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Szufla M, Roztocki K, Krawczuk A, Matoga D. One-step introduction of terminal sulfonic groups into a proton-conducting metal–organic framework by concerted deprotonation–metalation–hydrolysis reaction. Dalton Trans 2020; 49:9953-9956. [DOI: 10.1039/d0dt02017f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A one-step strategy for introducing terminal sulfonic groups from a hydrolysable precursor is demonstrated for a proton-conducting metal–organic framework.
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Rydz A, Gryl M, Krawczuk A, Stadnicka K. Understanding of chromic phenomena: the examples of violuric acid–amino acid based salts and co-crystals. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319091848] [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] Open
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Krawczuk A. Influence of a hydrogen bond on optical properties of materials. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319091101] [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] Open
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Rzęsikowska K, Krawczuk A, Kalinowska-Tłuścik J. Electrostatic potential and non-covalent interactions analysis for the design of selective 5-HT 7 ligands. J Mol Graph Model 2019; 91:130-139. [PMID: 31226573 DOI: 10.1016/j.jmgm.2019.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 01/01/2023]
Abstract
Despite the significant improvement of methodology in the field of the in silico drug discovery, the search for selective drugs is still far from trivial. This is especially relevant in the case of designing new medicaments for treatment of central nervous system disorders. In this work, we present a new approach based on the molecular docking and the following electronic properties analysis of ligands' binding poses (electrostatic potential distribution analysis and quantitative topological analysis of the electron density distribution). The proposed protocol significantly increases the success rate of the selective 5-HT7R ligands against 5-HT1AR selection from the prepared databases (the rise from 33.3% to 77.8% and from 22.7% to 62.5% for training and testing sets, respectively). The presented approach can be applied as a supportive method in the virtual screening of ligands databases.
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Gryl M, Rydz A, Wojnarska J, Krawczuk A, Kozieł M, Seidler T, Ostrowska K, Marzec M, Stadnicka KM. Origin of chromic effects and crystal-to-crystal phase transition in the polymorphs of tyraminium violurate. IUCRJ 2019; 6:226-237. [PMID: 30867920 PMCID: PMC6400187 DOI: 10.1107/s2052252518017037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Chromic materials are nowadays widely used in various technological applications, however understanding the effect and the possibility of tuning the obtained colour of a material are still challenging. Here a combined experimental and theoretical study is presented on the solvatochromic and crystallochromic effects in the (pseudo)polymorphs of tyraminium violurate. This organic material exhibits a large solvatochromic shift (ca 192 nm) associated with broad colour change (from yellow to dark violet). Tyraminum violurate crystallizes as red crystals of form (I) from water as a solvate, and as an unsolvated form [violet crystals of (II)] from methanol solution. Form (I), when heated, undergoes two crystal-to-crystal phase transformations associated with colour change of the crystals. Crystals of (II) show extreme birefringence (ca 0.46) and high refractive index (n γ above 1.90), which can be correlated with preferential orientation of the resultant dipole moments of the ions. Examination of optical effects (UV-Vis spectra) along with theoretical calculations (QTAIM, atomic and bond polarizabilities) enabled the description of the origin of colour in the studied materials.
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Dhibar S, Yadav P, Paul T, Sarkar K, Chattopadhyay AP, Krawczuk A, Dey B. A bio-relevant supramolecular Co(ii)-complex for selective fluorescence sensing of μM range inorganic As(iii) in aqueous medium and its intracellular tracking in bacterial systems. Dalton Trans 2019; 48:4362-4369. [DOI: 10.1039/c8dt04127j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bio-relevant fluorescent supramolecular Co(ii)-complex selectively detects μM range toxic inorganic As(iii) in water and in bacterial systems.
