45 results on '"Sharmarke Mohamed"'
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2. Mechanically robust amino acid crystals as fiber-optic transducers and wide bandpass filters for optical communication in the near-infrared
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Durga Prasad Karothu, Ghada Dushaq, Ejaz Ahmed, Luca Catalano, Srujana Polavaram, Rodrigo Ferreira, Liang Li, Sharmarke Mohamed, Mahmoud Rasras, and Panče Naumov
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Science - Abstract
Fiber-optics based on organic crystals could have potential for unique telecommunications applications but typically transmit visible wavelengths. Here the authors present mechanically robust organic crystals with favourable optical properties across the main telecommunication bands in the near-infrared.
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- 2021
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3. Solvent inclusion in the crystal structure of bis[(adamantan-1-yl)methanaminium chloride] 1,4-dioxane hemisolvate monohydrate explained using the computed crystal energy landscape
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Sharmarke Mohamed
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crystal energy landscape ,adamantanes ,solvent-accessible voids ,solvent inclusion ,Crystallography ,QD901-999 - Abstract
Repeated attempts to crystallize 1-adamantanemethylamine hydrochloride as an anhydrate failed but the salt was successfully crystallized as a solvate (2C11H20N+·2Cl−·0.5C4H8O2·H2O), with water and 1,4-dioxane playing a structural role in the crystal and engaging in hydrogen-bonding interactions with the cation and anion. Computational crystal-structure prediction was used to rationalize the solvent-inclusion behaviour of this salt by computing the solvent-accessible voids in the predicted low-energy structures for the anhydrate: the global lattice-energy minimum structure, which has the same packing of the ions as the solvate, has solvent-accessible voids that account for 3.71% of the total unit-cell volume and is 6 kJ mol−1 more stable than the next most stable predicted structure.
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- 2016
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4. Substituent Effect on Stimuli-Responsive Donor–Acceptor Framework-Based 2-Thiohydantoins for Monitoring Nonanal Vapors
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Pratiksha P. Gawas, Arbacheena Bora, Rence P. Reji, Buthanapalli Ramakrishna, Praveen B. Managutti, Christian R. Göb, Sharmarke Mohamed, Yoshiyuki Kawazoe, Surya Velappa Jayaraman, Yuvaraj Sivalingam, and Venkatramaiah Nutalapati
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General Energy ,Physical and Theoretical Chemistry ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Published
- 2023
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5. Advances in synthesis: general discussion
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Alexander Angerhofer, Matej Baláž, Viktor Balema, Ana M. Belenguer, Richard G. Blair, Elena Boldyreva, Carsten Bolm, Lars Borchardt, Adam B. Braunschweig, Duncan L. Browne, Stephen Craig, Lamis El Wenni, Franziska Emmerling, Michael Ferguson, Cecilia Fiore, Tomislav Friščić, Kimichika Fukushima, Felipe García, Lori Gonnet, Sven Grätz, Rafael A. Hernandez R., Hajime Ito, Stuart L. James, Deniz Karabiyikli, Jeung Gon Kim, Koji Kubota, Frédéric Lamaty, Giulio I. Lampronti, Jamie Leitch, Stipe Lukin, James Mack, Lucia Maini, Sharmarke Mohamed, Audrey Moores, Karthik Nagapudi, Francesco Puccetti, Mi Tian, and Qian Yu
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Physical and Theoretical Chemistry - Published
- 2023
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6. Shear processes and polymer mechanochemistry: general discussion
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Matej Baláž, Viktor Balema, Richard G. Blair, Elena Boldyreva, Carsten Bolm, Adam B. Braunschweig, Robert W. Carpick, Stephen L. Craig, Franziska Emmerling, James P. Ewen, Cecilia Fiore, Tomislav Friščić, Sven Grätz, Ivan Halasz, Ehsan Hamzehpoor, Hajime Ito, Jeung Gon Kim, Giulio I. Lampronti, Danielle Laurencin, James Mack, Lucia Maini, Paolo P. Mazzeo, Sharmarke Mohamed, Karthik Nagapudi, Allan Niidu, Jogirdas Vainauskas, and Caterina Zuffa
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Physical and Theoretical Chemistry - Published
- 2023
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7. Mechanical properties and peculiarities of molecular crystals
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Wegood M. Awad, Daniel W. Davies, Daichi Kitagawa, Jad Mahmoud Halabi, Marieh B. Al-Handawi, Ibrahim Tahir, Fei Tong, Gonzalo Campillo-Alvarado, Alexander G. Shtukenberg, Tamador Alkhidir, Yuki Hagiwara, Mubarak Almehairbi, Linfeng Lan, Shodai Hasebe, Durga Prasad Karothu, Sharmarke Mohamed, Hideko Koshima, Seiya Kobatake, Ying Diao, Rajadurai Chandrasekar, Hongyu Zhang, Changquan Calvin Sun, Christopher Bardeen, Rabih O. Al-Kaysi, Bart Kahr, and Panče Naumov
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General Chemistry - Abstract
Molecular crystals have shown remarkable adaptability in response to a range of external stimuli. Here, we survey this emerging field and provide a critical overview of the experimental, computational and instrumental tools being used to design and apply such materials.
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- 2023
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8. Scale up and industrial implementation: general discussion
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Matej Baláž, Viktor Balema, James D. Batteas, Richard G. Blair, Carsten Bolm, Lars Borchardt, Adam B. Braunschweig, Stephen L. Craig, Franziska Emmerling, Michael Ferguson, Tomislav Friščić, Stuart James, Jamie Leitch, James Mack, Sharmarke Mohamed, Karthik Nagapudi, Francesco Puccetti, and Maria Elena Rivas
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Physical and Theoretical Chemistry - Published
- 2023
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9. Unravelling the Origin of Solvate Formation in the Anticancer Drug Trametinib: Insights from Crystal Structure Analysis and Computational Modeling
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Ipsha Shruti, Mubarak Almehairbi, Zeinab M. Saeed, Tamador Alkhidir, Wesam A. Ali, Rampal Vishwakarma, Sharmarke Mohamed, and Deepak Chopra
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General Materials Science ,General Chemistry ,Condensed Matter Physics - Published
- 2022
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10. Recent advances in quantification and remediation technologies for toxic PAH mitigation from the environment
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Bhausaheb Dhokale, Zeinab M. Saeed, Wesam A. Ali, and Sharmarke Mohamed
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- 2023
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11. Contributors
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Ali Al Alili, Saeed M. Alhassan, Wesam A. Ali, Fawzi Banat, Saroj Sundar Baral, Delicia A. Barretto, G. Bharath, Ranjeet K. Bhore, Sheshanath V. Bhosale, Lakshangy Charya, Sandeep Chauhan, Bilel Chouchene, Avelyno H. D'Costa, Samantha Da Costa, G.H. Darshan, Pinaki Dey, Bhausaheb Dhokale, Swizzle Furtado, Vilas K. Gawade, Abdul Hai, Mohammad Abu Haija, Shadi W. Hasan, Chaithanya D. Jain, Amanpreet Kaur Jassal, Sumit B. Kamble, Meenal Kowshik, Cheng Chin Kui, Kiran Kumar, Gandhita Kundaikar, Dileep Maarisetty, Maithili Majithia, Harshad A. Mirgane, Hemant Mittal, Sharmarke Mohamed, Pranay P. Morajkar, Kerba S. More, Pavan More, Dinesh N. Nadimetla, Anjani P. Nagvenkar, Amarja P. Naik, Milind M. Naik, K. Rambabu, Vivek Rangarajan, Zeinab M. Saeed, Komal Salkar, Akshay V. Salkar, Subhranshu Samal, Aleksandra Schejn, Raphaël Schneider, Shamshad Shaikh, Sarvesha S. Shetgaonkar, Pooja V. Shreechippa, Vootla Shyamkumar, Pradeep Kumar Sow, and A. Thanigaivelan
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- 2023
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12. Expanding the Supramolecular Toolkit: Computed Molecular and Crystal Properties for Supporting the Crystal Engineering of Higher-Order Molecular Ionic Cocrystals
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Tamador Alkhidir, Zeinab M. Saeed, Abeer F. Shunnar, Eman Abujami, Runyararo M. Nyadzayo, Bhausaheb Dhokale, and Sharmarke Mohamed
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General Materials Science ,General Chemistry ,Condensed Matter Physics - Published
- 2021
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13. Experimental and theoretical characterization of the interfacial adhesion of 2D heterogeneous materials: A review
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Shoaib Anwer, Baosong Li, Shaohong Luo, Tamador Alkhidir, Sharmarke Mohamed, Vincent Chan, and Kin Liao
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Polymers and Plastics ,Mechanics of Materials ,Ceramics and Composites ,Atomic and Molecular Physics, and Optics - Abstract
Two-dimensional (2D) materials have been developed intensively over the last decade, and combining different 2D materials to form heterogeneous 2D materials is anticipated to be more attractive with broader applications. The precise evaluation and prediction of interfacial properties of 2D heterostructures are critical for designing more robust heterostructures and developing advanced, engineered molecular devices. Here, we present a brief review on experimental (namely, atomic force microscopy (AFM), in situ peel test, double cantilever beam, pressurized blister test and sheet-on-bead method) and theoretical techniques (namely, molecular dynamics and density functional theory) for probing the adhesion/interaction energy of the interface of 2D heterogeneous materials and paving the way for future applications.
