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Ludík J, Kostková V, Kocian Š, Touš P, Štejfa V, Červinka C. First-Principles Models of Polymorphism of Pharmaceuticals: Maximizing the Accuracy-to-Cost Ratio. J Chem Theory Comput 2024; 20:2858-2870. [PMID: 38531828 PMCID: PMC11008097 DOI: 10.1021/acs.jctc.4c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Accuracy and sophistication of in silico models of structure, internal dynamics, and cohesion of molecular materials at finite temperatures increase over time. Applicability limits of ab initio polymorph ranking that would be feasible at reasonable costs currently represent crystals of moderately sized molecules (less than 20 nonhydrogen atoms) and simple unit cells (containing rather only one symmetry-irreducible molecule). Extending the applicability range of the underlying first-principles methods to larger systems with a real-life significance, and enabling to perform such computations in a high-throughput regime represent additional challenges to be tackled in computational chemistry. This work presents a novel composite method that combines the computational efficiency of density-functional tight-binding (DFTB) methods with the accuracy of density-functional theory (DFT). Being rooted in the quasi-harmonic approximation, it uses a cheap method to perform all of the costly scans of how static and dynamic characteristics of the crystal vary with respect to its volume. Such data are subsequently corrected to agree with a higher-level model, which must be evaluated only at a single volume of the crystal. It thus enables predictions of structural, cohesive, and thermodynamic properties of complex molecular materials, such as pharmaceuticals or organic semiconductors, at a fraction of the original computational cost. As the composite model retains the solid physical background, it suffers from a minimum accuracy deterioration compared to the full treatment with the costly approach. The novel methodology is demonstrated to provide consistent results for the structural and thermodynamic properties of real-life molecular crystals and their polymorph ranking.
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Affiliation(s)
- Jan Ludík
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Veronika Kostková
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Štefan Kocian
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Petr Touš
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
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Experimental and Computational Study for the Design of Sulfathiazole Dosage Form with Clay Mineral. Pharmaceutics 2023; 15:pharmaceutics15020575. [PMID: 36839898 PMCID: PMC9967197 DOI: 10.3390/pharmaceutics15020575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/23/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Sulfathiazole is an antimicrobial belonging to the family of sulfonamides, which were the first antibiotics to be discovered. Sulfathiazole is generally administered orally, and its main disadvantage is that it has low aqueous solubility, requiring high doses for its administration. This fact has led to side effects and the generation of bacterial resistance to the drug over time. The improvement of its solubility would mean not having to administer such high doses in its treatment. At the same time, montmorillonite is a natural, low-cost, non-toxic, biocompatible clay with a high adsorption capacity. It is potentially useful as a nanocarrier to design sulfathiazole dosage forms. In this work, the interaction between the drug and the clay mineral has been studied from an experimental and computational atomistic point of view to improve the drug's biopharmaceutical profile. The results showed the potential enhancement of the drug solubility due to the correct adsorption of the sulfathiazole in the clay interlayer space. As a result of the inclusion of sulfathiazole in the interlayer of the clay mineral, the solubility of the drug increased by 220% concerning the pristine drug. Experimentally, it was not possible to know the number of drug molecules adsorbed in the interlayer space or the external surface of the carrier. Theoretical studies will enable the knowledge of the stoichiometry of the drug/clay hybrids, with three molecules in the interlayer space being the most favorable process. The resultant basal spacing was in agreement with the experimental results.
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Zeidan MA, Othman DI, Goda FE, Mostafa AS. Thiazole Ring-Cleavage: Versatile Products Obtained in The Course of Synthesis of Certain Sulfonamide Derivatives. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123690. [PMID: 35744821 PMCID: PMC9229234 DOI: 10.3390/molecules27123690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/22/2022] [Accepted: 05/29/2022] [Indexed: 11/17/2022]
Abstract
The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.
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Sandeep, Sudheendranath A, Venugopalan P, Kumar A, Thomas SP. Conformational preferences in a series of α-hydroxy ketone derivatives: interplay of conformational energies and lattice cohesive energies. CrystEngComm 2022. [DOI: 10.1039/d2ce00700b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A detailed structural analysis of a series of α-hydroxy ketone derivatives in terms of lattice energies and conformational energies reveals the competing factors of inter- and intramolecular interactions that direct conformational preferences.
