Jasrasaria
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of California, Berkeley, California 94609, United States
| | - Samuel P. Niblett
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of California, Berkeley, California 94609, United States
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94609, United States
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
2
|
Giordano N, Beavers CM, Campbell BJ, Eigner V, Gregoryanz E, Marshall WG, Peña-Álvarez M, Teat SJ, Vennari CE, Parsons S. High-pressure polymorphism in pyridine. IUCRJ 2020; 7:58-70. [PMID: 31949905 PMCID: PMC6949594 DOI: 10.1107/s2052252519015616] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Single crystals of the high-pressure phases II and III of pyridine have been obtained by in situ crystallization at 1.09 and 1.69 GPa, revealing the crystal structure of phase III for the first time using X-ray diffraction. Phase II crystallizes in P212121 with Z' = 1 and phase III in P41212 with Z' = ½. Neutron powder diffraction experiments using pyridine-d5 establish approximate equations of state of both phases. The space group and unit-cell dimensions of phase III are similar to the structures of other simple compounds with C 2v molecular symmetry, and the phase becomes stable at high pressure because it is topologically close-packed, resulting in a lower molar volume than the topologically body-centred cubic phase II. Phases II and III have been observed previously by Raman spectroscopy, but have been mis-identified or inconsistently named. Raman spectra collected on the same samples as used in the X-ray experiments establish the vibrational characteristics of both phases unambiguously. The pyridine molecules interact in both phases through CH⋯π and CH⋯N interactions. The nature of individual contacts is preserved through the phase transition between phases III and II, which occurs on decompression. A combination of rigid-body symmetry mode analysis and density functional theory calculations enables the soft vibrational lattice mode which governs the transformation to be identified.
Collapse
Affiliation(s)
- Nico Giordano
- Centre for Science at Extreme Conditions and EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkley, CA 94720, USA
| | - Christine M. Beavers
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
- Diamond Light Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
| | - Branton J. Campbell
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA
| | - Václav Eigner
- Centre for Science at Extreme Conditions and EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Institute of Physics of the AS CR, v.v.i., Cukrovarnicka 10, 162 00 Prague 6, Czech Republic
| | - Eugene Gregoryanz
- School of Physics and Astronomy and the Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Willliam G. Marshall
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot OX11 0QX, UK
| | - Miriam Peña-Álvarez
- School of Physics and Astronomy and the Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Simon J. Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkley, CA 94720, USA
| | - Cara E. Vennari
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Simon Parsons
- Centre for Science at Extreme Conditions and EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
| |
Collapse
|
3
|
Kodaya Y, Oki T, Yamakado H, Tokoyama H, Ohno K. Crystal Structure Exploration of Boron Nitride Polymorphs Using Anharmonic Downward Distortion Following Method with Potential Energy Surface Modified by the Inverse of Lattice Volume. CHEM LETT 2019. [DOI: 10.1246/cl.190520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yoshitomo Kodaya
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Takuto Oki
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Hideo Yamakado
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Hiroaki Tokoyama
- Institute for Quantum Chemical Exploration, 1-9-36 Konan, Minato-ku, Tokyo 108-0075, Japan
| | - Koichi Ohno
- Institute for Quantum Chemical Exploration, 1-9-36 Konan, Minato-ku, Tokyo 108-0075, Japan
- Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| |
Collapse
|
4
|
Abstract
We investigate, using molecular dynamics simulations, the spontaneous homogeneous melting of benzene phase I under a high pressure of 1.0 GPa. We find an apparent stepwise transition via a metastable crystal phase, unlike the direct melting observed at ambient pressure. The transition to the metastable phase is achieved by rotational motions, without the diffusion of the center of mass of benzene. The metastable crystal completely occupies the whole space and maintains its structure for at least several picoseconds, so that the phase seems to have a local free energy minimum. The unit cell is found to be unique—no such crystalline structure has been reported so far. Furthermore, we discuss the influence of pressure control on the melting behavior.