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- 2021
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14. Mechanosynthesis of Higher‐Order Cocrystals: Tuning Order, Functionality and Size in Cocrystal Design**
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Felix León, Wei Liang Teo, Sharmarke Mohamed, Yongxin Li, Yanli Zhao, Ying Sim, Felipe García, Rakesh Ganguly, Xiaoyan Shi, Zi Xuan Ng, Davin Tan, and School of Physical and Mathematical Sciences
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Materials science ,Intermolecular force ,Azane ,higher-order Cocrystals ,General Medicine ,General Chemistry ,Crystal engineering ,Cocrystal ,Catalysis ,Crystal ,chemistry.chemical_compound ,phosphazanes ,Cocrystals ,chemistry ,Chemical engineering ,Mechanochemistry ,Chemistry [Science] ,Mechanosynthesis ,Phosphazanes ,mechanochemistry ,Ternary operation ,Density Functional Theory ,Research Articles ,density functional theory ,Research Article - Abstract
The ability to rationally design and predictably construct crystalline solids has been the hallmark of crystal engineering research. To date, numerous examples of multicomponent crystals comprising organic molecules have been reported. However, the crystal engineering of cocrystals comprising both organic and inorganic chemical units is still poorly understood and mostly unexplored. Here, we report a new diverse set of higher‐order cocrystals (HOCs) based on the structurally versatile—yet largely unexplored—phosph(V/V)azane heterosynthon building block. The novel ternary and quaternary cocrystals reported are held together by synergistic and orthogonal intermolecular interactions. Notably, the HOCs can be readily obtained either via sequential or one‐pot mechanochemical methods. Computational modelling methods reveal that the HOCs are thermodynamically driven to form and that their mechanical properties strongly depend on the composition and intermolecular forces in the crystal, offering untapped potential for optimizing material properties., Mechanosynthesis gives ternary and quaternary hybrid organic‐inorganic cocrystals held together via synergistic intermolecular interactions. Notably, higher‐order ternary and quaternary cocrystals can be readily obtained either via serial synthetic routes from the individual components or via one‐pot approaches.
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- 2021
15. Diversity Makes Science Better: But Improving It Is a Continuous Process That Requires All of Us
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Sharmarke Mohamed
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General Materials Science ,General Chemistry ,Condensed Matter Physics - Published
- 2023
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16. Mechanoelectronics: Flexible Organic Semiconducting Single Crystals for Durable All-Flexible Field-Effect Transistors
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Ranita Samanta, Susobhan Das, Saikat Mondal, Tamador Alkhidir, Sharmarke Mohamed, Satyaprasad P Senanayak, and Chilla Malla Reddy
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Although many examples of mechanically flexible crystals are currently known, their utility in all-flexible devices is not yet demonstrated, despite their immense potential for fabricating high-performance flexible devices. We report two alkylated diketopyrrolopyrrole (DPP) semiconducting single crystals, one of which displays impressive elastic mechanical flexibility whilst the other is brittle. Using the single crystal structures and density functional theory (DFT) calculations, we show that the methylated diketopyrrolopyrrole (DPP-diMe) crystals, with dominant π-stacking interactions and large contributions from dispersive interactions, are superior in terms of their stress tolerance and field-effect mobility (µFET) when compared to the brittle crystals of ethylated diketopyrrolopyrrole derivative (DPP-diEt). The field effect transistors (FETs) made of flexible substrates using elastic microcrystals of DPPdiMe retained µFET (from 0.019 cm2/Vs to 0.014 cm2/Vs ) more efficiently even after 40 bending cycles when compared to the brittle microcrystals of DPP-diEt which showed a significant drop in µFET just after 10 bending cycles. Our results not only provide valuable insights into bending mechanism but also demonstrate the untapped potential of mechanically flexible semiconducting crystals for designing all flexible durable devices.
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- 2022
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17. Crystal Engineering of Binary Organic Eutectics: Significant Improvement in the Physicochemical Properties of Polycyclic Aromatic Hydrocarbons via the Computational and Mechanochemical Discovery of Composite Materials
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Panče Naumov, Sharmarke Mohamed, Hector H. Hernandez, Zeinab M. Saeed, Abeer F. Shunnar, Bhausaheb Dhokale, and Wegood M. Awad
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Materials science ,Chemical engineering ,Binary number ,General Materials Science ,General Chemistry ,Condensed Matter Physics ,Crystal engineering ,Eutectic system - Published
- 2021
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18. Investigating the solid-state assembly of pharmaceutically-relevant N,N-dimethyl-O-thiocarbamates in the absence of labile hydrogen bonds
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Yongxin Li, Felipe García, Rakesh Ganguly, Han Sen Soo, Sharmarke Mohamed, Davin Tan, Zi Xuan Ng, School of Physical and Mathematical Sciences, Divsion of Chemistry and Biological Chemistry, Chemistry Department, Shiv Nadar University, Gautam Buddha Nagar, India 201314, and Department of Chemistry, Khalifa University of Science and Technology, PO BOX 127788, Abu Dhabi, United Arab Emirates
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Active ingredient ,Chemistry ,Hydrogen bond ,Aryl ,Stacking ,Hydrogen Bonds ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Crystallography ,chemistry.chemical_compound ,Engineering ,Molecular geometry ,Thiocarbamates ,Molecule ,General Materials Science ,Isostructural - Abstract
There are many active pharmaceutical ingredients that lack N-H, O-H and S-H hydrogen-bond donor functional groups. N,N-disubstituted O-thiocarbamates are examples of molecules that display such a feature. Despite the desirable medicinal properties displayed by some N,N-disubstituted O-thiocarbamates, the study of the solid-state properties of these compounds has been relatively unexplored. Herein, we report the synthesis and analysis of the structures and properties of a series of N,N-dimethyl-O-thiocarbamates, and use X-ray diffraction techniques to gain insight into how these molecules self-assemble in the solid-state. As part of our work, we report for the first time the crystal structure of Tolnaftate, an active pharmaceutical ingredient that is indicated for the treatment of fungal infections. It was observed that the aryl-thiocarbamate C-O bonds are twisted such that the planar aryl and carbamate moieties are orthogonal. Such a non-planar molecular geometry affects the way the molecules pack and crystal structure analyses revealed four general modes in which the molecules can assemble in the solid-state, with some members of the series displaying isostructural relationships. Computational modelling of the cohesive energy densities in the crystals suggests that there is no single stacking type that is associated with greater stability. However, crystals with a combination of high packing index and π···π stacking interactions appear to display large cohesive energy densities. The lack of strong hydrogen bonding interactions in the crystals also leads to relatively low Young’s moduli that are within a narrow range of 10-15 GPa for all 14 crystal structures reported. Agency for Science, Technology and Research (A*STAR) Accepted version F.G. would like to thank A*STAR AME IRG (A1783c0003) and a NTU start-up grant (M4080552) for financial support. H.S.S. is grateful for the Singapore Ministry of Education Academic Research Fund Tier 1 grants RG 111/18 and RT 05/19. H.S.S. also acknowledges that this project is supported by A*STAR under the AME IRG grants A1783c0003, A1783c0002, and A1783c0007 D.T. would like to thank A*STAR for a postdoctoral research fellowship. .M. would like to acknowledge Khalifa University for financial support under the CIRA program (Project Code: CIRA-2018-068). The theoretical calculations were performed using the high-performance computing clusters of Khalifa University and the authors would like to acknowledge the support of the research computing department.
