Evaluation of the σ-Donation from Group 11 Metals (Cu, Ag, Au) to Silane, Germane, and Stannane Based on the Experimental/Theoretical Systematic Approach

Organometallics
Reactions of group 11 metal chlorides (CuCl, AgCl, AuCl) with {(o-Ph2P)C6H4}3E(F) (E = Si (1), Ge (2), Sn (3)) provide a complete series of metallasilatrane [{(o-Ph2P)C6H4}3(F)Si]MCl (E = Cu (4), Ag (5), Au (6)), metallagermatrane [{(o-Ph2P)C6H4}3(F)Ge]MCl (E = Cu (7), Ag (8), Au (9)), and metallastannatrane [{(o-Ph2P)C6H4}3(F)Sn]MCl (E = Cu (10), Ag (11), Au (12)) complexes. Structural analyses clearly show the presence of M→E interactions in all of these complexes and establish the presence of periodicity; heavier group 14 elements E act as stronger electron acceptor ligands, and heavier group 11 metals exhibit higher donor ability toward ER4. Density functional theory calculations fully...  Read more

A trispyrazolylborato iron cysteinato complex efficiently mimics the cysteine dioxygenation process: mechanistic insights

Chemical Communications
The O2 activation process by a CDO biomimetic system has been herein investigated to gain mechanistic details on the unknown reaction mechanism. The outcomes of the DFT study show that the functional model efficiently mimics the enzymatic process, the reaction proceeding with a feasible activation barrier via multistate reactivity patterns.Read more

The structure of monoclinic Na2B10H10: a combined diffraction, spectroscopy, and theoretical approach

CrystEngComm
Neutron powder diffraction measurements of a specially synthesized Na211B10D10 compound, buttressed by comparative measurements and calculations of vibrational dynamics, have led to an improved, Rietveld-refined, structural model for its low-temperature monoclinic phase. The detailed atomic arrangements and phases for this compound are important for an understanding of its potential roles for fast-ion-battery and hydrogen-storage applications. A comparison of the calculated phonon densities of states (PDOSs) based on density functional theory for both the previously published structure and our new modified structure show that the PDOS of the latter is in noticeably better agreement with that experimentally observed by neutron vibrational spectroscopy. Moreover, this improved structure is predicted to have a higher stability and exhibits more reasonable separations between all...  Read more

Dual-dehydrogenation-promoted catalytic oxidation of formaldehyde on alkali-treated Pt clusters at room temperature

Journal of Materials Chemistry A
The activity of the Pt catalyst toward room-temperature catalytic oxidation of formaldehyde (HCHO) known as a common indoor air pollutant can be remarkably improved by the addition of some alkali metal salts. The resulting enhancement in the catalytic activity of the Pt catalyst is generally attributed to the introduction of alkali metal ions. Theoretical simulations and experimental studies presented here show that the OH ions provided by alkali metal salts make a major contribution to the enhanced activity of Pt catalysts toward the room-temperature catalytic oxidation of HCHO instead of additional alkali metal ions. This is because Cl ions from the Pt precursor (H2PtCl6) are easily chemisorbed on prepared Pt catalysts, leading to their deactivation. The OH ions provided by some alkali metal salts can effectively substitute surface adsorbed...  Read more

Proton trapping in Y and Sn Co-doped BaZrO3

Journal of Materials Chemistry A
Recent experimental and computational works have shown that Y and Sn co-doped BaZrO3 (BZSY) exhibits superior hydration ability and improved power output performance to that of the traditional solid oxide fuel cell (SOFC) electrolyte, Y-doped BaZrO3 (BZY). BZSY is also chemically stable in both H2O and CO2 atmospheres and is thought to have great potential as a future electrolyte material in proton-conducting SOFCs. Herein, we report the use of potential-based calculations in the assessment of dopant–proton trapping in this exciting new material. We use a genetic algorithm to find the lowest energy BZSY configuration and then proceed to locate the lowest energy proton doping sites. Calculations of the binding energies between the proton and a range of trivalent dopants, commonly used for these kinds of electrolyte, reveal its dependence on local chemical structure and can range...  Read more

Revealing the binding mode between respiratory syncytial virus fusion protein and benzimidazole-based inhibitors

