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Title: ROY Revisited, Again: The Eighth Solved Structure

Abstract

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orange forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.

Authors:
 [1];  [1];  [2];  [3];  [4];  [5];  [1];  [6];  [2]
  1. New York Univ. (NYU), NY (United States). Dept. of Chemistry and Molecular Design Inst.
  2. Univ. of Nevada, Las Vegas, NV (United States). High Pressure Science and Engineering Center (HiPSEC), and Dept. of Physics and Astronomy
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS), X-ray Science Division
  4. Brookhaven National Lab. (BNL), Upton, NY (United States). National Synchrotron Light Source II (NSLS-II), Photon Sciences Division
  5. New York Univ. (NYU), NY (United States). Dept. of Chemistry and Molecular Design Inst.; Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology
  6. New York Univ. (NYU), NY (United States). Dept. of Chemistry and Molecular Design Inst.; Waseda Univ., Shinjuku (Japan). Dept. of Advanced Science and Engineering
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Science Foundation (NSF); National Institutes of Health (NIH); USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1436447
Alternate Identifier(s):
OSTI ID: 1461212; OSTI ID: 1487030
Report Number(s):
BNL-203633-2018-JAAM
Journal ID: ISSN 1359-6640; FDISE6
Grant/Contract Number:  
SC0012704; NA0001982; AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Faraday Discussions
Additional Journal Information:
Journal Volume: 211; Journal ID: ISSN 1359-6640
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE

Citation Formats

Tan, Melissa, Shtukenberg, Alexander G., Zhu, Shengcai, Xu, Wenqian, Dooryhee, Eric, Nichols, Shane M., Ward, Michael David, Kahr, Bart, and Zhu, Qiang. ROY Revisited, Again: The Eighth Solved Structure. United States: N. p., 2018. Web. doi:10.1039/C8FD00039E.
Tan, Melissa, Shtukenberg, Alexander G., Zhu, Shengcai, Xu, Wenqian, Dooryhee, Eric, Nichols, Shane M., Ward, Michael David, Kahr, Bart, & Zhu, Qiang. ROY Revisited, Again: The Eighth Solved Structure. United States. doi:10.1039/C8FD00039E.
Tan, Melissa, Shtukenberg, Alexander G., Zhu, Shengcai, Xu, Wenqian, Dooryhee, Eric, Nichols, Shane M., Ward, Michael David, Kahr, Bart, and Zhu, Qiang. Mon . "ROY Revisited, Again: The Eighth Solved Structure". United States. doi:10.1039/C8FD00039E. https://www.osti.gov/servlets/purl/1436447.
@article{osti_1436447,
title = {ROY Revisited, Again: The Eighth Solved Structure},
author = {Tan, Melissa and Shtukenberg, Alexander G. and Zhu, Shengcai and Xu, Wenqian and Dooryhee, Eric and Nichols, Shane M. and Ward, Michael David and Kahr, Bart and Zhu, Qiang},
abstractNote = {X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orange forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.},
doi = {10.1039/C8FD00039E},
journal = {Faraday Discussions},
issn = {1359-6640},
number = ,
volume = 211,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 8 works
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Figures / Tables:

Fig. 1 Fig. 1: ROY molecule (left). The torsion angles are indicated by θthio and θphen. Optical micrograph of spherulites of three ROY phases (YN, ON, R05) grown from the melt viewed with polarized light microscope (right).

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    Works referencing / citing this record:

    Growth Actuated Bending and Twisting of Single Crystals
    journal, January 2014

    • Shtukenberg, Alexander G.; Punin, Yurii O.; Gujral, Ankit
    • Angewandte Chemie International Edition, Vol. 53, Issue 3
    • DOI: 10.1002/anie.201301223

    DDT Polymorphism and the Lethality of Crystal Forms
    journal, June 2017

    • Yang, Jingxiang; Hu, C. T.; Zhu, Xiaolong
    • Angewandte Chemie International Edition, Vol. 56, Issue 34
    • DOI: 10.1002/anie.201703028

    Crystallization Force-A Density Functional Theory Concept for Revealing Intermolecular Interactions and Molecular Packing in Organic Crystals
    journal, November 2008

    • Li, Tonglei; Ayers, Paul W.; Liu, Shubin
    • Chemistry - A European Journal, Vol. 15, Issue 2
    • DOI: 10.1002/chem.200801056

    Conformational and Color Polymorphism of 5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile
    journal, November 1995