Collapse
|
5
|
Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Dispersion-Corrected Mean-Field Electronic Structure Methods. Chem Rev 2016; 116:5105-54. [DOI: 10.1021/acs.chemrev.5b00533] [Citation(s) in RCA: 799] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | | | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| |
Collapse
|
8
|
Sure R, Brandenburg JG, Grimme S. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources. ChemistryOpen 2016; 5:94-109. [PMID: 27308221 PMCID: PMC4906470 DOI: 10.1002/open.201500192] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/12/2022] Open
Abstract
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
Collapse
Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| |
Collapse
|
9
|
Yang J, Hu W, Usvyat D, Matthews D, Schütz M, Chan GKL. Ab initio determination of the crystalline benzene lattice energy to sub-kilojoule/mole accuracy. Science 2014; 345:640-3. [DOI: 10.1126/science.1254419] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Computation of lattice energies to an accuracy sufficient to distinguish polymorphs is a fundamental bottleneck in crystal structure prediction. For the lattice energy of the prototypical benzene crystal, we combined the quantum chemical advances of the last decade to attain sub-kilojoule per mole accuracy, an order-of-magnitude improvement in certainty over prior calculations that necessitates revision of the experimental extrapolation to 0 kelvin. Our computations reveal the nature of binding by improving on previously inaccessible or inaccurate multibody and many-electron contributions and provide revised estimates of the effects of temperature, vibrations, and relaxation. Our demonstration raises prospects for definitive first-principles resolution of competing polymorphs in molecular crystal structure prediction.
Collapse
Affiliation(s)
- Jun Yang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Weifeng Hu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Denis Usvyat
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg D-93040, Germany
| | - Devin Matthews
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 078712, USA
| | - Martin Schütz
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg D-93040, Germany
| | | |
Collapse
|
10
|
Yu TQ, Tuckerman ME. Temperature-accelerated method for exploring polymorphism in molecular crystals based on free energy. PHYSICAL REVIEW LETTERS 2011; 107:015701. [PMID: 21797550 DOI: 10.1103/physrevlett.107.015701] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/04/2011] [Indexed: 05/27/2023]
Abstract
The ability of certain organic molecules to form multiple crystal structures, known as polymorphism, has important ramifications for pharmaceuticals and high energy materials. Here, we introduce an efficient molecular dynamics method for rapidly identifying and thermodynamically ranking polymorphs. The new method employs high temperature and adiabatic decoupling to the simulation cell parameters in order to sample the Gibbs free energy of the polymorphs. Polymorphism in solid benzene is revisited, and a resolution to a long-standing controversy concerning the benzene II structure is proposed.
Collapse
Affiliation(s)
- Tang-Qing Yu
- Department of Chemistry, New York University, New York, 10003, USA.
| | | |
Collapse
|
11
|
|
12
|
Yao Y, Shen W, Nohra B, Lescop C, Réau R. Coordination-Driven Hierarchical Organization of π-Conjugated Systems: From Molecular to Supramolecular π-Stacked Assemblies. Chemistry 2010; 16:7143-63. [DOI: 10.1002/chem.201000621] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
13
|
Martoňák R, Laio A, Bernasconi M, Ceriani C, Raiteri P, Zipoli F, Parrinello M. Simulation of structural phase transitions by metadynamics. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.220.5.489.65078] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
We describe here in detail the recently introduced methodology for simulation of structural transitions in crystals. The applications of the new scheme are illus trated on various kinds of crystals and the advantages with respect to previous schemes are emphasized. The relevance of the new method for the problem of crystal structure prediction is also discussed.
Collapse
|
14
|
Dunitz JD, Gavezzotti A. How molecules stick together in organic crystals: weak intermolecular interactions. Chem Soc Rev 2009; 38:2622-33. [PMID: 19690742 DOI: 10.1039/b822963p] [Citation(s) in RCA: 201] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This tutorial review introduces the fundamentals of intermolecular interactions in terms of the underlying physics and goes on to illustrate the most popular methods for the computer simulation of intermolecular interactions, from atom-atom potentials to ab initio methods, including intermediate, hybrid methods, with an appreciation of their relative merits and costs. Typical results are critically presented, culminating in the most difficult exercise of all, the computer prediction of crystal structures. Perspectives on our present and future ability to understand and exploit intermolecular interactions are given.
Collapse
Affiliation(s)
- Jack D Dunitz
- Chemistry Department Organic Chemistry Laboratory, Swiss Federal Institute of Technology, ETHZ, CH 8093 Zurich, Switzerland.
| | | |
Collapse
|
15
|
Dzyabchenko AV. From molecule to solid: The prediction of organic crystal structures. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2008. [DOI: 10.1134/s0036024408100075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Podeszwa R, Rice BM, Szalewicz K. Predicting structure of molecular crystals from first principles. PHYSICAL REVIEW LETTERS 2008; 101:115503. [PMID: 18851295 DOI: 10.1103/physrevlett.101.115503] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Indexed: 05/26/2023]
Abstract
A recently developed method, symmetry-adapted perturbation theory based on the density-functional description of monomers [SAPT(DFT)], is shown to be sufficiently accurate and numerically efficient to facilitate predictions of the structure of molecular crystals from first principles. In one application, a SAPT(DFT) potential was used to generate and order polymorphs of the cyclotrimethylene trinitramine crystal, resulting in the lowest-energy structure in excellent agreement with the experimental crystal. In a different application, a SAPT(DFT)-based calculation reproduced the lattice energy of the benzene crystal to within a few percent.