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Affiliation(s)
- Sandeep
- Department of Chemistry, Panjab University, Chandigarh-160014, India
- Department of Applied Sciences, University Institute of Engineering and Technology, Panjab University, Chandigarh-160014, India
| | - Athul Sudheendranath
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, Delhi, India
| | | | - Anil Kumar
- Department of Applied Sciences, University Institute of Engineering and Technology, Panjab University, Chandigarh-160014, India
| | - Sajesh P. Thomas
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, Delhi, India
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6
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Hughes DS, Bingham AL, Hursthouse MB, Threlfall TL, Bond AD. The extensive solid-form landscape of sulfathiazole: geometrical similarity and interaction energies. CrystEngComm 2022. [DOI: 10.1039/d1ce01516h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sulfathiazole shows one of the most extensive solid-form landscapes known to date for an active pharmaceutical ingredient. A standardised structure set of 5 polymorphs, 59 co-crystals, 29 salts, and 3 other structures is established.
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Affiliation(s)
- David S. Hughes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ann L. Bingham
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Michael B. Hursthouse
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Terry L. Threlfall
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew D. Bond
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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Shteingolts SA, Saifina AF, Saifina LF, Semenov VE, Fukin GK, Fayzullin RR. X-ray charge density study of the 6-methyluracil derivative in the crystal: Revealing, consequences, and multipole refinement of minor static disorder. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Menon PK, Krishnaraj K, Anabha E, Devaky K, Thomas SP. Synthesis, crystal structure and electron density analysis of a sulfanyl 2-pyridone analogue: Tautomeric preference and conformation locking by S···O chalcogen bonding. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Dumitrescu DG, Roche GH, Moreau JJE, Dautel OJ, van der Lee A. A positive to negative uniaxial thermal expansion crossover in an organic benzothienobenzothiophene structure. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:661-673. [PMID: 32831285 DOI: 10.1107/s2052520620007702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Compound 6,6'-([1]benzothieno[3,2-b][1]benzothiophene-2,7-diyl)bis(butan-1-ol) (BTBT-C4OH) displays a continuous type 0 first-order isosymmetric phase transition at 200 K which is accompanied by a continuous change of the thermal expansion along the b axis from positive to negative. The equivalent isotropic atomic displacement parameters for all non-hydrogen atoms as well as all the eigenvalues of the anisotropic atomic displacement tensor show discontinuous behavior at the phase transition. The eigenvalues of the translational tensor in a rigid-body description of the molecule are all discontinuous at the phase transition, but the librational eigenvalues are discontinuous only in their temperature derivative. BTBT-C4OH displays a similar type of quasi-supercritical phase transition as bis(hydroxyhexyl)[1]benzothieno[3,2-b][1]benzothiophene (BTBT-C6OH), despite the difference in molecular packing and the very large difference in thermal expansion magnitudes.
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Affiliation(s)
- Dan G Dumitrescu
- Elettra, Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5 in AREA Science Park, Basovizza, Trieste 34149, Italy
| | - Gilles H Roche
- ICGM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Joël J E Moreau
- ICGM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Olivier J Dautel
- ICGM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Arie van der Lee
- Institut Européen des Membranes, IEM - UMR 5635, ENSCM, CNRS, Université de Montpellier, Montpellier, France
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Bora P, Saikia B, Sarma B. Oriented Crystallization on Organic Monolayers to Control Concomitant Polymorphism. Chemistry 2019; 26:699-710. [PMID: 31651064 DOI: 10.1002/chem.201903938] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/24/2019] [Indexed: 11/06/2022]
Abstract
Nucleation events and crystal growth can be guided by molecular recognition at interfaces through intermolecular interactions. The short-acting antimicrobial sulfa drug sulfathiazole is known for its concomitant crystallization, which has five known polymorphs, due to conformational flexibility and hydrogen-bond synthon variation. In its development stage of a drug the issue of concomitant crystallization needs to be addressed with respect to patent litigation, including legal actions to protect patents against infringement. A functional self-assembled monolayer (SAM) of organic thiol on a gold surface has been employed as an efficient approach to control concomitant nucleation of such flexible drugs. The crystallization on a SAM surface is mostly kinetically driven and often leads to the nucleation of novel metastable forms. Spectroscopic, thermal analysis and X-ray diffraction studies reveal that a previously unknown, sixth form of the drug nucleates on the designed SAM surface.