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- 2020
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19. Investigation of interfacial interaction of graphene oxide and Ti3C2Tx (MXene) via atomic force microscopy
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Shaohong Luo, Tamador Alkhidir, Sharmarke Mohamed, Shoaib Anwer, Baosong Li, Jing Fu, Kin Liao, and Vincent Chan
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History ,Polymers and Plastics ,General Physics and Astronomy ,Surfaces and Interfaces ,General Chemistry ,Business and International Management ,Condensed Matter Physics ,Industrial and Manufacturing Engineering ,Surfaces, Coatings and Films - Published
- 2023
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20. Exceptionally high work density of a ferroelectric dynamic organic crystal around room temperature
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Durga Prasad Karothu, Rodrigo Ferreira, Ghada Dushaq, Ejaz Ahmed, Luca Catalano, Jad Mahmoud Halabi, Zainab Alhaddad, Ibrahim Tahir, Liang Li, Sharmarke Mohamed, Mahmoud Rasras, and Panče Naumov
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Multidisciplinary ,General Physics and Astronomy ,General Chemistry ,General Biochemistry, Genetics and Molecular Biology - Abstract
Dynamic organic crystals are rapidly gaining traction as a new class of smart materials for energy conversion, however, they are only capable of very small strokes (
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- 2021
21. Importance of the donor unit on fluoranthene for selective detection of nitro aromatic explosives
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Kasthuri Selvaraj, Praveen B. Managutti, Sharmarke Mohamed, Satyanarayana Talam, and Venkatramaiah Nutalapati
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General Chemical Engineering ,General Physics and Astronomy ,General Chemistry - Published
- 2022
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22. Mechanically robust amino acid crystals as fiber-optic transducers and wide bandpass filters for optical communication in the near-infrared
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Panče Naumov, Mahmoud Rasras, Durga Prasad Karothu, Srujana Polavaram, Rodrigo Ferreira, Liang Li, Luca Catalano, Ghada Dushaq, Ejaz Ahmed, and Sharmarke Mohamed
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Threonine ,Optical fiber ,Materials science ,Fibre optics and optical communications ,Infrared ,C band ,Science ,Transducers ,Optical communication ,Physics::Optics ,General Physics and Astronomy ,Mechanical properties ,02 engineering and technology ,Crystallography, X-Ray ,010402 general chemistry ,01 natural sciences ,Article ,General Biochemistry, Genetics and Molecular Biology ,law.invention ,Band-pass filter ,Hardness ,law ,Elastic Modulus ,Fiber Optic Technology ,Amino Acids ,Anisotropy ,Multidisciplinary ,business.industry ,Communication ,Near-infrared spectroscopy ,Hydrogen Bonding ,General Chemistry ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Optical materials ,Optoelectronics ,Crystallization ,0210 nano-technology ,business ,Visible spectrum - Abstract
Organic crystals are emerging as mechanically compliant, light-weight and chemically versatile alternatives to the commonly used silica and polymer waveguides. However, the previously reported organic crystals were shown to be able to transmit visible light, whereas actual implementation in telecommunication devices requires transparency in the near-infrared spectral range. Here we demonstrate that single crystals of the amino acid L-threonine could be used as optical waveguides and filters with high mechanical and thermal robustness for transduction of signals in the telecommunications range. On their (00\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\bar 1$$\end{document}1¯) face, crystals of this material have an extraordinarily high Young’s modulus (40.95 ± 1.03 GPa) and hardness (1.98 ± 0.11 GPa) for an organic crystal. First-principles density functional theory calculations, used in conjunction with analysis of the energy frameworks to correlate the structure with the anisotropy in the Young’s modulus, showed that the high stiffness arises as a consequence of the strong charge-assisted hydrogen bonds between the zwitterions. The crystals have low optical loss in the O, E, S and C bands of the spectrum (1250−1600 nm), while they effectively block infrared light below 1200 nm. This property favors these and possibly other related organic crystals as all-organic fiber-optic waveguides and filters for transduction of information., Fiber-optics based on organic crystals could have potential for unique telecommunications applications but typically transmit visible wavelengths. Here the authors present mechanically robust organic crystals with favourable optical properties across the main telecommunication bands in the near-infrared.
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- 2021
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23. Direct and Telescopic Mechanochemical Synthesis of Higher-order Organic-Inorganic Hybrid Cocrystals: Tuning Order, Functionality and Size in Cocrystal Design
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Zi xuan Ng, Davin Tan, Wei Liang Teo, felix leon, Xiaoyan Shi, Ying Sim, yongxin Li, Rakesh Ganguly, Yanli Zhao, Sharmarke Mohamed, and Felipe Garcia
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chemistry.chemical_compound ,Materials science ,chemistry ,Chemical engineering ,Mechanochemistry ,Intermolecular force ,Azane ,Molecule ,Ionic bonding ,Crystal engineering ,Ternary operation ,Cocrystal - Abstract
The ability to rationally design and predictably construct crystalline solids has been the hallmark of crystal engineering research over the past two decades. When building higher-order multicomponent cocrystals (i.e. crystals containing more than two constituents), the differential and hierarchical way molecules interact and assemble in the solidstate is of pinnacle importance. To date, numerous examples of multicomponent crystals comprising organic molecules leading to salts, cocrystals or ionic cocrystals have been reported. However, the crystal engineering of hybrid organicinorganic cocrystals with sophisticated inorganic building blocks is still poorly understood and mostly unexplored. Here, we reveal the first efficient mechanochemical synthesis of higher-order hybrid organic-inorganic cocrystals based on the structurally versatile – yet largely unexplored – cyclodiphos(V/V)azane heterosynthon building block. The novel hybrid ternary and quaternary multicomponent cocrystals herein reported are held together by synergistic intermolecular interactions (e.g., hydrogen- and halogen-bonding, Se-π and ion-dipole interactions). Notably, higher-order ternary and quaternary cocrystals can be readily obtained either via direct synthetic routes from its individual components, or via unprecedented telescopic approaches from lower-order cocrystal sets. In addition, computational modelling has also revealed that the formation of higher-order cocrystals is thermodynamically driven, and that bulk moduli and compressibilities are strongly dependent on the chemical composition and intermolecular forces present in the crystals, which offer untapped potential for optimizing material properties.
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- 2021
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24. From serendipity to supramolecular design: assessing the utility of computed crystal form landscapes in inferring the risks of crystal hydration in carboxylic acids
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Liang Li and Sharmarke Mohamed
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Lattice energy ,Materials science ,Hydrogen bond ,Intermolecular force ,02 engineering and technology ,General Chemistry ,Crystal structure ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Atomic packing factor ,01 natural sciences ,Acceptor ,0104 chemical sciences ,law.invention ,Crystal ,Crystallography ,law ,General Materials Science ,Crystallization ,0210 nano-technology - Abstract
A set of calculated structural descriptors [% solvent accessible volumes per unit cell (% SAVs), the relative packing index and the estimated distance of polar/non-polar groups on the acid relative to the lattice positions corresponding to crystal voids] were used to assess the utility of predicted crystal form landscapes (CFLs) in warning against the risks of crystal hydration using model carboxylic acids that are known to crystallise as anhydrate, monohydrate and dihydrate crystal phases, respectively. The crystal structures of 1-adamantaneacetic acid and 3-bromoadamantane-1-acetic acid are reported as anhydrates following crystallisation screens for possible hydrates of both. The results show that % SAVs are a poor predictor of crystal hydration as the majority of the predicted anhydrate polymorphs (up to a relative lattice energy range of 10 kJ mol−1) for all systems did not display packings with solvent accessible voids. The relative packing index (ΔPI) of the known hydrates and the set of low energy predicted anhydrate polymorphs was found to be a useful predictor of crystal packing frustration. 4-Oxocyclohexanecarboxylic acid which crystallises as a monohydrate (INOGEX) displayed a CFL where 86% of the predicted anhydrate polymorphs within a relative lattice energy range of 10 kJ mol−1 displayed poorer crystal packings than the monohydrate. By contrast, in 2-pyrone-4,6-dicarboxylic acid which crystallises as a dihydrate (KISJEC), only 15% of predicted anhydrate polymorphs had a lower packing efficiency than the dihydrate, indicating that the crystal hydration for this system is not driven by poor crystal packing of the acid. Careful inspection of the hydrogen bond motifs adopted by the predicted anhydrate polymorphs has shown that crystal hydration in 2-pyrone-4,6-dicarboxylic acid may be driven by the need to satisfy all hydrogen bond donor/acceptor groups on the acid whilst in 4-oxocyclohexanecarboxylic acid, water inclusion is likely to be driven by poor crystal packing of the low energy anhydrate polymorphs for this molecule. The results suggest that careful analysis of the packing efficiencies and the lattice positions of the crystal voids in predicted anhydrate polymorphs can provide clues to the driving force for crystal hydration as well as the types of intermolecular acid–water interactions that may be observed in hydrated crystal forms.
