Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n?=?6–9 and k?=?2–4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (Lt) and the diameter (dt) of the pristine CNT has to be larger than 2, i.e., Lt/dt?>?2, in order to provide the observed experimental trends of C=C bond distances, as well as to maintain the atomic charges nearly constant and zero around the center of the tube. Therefore, the concepts of useful length and volume were developed and tested for the encapsulation process of HCN and C2H2 into CNTs. The energies involved in these processes, as well as the changes in molecular structure and electronic properties of the dopants and the CNTs are discussed and rationalized by the amount of charge transferred between dopant and CNT.
The effect of alkali metal oxides MnO (M?=?Li, Na, K; n?=?2, 3, 4) on the geometric, electronic, and linear and nonlinear optical properties of the Mg12O12 nanocage was investigated by density-functional-based methods. According to the computational results, these alkali metal oxides are adsorbed on the Mg12O12 nanocage because this adsorption reduces its energy gap. The static first hyperpolarizability (β0) of the nanocage is dramatically increased in the presence of the alkali metal oxides, with the greatest increase seen in the presence of the superalkalis (i.e., M3O; M?=?Li, Na, and K). The highest first hyperpolarizability (β0?≈?600,000 a.u.) was calculated for K3O@Mg12O12, which was considerably more than that for Mg12O12. The thermodynamic properties and relative stabilities of these inorganic compounds are discussed.
Natural bond orbital (NBO) analyses and dissected nucleus-independent chemical shifts (NICSπzz) were computed to evaluate the bonding (bond type, electron occupation, hybridization) and aromatic character of the three lowest-lying Si2CH2 (1-Si, 2-Si, 3-Si) and Ge2CH2 (1-Ge, 2-Ge, 3-Ge) isomers. While their carbon C3H2 analogs favor classical alkene, allene, and alkyne type bonding, these Si and Ge derivatives are more polarizable and can favor “highly electron delocalized”? and “non-classical”? structures. The lowest energy Si 2CH2 and Ge 2CH2 isomers, 1-Si and 1-Ge, exhibit two sets of 3–center 2–electron (3c-2e) bonding; a π-3c-2e bond involving the heavy atoms (C–Si–Si and C–Ge–Ge), and a σ-3c-2e bond (Si–H–Si, Ge–H–Ge). Both 3-Si and 3-Ge exhibit π and σ-3c-2e bonding involving a planar tetracoordinated carbon (ptC) center. Despite their highly electron delocalized nature, all of the Si2CH2 and Ge2CH2 isomers considered display only modest two π electron aromatic character (NICS(0)πzz=--6.2 to –8.9 ppm, computed at the heavy atom ring center) compared to the cyclic-C 3H2 (–13.3 ppm).
The electric dipole transitions between pure spin and mixed spin electronic states are calculated at the XMC-QDPT2 and MCSCF levels of theory, respectively, for different intermolecular distances of the C6H6 and O2 collisional complex. The magnetic dipole transition moment between the mixed-spin ground (“triplet”) and the first excited (“singlet”) states is calculated by quadratic response at MCSCF level of theory. The obtained results confirm the theory of intensity borrowing and increasing the intensity of electronic transitions in the C6H6?+?O2 collision. The calculation of magnetically induced current density is performed for benzene molecule being in contact with O2 at the distances from 3.5 to 4.5 Å. The calculation shows that the aromaticity of benzene is rising due to the conjugation of π-MOs of both molecules. The C6H6?+?O2 complex becomes nonaromatic at the short distances (r?<?3.5 Å). The computation of static polarizability in the excited electronic states of the C6H6?+?O2 collisional complex at various distances supports the theory of red solvatochromic shift of the a?→?X band.
The present study reports the geometries, electronic structures, growth behavior, and stabilities of neutral and ionized copper-doped germanium clusters containing 1–20 Ge atoms within the framework of linear combination of atomic orbitals density functional theory (DFT) under the spin-polarized generalized gradient approximation. It was found that Cu-capped Gen (or Cu-substituted Gen+1) and Cu-encapsulated Gen clusters mostly occur in the ground state at a particular cluster size (n). In order to explain the relative stabilities of the ground-state clusters, parameters such as the average binding energy per atom (BE), the embedding energy (EE), and the fragmentation energy (FE) of the clusters were calculated, and the resulting values are discussed. To explain the chemical stabilities of the clusters, parameters such as the energy gap between the highest occupied and the lowest unoccupied molecular orbitals (the HOMO–LUMO gap), the ionization energy (IP), the electron affinity (EA), the chemical potential (μ), the chemical hardness (η), and the polarizability were calculated, and the resulting values are also discussed. Natural atomic orbital (NAO) and natural bond orbital (NBO) analyses were also used to determine the electron-counting rule that should be applied to the most stable Ge10Cu cluster. Finally, the relevance of the calculated results to the design of Ge-based superatoms is discussed.
