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Hoser A, Zwolenik A, Makal A. On the importance of low-frequency modes in predicting pressure-induced phase transitions. Phys Chem Chem Phys 2024; 26:20745-20749. [PMID: 39078650 DOI: 10.1039/d4cp02368d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The occurrence of ultra-low frequency oscillation mode as observed by means of periodic DFT calculations at Γ point in a molecular crystal at ambient conditions can be a valuable predictor of imminent pressure-induced phase transition. We illustrate it with a series of polymorphs of diacetyl-pyrenes, for two of which such soft-modes indicated the trajectory of pressure-induced structural reorganization at ≈0.8 GPa. Notably, susceptibility to pressure-induced phase transformations could not be predicted based on material's thermodynamic characteristics, and there were no unequivocal clues in their crystal packing.
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Affiliation(s)
- Anna Hoser
- Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland.
| | - Aleksandra Zwolenik
- Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland.
| | - Anna Makal
- Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland.
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Anker S, McKechnie D, Mulheran P, Sefcik J, Johnston K. Assessment of GAFF and OPLS Force Fields for Urea: Crystal and Aqueous Solution Properties. CRYSTAL GROWTH & DESIGN 2024; 24:143-158. [PMID: 38188266 PMCID: PMC10767702 DOI: 10.1021/acs.cgd.3c00785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
Molecular simulations such as Monte Carlo, molecular dynamics, and metadynamics have been used to provide insight into crystallization phenomena, including nucleation and crystal growth. However, these simulations depend on the force field used, which models the atomic and molecular interactions, to adequately reproduce relevant material properties for the phases involved. Two widely used force fields, the General AMBER Force Field (GAFF) and the Optimized Potential for Liquid Simulations (OPLS), including several variants, have previously been used for studying urea crystallization. In this work, we investigated how well four different versions of the GAFF force field and five different versions of the OPLS force field reproduced known urea crystal and aqueous solution properties. Two force fields were found to have the best overall performance: a specific urea charge-optimized GAFF force field and the original all-atom OPLS force field. It is recommended that a suitable testing protocol involving both solution and solid properties, such as that used in this work, is adopted for the validation of force fields used for simulations of crystallization phenomena.
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Affiliation(s)
- Samira Anker
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow G1 1XJ, U.K
- Future Continuous Manufacturing and Advanced Crystallisation Research Hub, University of Strathclyde, Glasgow G1 1RD, U.K
| | - David McKechnie
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow G1 1XJ, U.K
- Future Continuous Manufacturing and Advanced Crystallisation Research Hub, University of Strathclyde, Glasgow G1 1RD, U.K
| | - Paul Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow G1 1XJ, U.K
| | - Jan Sefcik
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow G1 1XJ, U.K
- Future Continuous Manufacturing and Advanced Crystallisation Research Hub, University of Strathclyde, Glasgow G1 1RD, U.K
| | - Karen Johnston
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow G1 1XJ, U.K
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Napiórkowska E, Szeleszczuk Ł, Milcarz K, Pisklak DM. Density Functional Theory and Density Functional Tight Binding Studies of Thiamine Hydrochloride Hydrates. Molecules 2023; 28:7497. [PMID: 38005219 PMCID: PMC10673443 DOI: 10.3390/molecules28227497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Thiamine hydrochloride (THCL), also known as vitamin B1, is an active pharmaceutical ingredient (API), present on the list of essential medicines developed by the WHO, which proves its importance for public health. THCL is highly hygroscopic and can occur in the form of hydrates with varying degrees of hydration, depending on the air humidity. Although experimental characterization of the THCL hydrates has been described in the literature, the questions raised in previously published works suggest that additional research and in-depth analysis of THCL dehydration behavior are still needed. Therefore, the main aim of this study was to characterize, by means of quantum chemical calculations, the behavior of thiamine hydrates and explain the previously obtained results, including changes in the NMR spectra, at the molecular level. To achieve this goal, a series of DFT (CASTEP) and DFTB (DFTB+) calculations under periodic boundary conditions have been performed, including molecular dynamics simulations and GIPAW NMR calculations. The obtained results explain the differences in the relative stability of the studied forms and changes in the spectra observed for the samples of various degrees of hydration. This work highlights the application of periodic DFT calculations in the analysis of various solid forms of APIs.