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Affiliation(s)
- Pranita Bora
- Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
| | - Basanta Saikia
- Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
| | - Bipul Sarma
- Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
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Crystal Structure Optimization and Gibbs Free Energy Comparison of Five Sulfathiazole Polymorphs by the Embedded Fragment QM Method at the DFT Level. CRYSTALS 2019. [DOI: 10.3390/cryst9050256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Molecular crystal plays an important role in many fields of science and technology, but it often crystallizes in different polymorphs with different physical properties. To guide the experimental synthesis of candidate materials, the atomic-scale model is frequently used to predict the most stable polymorph and its structural properties. Here, we show how an ab initio method can be used to achieve a rapid and accurate prediction of sulfathiazole crystal polymorphs (an antibiotic drug), based on the Gibbs free energy calculation and Raman spectra analysis. At the atmospheric pressure and the temperature of 300 K, we demonstrate that form III (FIII) is the most stable structure of sulfathiazole. The agreement between the predicted and experimental crystal structures corresponds to the order of stability for five sulfathiazole polymorphs as FI < FV < FIV < FII < FIII, which is achieved by employing the density functional theory (DFT) calculations.
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13
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Multiple conformations and supramolecular synthons in almost fifty crystal structures of the anti-HIV/HBV drug lamivudine. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Trujillo C, Rozas I, Elguero J, Alkorta I, Sánchez-Sanz G. Modulating intramolecular chalcogen bonds in aromatic (thio)(seleno)phene-based derivatives. Phys Chem Chem Phys 2019; 21:23645-23650. [DOI: 10.1039/c9cp03694f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Intramolecular chalcogen interactions have been studied for four different derivatives of compounds within two different families, S or Se, to evaluate the effect of these IMChBs in the stability of the interacting and non-interacting systems.
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Affiliation(s)
- Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin 152-160 Pearse Street
- Dublin 2
- Ireland
| | - Isabel Rozas
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin 152-160 Pearse Street
- Dublin 2
- Ireland
| | - José Elguero
- Instituto de Química Médica
- CSIC
- Juan de la Cierva
- 3
- E-28006 Madrid
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- Juan de la Cierva
- 3
- E-28006 Madrid
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15
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Investigation of crystallization mechanisms for polymorphic and habit control from the Supercritical AntiSolvent process. J Supercrit Fluids 2018. [DOI: 10.1016/j.supflu.2017.11.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Lai F, Du JJ, Williams PA, Váradi L, Baker D, Groundwater PW, Overgaard J, Platts JA, Hibbs DE. A comparison of the experimental and theoretical charge density distributions in two polymorphic modifications of piroxicam. Phys Chem Chem Phys 2018; 18:28802-28818. [PMID: 27722530 DOI: 10.1039/c6cp02690g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental charge density distribution studies of two polymorphic forms of piroxicam, β-piroxicam (1) and piroxicam monohydrate (2), were carried out via high-resolution single crystal X-ray diffraction experiments and multipole refinement. The asymmetric unit of (2) consists of two discrete piroxicam molecules, (2a) and (2b), and two water molecules. Geometry differs between (1) and (2) due to the zwitterionic nature of (2) which results in the rotation of the pyridine ring around the C(10)-N(2) bond by approximately 180°. Consequently, the pyridine and amide are no longer co-planar and (2) forms two exclusive, strong hydrogen bonds, H(3)O(4) and H(2)O(3), with bond energies of 66.14 kJ mol-1 and 112.82 kJ mol-1 for (2a), and 58.35 kJ mol-1 and 159.51 kJ mol-1 for (2b), respectively. Proton transfer between O(3) and N(3) in (2) results in significant differences in surface electrostatic potentials. This is clarified by the calculation of atomic charges in the zwitterion that shows the formally positive charge of the pyridyl nitrogen which is redistributed over the whole of the pyridine ring instead of concentrating at N-H. Similarly, the negative charge of the oxygen is distributed across the benzothiazine carboxamide moiety. The multipole derived lattice energy for (1) is -304 kJ mol-1 and that for (2) is -571 kJ mol-1, which is in agreement with the experimentally determined observations of higher solubility and dissolution rates of (1) compared to (2).