Figure Contributions of the valance orbitals of the Ge and Cu atom(s) to the HOMO of the ground-state icosahedral Ge10Cu cluster obtained from NBO analysis. The numbers below the clusters represent the occupancies of the HOMO orbitals
Designing and synthesizing novel electron-donor polymers with the high photovoltaic performances has remained a major challenge and hot issue in organic electronics. In this work, the exciton-dissociation (kdis) and charge-recombination (krec) rates for the PC61BM-PTDPPSe system as a promising polymer-based solar cell candidate have been theoretically investigated by means of density functional theory (DFT) calculations coupled with the non-adiabatic Marcus charge transfer model. Moreover, a series of regression analysis has been carried out to explore the rational structure–property relationship. Results reveal that the PC61BM-PTDPPSe system possesses the large open-circuit voltage (0.77 V), middle-sized exiton binding energy (0.457 eV), and relatively small reorganization energies in exciton-dissociation (0.273 eV) and charge-recombination (0.530 eV) processes. With the Marcus model, the kdis, krec, and the radiative decay rate (ks), are estimated to be 3.167×1011 s?1, 3.767×1010 s?1, and 7.930×108 s?1 respectively in the PC61BM-PTDPPSe interface. Comparably, the kdis is as 1～3 orders of magnitude larger than the krec and the ks, which indicates a fast and efficient photoinduced exciton-dissociation process in the PC61BM-PTDPPSe interface.
Graphical Abstract PTDPPSe is predicted to be a promising electron donor polymer, and the PC61BM-PTDPPSe system is worthy of further device research by experiments.
The 1A1 ground and the first 1B2 excited states of the methylenecyclopropene (triafulvene) are described by localized wave functions, based on 20 structures valence bond structures. The results are compared to CASSCF(4,4) calculations for both the energetics and the dipole moment. Additional calculations with partial electronic delocalization are presented, and it is shown that the dipole moment modification does not correspond to a situation where the antiaromatic situation prevails (with 4n electrons in the cycle). Part of the analysis uses a “trust factor” that helps to decide if a wave function is appropriate to describe a given state. The trust factor compares the VB wave function to the CASSCF’s with their overlap. Finally, the valence bond density is used to produce density maps that illustrate the electron transfer upon excitation.
Graphical Abstract A projector-based method compares CASSCF wave functions to local wave functions, including Lewis structures as shown in the picture. A “trust factor” (τ) is obtained. Both the ground state and the first excited state of the methylenecyclopropene are discussed
Phospholipase A2 (PLA2) is one of the key enzymes involved in the formation of inflammatory mediators. Inhibition of PLA2 is considered to be one of the efficient methods to control inflammation. In silico docking studies of 160 selected indole derivatives performed against porcine pancreatic PLA2 (ppsPLA2) suggested that, CID2324681, CID8617 (indolebutyric acid or IBA), CID22097771 and CID802 (indoleacetic acid or IAA) exhibited highest binding energies. In silico analysis was carried out to predict some of the ADME properties. The binding potential of these compounds with human non pancreatic secretory PLA2 (hnpsPLA2) was determined using molecular docking studies. In order to corroborate the in silico results, enzyme kinetics and isothermal titration calorimetric analysis of the two selected compounds, IAA and IBA were performed against ppsPLA2. From the analysis, it was concluded that IAA and IBA can act as competitive inhibitors to the enzyme and may be used as anti inflammatory agents.
Carbohydrates have drawn considerable interest from researchers recently due to their affinity for CO2. However, most of the research in this field has focused on peracetylated derivatives. Compared with acetylated carbohydrates, which have already been studied in depth, methyl d-glucopyranoside derivatives are more stable and could have additional applications. Thus, in the present work, ab initio calculations were performed to elucidate the characteristics of the interactions of methylglucoside derivatives with CO2, and to investigate how the binding energy (ΔE) is affected by isomerization or the introduction of various acyl groups. Four methyl d-glucopyranosides (each with two anomers) bearing acetyl, propionyl, butyryl, and isobutyryl moieties, respectively, were designed as substrates, and the 1:1 complexes of a CO2 molecule with each of these sugar substrates were modeled. The results indicate that ΔE is mainly influenced by interaction distance and the number of negatively charged donors or interacting pairs in the complex; the structure of the acyl group present in the substrate is a secondary influence. Except in the case of methyl 2-O-acetyl-d-glucopyranose, the ΔE values of the α- and β-anomers of each methylglucoside were found to be almost the same. Therefore, we would expect the CO2 affinities of the four derivatives studied here to be as strong as or even stronger than that of peracetylated d-glucopyranose.
