1
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Schottdorf M, Yu G, Walker EY. Data science and its future in large neuroscience collaborations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585936. [PMID: 38585895 PMCID: PMC10996530 DOI: 10.1101/2024.03.20.585936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The rise of large scientific collaborations in neuroscience requires systematic, scalable, and reliable data management. How this is best done in practice remains an open question. To address this, we conducted a data science survey among currently active U19 grants, funded through the NIH's BRAIN Initiative. The survey was answered by both data science liaisons and Principal Investigators, speaking for ~500 researchers across 21 nation-wide collaborations. We describe the tools, technologies, and methods currently in use, and identify several shortcomings of current data science practice. Building on this survey, we develop plans and propose policies to improve data collection, use, publication, reuse and training in the neuroscience community.
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Affiliation(s)
- Manuel Schottdorf
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Guoqiang Yu
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA
| | - Edgar Y. Walker
- Department of Physiology and Biophysics, Computational Neuroscience Center, University of Washington, Seattle, WA, USA
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2
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Nakata M, Maeda T. PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules Using B3LYP/6-31G* Calculations. J Chem Inf Model 2023; 63:5734-5754. [PMID: 37677147 DOI: 10.1021/acs.jcim.3c00899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The presented "PubChemQC B3LYP/6-31G*//PM6" data set is composed of the electronic properties of 85,938,443 molecules, encompassing a broad spectrum of molecules from essential compounds to biomolecules with a molecular weight up to 1000. These molecules account for 94.0% of the original PubChem Compound catalog as of August 29, 2016. The electronic properties, including orbitals, orbital energies, total energies, dipole moments, and other pertinent properties, were computed by using the B3LYP/6-31G* and PM6 methods. The data set, available in three formats, namely, GAMESS quantum chemistry program files, selected JSON output files, and a PostgreSQL database, provides researchers with the ability to query molecular properties. It is further subdivided into five subdata sets for more specific data. The first two subsets encompass molecules with carbon, hydrogen, oxygen, and nitrogen with molecular weights under 300 and 500, respectively. The third and fourth subsets incorporate molecules with carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, fluorine, and chlorine, with molecular weights under 300 and 500, respectively. The fifth subset comprises molecules with carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, fluorine, chlorine, sodium, potassium, magnesium, and calcium, with a molecular weight of under 500. The coefficients of determination for the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap range from 0.892 (for CHON500) to 0.803 (for the whole data set). These comprehensive results pave the way for applications in drug discovery and materials science, among others. The data sets can be accessed under the Creative Commons Attribution 4.0 International license at the following web address: https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html.
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Affiliation(s)
- Maho Nakata
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiyuki Maeda
- Software Technology and Artificial Intelligence Research Laboratory, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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3
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Chauhan V, Mardia R, Patel M, Suhagia B, Parmar K. Technical and Formulation Aspects of Pharmaceutical Co‐Crystallization: A Systematic Review. ChemistrySelect 2022. [DOI: 10.1002/slct.202202588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Vishva Chauhan
- Affiliation: a-ROFEL Shri G.M. Bilakhia College of Pharmacy Namdha campus Vapi Gujarat India 396191
- Department of Pharmacy Dharmsinh Desai University Nadiad Gujarat India 387001 Corresponding author: Vishva Chauhan
| | - Rajnikant Mardia
- Department of Pharmacy Dharmsinh Desai University Nadiad Gujarat India 387001 Corresponding author: Vishva Chauhan
| | - Mehul Patel
- Department of Pharmacy Dharmsinh Desai University Nadiad Gujarat India 387001 Corresponding author: Vishva Chauhan
| | - Bhanu Suhagia
- Department of Pharmacy Dharmsinh Desai University Nadiad Gujarat India 387001 Corresponding author: Vishva Chauhan
| | - Komal Parmar
- Affiliation: a-ROFEL Shri G.M. Bilakhia College of Pharmacy Namdha campus Vapi Gujarat India 396191
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4
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Sarathi P, Padhi S. Insight of the various in silico screening techniques developed for assortment of cocrystal formers and their thermodynamic characterization. Drug Dev Ind Pharm 2022; 47:1523-1534. [PMID: 35164621 DOI: 10.1080/03639045.2022.2042554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Most of the widely used drugs have problems associated with their oral bioavailability either due to their poor aqueous solubility or due to their poor permeability. Co-crystallization is an efficient and economically feasible approach that offers a great opportunity for improvement in physicochemical properties such as solubility, stability, and bioavailability of such type of therapeutic agent. Selection of the best co-former plays a major role in co-crystallization. Various approaches have been developed for the selection of suitable co-formers with API. In recent years in silico screening, a computational tool paying more attention for screening of co-formers has been developed. Numerous approaches can be used for in silico screening such as the Autodocking tool, COSMORS, COSMOTHERM, etc. Autodocking can predict several numbers of co-former effectively screened in silico method to identify a suitable co-former with an API. Prediction of solubility and dissolution is also important for the development of co-crystal. In this review, we discuss in silico screening of coformer and thermodynamic approaches to determine the dissolution and solubility of co-crystal specially with reference to the drugs belonging to BCS class II group.
