Structural, mechanical and electronic properties of nano-fibriform silica and its organic functionalization by dimethyl silane: a SCC-DFTB approach

Self-consistent-charge density-functional tight-binding (SCC-DFTB) approximated method was employed to investigate the structural, mechanical and electronic properties of the zigzag and armchair nano-fibriform silica (SNTs) and their outer surface organic modified derivatives (MSNTs) with internal radii in the range of 8 to 36 Å. The strain energy curves showed that the nanotubes structures are energetically more stable compared to the respective sheet structures. External hydroxyl dihedral angles in silica nanotubes have small influence, about 0.5 meV.atom^?1, in the strain energy curve tendency of those materials favoring the zigzag chirality. The chemical modification of outer surface of SNTs by dimethyl silane group affects their relative stability favoring the armchair chirality in approximately 2 meV.atom^?1. MSNTs have axial elastic constants, Young’s moduli, determined at the harmonic approximation, around 100 GPa smaller than the respective SNTs. The Young’s moduli of zigzag and armchair SNTs are in the range of 150–195 GPa and 232–260 GPa, respectively. And for the zigzag and armchair MSNTs these values are in the range of 77–89 and 110–140 GPa, respectively. The SNTs and MSNTs were characterized as insulators with band gaps around 8–10 eV.

Theoretical design of donor-acceptor conjugated copolymers based on furo-, thieno-, and selenopheno[3,4-c] thiophene-4,6-dione and benzodithiophene units for organic solar cells

In this work, a series of donor-acceptor (D-A) copolymers (PBDTFPD(Pa1), PBDTTPD (Pa2) and PBDTSePD(Pa3)) were selected and theoretically investigated using O3LYP/6-31G(d), PBE0/6-31G(d), TD-O3LYP/6-31G(d)//O3LYP/6-31G(d) and periodic boundary conditions methods. The calculated results go well with the available experimental data of highest occupied and lowest unoccupied molecular orbital (HOMO/LUMO) energy levels and band gaps. A series of conjugated polymers (Pb1?~?Pb3) comprised of electron-deficient benzodithiophene and electron-rich furo-, thieno-, and selenopheno[3,4-c]thiophene-4,6-dione were further designed and studied. Compared with Pa1-Pa3, the designed polymers of Pb1?~?Pb3 show better performances with smaller band gaps, lower HOMO energy levels, red shift of absorption spectra, and larger open circuit voltage (Voc). For investigated polymers (Pa1, Pa2, Pa3, Pb1, Pb2, Pb3), the power conversion efficiencies (PCEs) of ~6.1 %, ~7.2 %, ~7.9 %, ~8.0 %, ~9.5 % and ~9.0 % are predicted by Scharber diagrams when they are used in combination with PC60BM as an acceptor. The results illustrate that these designed polymers which turn the electron-withdrawing capability in D-A conjugated polymers are expected to turn into highly efficient donor materials for organic solar cells.

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.

Assessing the quantum mechanical level of theory for prediction of linear and nonlinear optical properties of push-pull organic molecules

In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability (〈α〉) and total static first hyperpolarizability (β_t) were calculated for a set of benzene, styrene, biphenyl and stilbene derivatives using HF, MP2 and DFT (31 different functionals) levels and over 71 distinct basis sets. In addition, we propose two new basis sets, NLO-V and aNLO-V, for NLO properties calculations. As the main outcomes it is shown that long-range corrected DFT functionals such as M062X, ωB97, cam-B3LYP, LC-BLYP and LC-ωPBE work satisfactorily for NLO properties when appropriate basis sets such as those proposed here (NLO-V or aNLO-V) are used. For most molecules with β ranging from 0 to 190 esu, the average absolute deviation was 13.2 esu for NLO-V basis sets, compared to 27.2 esu for the standard 6-31 G(2d) basis set. Therefore, we conclude that the new basis sets proposed here (NLO-V and aNLO-V), together with the cam-B3LYP functional, make an affordable calculation scheme to predict NLO properties of large organic molecules.

Fine scale measurement and mapping of uranium in soil solution in soil and plant-soil microcosms, with special reference to depleted uranium

Background and aims

Residues from use of depleted uranium (DU) munitions pose a lasting environmental impact through persistent contamination of soils. Consequently, an understanding of the factors determining the fate of DU in soil is necessary. An understudied factor is the interaction of root exudates with DU. This study describes the use of ‘Single-Cell-Sampling-and-Analysis’ (SiCSA) for the first time in soil and investigates the effects of root exudates on DU dissolution.