Graphical Abstract The binding energy between methyl d-glucopyranoside derivatives with various substituted acyl groups and CO2 are evaluated by ab initio calculations. The strong interaction between these methyl dglucopyranoside derivatives and CO2 showed the potential of their application for CO2 capture
In this work we used a combination of classical molecular dynamics and simulated annealing techniques to shed more light on the conformational flexibility of 12 adenosine triphosphate (ATP) analogues in a water environment. We present simulations in AMBER force field for ATP and 12 published analogues [Shah et al. (1997) Proc Natl Acad Sci USA 94: 3565–3570]. The calculations were carried out using the generalized Born (GB) solvation model in the presence of the cation Mg2+. The ion was placed at a close distance (2 Å) from the charged oxygen atoms of the beta and gamma phosphate groups of the ?3 negatively charged ATP analogue molecules. Analysis of the results revealed the distribution of inter-proton distances H8–H1′ and H8–H2′ versus the torsion angle ψ (C4–N9-C1′–O4′) for all conformations of ATP analogues. There are two gaps in the distribution of torsion angle ψ values: the first is between ?30 and 30 degrees and is described by cis-conformation; and the second is between 90 and 175 degrees, which mostly covers a region of anti conformation. Our results compare favorably with results obtained in experimental assays [Jiang and Mao (2002) Polyhedron 21:435–438].
Biocidal natural substances of botanical origin offer a promising ecofriendly option for controlling toxic cyanobacteria. Herein, we study 11 essential oils and some of their major components for their activity on Aphanizomenon gracile. On the basis of our results we support that Origanum vulgare and O. dictamnus, Ocimum basilicum, Eucalyptus meliodora, Melissa officinalis, and Pimpinella anisum exhibited the strongest activities, and the IC50/1d values of the extracts were calculated to be between 168.43 and 241.97 μg mL?1. When the major components of the biocidal essential oils were tested individually, (E)-anethole was found active, exhibiting an IC50/1d value of 71.35 μg mL?1. On the other hand, the half-life (t1/2) of (E)-anethole was calculated at 1 h. A preliminary attempt of (E)-anethole microencapsulation was conducted, in order to slowly release this biocidal agent, increasing the residual life under open air conditions and thus the biological activity. Results were promising since the microencapsulated product exhibited better activity than did the non-formulated (E)-anethole. This is a first report on the biocidal activity of EOs and (E)-anethole on A. gracile and a preliminary indication of the microencapsulated (E)-anethole potential use as a natural biocidal in fresh waters.
In recent years, New Delhi metallo-beta-lactamases 1 (blaNDM-1) has been reported with increasing frequency and become prevalent. The present study was undertaken to investigate the epidemiological dissemination of the blaNDM-1 gene in Enterobacter cloacae isolates at a teaching hospital in Yunnan, China.
Methods
Antimicrobial susceptibility testing was performed using VITEK 2 system and E test gradient strips. The presence of integrons and insertion sequence common region 1 were examined by PCR and sequencing. Clonal relatedness was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Conjugation experiments and Southern blot hybridization were performed to determine the transferability of plasmids.
Results
Ten E. cloacae isolates and their Escherichia coli transconjugants were exhibited similar resistant patterns to carbapenems, cephalosporins and penicillins. 8 (80%) of E. cloacae isolates carried class 1 integron and 1 (12.5%) carried class 2 integron. Integron variable regions harbored the genes which encoded resistance to aminoglycosides (aadA1, aadA2, aadA5, aadB, aac(6′)-Ib-cr), sulfamethoxazole/trimethoprim (dfrA17, dfrA12, dfrA15) and Streptozotocin (sat2). Six E. cloacae isolates belonged to ST74 and exhibited highly similar PFGE patterns. Each isolate shared an identical plasmid with ~33.3 kb size that carried the blaNDM-1 gene, except T3 strain, of which the blaNDM-1 gene was located on a ~50 kb plasmid.