Molecular BioSystems
Human respiratory syncytial virus (HRSV) is a major respiratory pathogen in newborn infants and young children and can also be a threat to some elderly and high-risk adults with chronic pulmonary disease and the severely immunocompromised. The RSV fusion (RSVF) protein has been an attractive target for vaccine and drug development. Experimental results indicate a series of benzimidazole-based inhibitors which target RSVF protein to inhibit the viral entry of RSV. To reveal the binding mode between these inhibitors and RSVF protein, molecular docking and molecular dynamics simulations were used to investigate the interactions between the inhibitors and the core domain of RSVF protein. MD results suggest that the active molecules have stronger π–π stacking, cation–π, and other interactions than less active inhibitors. The binding free energy between the active inhibitor and RSVF protein is also found to be significantly lower than that of the less active one using MM/GBSA. Then,...  Read more

Supramolecular Polymerization: A Coarse Grained Molecular Dynamics Study

The Journal of Physical Chemistry B
A coarse-grained (CG) force field to model the self-assembly of benzene-1,3,5-tricarboxamide (BTA) class of compounds in nonpolar solvents has been developed. The model includes an intrinsic point dipole embedded on one of the CG beads so as to impart a macrodipole moment to the oligomer, one of its characteristic feature. Chemical specificity has been preserved by benchmarking against results, including dimerization and solvation free energies, obtained from an all-atom representation. Starting from a well-dispersed configuration in n-nonane, BTA molecules self-assemble to form one-dimensional stacks. Free energy (FE) changes for the various manner in which short oligomers can exchange between the assembled and the dispersed states have been calculated. These calculations show BTA to self-assemble via a downhill cooperative mechanism with a nucleus size of three.Read more

Methyl-substituted enhancement of antitumor activity in square-planar metal complex and analysis of ΔE, ΔG, CV, UV-vis and luminescence

New Journal of Chemistry
Two novel Ala-based copper(II) compounds with formulas [(1,10-Phen)Cu(Ala)·(H2O)]·Cl·H2O (1) and [(2,9-DMP)Cu(Ala)·(H2O)]·NO3·H2O (2) have been synthesized and determined by X-ray diffraction. The two complexes stack in a square-planar structure and exhibit excellent anticancer activities. In particular, complex 2 with methyl-substituted phenanthroline shows higher anticancer properties than complex 1 with Phen. Computational ΔEE1,10-Phen > ΔE1 and ΔE2,9-DMP > ΔE2) has shown that the two substituted methyl groups can activate the conjugated system of π1414...  Read more

The effect of terminal groups of viologens on their binding behaviors and thermodynamics upon complexation with sulfonated calixarenes

Organic & Biomolecular Chemistry
The binding modes, inclusion abilities, and thermodynamic parameters for the intermolecular complexation of p-sulfonatocalix[4]arene (SC4A), p-sulfonatocalix[5]arene (SC5A), and p-sulfonatothiacalix[4]arene (STC4A), with methyl viologen (MV2+), ethyl viologen (EV2+), propyl viologen (PV2+), butyl viologen (BV2+), and benzyl viologen (BnV2+), were systematically investigated by NMR spectroscopy, molecular mechanics calculation, and microcalorimetry in neutral aqueous solutions. The obtained results show that all the sulfonated calixarene hosts can form stable inclusion complexes with viologen guests driven by much favorable enthalpy changes. All the viologen guests are encapsulated into the smaller SC4A cavity in their axial orientation. The larger SC5A cavity can accommodate all the viologen guests at its upper-rim midsection in...  Read more

An experimental and theoretical study of the photoisomerization and thermal reversion on 5-arylmethylene-2-thioxoimidazolidin-4-one

Physical Chemistry Chemical Physics
Unraveling the photochemical behaviour of the green fluorescent protein chromophore has lately attracted widespread attention among scientists. In this paper we present the study of the photochemical isomerization ZE and the back reaction of the chromophore analog, 5-arylmethylene-2- thioxoimidazolidin-4-one. Experimental results are supported with ab initio calculations at the DFT, (B3LYP/6-31+g(d,p)), TD-DFT (B3LYP/6-311++g(3df,3pd)) and CASSCF levels. A first excitation to the S2 state, where the isomerization occurs, is proposed followed by two conical intersections to S1 and S0 respectively. Three different mechanisms were analyzed for thermal reversion, concluding that the preferred channel involves an intersystem crossing between the S0 and T1 states with the formation of a biradical.Read more