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Affiliation(s)
- Felcia Lai
- Faculty of Pharmacy, The University of Sydney, NSW 2006, Australia.
| | - Jonathan J Du
- Faculty of Pharmacy, The University of Sydney, NSW 2006, Australia.
| | - Peter A Williams
- Faculty of Pharmacy, The University of Sydney, NSW 2006, Australia. and School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Linda Váradi
- Faculty of Pharmacy, The University of Sydney, NSW 2006, Australia.
| | - Daniel Baker
- Rigaku Oxford Diffraction, Oxford Industrial Park, Yarnton, Oxfordshire, OX5 1QU, UK
| | | | - Jacob Overgaard
- Department of Chemistry, Center for Materials Crystallography, Aarhus University, Langelandsgade 140, Aarhus C, 8000, Denmark
| | - James A Platts
- School of Chemistry, Cardiff University, P.O. Box 912, Cardiff, CF13TB, Wales, UK
| | - David E Hibbs
- Faculty of Pharmacy, The University of Sydney, NSW 2006, Australia.
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Spackman MA. Towards the use of experimental electron densities to estimate reliable lattice energies. CrystEngComm 2018. [DOI: 10.1039/c8ce01108g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lattice energies derived from experimental charge densities are critically assessed, with a view to encouraging further research of this nature.
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Affiliation(s)
- Mark A. Spackman
- School of Molecular Sciences
- University of Western Australia
- Perth
- Australia
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18
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Recent progress of structural study of polymorphic pharmaceutical drugs. Adv Drug Deliv Rev 2017; 117:71-85. [PMID: 27940141 DOI: 10.1016/j.addr.2016.12.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 12/20/2022]
Abstract
This review considers advances in the understanding of active pharmaceutical ingredient polymorphism since around 2010 mainly from a structural view point, with a focus on twelve model drugs. New polymorphs of most of these drugs have been identified despite that the polymorphism of these old drugs has been extensively studied so far. In addition to the conventional modifications of preparative solvents, temperatures, and pressure, more strategic structure-based methods have successfully yielded new polymorphs. The development of analytical techniques, including X-ray analyses, spectroscopy, and microscopy has facilitated the identification of unknown crystal structures and also the discovery of new polymorphs. Computational simulations have played an important role in explaining and predicting the stability order of polymorphs. Furthermore, these make significant contributions to the design of new polymorphs by considering structure and energy. The new technologies and insights discussed in this review will contribute to the control of polymorphic forms, both during manufacture and in the drug formulation.
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Theoretical Study of Intramolecular Interactions in Peri-Substituted Naphthalenes: Chalcogen and Hydrogen Bonds. Molecules 2017; 22:molecules22020227. [PMID: 28157170 PMCID: PMC6155622 DOI: 10.3390/molecules22020227] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/26/2017] [Indexed: 01/19/2023] Open
Abstract
A theoretical study of the peri interactions, both intramolecular hydrogen (HB) and chalcogen bonds (YB), in 1-hydroxy-8YH-naphthalene, 1,4-dihydroxy-5,8-di-YH-naphthalene, and 1,5-dihydroxy-4,8-di-YH-naphthalene, with Y = O, S, and Se was carried out. The systems with a OH:Y hydrogen bond are the most stable ones followed by those with a chalcogen O:Y interaction, those with a YH:O hydrogen bond (Y = S and Se) being the least stable ones. The electron density values at the hydrogen bond critical points indicate that they have partial covalent character. Natural Bond Orbital (NBO) analysis shows stabilization due to the charge transfer between lone pair orbitals towards empty Y–H that correlate with the interatomic distances. The electron density shift maps and non-covalent indexes in the different systems are consistent with the relative strength of the interactions. The structures found on the CSD were used to compare the experimental and calculated results.