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- 2018
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25. Expanding the crystal form landscape: emerging computational tools for the discovery of eutectic composites and higher-order cocrystals of organic compounds
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Zeinab M. Saeed, Bhausaheb Dhokale, Abeer F. Shunnar, Durga P. Karothu, Panče Naumov, Hector H. Hernandez, and Sharmarke Mohamed
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Inorganic Chemistry ,Structural Biology ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry - Published
- 2021
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26. Efficient screening for ternary molecular ionic cocrystals using a complementary mechanosynthesis and computational structure prediction approach
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Sharmarke Mohamed, Abeer F. Shunnar, David H. Bowskill, Bhausaheb Dhokale, Hector H. Hernandez, Isaac J. Sugden, Panče Naumov, and Durga Prasad Karothu
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Chemistry, Multidisciplinary ,Ionic bonding ,SOLID-STATE LANDSCAPE ,Crystal structure ,010402 general chemistry ,Crystal engineering ,01 natural sciences ,POTENTIAL-FUNCTION MODELS ,Catalysis ,crystal structure prediction ,law.invention ,ENERGY ,Computational chemistry ,law ,Crystallization ,mechanosynthesis ,CO-CRYSTALS ,SUPRAMOLECULAR SYNTHONS ,Science & Technology ,Full Paper ,STABILITY ,010405 organic chemistry ,Chemistry ,green chemistry ,Organic Chemistry ,SALT ,DISTRIBUTED MULTIPOLE ANALYSIS ,General Chemistry ,Full Papers ,PHARMACEUTICAL COCRYSTALS ,0104 chemical sciences ,Crystal structure prediction ,X-ray diffraction ,crystal engineering ,X-ray crystallography ,Physical Sciences ,CRYSTAL-STRUCTURE PREDICTION ,Mechanosynthesis ,molecular ionic cocrystals ,Ternary operation ,03 Chemical Sciences - Abstract
The discovery of molecular ionic cocrystals (ICCs) of active pharmaceutical ingredients (APIs) widens the opportunities for optimizing the physicochemical properties of APIs whilst facilitating the delivery of multiple therapeutic agents. However, ICCs are often observed serendipitously in crystallization screens and the factors dictating their crystallization are poorly understood. We demonstrate here that mechanochemical ball milling is a versatile technique for the reproducible synthesis of ternary molecular ICCs in less than 30 min of grinding with or without solvent. Computational crystal structure prediction (CSP) calculations have been performed on ternary molecular ICCs for the first time and the observed crystal structures of all the ICCs were correctly predicted. Periodic dispersion‐corrected DFT calculations revealed that all the ICCs are thermodynamically stable (mean stabilization energy=−2 kJ mol−1) relative to the crystallization of a physical mixture of the binary salt and acid. The results suggest that a combined mechanosynthesis and CSP approach could be used to target the synthesis of higher‐order molecular ICCs with functional properties., Spot on predictions! The mechanosynthesis of ternary molecular ionic cocrystals (ICCs) with significantly different physicochemical properties has been achieved in less than 30 min of grinding. The crystal structures of the ICCs were successfully predicted by using computational methods. The results pave the way for the efficient screening of higher‐order multicomponent crystal forms with functional properties (see figure).
- Published
- 2019
27. Using crystal structure prediction to rationalize the hydration propensities of substituted adamantane hydrochloride salts
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Durga Prasad Karothu, Sharmarke Mohamed, and Panče Naumov
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Lattice energy ,Chemistry ,Hydrochloride ,Adamantane ,Inorganic chemistry ,Metals and Alloys ,Energy landscape ,02 engineering and technology ,Crystal structure ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,law.invention ,Crystal structure prediction ,Crystal ,chemistry.chemical_compound ,Crystallography ,law ,Materials Chemistry ,Crystallization ,0210 nano-technology - 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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- 2016
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28. Crystal structure evaluation: calculating relative stabilities and other criteria: general discussion
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J. Christian Schön, Matthew R. Ryder, Jonas Nyman, Seiji Tsuzuki, Alexandre Tkatchenko, Alan Hare, John B. O. Mitchell, Marcus A. Neumann, Julian Helfferich, Samuel Alexander Jobbins, Johannes Hoja, David H. Bowskill, Ivo B. Rietveld, Luca Iuzzolino, Pablo M. Piaggi, Michael T. Ruggiero, Sharmarke Mohamed, Sarah L. Price, Rui Guo, Mihails Arhangelskis, Qiang Zhu, Artem R. Oganov, Matthew Addicoat, Jason C. Cole, Gregory J. O. Beran, Graeme M. Day, Sten O. Nilsson Lill, Doris E. Braun, Scott M. Woodley, Christopher R. Taylor, Virginia M. Burger, German Sastre, Claire S. Adjiman, Noa Marom, Aurora J. Cruz-Cabeza, David McKay, Jan Gerit Brandenburg, Susan M. Reutzel-Edens, Grahame Woollam, Joost A. van den Ende, Volker L. Deringer, Respiratory Epidemiology and Public Health, Imperial College London-Royal Brompton Hospital-National Heart and Lung Institute [UK], Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Blackett Laboratory, Imperial College London, University of Cambridge [UK] (CAM), Brigham and Women's Hospital [Boston], Karlsruhe Institute of Technology (KIT), Institute for Computational Engineering and Sciences [Austin] (ICES), University of Texas at Austin [Austin], School of Engineering and Physical Sciences, Heriot-Watt University, Heriot-Watt University [Edinburgh] (HWU), University College of London [London] (UCL), Sciences et Méthodes Séparatives (SMS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Univ Politecnica Valencia Consejo Super Invest, Inst Tecnol Quim UPV CSIC, Valencia 46022, Spain, Max Planck Institute for Solid State Research, Max-Planck-Gesellschaft, National Institute of Advanced Industrial Science and Technology (AIST), and Department of Chemistry, University College London
- Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,Materials science ,010304 chemical physics ,0103 physical sciences ,Thermodynamics ,02 engineering and technology ,Crystal structure ,Physical and Theoretical Chemistry ,021001 nanoscience & nanotechnology ,0210 nano-technology ,01 natural sciences ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2018
- Full Text
- View/download PDF
29. Towards the systematic crystallisation of molecular ionic cocrystals: insights from computed crystal form landscapes
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Andrew J. Morris, Sharmarke Mohamed, Ahmad Almasri Alwan, Tomislav Friščić, and Mihails Arhangelskis
- Subjects
chemistry.chemical_classification ,010405 organic chemistry ,Hydrogen bond ,Carboxylic acid ,Intermolecular force ,Ionic bonding ,Crystal structure ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,law.invention ,Crystal ,chemistry.chemical_compound ,Crystallography ,chemistry ,law ,Carboxylate ,Physical and Theoretical Chemistry ,Crystallization - Abstract
The underlying molecular and crystal properties affecting the crystallisation of ionic cocrystals (ICCs) with the general formula A-B+N (A- = anion, B+ = cation and N = neutral acid molecule; 1 : 1 : 1 stoichiometry) are reported for a limited set of known crystal structures determined following the cocrystallisation of either 4-aminopyridine (which forms salts) or 4-dimethylaminopyridine (which forms salts and ICCs) with the same set of monoprotic acids with a single hydroxy or halogen substitution at the ortho or para position. Periodic density functional theory calculations (PBE + D2) on the energetic driving force for ICC crystallisation for a set of known crystal structures with well characterised acid, salt and ICC structures show that all but 1 of the 7 experimental ICC structures surveyed were more stable than the sum of their component salt and acid structures with 4 displaying relative stabilities (ΔEICC) ranging from 2.47-8.02 kJ mol-1. The majority of molecular ICCs that are more stable with respect to their component salt and acid structures display the formation of discrete intermolecular O-HacidOanion hydrogen bonds with the D11(2) graph set between the carboxylic acid OH donor and the carboxylate oxygen acceptor of the anion. Computed crystal form landscapes for model 1 : 1 salts derived from acid-base pairs (involving 4-dimethylaminopyridine) known to form molecular ICCs show that on average the most stable predicted polymorphs of the 1 : 1 salts have efficient packing of the ions with packing coefficients in the range 65-80% and this is comparable to the packing coefficients of the most stable predicted polymorphs of 1 : 1 salts (involving 4-aminopyridine) that have no ICCs reported. This suggests that the cocrystallisation of equimolar amounts of the 1 : 1 salt and the acid to form a 1 : 1 : 1 molecular ICC is a complicated phenomenon that cannot be explained on the basis of inefficiencies in the crystal packing of the salt ions.