Collapse
Affiliation(s)
- Rafał Podeszwa
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | | | | |
Collapse
|
17
|
Karamertzanis PG, Raiteri P, Parrinello M, Leslie M, Price SL. The Thermal Stability of Lattice-Energy Minima of 5-Fluorouracil: Metadynamics as an Aid to Polymorph Prediction. J Phys Chem B 2008; 112:4298-308. [DOI: 10.1021/jp709764e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Panagiotis G. Karamertzanis
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K., Computational Science, Department of Chemistry and Applied Biosciences, ETH, Zurich, USI Campus, Via Buffi 13, CH-6900 Lugano, Switzerland, and STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, U.K
| | - Paolo Raiteri
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K., Computational Science, Department of Chemistry and Applied Biosciences, ETH, Zurich, USI Campus, Via Buffi 13, CH-6900 Lugano, Switzerland, and STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, U.K
| | - Michele Parrinello
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K., Computational Science, Department of Chemistry and Applied Biosciences, ETH, Zurich, USI Campus, Via Buffi 13, CH-6900 Lugano, Switzerland, and STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, U.K
| | - Maurice Leslie
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K., Computational Science, Department of Chemistry and Applied Biosciences, ETH, Zurich, USI Campus, Via Buffi 13, CH-6900 Lugano, Switzerland, and STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, U.K
| | - Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K., Computational Science, Department of Chemistry and Applied Biosciences, ETH, Zurich, USI Campus, Via Buffi 13, CH-6900 Lugano, Switzerland, and STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, U.K
| |
Collapse
|
18
|
Mohapatra H, Eckhardt CJ. Elastic Constants and Related Mechanical Properties of the Monoclinic Polymorph of the Carbamazepine Molecular Crystal. J Phys Chem B 2008; 112:2293-8. [DOI: 10.1021/jp077014c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Himansu Mohapatra
- Department of Chemistry, Center for Materials Research and Analysis, University of NebraskaLincoln, Lincoln, Nebraska 68588-0304
| | - Craig J. Eckhardt
- Department of Chemistry, Center for Materials Research and Analysis, University of NebraskaLincoln, Lincoln, Nebraska 68588-0304
| |
Collapse
|
19
|
Dunitz JD, Schweizer WB. Molecular pair analysis: C-H...F interactions in the crystal structure of fluorobenzene? And related matters. Chemistry 2007; 12:6804-15. [PMID: 16862632 DOI: 10.1002/chem.200600092] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The crystal structure of fluorobenzene is compared with isomorphous crystal structures of molecules of roughly similar shape. The lowest-energy fluorobenzene dimers are identified by theoretical calculations. Molecular pair analysis of the crystal structure of fluorobenzene and of an isomorphous virtual low-energy polymorph of benzene suggests that the important intermolecular interactions in the two structures are closely similar. In particular, the intermolecular C-H...F interactions in the fluorobenzene crystal have approximately the same structure-directing ability and influence on the intermolecular energy as the corresponding C-H...H interactions in benzene. Molecular pair analysis of the isomorphous crystal structures of benzonitrile, alloxan, and cyclopentene-1,2,3-trione indicates that essentially the same crystal structure can be adopted with quite different patterns of pair energies and atom-atom interactions. The question as to whether the packing radius of organic fluorine is larger or smaller than that of hydrogen, is addressed, but not answered.
Collapse
Affiliation(s)
- Jack D Dunitz
- Organic Chemistry Laboratory, ETH-Zurich, 8093 Zurich, Switzerland.
| | | |
Collapse
|
20
|
Cruz Cabeza AJ, Pidcock E, Day GM, Motherwell WDS, Jones W. Space group selection for crystal structure prediction of solvates. CrystEngComm 2007. [DOI: 10.1039/b702073b] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
21
|
|
22
|
Raiteri P, Martonák R, Parrinello M. Exploring polymorphism: the case of benzene. Angew Chem Int Ed Engl 2006; 44:3769-73. [PMID: 15887199 DOI: 10.1002/anie.200462760] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Paolo Raiteri
- Computational Science, Departement für Chemie und Angewandte Biowissenschaften, ETHZ, USI Campus, Via Buffi 13, 6900 Lugano, Switzerland.
