Publications by authors named "Agnieszka J Rybarczyk-Pirek"

11 Publications

  • Page 1 of 1

Lack of Cooperativity in the Triangular X Halogen-Bonded Synthon?

Cryst Growth Des 2021 Jan 16;21(1):597-607. Epub 2020 Dec 16.

Department of Theoretical Chemistry and Amsterdam Centre for Multiscale Modelling, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

We have investigated 44 crystal structures, found in the Cambridge Structural Database, containing the X synthon (where X = Cl, Br, I) in order to verify whether three type II halogen-halogen contacts forming the synthon exhibit cooperativity. A hypothesis that this triangular halogen-bonded motif is stabilized by cooperative effects is postulated on the basis of structural data. However, theoretical investigations of simplified model systems in which the X motif is present demonstrate that weak synergy occurs only in the case of the I motif. In the present paper we computationally investigate crystal structures in which the X synthon is present, including halomesitylene structures, that are usually described as being additionally stabilized by a synergic interaction. Our computations find no cooperativity for halomesitylene trimers containing the X motif. Only in the case of two other structures containing the I synthon a very weak or weak synergy, i.e. the cooperative effect being stronger than -0.40 kcal mol, is found. The crystal structure of iodoform has the most pronounced cooperativity of all investigated systems, amounting to about 10% of the total interaction energy.
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http://dx.doi.org/10.1021/acs.cgd.0c01410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7792510PMC
January 2021

Simple -Platinum Complex Bearing 3-Aminoflavone Ligand Could Be a Useful Drug: Structure-Activity Relationship of Platinum Complex in Comparison with Cisplatin.

Int J Mol Sci 2020 Mar 19;21(6). Epub 2020 Mar 19.

Department of Bioinorganic Chemistry, Medical University of Lodz, 1 Muszynskiego St., 90-151 Łódź, Poland.

Following previous studies devoted to -Pt(3-af)Cl, in this paper, the molecular structure and intermolecular interactions of the title complex are compared with other cisplatin analogues of which the crystal structures are presented in the Cambridge Structural Database (CSD). Molecular Hirshfeld surface analysis and computational methods were used to examine a possible relationship between the structure and anticancer activity of -Pt(3-af)Cl. The purpose of the article was also to investigate the effect of hyperthermia on the anticancer activity of cisplatin, cytostatics used in the treatment of patients with ovarian cancer and a new analogue of cisplatin--Pt(3-af)Cl. The study was conducted on two cell lines of ovarian cancer sensitive to Caov-3 cytostatics and the OVCAR-3 resistant cisplatin line. The study used the MTT (3-(4,5-dimethylthiazol-2,5-diphenyltetrazolium bromide) cell viability assay, LDH (lactate dehydrogenase), and the quantitative evaluation method for measuring gene expression, i.e., qPCR with TagMan probes. Reduced survivability of OVCAR-3 and Caov-3 cells exposed to cytostatics at elevated temperatures (37 °C, 40 °C, 43 °C) was observed. Hyperthermia may increase the sensitivity of cells to platinum-based antineoplastic drugs and paclitaxel, which may be associated with the reduction of gene expression related to apoptotic processes.
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http://dx.doi.org/10.3390/ijms21062116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7139614PMC
March 2020

C-Br...S halogen bonds in novel thiourea N-oxide cocrystals: analysis of energetic and QTAIM parameters.

Acta Crystallogr C Struct Chem 2020 02 29;76(Pt 2):170-176. Epub 2020 Jan 29.

Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, Lodz 90-236, Poland.

Cocrystals of thiourea with 4-nitropyridine N-oxide, CHNO·2CHNS, (I), and 3-bromopyridine N-oxide, CHBrNO·CHNS, (II), crystallize in the monoclinic space group P2/c. In the crystals, molecules of both components are linked by N-H...O hydrogen bonds, creating R(6) synthons. The bromine substituent of the N-oxide component in (II) is a centre for C-Br...S halogen bonding to the thiourea molecule. Computations based on quantum chemistry methods (quantum theory of atoms in molecules, QTAIM) and atoms in molecules (AIM) theory were performed for a more detailed description of the observed type of halogen-bonding interaction.
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http://dx.doi.org/10.1107/S2053229620000947DOI Listing
February 2020

Crystal structure of 3,6-bis-(pyridin-2-yl)-1,4-di-hydro-1,2,4,5-tetra-zine.