Theoretical studies on the activation mechanism involving bifunctional tertiary amine–thioureas and isatylidene malononitriles

RSC Advances
Computational studies have been performed to elucidate the activation mechanism of the Michael addition reactions containing bifunctional tertiary amine–thioureas and isatylidene malononitriles by density functional theory (DFT) calculations at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level of theory. Results showed a difference of 6.47 kcal mol−1 between M1-O and M1-N, which suggest that it is the carbonyl group, instead of the malononitrile moiety of isatylidene malononitriles, that plays a dominating role in the activation of the electrophile by the catalysts. The predicted mechanism also successfully explains the experimentally observed enantioselectivity.Read more

Two-Dimensional Self-Assembly of a Pair of Triangular Macrocycles Studied by STM

The Journal of Physical Chemistry C
In this investigation, we reported the two-dimensional (2D) self-assembly of a pair of triangular macrocycles (TMC1 and TMC2) at a highly oriented pyrolytic graphite (HOPG)/1-phenyloctane interface. Although with the similar triangle-shaped phenyl backbones, TMC1 and TMC2 displayed different 2D nanopatterns. Control experiments with varying concentrations and temperatures have been carried out. Phase separations were recorded in the coassembly of TMC1 and TMC2. Scanning tunneling microscopy (STM) measurements, as well as density function theory (DFT) calculations, revealed the formation mechanism of the TMC1 and TMC2 nanoarrays. Moreover, minor ring-opening phenomena of TMC2 were detected by STM, which demonstrates the advantages of STM in trace content analysis.Read more

Mechanical properties and variation in SOC going from La to Nd in intermetallic RIn3 and RSn3 (R = La, Ce, Pr, Nd)

RSC Advances
First principle studies of the cubic rare-earth intermetallics RIn3 and RSn3 (R = La, Ce, Pr, Nd) have been carried out within the framework of density functional theory using the full potential linearized augmented plane waves plus local orbital method (FP-LAPW + lo). The calculated structural parameters with different functionals are found to be consistent with the experimental results. The effect of the Hubbard potential on the density of states is discussed in detail. It is observed that the inclusion of spin–orbit coupling (SOC) causes degeneracies of the electronic band structures in the vicinity of the Fermi level of these compounds. Furthermore, the SOC effect enhances as one goes from La to Nd in a compound, which demonstrates the interesting nature of this effect in the periodic table. The elastic constants, bulk moduli, shear moduli, Young’s moduli, anisotropy, Kleinman parameters, Poisson’s ratios, sound velocities...  Read more

Theoretical investigation of the mechanism of gold(I)-catalyzed hydrothiolation of alkynes and alkenes with phenthiol

RSC Advances
The mechanisms of the gold-catalyzed hydrothiolation of alkynes and alkenes with phenthiol have been investigated using density functional theory calculations done at the B3LYP/6-31G (d,p) (SDD for Au) level of theory. The solvent effect was taken into account by B3LYP/6-311++G (d,p) (SDD for Au) single-point calculations with the integral equation formalism polarizable continuum model (IEFPCM) and solvation model (SMD) in toluene. The calculations indicated that the reactions of the gold-catalyzed hydrothiolation proceed through two competing pathways and lead to Markovnikov-type sulfides or anti-Markovnikov-type products. The process of forming anti-Markovnikov-type products is more favored kinetically with barriers of 21.9 and 23.6 kcal mol−1 for alkyne and olefin versus >27.0 kcal mol−1 for the pathway of forming Markovnikov-type products. The computational results are consistent with the experimental observations...  Read more

Dynamic motion of an Lu pair inside a C76(Td) cage

RSC Advances
Relativistic density functional theory (DFT) computations were performed to investigate the dynamic motion of an encapsulated Lu pair inside a C76(Td) cage. The results revealed that the lowest-energy configuration of Lu2@C76(Td) adopts C2 symmetry; four electrons are transferred to the outer carbon cage and the two encapsulated Lu atoms form a metal–metal single bond (with an electronic structure of Lu24+@C764−), and the good electron delocalization in the C764−(Td) cage partially contributes the thermodynamic preference of...  Read more

High stability and superior catalytic reactivity of nitrogen-doped graphene supporting Pt nanoparticles as a catalyst for the oxygen reduction reaction: a density functional theory study

