Lattice density functional theory of molecular diffusion

A density functional theory of diffusion is developed for lattice fluids with molecular flux as a functional of the density distribution. The formalism coincides exactly with the generalized Ono-Kondo density functional theory when there is no gradient of chemical potential, i.e., at equilibrium. Away from equilibrium, it gives Fick's first law in the absence of a potential energy gradient, and it departs from Fickian behavior consistently with the Maxwell-Stefan formulation. The theory is applied to model a nanopore, predicting nonequilibrium phase transitions and the role of surface diffusion in the transport of capillary condensate.     

The size of sums of sets,II

We prove inequalities which give lower bounds for the Lebesgue measures of setsE +K whereK is a certain kind of Cantor set. For example, ifC is the Cantor middle-thirds subset of the circle groupT, then $$m(E)^{1 - log2/log3} \leqq m(E + C)$$ for every BorelE ?T.     

Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations.

NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl (13)C' CSA is computed for 103 conformations of the model peptide group N-methylacetamide (NMA). 2) The variations in computed (13)C' CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated (13)C' CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond-length and bond-angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca(2+)-saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for both R(1) and R(2) relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that (13)C' relaxation is a valid tool for measurement of interesting dynamical events in proteins.     

Phase transfer of metal cations by induced dynamic carrier agents: biphasic extraction based on dynamic covalent chemistry

In contrast to the classical method where a single molecule is designed to extract metal cations under specific conditions, dynamic covalent chemistry provides an approach based on the implementation of an adaptive dynamic covalent library for inducing the generation of the extractant species. This approach has been applied to the liquid–liquid extraction of copper(ii) nitrate based on a dynamic library of acylhydrazones constituents that self-build and distribute through the interface of a biphasic system. The addition of copper(ii) cations to this library triggers a modification of its composition and the up-regulation of the ligand molecules driven by coordination to the metal cations. Among these, one species has proven to be sufficiently lipophilic to play the role of carrier agent and its formation by component exchange enables the partial extraction of the copper(ii). The study of different pathways to generate the dynamic covalent library demonstrates the complete reversibility and the adaptability of the system. The detailed analytical investigation of the system provides a means to assess the mechanism of the dynamic extraction process.

Phase transfer of Cu(ii) cations is achieved by component exchange in a dynamic covalent library of acylhydrazone ligands. B1/B2 component exchange leads to the generation of a lipophilic carrier agent that extracts Cu(ii) into chloroform.     

Monolayers as models for supported catalysts: zirconium phosphonate films containing manganese(III) porphyrins

Organized monolayer films of a manganese tetraphenylporphyrin have been prepared and used as supported oxidation catalysts. Manganese 5,10,15,20-tetrakis(tetrafluorophenyl-4'-octadecyloxyphosphonic acid) porphyrin (1) has been immobilized as a monolayer film by a combination of Langmuir-Blodgett (LB) and self-assembled monolayer techniques that use zirconium phosphonate linkages to bind the molecule to the surface. Analysis by FTIR, XPS, UV-vis and polarized optical spectroscopy show that the films consist of noninteracting molecules effectively anchored and oriented nearly parallel to the surface. The monolayer films are stable to the solvent and temperature conditions needed to explore organic oxidations. The activity of films of 1 toward the epoxidation of cyclooctene using iodosylbenzene as the oxidant was compared to that of Manganese 5,10,15,20-tetrakis(pentafluorophenyl) porphyrin (2) and 1 under equivalent homogeneous conditions. The immobilized porphyrin 1 shows an enhanced activity relative to either homogeneous reaction. The main difference between 1 and 2 is the four alkyl phosphonate arms in 1 designed to incorporate the porphyrin within the films. The increased activity of immobilized 1 is a combination of the porphyrin structure, which prohibits the formation of mu-oxo dimers even in solution, and a change in conformation when anchored to the surface. The study demonstrates that careful monolayer studies can provide useful models for the design and study of supported molecular catalyst systems.     