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Affiliation(s)
- Ewa Napiórkowska
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland
- Doctoral School, Medical University of Warsaw, Żwirki i Wigury 81 Str., 02-093 Warsaw, Poland
| | - Łukasz Szeleszczuk
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland
| | - Katarzyna Milcarz
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland
| | - Dariusz Maciej Pisklak
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland
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Napiórkowska E, Milcarz K, Szeleszczuk Ł. Review of Applications of Density Functional Theory (DFT) Quantum Mechanical Calculations to Study the High-Pressure Polymorphs of Organic Crystalline Materials. Int J Mol Sci 2023; 24:14155. [PMID: 37762459 PMCID: PMC10532210 DOI: 10.3390/ijms241814155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Since its inception, chemistry has been predominated by the use of temperature to generate or change materials, but applications of pressure of more than a few tens of atmospheres for such purposes have been rarely observed. However, pressure is a very effective thermodynamic variable that is increasingly used to generate new materials or alter the properties of existing ones. As computational approaches designed to simulate the solid state are normally tuned using structural data at ambient pressure, applying them to high-pressure issues is a highly challenging test of their validity from a computational standpoint. However, the use of quantum chemical calculations, typically at the level of density functional theory (DFT), has repeatedly been shown to be a great tool that can be used to both predict properties that can be later confirmed by experimenters and to explain, at the molecular level, the observations of high-pressure experiments. This article's main goal is to compile, analyze, and synthesize the findings of works addressing the use of DFT in the context of molecular crystals subjected to high-pressure conditions in order to give a general overview of the possibilities offered by these state-of-the-art calculations.
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Affiliation(s)
| | | | - Łukasz Szeleszczuk
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-093 Warsaw, Poland; (E.N.); (K.M.)
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Walden DM, Bundey Y, Jagarapu A, Antontsev V, Chakravarty K, Varshney J. Molecular Simulation and Statistical Learning Methods toward Predicting Drug-Polymer Amorphous Solid Dispersion Miscibility, Stability, and Formulation Design. Molecules 2021; 26:E182. [PMID: 33401494 PMCID: PMC7794704 DOI: 10.3390/molecules26010182] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/20/2022] Open
Abstract
Amorphous solid dispersions (ASDs) have emerged as widespread formulations for drug delivery of poorly soluble active pharmaceutical ingredients (APIs). Predicting the API solubility with various carriers in the API-carrier mixture and the principal API-carrier non-bonding interactions are critical factors for rational drug development and formulation decisions. Experimental determination of these interactions, solubility, and dissolution mechanisms is time-consuming, costly, and reliant on trial and error. To that end, molecular modeling has been applied to simulate ASD properties and mechanisms. Quantum mechanical methods elucidate the strength of API-carrier non-bonding interactions, while molecular dynamics simulations model and predict ASD physical stability, solubility, and dissolution mechanisms. Statistical learning models have been recently applied to the prediction of a variety of drug formulation properties and show immense potential for continued application in the understanding and prediction of ASD solubility. Continued theoretical progress and computational applications will accelerate lead compound development before clinical trials. This article reviews in silico research for the rational formulation design of low-solubility drugs. Pertinent theoretical groundwork is presented, modeling applications and limitations are discussed, and the prospective clinical benefits of accelerated ASD formulation are envisioned.
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Affiliation(s)
| | | | | | | | | | - Jyotika Varshney
- VeriSIM Life Inc., 1 Sansome St, Suite 3500, San Francisco, CA 94104, USA; (D.M.W.); (Y.B.); (A.J.); (V.A.); (K.C.)
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Mazurek AH, Szeleszczuk Ł, Pisklak DM. Periodic DFT Calculations-Review of Applications in the Pharmaceutical Sciences. Pharmaceutics 2020; 12:E415. [PMID: 32369915 PMCID: PMC7284980 DOI: 10.3390/pharmaceutics12050415] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/31/2022] Open
Abstract
In the introduction to this review the complex chemistry of solid-state pharmaceutical compounds is summarized. It is also explained why the density functional theory (DFT) periodic calculations became recently so popular in studying the solid APIs (active pharmaceutical ingredients). Further, the most popular programs enabling DFT periodic calculations are presented and compared. Subsequently, on the large number of examples, the applications of such calculations in pharmaceutical sciences are discussed. The mentioned topics include, among others, validation of the experimentally obtained crystal structures and crystal structure prediction, insight into crystallization and solvation processes, development of new polymorph synthesis ways, and formulation techniques as well as application of the periodic DFT calculations in the drug analysis.
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Affiliation(s)
| | - Łukasz Szeleszczuk
- Chair and Department of Physical Pharmacy and Bioanalysis, Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 str., 02-093 Warsaw, Poland; (A.H.M.); (D.M.P.)
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