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Kumar V, Thaimattam R, Dutta S, Munshi P, Ramanan A. Structural landscape of multicomponent solids based on sulfa drugs. CrystEngComm 2017. [DOI: 10.1039/c7ce00217c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Broo A, Nilsson Lill SO. Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2016; 72:460-76. [DOI: 10.1107/s2052520616006831] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/22/2016] [Indexed: 11/10/2022]
Abstract
A new force field, here called AZ-FF, aimed at being used for crystal structure predictions, has been developed. The force field is transferable to a new type of chemistry without additional training or modifications. This makes the force field very useful in the prediction of crystal structures of new drug molecules since the time-consuming step of developing a new force field for each new molecule is circumvented. The accuracy of the force field was tested on a set of 40 drug-like molecules and found to be very good where observed crystal structures are found at the top of the ranked list of tentative crystal structures. Re-ranking with dispersion-corrected density functional theory (DFT-D) methods further improves the scoring. After DFT-D geometry optimization the observed crystal structure is found at the leading top of the ranking list. DFT-D methods and force field methods have been evaluated for use in predicting properties such as phase transitions upon heating, mechanical properties or intrinsic crystalline solubility. The utility of using crystal structure predictions and the associated material properties in risk assessment in connection with form selection in the drug development process is discussed.
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Sovago I, Gutmann MJ, Senn HM, Thomas LH, Wilson CC, Farrugia LJ. Electron density, disorder and polymorphism: high-resolution diffraction studies of the highly polymorphic neuralgic drug carbamazepine. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:39-50. [PMID: 26830795 DOI: 10.1107/s2052520615019538] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Analysis of neutron and high-resolution X-ray diffraction data on form (III) of carbamazepine at 100 K using the atoms in molecules (AIM) topological approach afforded excellent agreement between the experimental results and theoretical densities from the optimized gas-phase structure and from multipole modelling of static theoretical structure factors. The charge density analysis provides experimental confirmation of the partially localized π-bonding suggested by the conventional structural formula, but the evidence for any significant C-N π bonding is not strong. Hirshfeld atom refinement (HAR) gives H atom positional and anisotropic displacement parameters that agree very well with the neutron parameters. X-ray and neutron diffraction data on the dihydrate of carbemazepine strongly indicate a disordered orthorhombic crystal structure in the space group Cmca, rather than a monoclinic crystal structure in space group P2(1)/c. This disorder in the dihydrate structure has implications for both experimental and theoretical studies of polymorphism.
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Affiliation(s)
- Ioana Sovago
- WESTChem School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Matthias J Gutmann
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0QX, England
| | - Hans Martin Senn
- WESTChem School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Lynne H Thomas
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Chick C Wilson
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Louis J Farrugia
- WESTChem School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
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Sovago I, Thomas LH, Adam MS, Capelli SC, Wilson CC, Farrugia LJ. High resolution X-ray and neutron diffraction studies on molecular complexes of chloranilic acid and lutidines. CrystEngComm 2016. [DOI: 10.1039/c6ce01065b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Shi X, El Hassan N, Ikni A, Li W, Guiblin N, Spasojević de-Biré A, Ghermani NE. Experimental electron densities of neutral and zwitterionic forms of the drug piroxicam. CrystEngComm 2016. [DOI: 10.1039/c5ce02397a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electron and electrostatic properties of piroxicam (PX) were derived from high resolution X-ray diffraction experiments carried out at 100 K.