- Published
- 2018
30. CHAPTER 1. Integrating Computed Crystal Energy Landscapes in Crystal Form Discovery and Characterisation
- Author
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Sharmarke Mohamed
- Subjects
Structure (mathematical logic) ,Crystal ,Lattice energy ,Range (mathematics) ,Computer science ,media_common.quotation_subject ,Density functional theory ,Biochemical engineering ,Crystal structure ,Function (engineering) ,Crystal structure prediction ,media_common - Abstract
Over the past two decades, computational methods of crystal structure prediction (CSP) have shown enormous potential in complementing the efforts of crystal engineers to synthesise and characterise new solid forms of organic molecules. This chapter summarises the insights that can be gained from computational methods of CSP when integrated as part of experimental efforts to synthesise and characterise the crystal structures of organic molecules. The value of CSP methods is that they allow us to map the range of packing alternatives that a single-component or multi-component molecular system may adopt in the crystal as a function of the lattice energy. CSP methods can now handle large flexible organic molecules with the sort of complexity typically seen in pharmaceutical drug development pipelines, and it is now not unusual to find the experimentally observed crystal structure at, or close to, the global minimum in the crystal lattice energy landscape with the use of accurate dispersion-corrected density functional theory methods. The fundamental promise of CSP methods is to move us to a point where we can generate a set of plausible low-energy predicted structures for any molecule and be able to target the crystallisation and characterisation of a preferred structure.
- Published
- 2018
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- View/download PDF
31. Applications of crystal structure prediction – inorganic and network structures: general discussion
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Scott M. Woodley, Yi Li, John B. O. Mitchell, Peter R. Spackman, Frederik Claeyssens, Matthew S. Dyer, Graeme M. Day, Caroline Mellot-Draznieks, Daniel W. Davies, Sharmarke Mohamed, Michael T. Ruggiero, Matthew R. Ryder, J. Christian Schön, Sarah L. Price, Virginia M. Burger, Artem R. Oganov, Alan Hare, Qiang Zhu, German Sastre, Laboratoire de Chimie des Processus Biologiques (LCPB), and Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
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Materials science ,Network structure ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,computer.software_genre ,01 natural sciences ,0104 chemical sciences ,Crystal structure prediction ,Data mining ,[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph] ,Physical and Theoretical Chemistry ,0210 nano-technology ,computer ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2018
- Full Text
- View/download PDF
32. Structure searching methods: general discussion
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Scott M. Woodley, Stefanos Konstantinopoulos, Kim E. Jelfs, Claire S. Adjiman, J. Christian Schön, Matthew S. Dyer, David McKay, Shiyue Yang, Jan Gerit Brandenburg, Marcus A. Neumann, Virginia M. Burger, German Sastre, Peter R. Spackman, Volker L. Deringer, Graeme M. Day, Michael T. Ruggiero, Asbjoern Burow, Matthew Addicoat, Yanming Ma, Mihails Arhangelskis, Artem R. Oganov, Caroline Mellot-Draznieks, Julia A. Schmidt, Jonas Nyman, Qiang Zhu, Julian Keupp, Sten O. Nilsson Lill, Christopher Collins, Susan M. Reutzel-Edens, Sarah L. Price, Rochus Schmid, Gregory J. O. Beran, Yi Li, Alan Hare, Sharmarke Mohamed, Andrew Cooper, Doris E. Braun, Seiji Tsuzuki, Noa Marom, Laboratoire de Chimie des Processus Biologiques (LCPB), and Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
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Structure (mathematical logic) ,Materials science ,Information retrieval ,business.industry ,MEDLINE ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Text mining ,[CHIM.CRIS]Chemical Sciences/Cristallography ,[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph] ,Physical and Theoretical Chemistry ,0210 nano-technology ,business ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2018
- Full Text
- View/download PDF
33. Porous organic polymer composites as surging catalysts for visible-light-driven chemical transformations and pollutant degradation
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Shaoxian Song, Philippe M. Heynderickx, Ipsita Nath, Sharmarke Mohamed, Jeet Chakraborty, Anish Khan, and Francis Verpoort
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Pollutant ,Environmental remediation ,Chemistry ,Singlet oxygen ,Organic Chemistry ,Photoredox catalysis ,Nanotechnology ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Chemical reaction ,Catalysis ,0104 chemical sciences ,Conjugated microporous polymer ,chemistry.chemical_compound ,Organic reaction ,Photocatalysis ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
The promising aspect of photocatalysis to effectively utilize the abundant solar irradiation for promoting various chemical reactions and environmental remediation at greener, low-energy demanding conditions resulted in the recent surge in this research field. In this review, the synthesis and structure-property relationships of photoactive porous organic polymers (POPs) followed by their environmentally benign applications including various chemical transformations and decontamination of pollutants involving key intermediate reactive species have been critically discussed. The conditions required to generate these active species such as photo-generated electron and hole pair, singlet oxygen, superoxide, organic radical, etc. and their different quenching pathways are initially explained to clearly portray the favourable settings necessary for efficient POP-photocatalysis. This introductory discussion is further extrapolated to systematically illustrate the structure-application correlation of every visible-light-responsive POPs reported to date. The mechanisms adapted by POPs for photocatalytic organic reactions and degradation of wastewater pollutants have been comprehensively depicted. Initial discussion on reactive species is envisioned to provide a clear grasp on these later-explained mechanistic pathways. The review is finally concluded by crucially explaining the existing limitations and future development prospects of this field.
- Published
- 2019
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34. Report on the sixth blind test of organic crystal structure prediction methods
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Elia Schneider, Harald Oberhofer, Bouke P. van Eijck, Dennis M. Elking, Rafał Podeszwa, David P. McMahon, Angeles Pulido, Christina-Anna Gatsiou, Daniël T. de Jong, Constantinos C. Pantelides, D. W. M. Hofmann, Luca Iuzzolino, Artem R. Oganov, Chris J. Pickard, Marta B. Ferraro, Jan Gerit Brandenburg, Farren Curtis, Karsten Reuter, René de Gelder, Johannes Hoja, Yanchao Wang, Sharmarke Mohamed, Rona E. Watson, Graeme M. Day, Alston J. Misquitta, Wojciech Jankiewicz, Saswata Bhattacharya, Roberto Car, Richard I. Cooper, Murray G. Read, Marcus A. Neumann, Alexander Dzyabchenko, Katherine Cosburn, Álvaro Vázquez-Mayagoitia, Luca M. Ghiringhelli, Stefan Grimme, Alexandre Tkatchenko, Jian Lv, Jack Yang, Francesca Vacarro, Patrick McCabe, Herma M. Cuppen, L. N. Kuleshova, Joost A. van den Ende, Julio C. Facelli, Yanming Ma, Claire S. Adjiman, Krzysztof Szalewicz, Renu Chadha, Gilles A. de Wijs, Sarah L. Price, Frank J. J. Leusen, Mark E. Tuckerman, Noa Marom, Niek J. J. de Klerk, Manolis Vasileiadis, Richard J. Needs, Shigeaki Obata, Gabriel Ignacio Pagola, J.E. Campbell, Anthony M. Reilly, A. Daniel Boese, Qiang Zhu, Hsin-Yu Ko, Robert A. DiStasio, Rita Bylsma, Leslie Vogt, Hugo Meekes, Xiayue Li, Artëm E. Masunov, Colin R. Groom, John Kendrick, David H. Case, Pawanpreet Singh, Thomas S. Gee, Louise S. Price, Rebecca K. Hylton, Gregory P. Shields, Jason C. Cole, Michael P. Metz, Christoph Schober, Bartomeu Monserrat, Christopher R. Taylor, Hitoshi Goto, Isaac J. Sugden, Jonas Nyman, Peter J. Bygrave, Rui Guo, Albert M. Lund, Laszlo Fusti-Molnar, Sanjaya Lohani, Anita M. Orendt, Monserrat Sanchez, Bartomeu [0000-0002-4233-4071], Needs, Richard [0000-0002-5497-9440], Pickard, Christopher [0000-0002-9684-5432], and Apollo - University of Cambridge Repository
- Subjects
