Structural elucidation of supramolecular alpha-cyclodextrin dimer/aliphatic monofunctional molecules complexes

The structural elucidation of 2α-cyclodextrin/1-octanethiol, 2α-cyclodextrin/1-octylamine and 2α-cyclodextrin/1-nonanoic acid inclusion complexes by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling has been achieved. The detailed spatial configurations are proposed for the three inclusion complexes based on 2D NMR method. ROESY experiments confirm the inclusion of guest molecules inside the α-cyclodextrin (α-CD) cavity. On the other hand, the host-guest ratio observed was 2:1 for three complexes. The detailed spatial configuration proposed based on 2D NMR methods were further interpreted using molecular modeling studies. The theoretical calculations are in good agreement with the experimental data.

A theoretical study on the hydrogen adducts of diamidocarbenes and diaminocarbenes

The hybrid-meta GGA DFT functional M06-2X was used to examine the potential of N,N′-diamidocarbenes for use as hydrogen storage materials. We previously discovered that borylene, which is isoelectronic with an Arduengo-type carbene, was a suitable candidate for a hydrogen storage material. We compared the capabilities of N,N′-diamidocarbenes and N-heterocyclic carbenes as hydrogen storage materials. The results indicate that diamidocarbenes are not suitable hydrogen storage materials because the removal of H₂ is more endothermic for diamidocarbenes than for diaminocarbenes.

Exploration of various electronic properties along the reaction coordinate for hydration of Pt(II) and Ru(II) complexes; the CCSD, MPx, and DFT computational study

In the study behavior of molecular electrostatic potential, averaged local ionization energy, and reaction electronic flux along the reaction coordinate of hydration process of three representative Ru(II) and Pt(II) complexes were explored using both post-HF and DFT quantum chemical approximations. Previously determined reaction mechanisms were explored by more detailed insight into changes of electronic properties using ωB97XD functional and MP2 method with 6–311++G(2df,2pd) basis set and CCSD/6–31(+)G(d,p) approach. The dependences of all examined properties on reaction coordinate give more detailed understanding of the hydration process.

Erratum to: “Nano-characterization of Jagged-1-educated dendritic cells”

Paper by Xing et al. “Nano-characterization of Jagged-1-educated dendritic cells” in Volume 6, Issue 6, 981-989 / December 2011; DOI: 10.2478/s11535-011-0063-3 contains an error in the graphic file inserted as Figure 1 and also an incorrect figure caption. The corrected Figure 1, together with its caption is presented below.     

Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes

The adsorption of CO onto Ni-doped boron nitride nanotubes (BNNTs) was investigated using density functional theory at the B3LYP/LanL2DZ level of theory. The structures of the Ni-doped BNNTs and their CO-adsorbed configurations were obtained. It was found that the strength of adsorption of CO onto Ni-doped perfect BNNTs is higher than that on defective BNNTs. The electronic properties of all of the adsorption configurations of CO on Ni-doped BNNTs are reported.

Erratum to: “The Luc2 gene enhances reliability of bicistronic assays”

Paper by Masek et al. “The Luc2 gene enhances reliability of bicistronic assays” in Volume 8, Issue 5, 423–431 / May 2013; DOI: 10.2478/s11535-013-0151-z contains incomplete graphic file inserted as Figure 2. The correct Figure 2, together with its caption is presented below.     

Determination of key receptor–ligand interactions of dopaminergic arylpiperazines and the dopamine D2 receptor homology model

Interest in structure-based G-protein-coupled receptor (GPCR) ligand discovery is huge, given that almost 30 % of all approved drugs belong to this category of active compounds. The GPCR family includes the dopamine receptor subtype D2 (D2DR), but unfortunately—as is true of most GPCRs—no experimental structures are available for these receptors. In this publication, we present the molecular model of D2DR based on the previously published crystal structure of the dopamine D3 receptor (D3DR). A molecular modeling study using homology modeling and docking simulation provided a rational explanation for the behavior of the arylpiperazine ligand. The observed binding modes and receptor–ligand interactions provided us with fresh clues about how to optimize selectivity for D2DR receptors.

Penta- and heteropentadienyl ligands coordinated to beryllium

In this work we have performed a systematic study of new organometallic complexes containing penta- and heteropentadienyl (CH₂CHCHCHX, X?=?CH₂, O, NH, S) ligands coordinated to beryllium. Calculated complexes were studied using the density functional theory (PBE) in combination with the 6-311++G(3d,2p) basis set. The coordination number on the beryllium atom varies according to the type of ligand. Pentadienyl ligand shows hapticities η¹ and η⁵, while heteropentadienyl ligands display η¹ and η² hapticities. A Wiberg bond indices study was performed in order to get information about their bond orders.

Electric field effect on the zigzag (6,0) single-wall BC2N nanotube for use in nano-electronic circuits

We have analyzed the effect of external electric field on the zigzag (6,0) single-wall BC₂N nanotube using density functional theory calculations. Analysis of the structural parameters indicates that the nanotube is resistant against the external electric field strengths. Analysis of the electronic structure of the nanotube indicates that the applied parallel electric field strengths have a much stronger interaction with the nanotube with respect to the transverse electric field strengths and the nanotube is easier to modulate by the applied parallel electric field. Our results show that the properties of the nanotube can be controlled by the proper external electric field for use in nano-electronic circuits.