RSC Advances
We investigated the structural and electronic properties of Pt13 nanoparticles on various nitrogen (N)-doped graphene and their interaction with O by density functional theory (DFT) calculations. The results revealed that the N-doping can greatly enhance the binding strength of Pt13 nanoparticles on the graphene surface, thus ensuring their high stability. For NC doping (N atoms directly substituting for C atoms), the enhanced binding strength of the Pt13 cluster is attributed to the activation of the carbon atoms around the N-dopant, while the strong hybridization of the d states of the Pt13 cluster with the sp2 dangling bonds of the N atoms in defective N-doped graphenes contributes to the strong adsorption. Moreover, a certain amount of electrons are transferred from Pt13 to the substrate accompanied by...  Read more

Insights into the roles of two constituents CL-20 and HMX in the CL-20:HMX cocrystal at high pressure: a DFT-D study

RSC Advances
Density functional theory with dispersion corrections (DFT-D) was used to study pressure-induced effects in a novel energetic CL-20:HMX cocrystal and to understand what role its constituents CL-20 and HMX have. The structural, electronic, absorption, and mechanical properties of the cocrystal and its constituents were compared and analyzed in detail. The results indicate that the two constituents produce different effects on the crystal structure of the cocrystal in different directions. This distinct energy distribution in the cocrystal suggests that electron transitions may take place between the HMX and CL-20 molecules. The CL-20 in the cocrystal plays a leading role in the electronic structure of the cocrystal. The cocrystal has quite similar absorption spectra to ε-CL-20 but very different ones from β-HMX. Compared with the pure crystals, the mechanical properties of the cocrystal present a great anisotropy, which not only greatly strengthens the stiffness but also affects the...  Read more

Synthesis of Ni/Au/Co trimetallic nanoparticles and their catalytic activity for hydrogen generation from alkaline sodium borohydride aqueous solution

RSC Advances
A series of poly (N-vinyl-2-pyrrolidone) stabilized colloidal Ni/Au/Co trimetallic nanoparticles (TNPs) were synthesized by co-reduction of their corresponding metal precursors via dropwise addition of NaBH4. Ultraviolet-visible spectrophotometry (UV-Vis), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), powder X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HR-TEM) combined with energy dispersive spectrometry (EDS) were used to characterize the morphology, crystalline structure and electron distribution of the as-prepared TNPs. The effects of metal composition on the size distribution and hydrogen generation from catalytic hydrolysis of alkaline NaBH4 aqueous solutions were also investigated. The results indicated that the as-prepared alloy-structured Ni45Au45Co10 TNPs showed a...  Read more

Helical inner-wall texture prevents jamming in granular pipe flows

Soft Matter
Granular pipe flows are characterized by intermittent behavior and large, potentially destructive solid fraction variations in the transport direction. By means of particle-based numerical simulations of gravity-driven flows in vertical pipes, we show that it is possible to obtain steady material transport by adding a helical texture to the inner-wall of the pipe. The helical texture leads to a more homogeneous mass flux along the pipe, prevents the emergence of large density waves and substantially reduces the probability of plug formation thus avoiding jamming of the particulate flow. We show that the granular mass flux Q through a pipe of diameter D with a helical texture of wavelength λ follows the equation Q = Q0·{1 − B sin[arctan(2πD/λ)]}, where Q0 is the flow...  Read more

A Ferric–Peroxo Intermediate in the Oxidation of Heme by IsdI

Biochemistry
The canonical heme oxygenases (HOs) catalyze heme oxidation via a heme-bound hydroperoxo intermediate that is stabilized by a water cluster at the active site of the enzyme. In contrast, the hydrophobic active site of IsdI, a heme-degrading enzyme from Staphylococcus aureus, lacks a water cluster and is expected to oxidize heme by an alternative mechanism. Reaction of the IsdI–heme complex with either H2O2 or m-chloroperoxybenzoic acid fails to produce a specific oxidized heme iron intermediate, suggesting that ferric–hydroperoxo or ferryl derivatives of IsdI are not involved in the catalytic mechanism of this enzyme. IsdI lacks a proton-donating group in the distal heme pocket, so the possible involvement of a ferric–peroxo intermediate has been evaluated. Density functional theory (DFT) calculations indicate that heme oxidation involving a ferric–peroxo intermediate is energetically accessible, whereas the energy barrier for a reaction...  Read more