Ciencias Físicas ,02 engineering and technology ,Solid State Chemistry ,010402 general chemistry ,LATTICE ENERGIES ,01 natural sciences ,crystal structure prediction ,polymorphism ,Analytical Chemistry ,purl.org/becyt/ford/1 [https] ,lattice energies ,Prediction methods ,Materials Chemistry ,Chloride salt ,Cambridge Structural Database ,Theoretical Chemistry ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,Electronic Structure of Materials ,Complement (set theory) ,Structure (mathematical logic) ,Chemistry ,Metals and Alloys ,Organic crystal ,purl.org/becyt/ford/1.3 [https] ,021001 nanoscience & nanotechnology ,Atomic and Molecular Physics, and Optics ,CRYSTAL STRUCTURE PREDICTION ,POLYMORPHISM ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,Crystal structure prediction ,Astronomía ,Range (mathematics) ,Ranking ,CAMBRIDGE STRUCTURAL DATABASE ,0210 nano-technology ,Algorithm ,CIENCIAS NATURALES Y EXACTAS - 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. Fil: Reilly, Anthony M.. Cambridge Crystallographic Data Centre; Fil: Cooper, Richard I.. Chemistry Research Laboratory; Fil: Adjiman, Claire S.. Imperial College London; Reino Unido Fil: Bhattacharya, Saswata. Fritz Haber Institute Of The Max Planck Society; Fil: Boese, A. Daniel. Karl-franzens-universitat Graz; Austria Fil: Brandenburg, Jan Gerit. Colegio Universitario de Londres; Reino Unido. Universitat Bonn; Alemania Fil: Bygrave, Peter J.. University of Southampton; Reino Unido Fil: Bylsma, Rita. Radboud Universiteit Nijmegen; Países Bajos Fil: Campbell, Josh E.. University of Southampton; Reino Unido Fil: Car, Roberto. University of Princeton; Estados Unidos Fil: Case, David H.. University of Southampton; Reino Unido Fil: Chadha, Renu. University Institute Of Pharmaceutical Sciences India; India Fil: Cole, Jason C.. Cambridge Crystallographic Data Centre; Fil: Cosburn, Katherine. University of Tulane; Estados Unidos. University of Toronto; Canadá Fil: Cuppen, Herma M.. Radboud Universiteit Nijmegen; Países Bajos Fil: Curtis, Farren. University of Tulane; Estados Unidos. University of Carnegie Mellon; Estados Unidos Fil: Day, Graeme M.. University of Southampton; Reino Unido Fil: DiStasio, Robert A.. University of Princeton; Estados Unidos. Cornell University; Estados Unidos Fil: Dzyabchenko, Alexander. Karpov Institute Of Physical Chemistry; Fil: Van Eijck, Bouke P.. University of Utrecht; Países Bajos. Utrecht University; Países Bajos Fil: Elking, Dennis M.. Openeye Scientific Software, Inc; Fil: Van Den Ende, Joost A.. Radboud Universiteit Nijmegen; Países Bajos Fil: Facelli, Julio C.. University of Utah; Estados Unidos Fil: Ferraro, Marta B.. Universidad de Buenos Aires; Argentina Fil: Fusti-Molnar, Laszlo. Openeye Scientific Software, Inc; Fil: Gatsiou, Christina-Anna. Imperial College London; Reino Unido Fil: Gee, Thomas S.. University of Southampton; Reino Unido Fil: De Gelder, René. Radboud Universiteit Nijmegen; Países Bajos Fil: Ghiringhelli, Luca M.. Fritz Haber Institute Of The Max Planck Society; Fil: Goto, Hitoshi. Toyohashi University Of Technology; Fil: Grimme, Stefan. Universitat Bonn; Alemania Fil: Guo, Rui. Colegio Universitario de Londres; Reino Unido Fil: Hofmann, Detlef W. M.. Flexcryst; . Polaris; Fil: Hoja, Johannes. Fritz Haber Institute Of The Max Planck Society; Fil: Hylton, Rebecca K.. Colegio Universitario de Londres; Reino Unido Fil: Iuzzolino, Luca. Colegio Universitario de Londres; Reino Unido Fil: Jankiewicz, Wojciech. University Of Silesia In Katowice; Fil: De Jong, Daniël T.. Radboud Universiteit Nijmegen; Países Bajos Fil: Kendrick, John. University Of Bradford; Fil: De Klerk, Niek J. J.. Radboud Universiteit Nijmegen; Países Bajos Fil: Ko, Hsin-Yu. University of Princeton; Estados Unidos Fil: Kuleshova, Liudmila N.. Flexcryst; Fil: Li, Xiayue. University of Tulane; Estados Unidos. Argonne National Laboratory; Estados Unidos Fil: Lohani, Sanjaya. University of Tulane; Estados Unidos Fil: Leusen, Frank J. J.. University Of Bradford; Fil: Lund, Albert M.. University of Utah; Estados Unidos. Openeye Scientific Software, Inc; Fil: Lv, Jian. Jilin University; China Fil: Ma, Yanming. Jilin University; China Fil: Marom, Noa. University of Carnegie Mellon; Estados Unidos. University of Tulane; Estados Unidos Fil: Masunov, Artëm E.. University Of Central Florida; . National Research Nuclear University Mephi; Fil: McCabe, Patrick. Cambridge Crystallographic Data Centre; Fil: McMahon, David P.. University of Southampton; Reino Unido Fil: Meekes, Hugo. Radboud Universiteit Nijmegen; Países Bajos Fil: Metz, Michael P.. University Of Delaware; Fil: Misquitta, Alston J.. Queen Mary, University Of London; Fil: Mohamed, Sharmarke. Khalifa University Of Science And Technology; Fil: Monserrat, Bartomeu. Rutgers, The State University Of New Jersey; . University of Cambridge; Estados Unidos Fil: Needs, Richard J.. University of Cambridge; Estados Unidos Fil: Neumann, Marcus A.. No especifica; Fil: Nyman, Jonas. University of Southampton; Reino Unido Fil: Obata, Shigeaki. Toyohashi University Of Technology; Fil: Oberhofer, Harald. Universitat Technical Zu Munich; Alemania Fil: Oganov, Artem R.. Northwestern Polytechnical University; China. Skolkovo Institute Of Science And Technology; . Moscow Institute Of Physics And Technology; . Stony Brook University; Fil: Orendt, Anita M.. University of Utah; Estados Unidos Fil: Pagola, Gabriel Ignacio. Universidad de Buenos Aires; Argentina Fil: Pantelides, Constantinos C.. Imperial College London; Reino Unido Fil: Pickard, Chris J.. University of Cambridge; Estados Unidos. Colegio Universitario de Londres; Reino Unido Fil: Podeszwa, Rafal. University Of Silesia In Katowice; Fil: Price, Louise S.. Colegio Universitario de Londres; Reino Unido Fil: Price, Sarah L.. Colegio Universitario de Londres; Reino Unido Fil: Pulido, Angeles. University of Southampton; Reino Unido Fil: Read, Murray G.. Cambridge Crystallographic Data Centre; Fil: Reuter, Karsten. Universitat Technical Zu Munich; Alemania Fil: Schneider, Elia. University of New York; Estados Unidos Fil: Schober, Christoph. Universitat Technical Zu Munich; Alemania Fil: Shields, Gregory P.. Cambridge Crystallographic Data Centre; Fil: Singh, Pawanpreet. University Institute Of Pharmaceutical Sciences India; India Fil: Sugden, Isaac J.. Imperial College London; Reino Unido Fil: Szalewicz, Krzysztof. University Of Delaware; Fil: Taylor, Christopher R.. University of Southampton; Reino Unido Fil: Tkatchenko, Alexandre. University Of Luxembourg; . Fritz Haber Institute Of The Max Planck Society; Fil: Tuckerman, Mark E.. University of New York; Estados Unidos. New York University Shanghai; China. Courant Institute Of Mathematical Sciences; Fil: Vacarro, Francesca. University of Tulane; Estados Unidos. Loyola University New Orleans; Fil: Vasileiadis, Manolis. Imperial College London; Reino Unido Fil: Vazquez-Mayagoitia, Alvaro. Argonne National Laboratory; Estados Unidos Fil: Vogt, Leslie. University of New York; Estados Unidos Fil: Wang, Yanchao. Jilin University; China Fil: Watson, Rona E.. Colegio Universitario de Londres; Reino Unido Fil: De Wijs, Gilles A.. Radboud Universiteit Nijmegen; Países Bajos Fil: Yang, Jack. University of Southampton; Reino Unido Fil: Zhu, Qiang. Stony Brook University; Fil: Groom, Colin R.. Cambridge Crystallographic Data Centre
- Published
- 2016
35. Computational prediction of salt and cocrystal structures—Does a proton position matter?
- Author
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Sarah L. Price, Sharmarke Mohamed, and Derek A. Tocher
- Subjects
Models, Molecular ,Lattice energy ,Molecular Structure ,Pyridines ,Hydrogen bond ,Chemistry ,Intermolecular force ,Inorganic chemistry ,Pharmaceutical Science ,Crystal structure ,Benzoates ,Cocrystal ,Crystal structure prediction ,Crystallography ,chemistry.chemical_compound ,Nitriles ,Molecule ,Computer Simulation ,Salts ,Carboxylate ,Protons ,Crystallization - Abstract
The lattice energy landscape is calculated for three pyridinium carboxylate salts and the corresponding pyridine·carboxylic acid cocrystals. Experimentally, one system crystallizes as a salt, another as a cocrystal and the acidic proton in the third is disordered across the N(arom)...O hydrogen bond vector. A novel structure of a 1:1 4-cyanopyridine·4-fluorobenzoic acid cocrystal (I) was characterized to provide the cocrystal as a system with an isolated carboxylic acid-pyridine heterosynthon. By contrast, the 4-dimethylaminopyridinium maleate salt (GUKVUE) shows the effects of an internal hydrogen bond, and the proton-disordered pyridine·isophthalic acid crystal (IYUPEX) shows the effects of competing intermolecular hydrogen bonds. All three crystal structures were found low in energy on the lattice energy landscape for the correct proton connectivity. For all three systems, comparing the salt and cocrystal energy landscapes shows the importance of the proton position for the relative stabilities of structures, despite the expected similarities between the ionized and neutral forms of the carboxylic acid-pyridine heterosynthon. The systems with additional hydrogen bonds have some hydrogen bonding motifs that are only favourable for the salt or for the cocrystal. This illustrates the sensitivity of the range of thermodynamically plausible crystal structures to whether the molecules are assumed to be ionized or neutral.