Methods

Soil solutions from soil and plant-soil microcosms containing DU fragments were sampled and analysed using SiCSA and capillary electrophoresis/ICP-MS for organic acids and uranium.

Results

Nanolitre volumes of soil solution were sampled and analysed. Soils with DU fragments but no citrate addition showed low uranium concentrations in contrast to those with added citrate. Lupin root exudation gave concentrations up to 8 mM citrate and 4.4 mM malate in soil solution which solubilised DU fragments yielding transient solution concentrations of up to 30 mM.

Conclusions

Root exudates solubilise DU giving high localised soil solution concentrations. This should be considered when assessing the environmental risk of DU munitions. The SiCSA method was used successfully in soil for the first time and enables investigations with high spatial and temporal resolution in the rhizosphere.

Cubitane: a rare diterpenoid skeleton

There are only 15 diterpenoids known sharing the rare cubitane skeleton (1,3-diisopropyl-6,10-dimethylcyclododecane, Fig. 1) named after the natural product (+)-cubitene ((+)-1) from the termite Cubitermes umbratus. Cubitane-type diterpenoids (“cubitanoids”) have since then been isolated from gorgonian corals and there are reports that cubitene also occurs in plants. The twelve-membered ring of the cubitanoids is an interesting feature for which we have developed a novel synthesis involving bicyclic precursors. In this review, we discuss the state-of-research regarding isolation, structure elucidation, biological activity, biosynthesis, and total synthesis of cubitane-type diterpenoids.

Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation

The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 %?v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution and H-bonding are analyzed in the two organic media. Our results show that the changes in overall structure of the protein almost display a clear correlation with the water content in hexane media while to some extent U-shaped/bell-shaped dependence on the water content is observed in acetonitrile media with a minimum/maximum at 10–20 % water content. In contrast, the water content change in the two organic solvents does not play an observable role in the stability of catalytic hydrogen-bond network, which still exhibits high stability in all hydration levels, different from observations on the free enzyme system [Zhu L, Yang W, Meng YY, Xiao X, Guo Y, Pu X, Li M (2012) J Phys Chem B 116(10):3292–3304]. In low hydration levels, most water molecules mainly distribute near the protein surface and an increase in the water content could not fully exclude the organic solvent from the protein surface. However, the acetonitrile solvent displays a stronger ability to strip off water molecules from the protein than the hexane. In a summary, the difference in the calculated properties between the two organic solvents is almost significant in low water content (<10 %) and become to be small with increasing water content. In addition, some structural properties at 10?~?20 %?v/v hydration zone, to large extent, approach to those in aqueous solution.

Prodrugs for masking bitter taste of antibacterial drugs—a computational approach

DFT calculations for the acid-catalyzed hydrolysis of several maleamic acid amide derivatives revealed that the reaction rate-limiting step is determined on the nature of the amine leaving group. Further, it was established that when the amine leaving group was a secondary amine, acyclovir or cefuroxime moiety the tetrahedral intermediate formation was the rate-limiting step such as in the cases of acyclovir ProD 1- ProD 4 and cefuroxime ProD 1- ProD 4. In addition, the linear correlation between the calculated and experimental rates provided a credible basis for designing prodrugs for masking bitter taste of the corresponding parental drugs which have the potential to release the parent drug in a sustained release fashion. For example, based on the DFT calculated rates the predicted t_1/2 (a time needed for 50 % of the reactant to be hydrolyzed to products) for cefuroxime prodrugs, cefuroxime ProD 1- ProD 4, were 12 min, 18 min, 200 min and 123 min, respectively.

Do roots mind the gap?

Aims

Roots need to be in good contact with the soil to take up water and nutrients. However, when the soil dries and roots shrink, air-filled gaps form at the root-soil interface. Do gaps actually limit the root water uptake, or do they form after water flow in soil is already limiting?

Methods

Four white lupins were grown in cylinders of 20 cm height and 8 cm diameter. The dynamics of root and soil structure were recorded using X-ray CT at regular intervals during one drying/wetting cycle. Tensiometers were inserted at 5 and 18 cm depth to measure soil matric potential. Transpiration rate was monitored by continuously weighing the columns and gas exchange measurements.

Results

Transpiration started to decrease at soil matric potential ψ between ?5 kPa and ?10 kPa. Air-filled gaps appeared along tap roots between ψ?=??10 kPa and ψ?=??20 kPa. As ψ decreased below ?40 kPa, roots further shrank and gaps expanded to 0.1 to 0.35 mm. Gaps around lateral roots were smaller, but a higher resolution is required to estimate their size.