Conclusions
Our findings suggested that plasmid was able to contribute to the dissemination of blaNDM-1. Hence, more attention should be devoted to monitor the dissemination of the blaNDM-1 gene due to its horizontal transfer via plasmid. In addition, nosocomial surveillance system should actively monitor the potential endemic clone of ST74 to prevent their further spread.
A density functional theory (DFT) study of cct-As, ccc, and cct-CO isomers of the ruthenium dihydride complex RuH2(CO)2(AsMe2Ph)2 is reported (see Scheme for the labeling isomer 34 structures of RuH2(CO)2(AsMe2Ph)2). Complex geometries and relative energies of different isomers have been calculated with both B3LYP and M06-2X functionals. The results show that the B3LYP calculated Boltzmann populations of cct-As, ccc, and cct-CO isomers are 65.5, 34.2, and 0.3%, respectively. These are in better agreement with the experimental data than those calculated at the M06-2X level. However, the calculations of 1H NMR chemical shifts were found to be better described with M06-2X than with B3LYP or with HF level of theories. In addition, a transition state between the two most stable isomers was determined through DFT/(B3LYP or M06-2X) calculations.
A perfectly planar Al13+ cluster (CI) and a quasi-planar Al13+ cluster (CII) have been found for the first time. Both clusters have a triangular core surrounded by a set of ten Al atoms in the form of a ring. These cationic clusters have substantial aromatic character. The planar CI cluster has local antiaromatic patches within global aromatic sea. It is doubly aromatic having both σ and π aromatic character. The quasi-planar CII cluster is also aromatic but it has more σ-delocalization.
Rv0045c is an esterase involved in lipid metabolism of Mycobacterium tuberculosis. It belongs to the α/β hydrolase family. In the current study, we performed sequence- and structure-based analysis of Rv0045c followed by molecular dynamics (MD) simulation for 100 ns to investigate conformational changes in the enzyme. Sequence analysis revealed that this enzyme is possibly a hormone-sensitive lipase. Further, through structural analysis, a putative catalytic tetrad containing “Ser-Asp-Ser-His” and residues involved in the formation of an oxyanion hole were identified. MD simulation of Rv0045c revealed a conformational transition from an open to a closed state. The active site pocket was found to be gated by four loops. The potential role of the cap domain and the mobile histidine is discussed. From the simulation, we see that the conformational changes mimic the different stages in the reaction mechanism of Rv0045c. These results support the hypothesis that free enzyme simulation encompasses all the conformations necessary for the different stages of catalysis. Our findings add to the growing knowledge of an important family of esterases in Mycobacterium tuberculosis.
A computational study of metal difluorides (MF2; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca–F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn–Teller effect in nonlinear MF2 molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal. The interactions of CO2 with ScF2 (Scc3 geometry) and TiF2 (Tic2 geometry) caused CO2 to shift from its usual linear geometry to a bent geometry (η2(C=O) binding mode), while it retained its linear geometry (η1(O) binding mode) when it interacted with the other metal difluorides. Energy decomposition analysis showed that, among the various geometries considered, the Scc3 and Tic2 geometries possessed the highest interaction energies and orbital interaction energies. Heavier transition metal difluorides showed stronger affinities for H2O, whereas the lighter transition metal (Sc and Ti) difluorides preferred CO2. Overall, the results of this study suggest that fluorides of lighter transition metals with partially filled d orbitals (e.g., Sc and Ti) could be used for CO2 capture under moist conditions.
Despite extensive studies on effects of elevated CO2 concentration ([CO2]e) on plant growth, few studies have investigated the responses of native grassland plant species to [CO2]e in terms of nutrient acquisition.
Methods
The effects of [CO2]e (769 ± 23 ppm) on Artemisia frigida and Stipa krylovii, two dominant species in Inner Mongolia steppe were investigated by growing them for 7 weeks in Open-Top Chambers (OTC).
Results
Exposure to [CO2]e enhanced shoot and root growth of A. frigida and S. krylovii. Elevated [CO2] increased photosynthetic rates (Pn) by 34 % in A. frigida but decreased Pn by 52 % in S. krylovii. Moreover, root-secreted acid phosphatase activity in A. frigida was stimulated by [CO2]e, while exudation of malate from roots of S. krylovii was suppressed by [CO2]e. Exposure to [CO2]e led to a decrease in P concentration in shoots and roots of A. frigida and S. krylovii, but total amount of P accumulated in shoots and roots of both species was increased by [CO2]e.
Conclusions
The two dominant species in temperate steppes differed in their responses to [CO2]e, such that A. frigida was more adapted to [CO2]e than S. krylovii under low availability of soil P.
