Electron delocalization in planar metallacycles : Hückel or Möbius aromatic?

In this work the relationship between the formal number of π-electrons, d-orbital conjugation topology, π-electron delocalization and aromaticity in d-block metallacycles is investigated in the context of recent findings concerning the correlation of π-HOMO topology and the magnetic aromaticity indices in these species. It is demonstrated that for π-electron rich d-metallacycles the direct link between aromaticity, the number of π-electrons and the frontier π-orbital topology does not strictly hold and for such systems it is very difficult to unambiguously associate their aromaticity with the '4n+2' (Hückel) and '4n' (Möbius) rules. It is also shown that the recently proposed electron density of delocalized bonds (EDDB) method can successfully be used not only to quantify and visualize aromaticity in such difficult cases, but also - in contrast to magnetic aromaticity descriptors - to provide a great deal of information on the real role of d-orbitals in metallacycles without the ambiguity of bookkeeping of electrons in the π-subsystem of the molecular ring. Interestingly, some of the metallacycles studied cannot be classified exclusively as Hückel or Möbius because they have a hybrid Hückel-Möbius or even quasi-aromatic natur

Theoretical description of hydrogen bonding in oxalic acid dimer and trimer based on the combined extended-transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV)

In the present study we have analyzed hydrogen bonding in dimer and trimer of oxalic acid, based on a recently proposed charge and energy decomposition scheme (ETS-NOCV). In the case of a dimer, two conformations, α and β, were considered. The deformation density contributions originating from NOCV’s revealed that the formation of hydrogen bonding is associated with the electronic charge deformation in both the σ—(Δρσ) and π-networks (Δρπ). It was demonstrated that σ-donation is realized by electron transfer from the lone pair of oxygen on one monomer into the empty \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\rho_{H - O}^*$$\end{document} orbital of the second oxalic acid fragment. In addition, a covalent contribution is observed by the density transfer from hydrogen of H-O group in one oxalic acid monomer to the oxygen atom of the second fragment. The resonance assisted component (Δρπ), is based on the transfer of electron density from the π—orbital localized on the oxygen of OH on one oxalic acid monomer to the oxygen atom of the other fragment. ETS-NOCV allowed to conclude that the σ(O---HO) component is roughly eight times as important as π (RAHB) contribution in terms of energetic estimation. The electrostatic factor (ΔEelstat) is equally as important as orbital interaction term (ΔEorb). Finally, comparing β-dimer of oxalic acid with trimer we found practically no difference concerning each of the O---HO bonds, neither qualitative nor quantitative

Supplementary data for article: Mitoraj, M. P.; Janjić, G. V.; Medaković, V. B.; Veljković, D. Ž.; Michalak, A.; Zarić, S. D.; Milčić, M. K. Nature of the Water/Aromatic Parallel Alignment Interactions. Journal of Computational Chemistry 2015, 36 (3), 171–180. https://doi.org/10.1002/jcc.23783

Supporting information for: [https://doi.org/10.1002/jcc.23783]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1892

Lead(ii) Coordination Polymers Driven by Pyridine-Hydrazine Donors: From Anion-Guided Self-Assembly to Structural Features