Conclusions

Gaps formed after the transpiration rate decreased. We conclude that gaps are not the cause but a consequence of reduced water availability for lupins.     

Competition between halogen, dihalogen and hydrogen bonds in bromo- and iodomethanol dimers

O-H…X and O-H…O H-bonds as well as C-X…X dihalogen and C-X…O halogen bonds have been investigated in halomethanol dimers (bromomethanol dimer, iodomethanol dimer, difluorobromomethanol…bromomethanol complex and difluoroiodomethanol…iodomethanol complex). Structures of all complexes were optimized at the counterpoise-corrected MP2/cc-pVTZ level and single-point energies were calculated at the CCSD(T)/aug-cc-pVTZ level. Energy decomposition for the bromomethanol dimer complex was performed using the DFT-SAPT method based on the aug-cc-pVTZ basis set. OH…O and OH…X H-bonds are systematically the strongest in all complexes investigated, with the former being the strongest bond. Halogen and dihalogen bonds, being of comparable strength, are weaker than both H-bonds but are still significant. The strongest bonds were found in the difluoroiodomethanol…iodomethanol complex, where the O-H…O H-bond exceeds 7 kcal mol^-1, and the halogen and dihalogen bonds exceed 2.5 and 2.3 kcal mol^-1, respectively. Electrostatic energy is dominant for H-bonded structures, in halogen bonded structures electrostatic and dispersion energies are comparable, and, finally, for dihalogen structures the dispersion energy is clearly dominant.

MD simulation of self-diffusion and structure in some n-alkanes over a wide temperature range at high pressures

Self-diffusion and structural properties of n-alkanes have been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 600 K at pressures up to 300 MPa. The simulated results of lower n-alkanes are in good agreement with the existing experimental data, and support the reliability of results of the simulations of self-diffusion coefficients obtained at the extreme conditions. We predict the self-diffusion coefficients for methane, ethane, propane and n-butane at the similar reduced temperatures and pressures to draw a comparison between them. Then the correlation between self-diffusion and structural properties are further investigated by calculating the coordination numbers. Moreover, we define four distances and their corresponding relative deviations to characterize the flexibility of long-chain n-alkanes. The simulated results show that the self-diffusion of n-alkane molecules is mainly affected by the close packing, and the flexibility has a strong impact on the self-diffusion of longer n-alkane molecules.

DFT calculation of the electronic properties of fluorene-1,3,4-thiadiazole oligomers

Thiadiazole derivatives have been widely employed in the areas of pharmaceutical, agricultural, industrial, and polymer chemistry. The electronic and molecular structures of thiadiazoles are of interest because they have an equal number of valence electrons and similar molecular structures to thiophenes, which are currently used in the construction of organic solar cells due to their relatively high hole mobilities and good light-harvesting properties. For this reason, the electronic properties of fluorene-1,3,4-thiadiazole oligomers warrant investigation. In the present work, the structure of fluorene-1,3,4-thiadiazole with one thiadiazole unit in the structure was analyzed. This molecule was then expanded until there were 10 thiadiazole units in the structure. The band gap, HOMO and LUMO distributions, and absorption spectrum were analyzed for each molecule. All calculations were performed by applying the B3LYP/6-31G(d) chemical model in the Gaussian 03W and GaussView software packages. The electronic properties were observed to significantly enhance as the number of monomeric units increased, which also caused the gap energy to decrease from 3.51 eV in the oligomer with just one thiadiazole ring to 2.33 eV in the oligomer with 10 units. The HOMO and LUMO regions were well defined and separated for oligomers with at least 5 monomer units of thiadiazole.

Theoretical studies of the interaction between enflurane and water

Increase of the atmospheric concentration of halogenated organic compounds is partially responsible for a change of the global climate. In this work we have investigated the interaction between halogenated ether and water, which is one of the most important constituent of the atmosphere. The structures of the complexes formed by the two most stable conformers of enflurane (a volatile anaesthetic) with one and two water molecules were calculated by means of the counterpoise CP-corrected gradient optimization at the MP2/6–311++G(d,p) level. In these complexes the CH…O_w hydrogen bonds are formed, with the H…O_w distances varying between 2.23 and 2.32 Å. A small contraction of the CH bonds and the blue shifts of the ν(CH) stretching vibrations are predicted. There is also a weak interaction between one of the F atoms and the H atom of water, with the H_w…F distances between 2.41 and 2.87 Å. The CCSD(T)/CBS calculated stabilization energies in these complexes are between ?5.89 and ?4.66 kcal?mol^?1, while the enthalpies of formation are between ?4.35 and ?3.22 kcal?mol^?1. The Cl halogen bonding between enflurane and water has been found in two complexes. The intermolecular (Cl···O) distance is smaller than the sum of the corresponding van der Waals radii. The CCSD(T)/CBS stabilization energies for these complexes are about ?2 kcal?mol^?1.