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Affiliation(s)
- Parth Sarathi
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, India
| | - Swarupanjali Padhi
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, India
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5
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Carrascoza F, Antczak M, Miao Z, Westhof E, Szachniuk M. Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. RNA (NEW YORK, N.Y.) 2022; 28:250-262. [PMID: 34819324 PMCID: PMC8906551 DOI: 10.1261/rna.078685.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1052 RNA 3D structures, including 1030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analyzed. The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity, or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modeling approaches.
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Affiliation(s)
- Francisco Carrascoza
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
| | - Maciej Antczak
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire CNRS, Architecture et Réactivité de l'ARN, 67084 Strasbourg, France
| | - Marta Szachniuk
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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6
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Tremouilhac P, Lin CL, Huang PC, Huang YC, Nguyen A, Jung N, Bach F, Ulrich R, Neumair B, Streit A, Bräse S. The Repository Chemotion: Infrastructure for Sustainable Research in Chemistry*. Angew Chem Int Ed Engl 2020; 59:22771-22778. [PMID: 32785962 PMCID: PMC7756630 DOI: 10.1002/anie.202007702] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Pierre Tremouilhac
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Chia-Lin Lin
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pei-Chi Huang
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Yu-Chieh Huang
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - An Nguyen
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Felix Bach
- Steinbuch Centre for Computing (SCC), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Robert Ulrich
- KIT Library, Karlsruhe Institute of Technology, Straße am Forum 2, 76131, Karlsruhe, Germany
| | - Bernhard Neumair
- Steinbuch Centre for Computing (SCC), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Achim Streit
- Steinbuch Centre for Computing (SCC), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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7
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Tremouilhac P, Lin C, Huang P, Huang Y, Nguyen A, Jung N, Bach F, Ulrich R, Neumair B, Streit A, Bräse S. Das Repositorium Chemotion: Infrastruktur für nachhaltige Wissenschaft in der Chemie**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Pierre Tremouilhac
- Institut für Biologische und Chemische Systeme – Funktionelle Molekulare Systeme (IBCS-FMS) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Chia‐Lin Lin
- Institut für Biologische und Chemische Systeme – Funktionelle Molekulare Systeme (IBCS-FMS) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Pei‐Chi Huang
- Institut für Biologische und Chemische Systeme – Funktionelle Molekulare Systeme (IBCS-FMS) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Yu‐Chieh Huang
- Institut für Biologische und Chemische Systeme – Funktionelle Molekulare Systeme (IBCS-FMS) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - An Nguyen
- Institut für Biologische und Chemische Systeme – Funktionelle Molekulare Systeme (IBCS-FMS) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Nicole Jung
- Institut für Biologische und Chemische Systeme – Funktionelle Molekulare Systeme (IBCS-FMS) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
- Institut für Organische Chemistry (IOC) Karlsruher Institut für Technologie Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Felix Bach
- Steinbuch Centre for Computing (SCC) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Robert Ulrich
- KIT Bibliothek Karlsruher Institut für Technologie Straße am Forum 2 76131 Karlsruhe Deutschland
| | - Bernhard Neumair
- Steinbuch Centre for Computing (SCC) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Achim Streit
- Steinbuch Centre for Computing (SCC) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Stefan Bräse
- Institut für Biologische und Chemische Systeme – Funktionelle Molekulare Systeme (IBCS-FMS) Karlsruher Institut für Technologie Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
- Institut für Organische Chemistry (IOC) Karlsruher Institut für Technologie Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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8