- Published
- 2011
- Full Text
- View/download PDF
36. Towards crystal structure prediction of complex organic compounds - a report on the fifth blind test
- Author
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Marcus A. Neumann, Louise S. Price, Marta B. Ferraro, Harold A. Scheraga, Andrei V. Kazantsev, Damián A. Grillo, K. V. Jovan Jose, D. W. M. Hofmann, Julio C. Facelli, John Kendrick, Rumpa Pal, Chris J. Pickard, Graeme M. Day, Alston J. Misquitta, Panagiotis G. Karamertzanis, Aurora J. Cruz-Cabeza, Richard J. Needs, Stephan X. M. Boerrigter, Denis Nikylov, L. N. Kuleshova, Matthew Habgood, Frank J. J. Leusen, Jacco van de Streek, Constantinos C. Pantelides, Ilia K. Zhitkov, Sharmarke Mohamed, Doris E. Braun, David A. Bardwell, Fridolin Hofmann, Andrey V. Maleev, Claire S. Adjiman, Sarah L. Price, Yelena A. Arnautova, Gautam R. Desiraju, Raffaele Guido Della Valle, Tejender S. Thakur, Bouke P. van Eijck, Elisabetta Venuti, Siddharth Tiwari, Ekaterina V. Bartashevich, Anita M. Orendt, D.A. Bardwell, C.S. Adjiman, Y.A. Arnautova, E. Bartashevich, S.X.M. Boerrigter, D.E. Braun, A.J. Cruz-Cabeza, G.M. Day, R.G. Della Valle, G.R. Desiraju, B.P. van Eijck, J.C. Facelli, M.B. Ferraro, D. Grillo, M. Habgood, D.W.M. Hofmann, F. Hofmann, K.V.J. Jose, P.G. Karamertzani, A.V. Kazantsev, J. Kendrick, L.N. Kuleshova, F.J.J. Leusen, A.V. Maleev, A.J. Misquitta, S. Mohamed, R.J. Need, M.A. Neumann, D. Nikylov, A.M. Orendt, R. Pal, C.C. Pantelide, C.J. Pickard, L.S. Price, S.L. Price, H.A. Scheraga, J. van de Streek, T.S. Thakur, S. Tiwari, E. Venuti, I.K. Zhitkov, and Simulation of Biomolecular Systems (HIMS, FNWI)
- Subjects
Models, Molecular ,organic compound ,Databases, Factual ,polymorph ,Complex system ,Crystallographic data ,Nanotechnology ,02 engineering and technology ,010402 general chemistry ,Collaborative projects ,Complex organic compounds ,chemistry ,Crystallography, X-Ray ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,crystal structure prediction ,Organic molecules ,Flexible molecules ,Group (periodic table) ,X ray methods ,Blind test ,Hydrates ,Organic Chemicals ,Rigid molecules ,Organic chemicals ,Chemistry ,Crystal structure ,Cambridge ,article ,methodology ,General Medicine ,prediction ,X ray crystallography ,Molecules ,021001 nanoscience & nanotechnology ,Research Papers ,BLIND TEST ,CRYSTAL STRUCTURE PREDICTION ,0104 chemical sciences ,Crystal structure prediction ,Range (mathematics) ,factual database ,Density functional theory ,chemical structure ,0210 nano-technology ,Algorithm ,Forecasting - Abstract
The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed., Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
- Published
- 2011
37. Salt or Cocrystal? A New Series of Crystal Structures Formed from Simple Pyridines and Carboxylic Acids
- Author
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Martin Vickers, Sharmarke Mohamed, Panagiotis G. Karamertzanis, Sarah L. Price, and Derek A. Tocher
- Subjects
Terephthalic acid ,chemistry.chemical_classification ,Fumaric acid ,Maleic acid ,Chemistry ,Salt (chemistry) ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Cocrystal ,law.invention ,chemistry.chemical_compound ,law ,Polymer chemistry ,Pyridine ,Organic chemistry ,General Materials Science ,Crystallization - Abstract
The two-component crystals formed from pyridine or 4-dimethylaminopyridine with maleic, fumaric, phthalic, isophthalic, or terephthalic acids were characterized by X-ray diffraction. The two-component solid forms involving pyridine included both salts and cocrystals, while 4-dimethylaminopyridine crystallized exclusively as a salt, in agreement with the differences in the pKa values. Five previously unknown salt solid forms of 4-dimethylaminopyridine and the crystal structure of a pyridine fumaric acid (2:1) cocrystal are reported. An in-situ base catalyzed isomerization of maleic acid was observed in cocrystallization experiments involving pyridine. The salts formed between 4-dimethylaminopyridine and fumaric acid included one or two fumaric acid molecules within the crystal lattice. Thus, the reported grid of crystal forms demonstrates the limitations of empirical rules for predicting the stoichiometry and covalent bonding of the acidic proton within salts and cocrystals. Many of the crystal structures ...
- Published
- 2009
- Full Text
- View/download PDF
38. Discovery of three polymorphs of 7-fluoroisatin reveals challenges in using computational crystal structure prediction as a complement to experimental screening
- Author
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Charlotte K. Leech, Sarah L. Price, Kenneth Shankland, Derek A. Tocher, Sharmarke Mohamed, and Sarah A. Barnett
- Subjects
Chemistry ,Hydrogen bond ,Nucleation ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Crystal structure prediction ,law.invention ,Crystal ,Crystallography ,law ,Metastability ,Molecule ,General Materials Science ,Crystallization - Abstract
A combined computational and experimental polymorph search was undertaken to establish the crystal forms of 7-fluoroisatin, a simple molecule with no reported crystal structures, to evaluate the value of crystal structure prediction studies as an aid to solid form discovery. Three polymorphs were found in a manual crystallisation screen, as well as two solvates. Form I (P21/c, Z′ = 1), found from the majority of solvent evaporation experiments, corresponded to the most stable form in the computational search of Z′ = 1 structures. Form III (P21/a, Z′ = 2) is probably a metastable form, which was only found concomitantly with form I, and has the same dimeric R22(8) hydrogen bonding motif as form I and the majority of the computed low energy structures. However, the most thermodynamically stable polymorph, form II (P, Z′ = 2), has an expanded four molecule R44(18) hydrogen bonding motif, which could not have been found within the routine computational study. The computed relative energies of the three forms are not in accord with experimental results. Thus, the experimental finding of three crystalline polymorphs of 7-fluoroisatin illustrates the many challenges for computational screening to be a tool for the experimental crystal engineer, in contrast to the results for an analogous investigation of 5-fluoroisatin.
- Published
- 2008
- Full Text
- View/download PDF
39. Commercial prospects for genomic sequencing technologies
- Author
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Sharmarke Mohamed and Basharut A. Syed
- Subjects
Pharmacology ,Pharmacogenetics ,Pharmacogenomics ,Genomic sequencing ,Drug Discovery ,Health Care Sector ,Genomics ,General Medicine ,Computational biology ,Biology ,Sequence Analysis ,health care economics and organizations - Abstract
This article analyses the evolution of the market for genomic sequencing technologies in the light of major reductions in sequencing costs and time, and the growth in potential pharmacogenomics applications.