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Affiliation(s)
- X. Shi
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- Université Paris Saclay
- CentraleSupélec, UMR CNRS 8580
- 92295 Châtenay-Malabry, France
| | - N. El Hassan
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- Université Paris Saclay
- CentraleSupélec, UMR CNRS 8580
- 92295 Châtenay-Malabry, France
| | - A. Ikni
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- Université Paris Saclay
- CentraleSupélec, UMR CNRS 8580
- 92295 Châtenay-Malabry, France
| | - W. Li
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- Université Paris Saclay
- CentraleSupélec, UMR CNRS 8580
- 92295 Châtenay-Malabry, France
| | - N. Guiblin
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- Université Paris Saclay
- CentraleSupélec, UMR CNRS 8580
- 92295 Châtenay-Malabry, France
| | - A. Spasojević de-Biré
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- Université Paris Saclay
- CentraleSupélec, UMR CNRS 8580
- 92295 Châtenay-Malabry, France
| | - N. E. Ghermani
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- Université Paris Saclay
- CentraleSupélec, UMR CNRS 8580
- 92295 Châtenay-Malabry, France
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Hathwar VR, Sist M, Jørgensen MRV, Mamakhel AH, Wang X, Hoffmann CM, Sugimoto K, Overgaard J, Iversen BB. Quantitative analysis of intermolecular interactions in orthorhombic rubrene. IUCRJ 2015; 2:563-74. [PMID: 26306198 PMCID: PMC4547824 DOI: 10.1107/s2052252515012130] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/24/2015] [Indexed: 05/24/2023]
Abstract
Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ⋯Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H-H interactions. The electron density features of H-H bonding, and the interaction energy of molecular dimers connected by H-H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.
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Affiliation(s)
- Venkatesha R. Hathwar
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Mattia Sist
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Mads R. V. Jørgensen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Aref H. Mamakhel
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Xiaoping Wang
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, PO Box 2008 - MS 6475, Oak Ridge, TN 37831, USA
| | - Christina M. Hoffmann
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, PO Box 2008 - MS 6475, Oak Ridge, TN 37831, USA
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute, I-I-I, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Jacob Overgaard
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Bo Brummerstedt Iversen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
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Abstract
Abstract
The crystal and molecular structures of three ammonium salts derived from sulfathiazole are described. In each case, the anion is in the azanide form, features an intramolecular S←O interaction, and adopts a U-shape. The structures of two cations, [R(HOCH2CH2)NH2]+, namely for R = Me (1) and iPr (2), are unprecedented in the crystallographic literature. Extensive hydrogen bonding is observed in all crystal structures and leads to a two-dimensional array for 1, and three-dimensional architectures for each of 2 and 3 (R = CH2CH2OH). The salts exhibited anti-microbial activity against a range of Gram-positive and Gram-negative bacteria, and proved bactericidal toward Vibrio parahaemolyticus, but had no advantage over sulfathiazole itself.
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Thomas SP, Jayatilaka D, Guru Row TN. S⋯O chalcogen bonding in sulfa drugs: insights from multipole charge density and X-ray wavefunction of acetazolamide. Phys Chem Chem Phys 2015; 17:25411-20. [DOI: 10.1039/c5cp04412j] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental charge density analysis combined with the quantum crystallographic technique of X-ray wavefunction refinement (XWR) provides quantitative insights into the intra- and intermolecular interactions formed by acetazolamide, a diuretic drug.
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Affiliation(s)
- Sajesh P. Thomas
- School of Chemistry and Biochemistry
- The University of Western Australia
- Crawley
- Australia
- Solid state and Structural Chemistry Unit
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry
- The University of Western Australia
- Crawley
- Australia
| | - T. N. Guru Row
- Solid state and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore
- India
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Bond AD. processPIXEL: a program to generate energy-vector models from Gavezzotti'sPIXELcalculations. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714016446] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A command-line program is presented to convert the output from Gavezzotti'sPIXELcalculations to Shishkin's energy-vector models representing the intermolecular interaction topology. The output models comprise sets of vectors joining the centres of the molecules in a crystal structure, scaled so that the vector representing the most stabilizing pairwise interaction has length equal to half of the corresponding intermolecular separation. When the energy-vector model is packed, the most stabilizing pairwise interaction is represented as a continuous line between interacting molecules, while the other intermolecular interactions are shown as discontinuous lines, with a smaller gap representing a more stabilizing interaction. The energy-vector models can be overlaid on the crystal structure using theMercuryvisualizer to enable convenient visualization of structural motifs that contribute significantly to the overall crystal packing energy.
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