Papers by Vesna Medakovic
Acta crystallographica Section B, Structural science, crystal engineering and materials, 2018
The interactions between phosphines and boranes in crystal structures have been investigated by a... more The interactions between phosphines and boranes in crystal structures have been investigated by analyzing data from the Cambridge Structural Database (CSD). The interactions between phosphines and boranes were classified into three types; two types depend on groups on the boron atom, whereas the third one involves frustrated Lewis pairs (FLPs). The data enabled geometric parameters in structures to be compared with phosphine-borane FLPs with classical Lewis pairs. Most of the crystal structures (78.1%) contain BH as the borane group. In these systems, the boron-phosphorus distance is shorter than systems where the boron atom is surrounded by groups other than hydrogen atoms. The analysis of the CSD data has shown that FLPs have a tendency for the longest boron-phosphorus distance among all phosphine-borane pairs, as well as different other geometrical parameters. The results show that most of the frustrated phosphine-borane pairs found in crystal structures are bridged ones. The min...
Journal of Computational Chemistry, 2014
The water/aromatic parallel alignment interactions are interactions where the water molecule or o... more The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its OAH bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to DE CCSD(T)(limit) 5 22.45 kcal mol 21 at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CHÁÁÁO water/benzene interactions, but weaker than OHÁÁÁp interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type p ! r*(OAH) between the monomers also exists. V
International Journal of Molecular Sciences, 2004
Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H•••π interact... more Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H•••π interactions with a chelate ring of coordinated porphyrin. It was found 154 crystal structures with 244 intramolecular C−H•••π interactions in transition metal complexes with derivatives of porphyrin. Comparison of interacting distances indicates that interactions of hydrogen atoms in positions 2 and 6 of axially coordinated pyridine are more favorable with ruffled than with planar porphyrin.
CrystEngComm, 2014
The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of... more The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.
Journal of Inorganic Biochemistry, 2012
CH/π interactions in metal porphyrinato complexes were studied by analyzing data in crystal struc... more CH/π interactions in metal porphyrinato complexes were studied by analyzing data in crystal structures from the Cambridge Structural Database (CSD) and by quantum chemical calculations. The analysis of the data in the CSD shows that both five-membered pyrrole and six-membered chelate rings form CH/π interactions. The interactions occur more frequently with five-membered rings. The analysis of distances in crystal structures and calculated energies show stronger interactions with six-membered chelate rings, indicating that a larger number of interactions with five-membered rings are not the consequence of stronger interactions, but better accessibility of five-membered pyrrole rings. The calculated energies of the interactions with positions in six-membered rings are − 2.09 to −2.83 kcal/mol, while the energies with five-membered rings are − 2.05 to −2.26 kcal/mol. The results reveal that stronger interactions of six-membered rings are the consequence of stronger electrostatic interactions. Substituents on the porphyrin ring significantly strengthen the interactions. Substituents on the six-membered ring strengthen the interaction energy by about 20%. The results show that CH/π interactions play an important role in molecular recognition of metalloporphyrins. The significant influence of the substituents on interaction energies can be very important for the design of model systems in bioinorganic chemistry.
Journal of Inorganic Biochemistry, 2006
Many properties of cytochromes and model systems depend on orientations of axial ligands. In this... more Many properties of cytochromes and model systems depend on orientations of axial ligands. In this work, we elucidated the role of porphyrin substituents on orientation of axial ligands in model systems of cytochromes. The orientations of axially coordinated imidazoles and pyridines in crystal structures of model systems of cytochromes were analyzed and data were compared with previous quantumchemical calculations. The results show that eight ethyl groups on porphyrin ring strongly favor parallel orientation, hence, in all these complexes axial ligands, pyridines or imidazoles, are mutually parallel. Four phenyl or mesityl groups at meso-carbons also favor parallel orientation but less strongly. Hence, in most of the bis-imidazole complexes the orientation is parallel, while in bis-pyridine complexes the orientation of pyridines depends on oxidation state of Fe. In bis-pyridine Fe(II) complexes orientation is parallel, in Fe(III) it is orthogonal. This analysis is in agreement with previous quantum-chemical calculations.
JBIC Journal of Biological Inorganic Chemistry, 2007
Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that th... more Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that the pi system of every porphyrin ring is involved in XH/pi interactions, with most of the porphyrins having several interactions. Both five-membered pyrrole rings and six-membered chelate rings are involved in XH/pi interactions; the number of interactions with five-membered rings is larger than the number of interactions with six-membered rings. We found interactions with C-H and N-H groups as hydrogen-atom donors; however, the number of CH/pi interactions is much larger than the number of NH/pi interactions. The amino acids involved in the interactions show a high conservation score. Our results that every porphyrin is involved in XH/pi interactions and that amino acids involved in these interactions are highly conserved demonstrate that XH/pi interactions play an important role in porphyrin-protein stability.
Inorganica Chimica Acta, 2003
The quantum chemical (DFT) calculations were performed on heme model systems with non-substituted... more The quantum chemical (DFT) calculations were performed on heme model systems with non-substituted Fe-porphyrin core for the different orientations of the axially coordinated imidazoles of [Fe II (por)(im) 2 ] and [Fe III (por)(im) 2 ] ' complexes. These calculations show that the energy difference between parallel and perpendicular orientations of imidazoles is very small for both Fe(II) and Fe(III) complexes, and that there is almost no preference for one or other orientation.