| | | | | |
Collapse
|
23
|
Motherwell WDS. Crystal Structure Prediction and the Cambridge Structural Database. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/10587250108023734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- W. D. S. Motherwell
- a Cambridge Crystallographic Data Centre , 12 Union Road, Cambridge , CB2 1EZ , U.K
| |
Collapse
|
24
|
Dunitz JD, Gavezzotti A. Molecular recognition in organic crystals: directed intermolecular bonds or nonlocalized bonding? Angew Chem Int Ed Engl 2006; 44:1766-87. [PMID: 15685679 DOI: 10.1002/anie.200460157] [Citation(s) in RCA: 376] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Molecules are held together mainly by forces acting between individual atoms. Does the same apply to molecular clusters? Does intermolecular cohesion depend on weak bonds between individual atoms in different molecules or on less localized, more diffuse interactions between molecules? We discuss these questions from several viewpoints and in particular compare interpretations based on the extension of Bader's atoms in molecules (AIM) theory to cover closed-shell intermolecular interactions with interpretations based on the new pixel method for the calculation of coulombic, polarization, dispersion, and repulsion energies from the electron density of molecular clusters.
Collapse
Affiliation(s)
- Jack D Dunitz
- Organic Chemistry Laboratory, Swiss Federal Institute of Technology, ETH-Hönggerberg HCI H333, 8093 Zurich, Switzerland.
| | | |
Collapse
|
25
|
Raiteri P, Martoňák R, Parrinello M. Vorhersage polymorpher Strukturen: der Fall Benzol. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462760] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
26
|
Dunitz JD, Gavezzotti A. Molekulare Erkennung in organischen Kristallen: gerichtete intermolekulare oder nichtlokalisierte Bindungen? Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200460157] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
27
|
Zhao XS, Chen B, Karaborni S, Siepmann JI. Vapor−Liquid and Vapor−Solid Phase Equilibria for United-Atom Benzene Models near Their Triple Points: The Importance of Quadrupolar Interactions. J Phys Chem B 2005; 109:5368-74. [PMID: 16863203 DOI: 10.1021/jp046339f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gibbs ensemble Monte Carlo simulations were used to calculate the vapor-liquid and vapor-solid coexistence curves for benzene using two simple united-atom models. An extension of the Gibbs ensemble method that makes use of an elongated box containing a slab of the condensed phase with a vapor phase along one axis was employed for the simulations of the vapor-solid equilibria and the vapor-liquid equilibria at very low reduced temperatures. Configurational-bias and aggregation-volume-bias Monte Carlo techniques were applied to improve the sampling of particle transfers between the two simulation boxes and between the vapor and condensed-phase regions of the elongated box. An isotropic united-atom representation with six Lennard-Jones sites at the positions of the carbon atoms was used for both force fields, but one model contained three additional out-of-plane partial charge sites to explicitly represent benzene's quadrupolar interactions. Both models were fitted to reproduce the critical temperature and density of benzene and yield a fair representation of the vapor-liquid coexistence curve. In contrast, differences between the models are very large for the vapor-solid coexistence curve. In particular, the lack of explicit quadrupolar interactions for the 6-site model greatly reduces the energetic differences between liquid and solid phases, and this model yields a triple point temperature that is about a factor of 2 too low. In contrast, the 9-site model predicts a triple point of benzene at T = 253 +/- 6 K and p = 2.3 +/- 0.8 kPa in satisfactory agreement with the experimental data (T = 278.7 K and p = 4.785 kPa).
Collapse
Affiliation(s)
- Xin S Zhao
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
| | | | | | | |
Collapse
|
28
|
Pillardy J, Arnautova YA, Czaplewski C, Gibson KD, Scheraga HA. Conformation-family Monte Carlo: a new method for crystal structure prediction. Proc Natl Acad Sci U S A 2001; 98:12351-6. [PMID: 11606783 PMCID: PMC60057 DOI: 10.1073/pnas.231479298] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new global optimization method, Conformation-family Monte Carlo, has been developed recently for searching the conformational space of macromolecules. In the present paper, we adapted this method for prediction of crystal structures of organic molecules without assuming any symmetry constraints except the number of molecules in the unit cell. This method maintains a database of low energy structures that are clustered into families. The structures in this database are improved iteratively by a Metropolis-type Monte Carlo procedure together with energy minimization, in which the search is biased toward the regions of the lowest energy families. The Conformation-family Monte Carlo method is applied to a set of nine rigid and flexible organic molecules by using two popular force fields, AMBER and W99. The method performed well for the rigid molecules and reasonably well for the molecules with torsional degrees of freedom.