    • Stephenson, G. A.; Borchardt, T. B.; Byrn, S. R.
    • Journal of Pharmaceutical Sciences, Vol. 84, Issue 11
    • DOI: 10.1002/jps.2600841122

    Ab initio molecular simulations with numeric atom-centered orbitals
    journal, November 2009

    • Blum, Volker; Gehrke, Ralf; Hanke, Felix
    • Computer Physics Communications, Vol. 180, Issue 11
    • DOI: 10.1016/j.cpc.2009.06.022

    New developments in evolutionary structure prediction algorithm USPEX
    journal, April 2013

    • Lyakhov, Andriy O.; Oganov, Artem R.; Stokes, Harold T.
    • Computer Physics Communications, Vol. 184, Issue 4
    • DOI: 10.1016/j.cpc.2012.12.009

    Multichannel Mueller matrix ellipsometer based on the dual rotating compensator principle
    journal, May 2004


    The Third Ambient Aspirin Polymorph
    journal, May 2017

    • Shtukenberg, Alexander G.; Hu, Chunhua T.; Zhu, Qiang
    • Crystal Growth & Design, Vol. 17, Issue 6
    • DOI: 10.1021/acs.cgd.7b00673

    Modeling Polymorphic Molecular Crystals with Electronic Structure Theory
    journal, March 2016


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    journal, September 2010


    Comparison of Polymorphic Molecular Crystal Structures through Hirshfeld Surface Analysis
    journal, April 2007

    • McKinnon, Joshua J.; Fabbiani, Francesca P. A.; Spackman, Mark A.
    • Crystal Growth & Design, Vol. 7, Issue 4
    • DOI: 10.1021/cg060773k

    Evaluating the Roles of Conformational Strain and Cohesive Binding in Crystalline Polymorphs of Aripiprazole
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    • Delaney, Sean P.; Pan, Duohai; Yin, Shawn X.
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    Parametrization and Benchmark of DFTB3 for Organic Molecules
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    • Gaus, Michael; Goez, Albrecht; Elstner, Marcus
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    • Rappe, Anthony K.; Goddard, William A.
    • The Journal of Physical Chemistry, Vol. 95, Issue 8
    • DOI: 10.1021/j100161a070

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    • Chen, Shuang; Guzei, Ilia A.; Yu, Lian
    • Journal of the American Chemical Society, Vol. 127, Issue 27
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    Cross-Nucleation between ROY Polymorphs
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    • Chen, Shuang; Xi, Hanmi; Yu, Lian
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    • DOI: 10.1021/ja056072d

    Nonamorphism in Flufenamic Acid and a New Record for a Polymorphic Compound with Solved Structures
    journal, June 2012

    • López-Mejías, Vilmalí; Kampf, Jeff W.; Matzger, Adam J.
    • Journal of the American Chemical Society, Vol. 134, Issue 24
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    Thermochemistry and Conformational Polymorphism of a Hexamorphic Crystal System
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    • Yu, Lian; Stephenson, Gregory A.; Mitchell, Christine A.
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    Resorcinol Crystallization from the Melt: A New Ambient Phase and New “Riddles”
    journal, March 2016

    • Zhu, Qiang; Shtukenberg, Alexander G.; Carter, Damien J.
    • Journal of the American Chemical Society, Vol. 138, Issue 14
    • DOI: 10.1021/jacs.6b01120

    Dichroism in Helicoidal Crystals
    journal, September 2016

    • Cui, Xiaoyan; Nichols, Shane M.; Arteaga, Oriol
    • Journal of the American Chemical Society, Vol. 138, Issue 37
    • DOI: 10.1021/jacs.6b06278

    DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method
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    • Aradi, B.; Hourahine, B.; Frauenheim, Th.
    • The Journal of Physical Chemistry A, Vol. 111, Issue 26
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    A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
    journal, April 2010

    • Grimme, Stefan; Antony, Jens; Ehrlich, Stephan
    • The Journal of Chemical Physics, Vol. 132, Issue 15
    • DOI: 10.1063/1.3382344

    Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory
    journal, September 2012

    • Klimeš, Jiří; Michaelides, Angelos
    • The Journal of Chemical Physics, Vol. 137, Issue 12
    • DOI: 10.1063/1.4754130

    The General Utility Lattice Program ( GULP )
    journal, May 2003


    Ab initio determination of the crystalline benzene lattice energy to sub-kilojoule/mole accuracy
    journal, August 2014


    Monte Carlo indexing with McMaille
    journal, September 2004


      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.