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Gryl M, Seidler T, Krawczuk A, Ostrowska K, Stadnicka K. Cocrystallisation enhanced optical properties of organic materials – quantum crystallography meets crystal engineering. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318093567] [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] Open
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33
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Krawczuk A, Kaczmarczyk M. Influence of chosen synthons on the polarizabilities of functional groups. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318090587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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34
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Kalinowska-Tłuścik J, Staroń J, Krawczuk A, Mordalski S, Warszycki D, Satała G, Hogendorf AS, Bojarski AJ. The effect of the intramolecular C–H⋯O interactions on the conformational preferences of bis-arylsulfones – 5-HT6 receptor antagonists and beyond. RSC Adv 2018; 8:18672-18681. [PMID: 35541096 PMCID: PMC9080534 DOI: 10.1039/c8ra03107j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/15/2018] [Indexed: 11/21/2022] Open
Abstract
The development of compounds with enhanced activity and selectivity by a conserved spatial orientation of the pharmacophore elements has a long history in medicinal chemistry. Rigidified compounds are an example of this concept. However, the intramolecular interactions were seldom used as a basis for conformational restraints. Here, we show the weak intramolecular interactions that contribute to the relatively well-conserved geometry of N1-arylsulfonyl indole derivatives. The structure analysis along with quantum mechanics calculations revealed a crucial impact of the sulfonyl group on the compound geometry. The weak intramolecular C–H⋯O interaction stabilizes the mutual "facing" orientation of two aromatic fragments. These findings extend the pharmacological interpretation of the sulfonyl group role from the double hydrogen bond acceptor to the conformational scaffold based on intramolecular forces. This feature has, to date, been omitted in in silico drug discovery. Our results should increase the awareness of researchers to consider the conformational preference when designing new compounds or improving computational methods. The impact of weak intramolecular C–H⋯O interactions on the conformational stability of bis-arylsulfones is discussed, suggesting different role of sulfonyl group in the ligand – 5HT6 receptor interaction.![]()
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Kocira S, Sujak A, Oniszczuk T, Szparaga A, Szymanek M, Karakuła-Juchnowicz H, Krawczuk A, Kupryaniuk K. Improvement of the photosynthetic activity of Moldavian dragonhead ( Dracocephalum moldavicaL.) through foliar application of a nitrophenolate–based biostimulant. BIO WEB OF CONFERENCES 2018. [DOI: 10.1051/bioconf/20181001009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Application of biostimulants instigates many physiological processes that enhance nutrition efficiency, abiotic stress tolerance, and quality traits of crops, regardless of their nutrient content. One of such preparations is Atonik which contains nitrophenol compounds naturally occurring in plant cells. Several studies have confirmed its beneficial effect on the growth, development, and improved metabolic activity of plants. Therefore, it seems advisable to investigate the effect of Atonik preparation on the photosynthetic activity of Moldavian dragonhead (Dracocephalum moldavicaL.). The reported study was carried out in 2014 in Perespa, Poland. Over the growing season, Atonik was foliar-applied at a dose of 0.3 L/ha (0.1%) and 0.6 L/ha (0.2%) by single and double spraying of plants. Chlorophyll content and nitrogen status (N) were estimated by a Chlorophyll Meter SPAD-502 Plus. The foliar application of Atonik was found to improve the efficiency of the photosynthetic apparatus and chlorophyll content in the leaves ofDracocephalum moldavicaplants, but the results were dependent on biostimulant concentration and number of its applications, and on the date of measurement. To conclude, Atonik is an environmental-friendly preparation which has a positive impact on the metabolic processes of plants.
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Ernst M, Dos Santos LHR, Krawczuk A, Macchi P. Cluster analysis of functional-group polarizabilities. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317087733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Krawczuk A, Chojnacka A. Negative thermal expansion in isostructural Zn II and Co II
L-malates. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317086569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Macchi P, Ragaini F, Casati N, Krawczuk A, Sironi A. Experimental and theoretical electron density of intermediates in palladium-phenanthroline catalyzed carbonylation of amines and reductive carbonylation of nitroarenes. J Comput Chem 2017; 39:581-586. [DOI: 10.1002/jcc.25115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/21/2017] [Accepted: 11/01/2017] [Indexed: 11/11/2022]
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Casati N, Genoni A, Meyer B, Krawczuk A, Macchi P. Exploring charge density analysis in crystals at high pressure: data collection, data analysis and advanced modelling. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:584-597. [DOI: 10.1107/s2052520617008356] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/06/2017] [Indexed: 11/10/2022]
Abstract
The possibility to determine electron-density distribution in crystals has been an enormous breakthrough, stimulated by a favourable combination of equipment for X-ray and neutron diffraction at low temperature, by the development of simplified, though accurate, electron-density models refined from the experimental data and by the progress in charge density analysis often in combination with theoretical work. Many years after the first successful charge density determination and analysis, scientists face new challenges, for example: (i) determination of the finer details of the electron-density distribution in the atomic cores, (ii) simultaneous refinement of electron charge and spin density or (iii) measuring crystals under perturbation. In this context, the possibility of obtaining experimental charge density at high pressure has recently been demonstrated [Casatiet al.(2016).Nat. Commun.7, 10901]. This paper reports on the necessities and pitfalls of this new challenge, focusing on the speciessyn-1,6:8,13-biscarbonyl[14]annulene. The experimental requirements, the expected data quality and data corrections are discussed in detail, including warnings about possible shortcomings. At the same time, new modelling techniques are proposed, which could enable specific information to be extracted, from the limited and less accurate observations, like the degree of localization of double bonds, which is fundamental to the scientific case under examination.