In this work, we report extensive experimental and theoretical investigations on a new series of PbII coordination polymers exhibiting extended supramolecular architectures, namely [Pb2(LI)(NCS)4]n (1), [Pb(HLII)I2]n (2), [Pb(LIII)I]n (3) and [Pb(HLIV)(NO3)2]n·nMeOH (4), which were self-assembled from different PbII salts and various pyridine-hydrazine based linkers, namely 1,2-bis(pyridin-3-ylmethylene)hydrazine (LI), (pyridin-4-ylmethylene)isonicotinohydrazide (HLII), 1-(pyridin-2-yl)ethylidenenicotinohydrazide (HLIII) and phenyl(pyridin-2-yl)methylenenicotinohydrazide (HLIV), respectively. It is recognized that the origin of self-assembling is fundamentally rooted in a dual donor (6s2/6p0 hybridized lone electron pair) and electrophilic behaviour of PbII. This allows production of extended topologies from a 1D polymeric chain in 4 through a 2D layer in 2 to the 3D frameworks in 1 and 3, predominantly due to the cooperative action of both covalent and non-covalent tetrel interactions of the overall type Pb-X (X = O, N, S, I). Counterintuitively, the latter, seemingly weak interactions, have appeared to be even stronger than the typical covalent bonds due to the presence of a bunch of supportive London dispersion dominated contacts: π⋯π, Lp⋯π, C-H⋯O, C-H⋯I, C-H⋯H-C as well as more typical mainly electrostatically driven N-H⋯O or N/O-H⋯O hydrogen bonds. It is revealed that the constituting generally strong tetrel type Pb-X (X = O, N, S, I) bonds, though dominated by a classic Coulomb term, are therefore characterized by a very important London dispersion constituent, extremely strong relativistic effects and the two way dative-covalent Pb ↔ X electron charge delocalization contribution as revealed by the Extended Transition State Natural Orbital for Chemical Valence (ETS-NOCV) charge and energy decomposition scheme. It unravels that the pyridine-hydrazine linkers are also excellent London dispersion donors, and that together with the donor-acceptor properties of the heavy (relativistic) PbII atoms and nucleophilic counterions lead to extended self-assembling of 1-4. © 2020 The Royal Society of Chemistry.We are grateful to the University of Maragheh for the financial support of this research. The publication has been prepared with the support from the “RUDN University Program 5-100” (recipient F. I. Zubkov, synthesis of the ligands). DFT calculations were partially performed using the PL-Grid Infrastructure and resources provided by the ACC Cyfronet AGH (Cracow, Poland). A. M. Kirillov acknowledges the FCT and Portugal 2020 (LISBOA-01-0145-FEDER-029697 and UIDB/ 00100/2020). ICMAB acknowledges the Severo Ochoa Program (MINECO, SEV-2015-0496). M. P. Mitoraj acknowledges the financial support from the Polish National Science Center within the Sonata Bis Project 2017/26/E/ST4/00104

Dynamics of Vulmar/VulMITE group of transposable elements in Chenopodiaceae subfamily Betoideae

Transposable elements are important factors driving plant genome evolution. Upon their mobilization, novel insertion polymorphisms are being created. We investigated differences in copy number and insertion polymorphism of a group of Mariner-like transposable elements Vulmar and related VulMITE miniature inverted-repeat transposable elements (MITEs) in species representing subfamily Betoideae. Insertion sites of these elements were identified using a modified transposon display protocol, allowing amplification of longer fragments representing regions flanking insertion sites. Subsequently, a subset of TD fragments was converted into insertion site-based polymorphism (ISBP) markers. The investigated group of transposable elements was the most abundant in accessions representing the section Beta, showing intraspecific insertion polymorphisms likely resulting from their recent activity. In contrast, no unique insertions were observed for species of the genus Beta section Corollinae, while a set of section-specific insertions was observed in the genus Patellifolia, however, only two of them were polymorphic between P. procumbens and P. webbiana. We hypothesize that Vulmar and VulMITE elements were inactivated in the section Corollinae, while they remained active in the section Beta and the genus Patellifolia. The ISBP markers generally confirmed the insertion patterns observed with TD markers, including presence of distinct subsets of TE insertions specific to Beta and Patellifolia

Lead(ii) Coordination Polymers Driven by Pyridine-Hydrazine Donors: From Anion-Guided Self-Assembly to Structural Features