Inorganica Chimica Acta, 2006
The calculations have been done for CH/p interaction with p-system of Ni(II)-acetylacetonato chel... more The calculations have been done for CH/p interaction with p-system of Ni(II)-acetylacetonato chelate ring. The results show that there is an attractive electrostatic interaction, while dispersion component is a major source of attractive interacting energies. The interaction was compared with CH/p interaction between two benzene rings. The comparison shows that two interactions are quite similar, enabling to estimate the energy of CH/p interaction with p-system of Ni(II)-acetylacetonato chelate ring to be about 10.5 kJ/mol. The results indicate that CH/p interactions of chelate ring in various molecular systems can be as important as CH/p interactions of phenyl ring.
Inorganic Chemistry, 2006
CH/pi interactions between the coordinated acetylacetonato ligand and phenyl rings were analyzed ... more CH/pi interactions between the coordinated acetylacetonato ligand and phenyl rings were analyzed in the crystal structures from the Cambridge Structural Database and by quantum chemical calculations. The acetylacetonato ligand may engage in two types of interactions: it can be hydrogen atom donor or acceptor. The analysis of crystal structures and calculations show that interactions with the acetylacetonato ligand acting as hydrogen atom donor depend on the metal in an acetylacetonato chelate ring; the chelate rings with soft metals make stronger interactions. The same trend was not observed in the interactions where the acetylacetonato chelate ring acts as the hydrogen atom acceptor.
Colloids and Surfaces B: Biointerfaces, 2005
Adsorption of zearalenone (ZEN), ochratoxin A (OCHRA) and aflatoxin B1 (AFB1) on natural zeolite,... more Adsorption of zearalenone (ZEN), ochratoxin A (OCHRA) and aflatoxin B1 (AFB1) on natural zeolite, clinoptilolite, modified with different amounts of octadecyldimethylbenzyl ammonium (ODMBA) ions was investigated. Results showed that adsorption of hydrophobic ionizable ZEN on unmodified zeolite tuff was very low and that adsorption on organozeolites increased with increasing hydrophobicity of the zeolitic surface. The adsorption was independent of the form of ZEN in solution and the solution pH, indicating that hydrophobic interactions with ODMBA are responsible for ZEN adsorption. Adsorption of low polar ionizable OCHRA on organozeolites also increased with increasing hydrophobicity of the zeolitic surface, however, OCHRA showed moderate adsorption on unmodified zeolitic tuff at pH 3. OCHRA adsorption on unmodified zeolite as well as on lower surface coverage of organozeolite was dependent on the form of OCHRA in solution; there was a decrease of adsorption at high pH, where OCHRA is in the anionic form. It indicated that at acidic pH, low surface coverage allows some combination of hydrophobic interaction with ODMBA and interactions with the surface of the zeolite. At higher surface coverage, the OCHRA adsorption was higher and practically independent of pH, indicating that the hydrophobic interactions of OCHRA with ODMBA are responsible for its adsorption. Nonionizable low polar AFB1 had a high affinity for the unmodified zeolitic tuff and the adsorption of AFB1 was greatly reduced for organozeolites, indicating that AFB1 does not have high tendency for hydrophobic interactions with ODMBA. pH dependence of AFB1 adsorption, while AFB1 has the same form at all pHs, demonstrated that the surface modification of the zeolite depends on pH and that these modifications have influence on its adsorption. The calculated dipole moments of neutral mycotoxin molecules: AFB1-9.5D, OCHRA-6.9D and ZEN-2.2D are in qualitative agreement with adsorption experimental data.
Acta Crystallographica Section A Foundations of Crystallography, 2005
The aim of this work is the study of weak intermolecular interactions in molecular crystals, by b... more The aim of this work is the study of weak intermolecular interactions in molecular crystals, by both diffraction methods and ab initio calculations using the new version of the CRYSTAL [1] program, which is designed to treat infinite periodic systems. Two molecular systems were chosen: i) formamide [2]: each molecule is linked to three other molecules by two types of hydrogen bonds; ii) boric acid [3]: each molecule forms six almost equivalent hydrogen bonds with three neighbouring molecules. The CRYSTAL03 calculations were carried out employing the HF and DFT (B3LYP) methods with the 6-31G(d,p) basis set, also using the new geometry optimisation options. The electron density, the electrostatic potential, the binding energies and the structure factors were derived. In formamide the cooperative effects of packing on the hydrogen bond interactions leading to the formation of linear chains and on those connecting the chains were analyzed. Hydrogen bonded molecules of boric acid form layers held together by weak B-O interactions, which may play a role in dictating the inter-layer packing. The comparison of the experimental and theoretical results and the most recent results obtained using the geometry optimisation facilities in CRYSTAL03 will be presented.
Acta Crystallographica Section A Foundations of Crystallography, 2005
The aim of this work is the study of weak intermolecular interactions in molecular crystals, by b... more The aim of this work is the study of weak intermolecular interactions in molecular crystals, by both diffraction methods and ab initio calculations using the new version of the CRYSTAL [1] program, which is designed to treat infinite periodic systems. Two molecular systems were chosen: i) formamide [2]: each molecule is linked to three other molecules by two types of hydrogen bonds; ii) boric acid [3]: each molecule forms six almost equivalent hydrogen bonds with three neighbouring molecules. The CRYSTAL03 calculations were carried out employing the HF and DFT (B3LYP) methods with the 6-31G(d,p) basis set, also using the new geometry optimisation options. The electron density, the electrostatic potential, the binding energies and the structure factors were derived. In formamide the cooperative effects of packing on the hydrogen bond interactions leading to the formation of linear chains and on those connecting the chains were analyzed. Hydrogen bonded molecules of boric acid form layers held together by weak B-O interactions, which may play a role in dictating the inter-layer packing. The comparison of the experimental and theoretical results and the most recent results obtained using the geometry optimisation facilities in CRYSTAL03 will be presented.
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Papers by Vesna Medakovic