- Published
- 2013
- Full Text
- View/download PDF
40. Screening for cocrystals of succinic acid and 4-aminobenzoic acid
- Author
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Sarah L. Price, Derek A. Tocher, Sharmarke Mohamed, Sarah A. Barnett, Royston C. B. Copley, Doris E. Braun, and Nizar Issa
- Subjects
Steric effects ,Chemistry ,Hydrogen bond ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Cocrystal ,Crystal structure prediction ,law.invention ,chemistry.chemical_compound ,law ,Succinic acid ,Molecule ,Organic chemistry ,General Materials Science ,Crystallization - Abstract
The ability of the pharmaceutically acceptable cocrystallising agents, succinic acid and 4-aminobenzoic acid, to form cocrystals with ten small organic molecules with hydrogen bonding acceptors but no donors, was investigated by grinding, hot-stage microscopy and solution based crystallisation experiments. The reproducible results obtained by different methods showed that only six cocrystals formed. The crystal structures of the four novel cocrystals, succinic acid·2,2′-bipyridine (1 : 1, P21/c, I), succinic acid·diphenylcyclopropenone (1 : 2, P21/c, II), 4-aminobenzoic acid·antipyrine (1 : 1, P21, III) and 4-aminobenzoic acid·phenazine (1 : 2, P, IV), are reported. The computed crystal energy landscapes of the cocrystals and their components show why succinic acid·1,4-dicyanobenzene did not form a cocrystal as well as predicting the observed structure of succinic acid·2,2′-bipyridine as the most stable. The most stable hypothetical structures of a 1 : 1 succinic acid·1,4-dicyanobenzene cocrystal are closely related to those of the components. The results demonstrate that cocrystal formation requires both hydrogen bonding and close packing, and so markedly non-planar pharmaceuticals will be quite specific in the steric and hydrogen bonding disposition requirement of coformers.
- Published
- 2012
- Full Text
- View/download PDF
41. 7-Fluoroisatin–1,4-dioxane (1/1)
- Author
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Kenneth Shankland, Derek A. Tocher, Sharmarke Mohamed, Charlotte K. Leech, and Sarah A. Barnett
- Subjects
Solvent ,chemistry.chemical_compound ,Crystallography ,Chemistry ,law ,General Materials Science ,General Chemistry ,1,4-Dioxane ,Crystallization ,Condensed Matter Physics ,Inversion (discrete mathematics) ,law.invention - Abstract
The title 1,4-dioxane solvate, C8H4FNO2·C4H8O2, was isolated during a manual crystallization screen on 7-fluoroisatin (7-fluoroindoline-2,3-dione). The 7-fluoroisatin molecule occupies a general position and each of the independent molecules of 1,4-dioxane is disposed about a centre of inversion, with half of each in the asymmetric unit. Hydrogen-bonded ribbons of 7-fluoroisatin are linked by 1,4-dioxane to form sheets parallel to (30\overline{1}). Whilst one solvent molecule has an active role in the sheet formation, the other simply fills the cavity formed within the sheet.
- Published
- 2007
- Full Text
- View/download PDF
42. 5-Fluoro-3-hydroxy-3-(nitromethyl)-1H-indol-2(3H)-one
- Author
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Sarah A. Barnett, Sharmarke Mohamed, and Derek A. Tocher
- Subjects
Crystallography ,chemistry.chemical_compound ,chemistry ,General Materials Science ,Center (algebra and category theory) ,Oxindole ,General Chemistry ,Condensed Matter Physics - Abstract
The title compound, C9H7FN2O4, was isolated during a manual crystallization screen on 5-fluoroisatin (5-fluoroindoline-2,3-dione). Hydrogen-bonded ribbons of the oxindole are formed through pairs of N-H center dot center dot center dot O and O-H center dot center dot center dot O interactions. These ribbons then pack parallel to (09 (2) over bar) and (091) such that a herring-bone motif is established.
- Published
- 2007
- Full Text
- View/download PDF
43. 5-Fluoroisatin–dimethyl sufoxide (1/1)
- Author
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Sharmarke Mohamed, Derek A. Tocher, and Sarah A. Barnett
- Subjects
chemistry.chemical_compound ,Crystallography ,Chemistry ,Dimethyl sulfoxide ,law ,Molecule ,General Materials Science ,Center (algebra and category theory) ,General Chemistry ,Crystallization ,Condensed Matter Physics ,law.invention - Abstract
The title dimethyl sulfoxide (DMSO) solvate, C8H4FNO2 center dot-C2H6OS, was isolated during a manual crystallization screen on 5-fluoroisatin (5-fluoroindoline-2,3-dione). Molecules of 5-fluoroisatin are linked via C-H center dot center dot center dot O interactions to form chains parallel to (0 (1) over bar1) from which N-H center dot center dot center dot O hydrogen-bonded DMSO molecules protrude.
- Published
- 2007
- Full Text
- View/download PDF
44. Salt or Cocrystal? A New Series of Crystal Structures Formed from Simple Pyridines and Carboxylic Acids.
- Author
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Sharmarke Mohamed, Derek A. Tocher, Martin Vickers, Panagiotis G. Karamertzanis, and Sarah L. Price
- Subjects
- *
MOLECULAR crystals , *SALTS , *MOLECULAR structure , *PYRIDINE , *CARBOXYLIC acids , *X-ray diffraction , *CRYSTALLIZATION , *FUMARATES - Abstract
The two-component crystals formed from pyridine or 4-dimethylaminopyridine with maleic, fumaric, phthalic, isophthalic, or terephthalic acids were characterized by X-ray diffraction. The two-component solid forms involving pyridine included both salts and cocrystals, while 4-dimethylaminopyridine crystallized exclusively as a salt, in agreement with the differences in the pKavalues. Five previously unknown salt solid forms of 4-dimethylaminopyridine and the crystal structure of a pyridine fumaric acid (2:1) cocrystal are reported. An in-situ base catalyzed isomerization of maleic acid was observed in cocrystallization experiments involving pyridine. The salts formed between 4-dimethylaminopyridine and fumaric acid included one or two fumaric acid molecules within the crystal lattice. Thus, the reported grid of crystal forms demonstrates the limitations of empirical rules for predicting the stoichiometry and covalent bonding of the acidic proton within salts and cocrystals. Many of the crystal structures displayed either the neutral or the ionic form of the carboxylic acid−pyridine heterosynthon, and the similarity in crystal structures between the neutral and the ionized molecules makes the visual distinction between a salt or cocrystal dependent on the experimental location of the acidic proton. Computational modelling experiments, by relocating the acid protons in the salts to produce cocrystals and vice versa, show that the crystal structure can be better modelled when the crystallographic designation of salt or cocrystal is used. Periodic electronic structure calculations also show that there is generally a significant energy penalty to relocate the acidic proton, which is considerably reduced when experiments indicate the presence of disorder in the acidic proton position. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
45. Discovery of three polymorphs of 7-fluoroisatin reveals challenges in using computational crystal structure prediction as a complement to experimental screeningElectronic supplementary information (ESI) available: Morphologies and ORTEP plots of all three forms of 1. Details of the low energy hypothetical crystal structures found in the computational searches for 1 and 2. The low energy structures are stored on the STFC Data Portal and are available from the authors on request. Details and results of the manual crystallisation screens of 1 and 2. Overlay of DSC traces of all three forms of 1. Overlay of powder patterns of form II of 1 and the commercial sample. See DOI: 10.1039/b714566g
- Author
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Sharmarke Mohamed, Sarah A. Barnett, Derek A. Tocher, Sarah L. Price, Kenneth Shankland, and Charlotte K. Leech
- Subjects
- *
PHYSICAL & theoretical chemistry , *MORPHOLOGY , *MATHEMATICAL crystallography , *CRYSTALLIZATION - Abstract
A combined computational and experimental polymorph search was undertaken to establish the crystal forms of 7-fluoroisatin, a simple molecule with no reported crystal structures, to evaluate the value of crystal structure prediction studies as an aid to solid form discovery. Three polymorphs were found in a manual crystallisation screen, as well as two solvates. Form I (P21/c, Z′ = 1), found from the majority of solvent evaporation experiments, corresponded to the most stable form in the computational search of Z′ = 1 structures. Form III (P21/a, Z′ = 2) is probably a metastable form, which was only found concomitantly with form I, and has the same dimeric R22(8) hydrogen bonding motif as form I and the majority of the computed low energy structures. However, the most thermodynamically stable polymorph, form II (P1̄, Z′ = 2), has an expanded four molecule R44(18) hydrogen bonding motif, which could not have been found within the routine computational study. The computed relative energies of the three forms are not in accord with experimental results. Thus, the experimental finding of three crystalline polymorphs of 7-fluoroisatin illustrates the many challenges for computational screening to be a tool for the experimental crystal engineer, in contrast to the results for an analogous investigation of 5-fluoroisatin. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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