Periodic DFT Calculations—Review of Applications in the Pharmaceutical Sciences

Mazurek, Anna; Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej

doi:10.3390/pharmaceutics12050415

Cited by 47 publications

(26 citation statements)

References 216 publications

(216 reference statements)

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“…requires the use of periodic DFT methods [123,124]. There are a number of methods and programs for performing this type of calculation [125,126]. In computational methods of solid-state physics, approaches that utilize basic sets of plane waves are usually used [117], and in solid state chemistry, basic sets of the Gaussian type are used [116].…”

Section: The Energies Of Intermolecular Interactions Of H2o2 In Organic Crystals: Calculations By the Kohn-sham Methods With Periodic Boumentioning

confidence: 99%

Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions

et al. 2020

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Despite the technological importance of urea perhydrate (percarbamide) and sodium percarbonate, and the growing technological attention to solid forms of peroxide, fewer than 45 peroxosolvates were known by 2000. However, recent advances in X-ray diffractometers more than tripled the number of structurally characterized peroxosolvates over the last 20 years, and even more so, allowed energetic interpretation and gleaning deeper insight into peroxosolvate stability. To date, 134 crystalline peroxosolvates have been structurally resolved providing sufficient insight to justify a first review article on the subject. In the first chapter of the review, a comprehensive analysis of the structural databases is carried out revealing the nature of the co-former in crystalline peroxosolvates. In the majority of cases, the coformers can be classified into three groups: (1) salts of inorganic and carboxylic acids; (2) amino acids, peptides, and related zwitterions; and (3) molecular compounds with a lone electron pair on nitrogen and/or oxygen atoms. The second chapter of the review is devoted to H-bonding in peroxosolvates. The database search and energy statistics revealed the importance of intermolecular hydrogen bonds (H-bonds) which play a structure-directing role in the considered crystals. H2O2 always forms two H-bonds as a proton donor, the energy of which is higher than the energy of analogous H-bonds existing in isostructural crystalline hydrates. This phenomenon is due to the higher acidity of H2O2 compared to water and the conformational mobility of H2O2. The dihedral angle H-O-O-H varies from 20 to 180° in crystalline peroxosolvates. As a result, infinite H-bonded 1D chain clusters are formed, consisting of H2O2 molecules, H2O2 and water molecules, and H2O2 and halogen anions. H2O2 can form up to four H-bonds as a proton acceptor. The third chapter of the review is devoted to energetic computations and in particular density functional theory with periodic boundary conditions. The approaches are considered in detail, allowing one to obtain the H-bond energies in crystals. DFT computations provide deeper insight into the stability of peroxosolvates and explain why percarbamide and sodium percarbonate are stable to H2O2/H2O isomorphic transformations. The review ends with a description of the main modern trends in the synthesis of crystalline peroxosolvates, in particular, the production of peroxosolvates of high-energy compounds and mixed pharmaceutical forms with antiseptic and analgesic effects.

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Section: The Energies Of Intermolecular Interactions Of H2o2 In Organic Crystals: Calculations By the Kohn-sham Methods With Periodic Boumentioning

confidence: 99%

Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions

et al. 2020

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“…Studying molecular crystals and their phase transitions is of great importance for many scientific fields such as crystallography [1,2], thermodynamics [3,4], computational [5][6][7] and solid state chemistry [8][9][10], etc. Solid forms of many organic molecules are being developed, studied, and produced in the pharmaceutical industry [11][12][13][14][15] and in arising subfields of materials science [16][17][18]. The last one, among others, focuses the attention on the mechanical properties of molecular crystals [19][20][21][22][23][24][25] and metal-organic complexes [26][27][28].…”

Section: Introductionmentioning

confidence: 99%

Low Temperature and High-Pressure Study of Bending L-Leucinium Hydrogen Maleate Crystals

Skakunova

Rychkov

2021

Crystals

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The polymorphism of molecular crystals is a well-known phenomenon, resulting in modifications of physicochemical properties of solid phases. Low temperatures and high pressures are widely used to find phase transitions and quench new solid forms. In this study, L-Leucinium hydrogen maleate (LLHM), the first molecular crystal that preserves its anomalous plasticity at cryogenic temperatures, is studied at extreme conditions using Raman spectroscopy and optical microscopy. LLHM was cooled down to 11 K without any phase transition, while high pressure impact leads to perceptible changes in crystal structure in the interval of 0.0–1.35 GPa using pentane-isopentane media. Surprisingly, pressure transmitting media (PTM) play a significant role in the behavior of the LLHM system at extreme conditions—we did not find any phase change up to 3.05 GPa using paraffin as PTM. A phase transition of LLHM to amorphous form or solid–solid phase transition(s) that results in crystal fracture is reported at high pressures. LLHM stability at low temperatures suggests an alluring idea to prove LLHM preserves plasticity below 77 K.

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“…Such methodology has been recently used to study crystal structures of 17β-estradiol. As a result, an estradiol hemihydrate has been computationally determined [ 150 ]. DFT calculations are also often necessary to refine a crystal structure obtained from powder X-ray diffraction (PXRD) experiments.…”

Section: Application Of Molecular Modelling Methods In the Study Omentioning

confidence: 99%

Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

Mazurek

Szeleszczuk

Simonson

et al. 2020

IJMS

Self Cite

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In this review, applications of various molecular modelling methods in the study of estrogens and xenoestrogens are summarized. Selected biomolecules that are the most commonly chosen as molecular modelling objects in this field are presented. In most of the reviewed works, ligand docking using solely force field methods was performed, employing various molecular targets involved in metabolism and action of estrogens. Other molecular modelling methods such as molecular dynamics and combined quantum mechanics with molecular mechanics have also been successfully used to predict the properties of estrogens and xenoestrogens. Among published works, a great number also focused on the application of different types of quantitative structure–activity relationship (QSAR) analyses to examine estrogen’s structures and activities. Although the interactions between estrogens and xenoestrogens with various proteins are the most commonly studied, other aspects such as penetration of estrogens through lipid bilayers or their ability to adsorb on different materials are also explored using theoretical calculations. Apart from molecular mechanics and statistical methods, quantum mechanics calculations are also employed in the studies of estrogens and xenoestrogens. Their applications include computation of spectroscopic properties, both vibrational and Nuclear Magnetic Resonance (NMR), and also in quantum molecular dynamics simulations and crystal structure prediction. The main aim of this review is to present the great potential and versatility of various molecular modelling methods in the studies on estrogens and xenoestrogens.

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Periodic DFT Calculations—Review of Applications in the Pharmaceutical Sciences

Cited by 47 publications

References 216 publications

Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions

Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions

Low Temperature and High-Pressure Study of Bending L-Leucinium Hydrogen Maleate Crystals

Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

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