Acta Crystallogr E Crystallogr Commun 2019 Jan 1;75(Pt 1):86-88. Epub 2019 Jan 1.

Group of Theoretical and Structural Chemistry, Department of Physical Chemistry, Faculty of Chemistry, University of Łódź, Pomorska 163/165, 90-236, Łódź, Poland.

The structure of the title compound, CHN, at 100 K has monoclinic (2/) symmetry. Crystals were obtained as a yellow solid by reduction of 3,6-bis-(pyridin-2-yl)-1,2,4,5-tetra-zine. The structure displays inter-molecular hydrogen bonding of the N-H⋯N type, ordering mol-ecules into infinite ribbons extending along the [100] direction.
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http://dx.doi.org/10.1107/S205698901801753XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323887PMC
January 2019

N-Oxide-N-oxide interactions and Cl...Cl halogen bonds in pentachloropyridine N-oxide: the many-body approach to interactions in the crystal state.

Acta Crystallogr C Struct Chem 2018 02 9;74(Pt 2):113-119. Epub 2018 Jan 9.

Group of Theoretical and Structural Chemistry, Department of Physical Chemistry, Faculty of Chemistry, University of Łódź, Pomorska 163/165, 90-236 Łódź, Poland.

Pentachloropyridine N-oxide, CClNO, crystallizes in the monoclinic space group P2/c. In the crystal structure, molecules are linked by C-Cl...Cl halogen bonds into infinite ribbons extending along the crystallographic [100] direction. These molecular aggregates are further stabilized by very short intermolecular N-oxide-N-oxide interactions into herringbone motifs. Computations based on quantum chemistry methods allowed for a more detailed description of the N-oxide-N-oxide interactions and Cl...Cl halogen bonds. For this purpose, Hirshfeld surface analysis and the many-body approach to interaction energy were applied.
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http://dx.doi.org/10.1107/S2053229617017922DOI Listing
February 2018

The nature of NO-bonding in N-oxide group.

Phys Chem Chem Phys 2015 Jul 5;17(25):16375-87. Epub 2015 Jun 5.

Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łódź, 163/165 Pomorska St., 90-236 Łódź, Poland.

The nature of the NO-bond in the N-oxide group was investigated by means of combined theoretical calculations (including QTAIM and NBO approaches) and statistical analyses of the contents of crystal structure databases. The N-O bond in the N-oxide group should be classified as the NO donating bond with an important contribution of ON back-donation (of the π-electron type, when available). The visualization of the Laplacian of electron density in the region of an oxygen valence sphere suggests the presence of two lone pairs for the imine-N-oxide group (characterized by effective ON back-donation). A detailed bonding analysis performed by means of natural resonance theory indicates that the N→O bond is of an order of magnitude clearly greater than 1. In addition, the stability of the N→O bond in various N-oxides was estimated. The analyses of the hydrogen- and halogen-bonded complexes of the N-oxides reveal strong Lewis basicity of the N-oxide group. The formation of H- and X-bonding leads to N→O bond elongation due to its structural, topological and spectroscopic characteristics. Moreover, in pyridine-N-oxide, the electron-withdrawing -NO2 group additionally stabilizes the N→O bond, whereas the opposite effect can be observed for the electron-donating-NH2 substituent. This is due to a substituent effect on the π-type ON back-donation. As a result, the oxygen atom in pyridine-N-oxide may change its availability during intermolecular interaction formation, as revealed in the interaction energy, which changes by about half of the estimated total interaction energy.
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http://dx.doi.org/10.1039/c5cp02148kDOI Listing
July 2015

trans-Platinum(II) complex of 3-aminoflavone - synthesis, X-ray crystal structure and biological activities in vitro.

Dalton Trans 2015 Jan;44(3):938-47

Department of Bioinorganic Chemistry, 1 Muszyńskiego St., Medical University, 90-151 Łódź, Poland.