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Arenas AE, Goh JM, Matthews B. Identifying the business model dimensions of data sharing: A value‐based approach. J Assoc Inf Sci Technol 2019. [DOI: 10.1002/asi.24180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Jie Mein Goh
- Beedie School of BusinessSimon Fraser University Burnaby Canada
| | - Brian Matthews
- Scientific Computing DepartmentScience and Technology Facilities Council Didcot United Kingdom
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9
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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10
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Sturluson A, Huynh MT, Kaija AR, Laird C, Yoon S, Hou F, Feng Z, Wilmer CE, Colón YJ, Chung YG, Siderius DW, Simon CM. The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation. MOLECULAR SIMULATION 2019; 45:10.1080/08927022.2019.1648809. [PMID: 31579352 PMCID: PMC6774364 DOI: 10.1080/08927022.2019.1648809] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/15/2019] [Indexed: 01/10/2023]
Abstract
Metal-organic frameworks (MOFs) are highly tuneable, extended-network, crystalline, nanoporous materials with applications in gas storage, separations, and sensing. We review how molecular models and simulations of gas adsorption in MOFs have informed the discovery of performant MOFs for methane, hydrogen, and oxygen storage, xenon, carbon dioxide, and chemical warfare agent capture, and xylene enrichment. Particularly, we highlight how large, open databases of MOF crystal structures, post-processed to enable molecular simulations, are a platform for computational materials discovery. We discuss how to orient research efforts to routinise the computational discovery of MOFs for adsorption-based engineering applications.
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Affiliation(s)
- Arni Sturluson
- School of Chemical, Biological, and Environmental Engineering, Oregon State University. Corvallis, OR, USA
| | - Melanie T. Huynh
- School of Chemical, Biological, and Environmental Engineering, Oregon State University. Corvallis, OR, USA
| | - Alec R. Kaija
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Caleb Laird
- School of Chemical, Biological, and Environmental Engineering, Oregon State University. Corvallis, OR, USA
| | - Sunghyun Yoon
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, Korea (South)
| | - Feier Hou
- Western Oregon University. Department of Chemistry, Monmouth, OR, USA
| | - Zhenxing Feng
- School of Chemical, Biological, and Environmental Engineering, Oregon State University. Corvallis, OR, USA
| | - Christopher E. Wilmer
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yamil J. Colón
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Yongchul G. Chung
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, Korea (South)
| | - Daniel W. Siderius
- Chemical Sciences Division, National Institute of Standards and Technology. Gaithersburg, MD, USA
| | - Cory M. Simon
- School of Chemical, Biological, and Environmental Engineering, Oregon State University. Corvallis, OR, USA
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11
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Becker S. The crystal structure of [Fe 2(PIMIC6)(AnthCO 2)(CH 3CN)]·[Fe 2(PIMIC6)(AnthCO 2)(CH 3CN) 0.9(CH 2Cl 2) 0.1]·[Fe 2(PIMIC6)(AnthCO 2)(OH 2)]·0.75CH 3CN: a crystallographer's nightmare or a fascinating case of disorder? ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2018; 74:122-131. [PMID: 29616987 DOI: 10.1107/s2052520618000689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
Refinement of large crystal structures as well as that of disordered structures can be challenging. If both features come together, structure refinement has the potential of becoming a crystallographer's nightmare. Here, the refinement of the large and highly disordered structure of [Fe2(PIMIC6)(AnthCO2)(CH3CN)]·[Fe2(PIMIC6)(AnthCO2)(CH3CN)0.9(CH2Cl2)0.1]·[Fe2(PIMIC6)(AnthCO2)(OH2)]·0.75CH3CN [(1), PIMIC6 is a phenol-imine-based macrocycle, AnthCO2 is an anthracene acid anion] is described and discussed. A total of 5311 parameters had to be refined to generate a model that allows for 14 400 possible arrangements of (1) in the asymmetric unit, making this structure one of the most complex structures in the Cambridge Structural Database to date. All disorders are exceptionally well resolved and exhaustive parameterizing affords a refinement model that is unique with respect to the detail of disorder refinement.