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Dos Santos LHR, Krawczuk A, Macchi P. Distributed Atomic Polarizabilities of Amino Acids and their Hydrogen-Bonded Aggregates. J Phys Chem A 2015; 119:3285-98. [DOI: 10.1021/acs.jpca.5b00069] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Krawczuk A, Macchi P. Charge density analysis for crystal engineering. Chem Cent J 2014; 8:68. [PMID: 25520749 PMCID: PMC4266768 DOI: 10.1186/s13065-014-0068-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/30/2014] [Indexed: 05/28/2023] Open
Abstract
This review reports on the application of charge density analysis in the field of crystal engineering, which is one of the most growing and productive areas of the entire field of crystallography. While methods to calculate or measure electron density are not discussed in detail, the derived quantities and tools, useful for crystal engineering analyses, are presented and their applications in the recent literature are illustrated. Potential developments and future perspectives are also highlighted and critically discussed. Graphical abstractᅟ
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Krawczuk A, Pérez D, Macchi P. PolaBer: a program to calculate and visualize distributed atomic polarizabilities based on electron density partitioning. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714010838] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This paper describes the program PolaBer, which calculates atomic polarizability tensors from electric field perturbations of a partitioned electron density distribution. Among many possible partitioning schemes, PolaBer is currently using the quantum theory of atoms in molecules and it is interfaced to programs that apply such a partitioning. The calculation of the atomic tensors follows the idea suggested by Keith [The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design, (2007), edited by C. F. Matta & R. J. Boyd. Weinheim: Wiley-VCH], which enables the removal of the intrinsic origin dependence of the atomic charge contributions to the molecular dipole moment. This scheme allows the export, within chemically equivalent functional groups, of properties calculated from atomic dipoles, such as for example the atomic polarizabilities. The software permits visualization of the tensors and calculation of straightforward optical properties of a molecule (like the molar refractive index) or a crystal (assuming the molecule in a given crystal lattice).
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Krawczuk A, Stadnicka K. Experimental and Theoretical Charge Density Study of the Chemical Bonding in Chlorokojic Acid Crystal Structure. J Phys Chem A 2012; 116:9759-68. [DOI: 10.1021/jp3058614] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Krawczuk A, Kowalska E, Wiśniewski L. Genetic and endocrinological studies in a patient with the XYY syndrome. Andrologia 2009; 4:69-74. [PMID: 4649074 DOI: 10.1111/j.1439-0272.1972.tb01194.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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46
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Kazanowska W, Krawczuk A. The usefulness of fluorescence investigation technics In the human semen estimation. Andrologia 2009. [DOI: 10.1111/j.1439-0272.1970.tb00442.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Gryl M, Krawczuk A, Stadnicka K. Polymorphism of urea-barbituric acid co-crystals. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2008; 64:623-32. [PMID: 18799850 DOI: 10.1107/s0108768108026645] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 08/18/2008] [Indexed: 11/10/2022]
Abstract
The crystal structures of three polymorphs found for the addition complex of urea and barbituric acid are described and compared. Two polymorphs are monoclinic, space groups P2(1)/c and Cc, whereas the third is triclinic, P1. The displacement of electron density towards the mesomeric forms, corresponding to the tautomeric forms of higher stability, of the barbituric acid molecule seem to influence the type of hydrogen bonds formed, which in turn determines the different packing topology in the polymorphs. While the polymorphic forms can be easily differentiated at the first-level graph-set analysis of their hydrogen-bonding patterns, a higher-level analysis enables important features of the mutual spatial arrangement of the structural components to be revealed.
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Gryl M, Krawczuk A, Stadnicka K. Crystal engineering of materials with potential NLO properties using barbituric acid as component. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308084341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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49
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Krawczuk A, Stadnicka K. Hydrogen bonding in diaquatetrakis(urea-κO)MIIdinitrates, withM= Ni and Co. Acta Crystallogr C 2007; 63:m448-50. [DOI: 10.1107/s0108270107040437] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Accepted: 08/14/2007] [Indexed: 11/10/2022] Open
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50
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Krawczuk A, Stadnicka K. Recognition of structural helices responsible for optical activity of selected urea adducts. Acta Crystallogr A 2006. [DOI: 10.1107/s0108767306095663] [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] Open
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