Inactivation of Cryptosporidium parvum Oocysts and Clostridium perfringens Spores by a Mixed-Oxidant Disinfectant and by Free Chlorine

Volume 63, no. 4, p. 1600: The caption to Table 2 should read as follows: "Inactivation of Clostridium perfringens spores by 5-mg/liter doses of mixed oxidants or free chlorine in buffer at pH 7 at 25(deg)C." [This corrects the article on p. 1598 in vol. 63.].     

Theoretical study of the decomposition of ethyl and ethyl 3-phenyl glycidate

The mechanism of the decomposition of ethyl and ethyl 3-phenyl glycidate in gas phase was studied by density functional theory (DFT) and MP2 methods. A proposed mechanism for the reaction indicates that the ethyl side of the ester is eliminated as ethylene through a concerted six-membered cyclic transition state, and the unstable intermediate glycidic acid decarboxylates rapidly to give the corresponding aldehyde. Two possible pathways for glycidic acid decarboxylation were studied: one via a five-membered cyclic transition state, and the other via a four-membered cyclic transition state. The results of the calculations indicate that the decarboxylation reaction occurs via a mechanism with five-membered cyclic transition state.

Structural characterization of the (MeSH)4 potential energy surface

A random walk on the PES for (MeSH)₄ clusters produced 50 structural isomers held together by hydrogen-bonding networks according to calculations performed at the B3LYP/6–311++G** and MP2/6–311++G** levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted.

CO2 adsorption on polar surfaces of ZnO

Physical and chemical adsorption of CO₂ on ZnO surfaces were studied by means of two different implementations of periodic density functional theory. Adsorption energies were computed and compared to values in the literature. In particular, it was found that the calculated equilibrium structure and internuclear distances are in agreement with previous work. CO₂ adsorption was analyzed by inspection of the density of states and electron localization function. Valence bands, band gap and final states of adsorbed CO₂ were investigated and the effect of atomic displacements analyzed. The partial density of states (PDOS) of chemical adsorption of CO₂ on the ZnO(0001) surface show that the p orbitals of CO₂ were mixed with the ZnO valence band state appearing at the top of the valence band and in regions of low-energy conduction band.

Cytotoxic effect and molecular docking of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide—a novel topoisomerase II inhibitor

The preliminary cytotoxic effect of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide hydrochloride (1)—a potent topoisomerase II inhibitor—was measured using a MTT assay. It was found that the compound decreased the number of viable cells in both estrogen receptor-positive MCF-7 and estrogen receptor-negative MDA-MB-231breast cancer cells, with IC₅₀ values of 146?±?2 and 132?±?2 μM, respectively. To clarify the molecular basis of the inhibitory action of 1, molecular docking studies were carried out. The results suggest that 1 targets the ATP binding pocket.

Electronic structures of bisnoradamantenyl and bisnoradamantanyl dications and related species

The highly pyramidalized molecule bisnoradamantene is extremely reactive toward nucleophiles and dienes. In this work, we studied the electronic structure of bisnoaradamantene, as well as those of its cation and dication, which are previously unreported carbonium ions. According to QTAIM and MO analysis, there is a 3c-2e bonding system in the bisnoradamantenyl cation and a 4c-2e bonding system in the bisnoradamantenyl dication. A topological study indicated that, on going from bisnoradamantene to its dication, π-bond interaction with the bridgehead carbon atom increases. Additional study of the bisnoradamantanyl dication also indicated that it has two multicenter bonding systems. Comparison of the D3BIA and NICS aromaticity indices of these molecules and other derivatives indicates that these indices are well correlated, and analysis of these indices shows that the cationic and dicationic bisnoradamantenyl species are homoaromatic.

Erratum

The cover caption for the August issue of Plant & Cell Physiologyshould     

Role of gold in a complex cascade reaction involving two electrocyclization steps

Quantum chemical computations (B3LYP/LACVP**) were applied to assess the impact of Au(I) complexation on activation barriers for sequential electrocyclization reactions (one a 1,2-dihydroazete ring-opening and another a pentadienyl cation ring-closure) proposed to occur during a complex reaction cascade that converts alkynes and imines to cyclopentenimines.

A B3LYP and MP2(full) theoretical investigation into the strength of the C–NO2 bond upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced and the charge of nitro group turned more negative in complex in comparison with those in isolated nitrotriazole molecule. The increment of the C–NO₂ bond dissociation energies correlated well with the intermolecular H-bonding interaction energies. Electron density shifts analyses showed that the electron density shifted toward the C–NO₂ bond upon complex formation, leading to the strengthened C–NO₂ bond and the possibly reduced explosive sensitivity.

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2 bond upon the formation of the molecule-cation interaction between Na+ and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the molecule-cation interaction between Na⁺ and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO₂ bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis showed that the electron density shifted toward the C-NO₂ bond upon complex formation, leading to the strengthened C-NO₂ bond and the possibly reduced explosive sensitivity.

A molecular dynamics study on sI hydrogen hydrate

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.