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Affiliation(s)
- Sabine Becker
- Fachbereich Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße 54/684, Kaiserslautern, 67663, Germany
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12
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Ross SA, Lamprou DA, Douroumis D. Engineering and manufacturing of pharmaceutical co-crystals: a review of solvent-free manufacturing technologies. Chem Commun (Camb) 2018; 52:8772-86. [PMID: 27302311 DOI: 10.1039/c6cc01289b] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Design and synthesis of pharmaceutical cocrystals have received great interest in recent years. Cocrystallization of drug substances offers a tremendous opportunity for the development of new drug products with superior physical and pharmacological properties such as solubility, stability, hydroscopicity, dissolution rates and bioavailability. It is now possible to engineer and develop cocrystals via 'green chemistry' and environmentally friendly approaches such as solid-state synthesis in the absence of organic solvents. In addition, significant efforts have been directed towards computational screening, cocrystal manufacturing in a continuous manner and real-time monitoring for quality purposes by using various analytical tools. Pharmaceutical cocrystals are not fully exploited yet and there is a lot of ground to cover before they can be successfully utilized as medical products.
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Affiliation(s)
- S A Ross
- Faculty of Engineering and Science, University of Greenwich, Medway Campus, Chatham Maritime, Kent ME4 4TB, UK.
| | - D A Lamprou
- Strathclyde Institute of Pharmacy and Biomedical Science (SIPBS)s, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK. and EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation (CMAC), University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1 RD, UK
| | - D Douroumis
- Faculty of Engineering and Science, University of Greenwich, Medway Campus, Chatham Maritime, Kent ME4 4TB, UK.
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13
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Rudshteyn B, Acharya A, Batista VS. Is the Supporting Information the Venue for Reproducibility and Transparency? J Phys Chem B 2017; 121:11425-11426. [DOI: 10.1021/acs.jpcb.7b11664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Rudshteyn
- Department of Chemistry and
Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - Atanu Acharya
- Department of Chemistry and
Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - Victor S. Batista
- Department of Chemistry and
Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
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14
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Rudshteyn B, Acharya A, Batista VS. Is the Supporting Information the Venue for Reproducibility and Transparency? J Phys Chem A 2017; 121:9680-9681. [PMID: 29281886 DOI: 10.1021/acs.jpca.7b11663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Rudshteyn
- Department of Chemistry and Energy Sciences Institute, Yale University , New Haven, Connecticut 06520, United States
| | - Atanu Acharya
- Department of Chemistry and Energy Sciences Institute, Yale University , New Haven, Connecticut 06520, United States
| | - Victor S Batista
- Department of Chemistry and Energy Sciences Institute, Yale University , New Haven, Connecticut 06520, United States
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15
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Malamatari M, Ross SA, Douroumis D, Velaga SP. Experimental cocrystal screening and solution based scale-up cocrystallization methods. Adv Drug Deliv Rev 2017; 117:162-177. [PMID: 28811184 DOI: 10.1016/j.addr.2017.08.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 12/20/2022]
Abstract
Cocrystals are crystalline single phase materials composed of two or more different molecular and/or ionic compounds generally in a stoichiometric ratio which are neither solvates nor simple salts. If one of the components is an active pharmaceutical ingredient (API), the term pharmaceutical cocrystal is often used. There is a growing interest among drug development scientists in exploring cocrystals, as means to address physicochemical, biopharmaceutical and mechanical properties and expand solid form diversity of the API. Conventionally, coformers are selected based on crystal engineering principles, and the equimolar mixtures of API and coformers are subjected to solution-based crystallization that are commonly employed in polymorph and salt screening. However, the availability of new knowledge on cocrystal phase behaviour in solid state and solutions has spurred the development and implementation of more rational experimental cocrystal screening as well as scale-up methods. This review aims to provide overview of commonly employed solid form screening techniques in drug development with an emphasis on cocrystal screening methodologies. The latest developments in understanding and the use of cocrystal phase diagrams in both screening and solution based scale-up methods are also presented. Final section is devoted to reviewing the state of the art research covering solution based scale-up cocrystallization process for different cocrystals besides more recent continuous crystallization methods.