Collapse
Affiliation(s)
- J Pillardy
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | | | | | | | | |
Collapse
|
29
|
YONETANI YOSHITERU, YOKOI KOHEI. Solid structures of benzene at high pressures: molecular dynamics study. Mol Phys 2001. [DOI: 10.1080/00268970110067913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
30
|
Beyer T, Day GM, Price SL. The prediction, morphology, and mechanical properties of the polymorphs of paracetamol. J Am Chem Soc 2001; 123:5086-94. [PMID: 11457339 DOI: 10.1021/ja0102787] [Citation(s) in RCA: 225] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The analgesic drug paracetamol (acetaminophen) has two reported metastable polymorphs, one with better tableting properties than the stable form, and another which remains uncharacterized. We have therefore performed a systematic crystal structure prediction search for minima in the lattice energy of crystalline paracetamol. The stable monoclinic form is found as the global lattice-energy minimum, but there are at least a dozen energetically feasible structures found, including the well-characterized metastable orthorhombic phase. Hence, we require additional criteria to reduce the number of hypothetical crystal structures that can be considered as potential polymorphs. For this purpose the elastic properties and vapor growth morphology of the known and predicted structures have been estimated using second-derivative analysis and the attachment-energy model. These inexpensive calculations give reasonable agreement with the available experimental data for the known polymorphs. Some of the hypothetical structures are predicted to have a low growth rate and plate-like morphology, and so are unlikely to be observed. Another is only marginally mechanically stable. Thus, this first consideration of such properties in a crystal-structure prediction study appears to reduce the number of predicted polymorphs while leaving a few candidates for the uncharacterized form.
Collapse
Affiliation(s)
- T Beyer
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | | | | |
Collapse
|
31
|
Yonetani Y, Yokoi K. Promotion of Crystal Phase Transitions by Mass-of-cell Control in Molecular Dynamics Simulations: Phase Transitions in Benzene Crystals. MOLECULAR SIMULATION 2001. [DOI: 10.1080/08927020108024508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
32
|
Schroer JW, Monson PA. Phase equilibrium in a quadrupolar hard sphere interaction site model of benzene. J Chem Phys 2001. [DOI: 10.1063/1.1341232] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
33
|
Beyer T, Lewis T, Price SL. Which organic crystal structures are predictable by lattice energy minimisation? CrystEngComm 2001. [DOI: 10.1039/b108135g] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Pillardy J, Wawak RJ, Arnautova YA, Czaplewski C, Scheraga HA. Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions. J Am Chem Soc 2000. [DOI: 10.1021/ja9929990] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jaroslaw Pillardy
- Contribution from the Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301
| | - Ryszard J. Wawak
- Contribution from the Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301
| | - Yelena A. Arnautova
- Contribution from the Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301
| | - Cezary Czaplewski
- Contribution from the Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301
| | - Harold A. Scheraga
- Contribution from the Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301
| |
Collapse
|
35
|
Mooij WTM, van Eijck BP, Kroon J. Transferable ab Initio Intermolecular Potentials. 2. Validation and Application to Crystal Structure Prediction. J Phys Chem A 1999. [DOI: 10.1021/jp991640v] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wijnand T. M. Mooij
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bouke P. van Eijck
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jan Kroon
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
36
|
Dunitz JD, Gavezzotti A. Attractions and Repulsions in Molecular Crystals: What Can Be Learned from the Crystal Structures of Condensed Ring Aromatic Hydrocarbons? Acc Chem Res 1999. [DOI: 10.1021/ar980007+] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jack D. Dunitz
- Organic Chemistry Laboratory, Swiss Federal Institute of Technology, CH-8092 Zurich, Switzerland
| | - Angelo Gavezzotti
- Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Università di Milano, 20133 Milano, Italy
| |
Collapse
|
37
|
|
38
|
van Eijck BP, Kroon J. Upack program package for crystal structure prediction: Force fields and crystal structure generation for small carbohydrate molecules. J Comput Chem 1999; 20:799-812. [DOI: 10.1002/(sici)1096-987x(199906)20:8<799::aid-jcc6>3.0.co;2-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/1998] [Accepted: 01/15/1999] [Indexed: 11/10/2022]
|
39
|
Dzyabchenko AV, Agafonov V, Davydov VA. A Theoretical Study of the Pressure-Induced Dimerization of C60 Fullerene. J Phys Chem A 1999. [DOI: 10.1021/jp983951w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Viatcheslav Agafonov
- Laboratoire de Chimie Physique, J.E. 1990, Faculté de Pharmacie de l'Université de Tours, 31 av. Monge, 37200 Tours, France
| | - Valery A. Davydov
- Institute of High-Pressure Physics, Russian Academy of Sciences, 142092 Troitsk, Moscow Region, Russia
| |
Collapse
|