This paper describes the synthesis of trans-bis-(3-aminoflavone)dichloridoplatinum(ii) (trans-Pt(3-af)2Cl2; TCAP) for use as a potential anticancer compound, and the evaluation of its structure by elemental and spectral analyses, and X-ray crystallography. The complex demonstrated a significant cytotoxic effect against human and murine cancer cell lines, as well as weaker toxicity towards healthy cells (human peripheral blood lymphocytes) in comparison with cisplatin. Various biochemical and morphological methods confirm that the proapoptotic activity of trans-Pt(3-af)2Cl2 is markedly higher than the reference cisplatin. Our results suggest that trans-Pt(3-af)2Cl2 may have a different antitumour specificity from that of cisplatin.
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http://dx.doi.org/10.1039/c4dt01501kDOI Listing
January 2015

Experimental and theoretical electron-density study of three isoindole derivatives: topological and Hirshfeld surface analysis of weak intermolecular interactions.

Acta Crystallogr B 2011 Dec 17;67(Pt 6):569-81. Epub 2011 Nov 17.

Structural Chemistry and Crystallography Group, University of Lodz, Tamka 12, Lodz 91 403, Poland.

A combined experimental and theoretical study of three isoindole derivatives was made on the basis of a topological analysis of their electron-density distributions. Experimental electron densities were determined from high-resolution X-ray diffraction data sets measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using DFT methods at the B3LYP\6-311++G(3df,3pd) level of approximation. Both experimental and theoretical models are in good agreement with each other. Since the analysed structures possess a variety of hydrogen-bonding interactions, weak intermolecular contacts of C-H···C(π), C,N(π)···C,N(π) and H···H types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment.
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http://dx.doi.org/10.1107/S0108768111041747DOI Listing
December 2011

O-phenyl (triphenylphosphoniomethyl)phosphonate phenol solvate: supramolecular structure generated by O-H...O, C-H...O and C-H...pi(arene) hydrogen bonds.

Acta Crystallogr C 2007 Sep 9;63(Pt 9):o504-6. Epub 2007 Aug 9.

Department of Crystallography and Crystal Chemistry, University of Łódź, Pomorska 149/153, 90 236 Łódź, Poland.

The title compound, C(25)H(22)O(3)P(2).C(6)H(6)O, has a zwitterionic betaine-like structure and crystallizes as a phenol solvate. The two molecular components are held together by an almost linear intermolecular O-H...O hydrogen bond. The structure also contains three weak C-H...O and two C-H...pi(arene) interactions.
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http://dx.doi.org/10.1107/S0108270107032453DOI Listing
September 2007

trans-bis(3-aminoflavone-kappa2N,O)bis(perchlorato-kappaO)copper(II), a new potential antitumour agent.

Acta Crystallogr C 2007 Sep 17;63(Pt 9):m410-2. Epub 2007 Aug 17.

Department of Crystallography and Crystal Chemistry, University of Łódź, Pomorska 149/153, PL-90236 Łódź, Poland.

The title compound, trans-bis(3-amino-2-phenyl-4H-1-benzopyran-4-one-kappa(2)N,O(4))bis(perchlorato-kappaO)copper(II), [Cu(ClO4)2(C(15)H(11)NO(2))2], is composed of mononuclear units wherein the central Cu(II) cation occupies a crystallographic inversion centre. The cation is coordinated by two bidentate 3-aminoflavone ligands occupying the equatorial sites and by two perchlorate anions in the apical positions, thereby giving rise to a markedly elongated octahedral coordination geometry. Two symmetry-related intermolecular N-H...O hydrogen bonds link the molecules into chains of rings running parallel to the [100] direction, while intramolecular N-H...O hydrogen bonds help to determine the orientation of the apical perchlorate anions.
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http://dx.doi.org/10.1107/S010827010703747XDOI Listing
September 2007

A benzopyran derivative substituted at position 3.

Acta Crystallogr C 2002 Jul 20;58(Pt 7):o405-6. Epub 2002 Jun 20.

Department of Crystallography and Crystallochemistry, University of Łódź, Pomorska 149/153, PL-90236 Łódź, Poland.

In (E)-3-[[(diphenoxyphosphoryl)methylhydrazono]methyl]-4H-1-benzopyran-4-one, C(23)H(19)N(2)O(5)P, the benzopyran-methylhydrazone moiety is planar and the two phenoxy phenyl rings are inclined at angles of 21.29 (6) and 89.33 (5) degrees. Weak C[bond]H...O and C[bond]H...N intramolecular interactions exert some influence on the planarity and orientation of that moiety.
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http://dx.doi.org/10.1107/s0108270102008508DOI Listing
July 2002