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16
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Lu N, Wei RJ, Lin KY, Alagesan M, Wen YS, Liu LK. Weak hydrogen bonding and fluorous interactions in the chloride and bromide salts of 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:343-349. [PMID: 28378719 DOI: 10.1107/s2053229617004016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/13/2017] [Indexed: 11/10/2022]
Abstract
Neutralization of 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridine with hydrohalo acids HX (X = Cl and Br) yielded the pyridinium salts 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium chloride, C9H10F4NO+·Cl-, (1), and 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium bromide, C9H10F4NO+·Br-, (2), both carrying a fluorous side chain at the para position of the pyridinium ring. Single-crystal X-ray diffraction techniques revealed that (1) and (2) are isomorphous. The halide anions accept four hydrogen bonds from N-H, ortho-C-H and CF2-H groups. Two cations and two anions form a centrosymmetric dimeric building block, utilizing complimentary N-H...X...H-Csp3 connections. These dimers are further crosslinked, utilizing another complimentary Csp2-H...X...H-Csp2 connection. The pyridinium rings are π-stacked, forming columns running parallel to the a axis that make angles of ca 44-45° with the normal to the pyridinium plane. There are also supramolecular C-H...F-C interactions, namely bifurcated C-H...F and bifurcated C-F...H interactions; additionally, one type II C-F...F-C halogen bond has been observed.
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Affiliation(s)
- Norman Lu
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| | - Rong Jyun Wei
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| | - Kwan Yu Lin
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| | - Mani Alagesan
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
| | - Yuh Sheng Wen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Ling Kang Liu
- Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
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17
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Stehr V, Fink RF, Deibel C, Engels B. Charge carrier mobilities in organic semiconductor crystals based on the spectral overlap. J Comput Chem 2016; 37:2146-56. [DOI: 10.1002/jcc.24441] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/10/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Vera Stehr
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg; Würzburg 97074 Germany
| | - Reinhold F. Fink
- Institut für Physikalische und Theoretische Chemie, Universität Tübingen; Tübingen 72076 Germany
| | - Carsten Deibel
- Institut für Physik, Technische Universität Chemnitz; Chemnitz 09126 Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg; Würzburg 97074 Germany
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18
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Groom CR, Bruno IJ, Lightfoot MP, Ward SC. The Cambridge Structural Database. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:171-9. [PMID: 27048719 PMCID: PMC4822653 DOI: 10.1107/s2052520616003954] [Citation(s) in RCA: 5865] [Impact Index Per Article: 733.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/08/2016] [Indexed: 05/03/2023]
Abstract
The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.
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Affiliation(s)
- Colin R. Groom
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Ian J. Bruno
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Matthew P. Lightfoot
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Suzanna C. Ward
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
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19
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Storing the Wisdom: Chemical Concepts and Chemoinformatics. INFORMATICS 2015. [DOI: 10.3390/informatics2040050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Harvey MJ, Mason NJ, McLean A, Rzepa HS. Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers. J Cheminform 2015; 7:37. [PMID: 26257829 PMCID: PMC4528360 DOI: 10.1186/s13321-015-0081-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the persistent identifier of the dataset with optional specification of the attributes of the data document such as filename or media type. RESULTS The procedures are demonstrated using the JSmol molecular visualizer as a component of a web page and Avogadro as a stand-alone modelling program. We compare our methods for automated retrieval of data from a standards-compliant data repository with those currently in operation for a selection of existing molecular databases and repositories. CONCLUSIONS Our methods illustrate the importance of adopting a standards-based approach of using metadata declarations to increase access to and discoverability of repository-based data. Graphical abstract.
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Affiliation(s)
- Matthew J Harvey
- />High Performance Computing Service, Imperial College London, London, UK
| | - Nicholas J Mason
- />Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ UK
| | - Andrew McLean
- />High Performance Computing Service, Imperial College London, London, UK
| | - Henry S Rzepa
- />Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ UK
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21
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Aakeröy C. Is there any point in making co-crystals? ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2015. [DOI: 10.1107/s2052520615010872] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Many aspects of co-crystals, including their synthesis, characterization and possible applications, are receiving considerable attention from academia and industry alike. The question is, can this interdisciplinary activity be translated into new fundamental insight and new solid forms of high-value materials with improved performances.
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Sheldrick GM. Crystal structure refinement with SHELXL. Acta Crystallogr C Struct Chem 2015; 71:3-8. [PMID: 25567568 PMCID: PMC4294323 DOI: 10.1107/s2053229614024218] [Citation(s) in RCA: 24891] [Impact Index Per Article: 2765.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/02/2014] [Indexed: 11/23/2022] Open
Abstract
The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
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Affiliation(s)
- George M. Sheldrick
- Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077, Germany
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