Theoretical investigation into optical and electronic properties of 1,8-naphthalimide derivatives

A series of 1,8-naphthalimide derivatives has been designed to explore their optical, electronic, and charge transport properties as charge transport and/or luminescent materials for organic light-emitting diodes (OLEDs). The frontier molecular orbitals (FMOs) analysis have shown that the vertical electronic transitions of absorption and emission are characterized as intramolecular charge transfer (ICT) for electron-donating and aromatic groups substituted derivatives. However, the ICT character of the electron-withdrawing substituted derivatives is not significant. The calculated results show that their optical and electronic properties are affected by the substituent groups in 4-position of 1,8-naphthalimide. Our results suggest that 1,8-naphthalimide derivatives with electron-donating ?OCH₃ and ?N(CH₃)₂ (1 and 2), electron-withdrawing ?CN and?COCH₃ (3 and 4), 2-(thiophen-2-yl)thiophene (5), 2,3-dihydrothieno[3,4-b][1, 4]dioxine (6), 2-phenyl-1,3,4-oxadiazole (7), and benzo[c][1,2,5]thiadiazole (8) fragments are expected to be promising candidates for luminescent materials for OLEDs, particularly for 5 and 7. In addition, 3 and 7 can be used as promising hole transport materials for OLEDs. This study should be helpful in further theoretical investigations on such kind of systems and also to the experimental study for charge transport and/or luminescent materials for OLEDs.

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.

Tunable differential conductance of single wall C/BN nanotube heterostructure

The transport properties and differential conductance of the heterostructures constructed by (5,5) single wall carbon nanotube (SWCNT) and (5,5) single wall boron nitride nanotube (SWBNNT) are investigated using density functional theory in combination with non-equilibrium Green’s functions. We find that the transmission conductance of (5,5) BN/C nanotube heterostructure is not only continually depressed as the BNNT region increases but also the drop of the conductance is uniform in the energy window (?1.43 eV, 1 eV), which leads to linear I–V dependence for the systems when the bias is within this energy range. Moreover, the differential conductance linearly decreases when n?≤?3 but exponentially decreases when n?≥?3 for (5,5)(BN) _n /C heterostructure. Such tunable differential conductance of (5,5) BN/C nanotube heterostructure mainly derives from the blockage of the transport channels induced by the semiconductive BN segment.

Modulating weak intramolecular interactions through the formation of beryllium bonds: complexes between squaric acid and BeH2

The electronic structure of the two most stable isomers of squaric acid and their complexes with BeH₂ were investigated at the B3LYP/6-311?+?G(3df,2p)// B3LYP/6-31?+?G(d,p) level of theory. Squaric acid forms rather strong beryllium bonds with BeH₂, with binding energies of the order of 60 kJ?mol^?1. The preferential sites for BeH₂ attachment are the carbonyl oxygen atoms, but the global minima of the potential energy surfaces of both EZ and ZZ isomers are extra-stabilized through the formation of a BeH···HO dihydrogen bond. More importantly, analysis of the electron density of these complexes shows the existence of significant cooperative effects between the beryllium bond and the dihydrogen bond, with both becoming significantly reinforced. The charge transfer involved in the formation of the beryllium bond induces a significant electron density redistribution within the squaric acid subunit, affecting not only the carbonyl group interacting with the BeH₂ moiety but significantly increasing the electron delocalization within the four membered ring. Accordingly the intrinsic properties of squaric acid become perturbed, as reflected in its ability to self-associate.

Computational investigation on microsolvation of the osmolyte glycine betaine [GB (H2O)1-7]

The preferential interactions of glycine betaine (GB) with solvent components and the effect of solvent on its stability have been examined. In particular, the microsolvation of organic osmolyte and widely important osmoprotectant in nature as glycine betaine has been reported by using M06 method. A number of configurations (b_X (a-z)) of the clusters for one to seven water molecules (×?=?1-7) have been considered for the microsolvation. Structures of stable conformers are obtained and denoted as b1a, b2a, b3a, b4a, b5a, b6a and b7a. It is observed from the interaction energy difference (?E) that only seven water molecules can be accommodated in the first solvation shell to stabilize GB. It is also observed that the calculated relative energy using M06 is in close agreement with calculations at the MP2 level of theory.

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.