In this work, we report extensive experimental and theoretical investigations on a new series of PbII coordination polymers exhibiting extended supramolecular architectures, namely [Pb2(LI)(NCS)4]n (1), [Pb(HLII)I2]n (2), [Pb(LIII)I]n (3) and [Pb(HLIV)(NO3)2]n·nMeOH (4), which were self-assembled from different PbII salts and various pyridine-hydrazine based linkers, namely 1,2-bis(pyridin-3-ylmethylene)hydrazine (LI), (pyridin-4-ylmethylene)isonicotinohydrazide (HLII), 1-(pyridin-2-yl)ethylidenenicotinohydrazide (HLIII) and phenyl(pyridin-2-yl)methylenenicotinohydrazide (HLIV), respectively. It is recognized that the origin of self-assembling is fundamentally rooted in a dual donor (6s2/6p0 hybridized lone electron pair) and electrophilic behaviour of PbII. This allows production of extended topologies from a 1D polymeric chain in 4 through a 2D layer in 2 to the 3D frameworks in 1 and 3, predominantly due to the cooperative action of both covalent and non-covalent tetrel interactions of the overall type Pb-X (X = O, N, S, I). Counterintuitively, the latter, seemingly weak interactions, have appeared to be even stronger than the typical covalent bonds due to the presence of a bunch of supportive London dispersion dominated contacts: π⋯π, Lp⋯π, C-H⋯O, C-H⋯I, C-H⋯H-C as well as more typical mainly electrostatically driven N-H⋯O or N/O-H⋯O hydrogen bonds. It is revealed that the constituting generally strong tetrel type Pb-X (X = O, N, S, I) bonds, though dominated by a classic Coulomb term, are therefore characterized by a very important London dispersion constituent, extremely strong relativistic effects and the two way dative-covalent Pb ↔ X electron charge delocalization contribution as revealed by the Extended Transition State Natural Orbital for Chemical Valence (ETS-NOCV) charge and energy decomposition scheme. It unravels that the pyridine-hydrazine linkers are also excellent London dispersion donors, and that together with the donor-acceptor properties of the heavy (relativistic) PbII atoms and nucleophilic counterions lead to extended self-assembling of 1-4. © 2020 The Royal Society of Chemistry.We are grateful to the University of Maragheh for the financial support of this research. The publication has been prepared with the support from the “RUDN University Program 5-100” (recipient F. I. Zubkov, synthesis of the ligands). DFT calculations were partially performed using the PL-Grid Infrastructure and resources provided by the ACC Cyfronet AGH (Cracow, Poland). A. M. Kirillov acknowledges the FCT and Portugal 2020 (LISBOA-01-0145-FEDER-029697 and UIDB/ 00100/2020). ICMAB acknowledges the Severo Ochoa Program (MINECO, SEV-2015-0496). M. P. Mitoraj acknowledges the financial support from the Polish National Science Center within the Sonata Bis Project 2017/26/E/ST4/00104

Visible Light Responsive Photocatalyst Induces Progressive and Apical-Terminus Preferential Damages on Escherichia coli Surfaces

BACKGROUND: Recent research shows that visible-light responsive photocatalysts have potential usage in antimicrobial applications. However, the dynamic changes in the damage to photocatalyzed bacteria remain unclear. METHODOLOGY/PRINCIPAL FINDINGS: Facilitated by atomic force microscopy, this study analyzes the visible-light driven photocatalyst-mediated damage of Escherichia coli. Results show that antibacterial properties are associated with the appearance of hole-like structures on the bacteria surfaces. Unexpectedly, these hole-like structures were preferentially induced at the apical terminus of rod shaped E. coli cells. Differentiating the damages into various levels and analyzing the percentage of damage to the cells showed that photocatalysis was likely to elicit sequential damages in E. coli cells. The process began with changing the surface properties on bacterial cells, as indicated in surface roughness measurements using atomic force microscopy, and holes then formed at the apical terminus of the cells. The holes were then subsequently enlarged until the cells were totally transformed into a flattened shape. Parallel experiments indicated that photocatalysis-induced bacterial protein leakage is associated with the progression of hole-like damages, further suggesting pore formation. Control experiments using ultraviolet light responsive titanium-dioxide substrates also obtained similar observations, suggesting that this is a general phenomenon of E. coli in response to photocatalysis. CONCLUSION/SIGNIFICANCE: The photocatalysis-mediated localization-preferential damage to E. coli cells reveals the weak points of the bacteria. This might facilitate the investigation of antibacterial mechanism of the photocatalysis

Synthesis and characterization of Sn‑doped TiO2 flm for antibacterial applications

Simple sol–gel method has been exploited to deposit Sn-doped TiO2 thin flms on glass substrates. The resultant coatings were characterized by X-ray difraction (XRD), UV–visible techniques (UV–Vis), Fourier transform infrared spectroscopy (FTIR), and photoluminescence analysis (PL). The XRD pattern reveals an increase in crystallite size of the prepared samples with the increasing doping concentration. A decrease in doping concentrating resulted in the decrease in bandgap values. The diferent chemical bonds on these flms were identifed from their FTIR spectra. The photoluminescence analysis shows an increase in the emission peak intensity with increasing dopant concentration, and this can be attributed to the efect created due to surface states. The prepared samples were tested as antibacterial agent toward both Gram-positive and Gram-negative bacteria like S.aureus (Staphylococcus aureus) and E.coli (Escherichia coli), respectively. The size of the inhibition zones indicates that the sample shows maximum inhibitory property toward E.coli when compared to S.aureus