New synthetic routes to cationic rhenium tricarbonyl bipyridine complexes with labile ligands

Triflate abstraction from the complex [Re(OTf)(CO)(3)(bipy)] (1) using the salt NaBAr'(4) (Ar' = 3,5-bis(trifluoromethyl)phenyl) in dichloromethane solution in the presence of L = PPh(3), NCMe, NCPh, imines, ketones, Et(2)O, THF, MeOH, and MeI affords cationic complexes [Re(L)(CO)(3)(bipy)](+) as their BAr'(4)(-) salts. The new complexes have been characterized spectroscopically and, for [Re(eta(1)-O=C(Me)R)(CO)(3)(bipy)]BAr'(4) (R = CH(3), 6a; R = Ph, 6b), and [Re(THF)(CO)(3)(bipy)]BAr'(4) (9), also by single-crystal X-ray diffraction. Compared with conventional methodologies, the route reported here allows the coordination of a broader range of weakly coordinating ligands and requires considerably milder conditions. On the other hand, the reactions of lithium acetylides with [Re(THF)(CO)(3)(bipy)]BAr'(4) (9) can be used for the high-yield syntheses of rhenium alkynyls [Re(Ctbd1;CR)(CO)(3)(bipy)] (R = Ph, 12; R = SiMe(3), 13). Complex 9 was found to catalyze the aziridination of benzylideneaniline with ethyl diazoacetate.     

Rational incorporation of defects within metal–organic frameworks generates highly active electrocatalytic sites

The allure of metal–organic frameworks (MOFs) in heterogeneous electrocatalysis is that catalytically active sites may be designed a priori with an unparalleled degree of control. An emerging strategy to generate coordinatively-unsaturated active sites is through the use of organic linkers that lack a functional group that would usually bind with the metal nodes. To execute this strategy, we synthesize a model MOF, Ni-MOF-74 and incorporate a fraction of 2-hydroxyterephthalic acid in place of 2,5-dihydroxyterephthalic acid. The defective MOF, Ni-MOF-74D, is evaluated vs. the nominally defect-free Ni-MOF-74 with a host of ex situ and in situ spectroscopic and electroanalytical techniques, using the oxidation of hydroxymethylfurtural (HMF) as a model reaction. The data indicates that Ni-MOF-74D features a set of 4-coordinate Ni–O₄ sites that exhibit unique vibrational signatures, redox potentials, binding motifs to HMF, and consequently superior electrocatalytic activity relative to the original Ni-MOF-74 MOF, being able to convert HMF to the desired 2,5-furandicarboxylic acid at 95% yield and 80% faradaic efficiency. Furthermore, having such rationally well-defined catalytic sites coupled with in situ Raman and infrared spectroelectrochemical measurements enabled the deduction of the reaction mechanism in which co-adsorbed *OH functions as a proton acceptor in the alcohol oxidation step and carries implications for catalyst design for heterogeneous electrosynthetic reactions en route to the electrification of the chemical industry.

The allure of metal–organic frameworks (MOFs) in heterogeneous electrocatalysis is that catalytically active sites may be designed a priori with an unparalleled degree of control.     

Site-to-site peptide transport on a molecular platform using a small-molecule robotic arm

Peptides attached to a cysteine hydrazide ‘transporter module’ are transported selectively in either direction between two chemically similar sites on a molecular platform, enabled by the discovery of new operating methods for a molecular transporter that functions through ratcheting. Substrate repositioning is achieved using a small-molecule robotic arm controlled by a protonation-mediated rotary switch and attachment/release dynamic covalent chemistry. A polar solvent mixtures were found to favour Z to E isomerization of the doubly-protonated switch, transporting cargo in one direction (arbitrarily defined as ‘forward’) in up to 85% yield, while polar solvent mixtures were unexpectedly found to favour E to Z isomerization enabling transport in the reverse (‘backward’) direction in >98% yield. Transport of the substrates proceeded in a matter of hours (compared to 6 days even for simple cargoes with the original system) without the peptides at any time dissociating from the machine nor exchanging with others in the bulk. Under the new operating conditions, key intermediates of the switch are sufficiently stabilized within the macrocycle formed between switch, arm, substrate and platform that they can be identified and structurally characterized by ¹H NMR. The size of the peptide cargo has no significant effect on the rate or efficiency of transport in either direction. The new operating conditions allow detailed physical organic chemistry of the ratcheted transport mechanism to be uncovered, improve efficiency, and enable the transport of more complex cargoes than was previously possible.

Peptides are transported in either direction between chemically similar sites on a molecular platform, substrate repositioning is achieved using a cysteine hydrazide transporter module and a small-molecule robotic arm controlled by a rotary switch.     

A supramolecular microfluidic optical chemosensor

A supramolecular microfluidic optical chemosensor (muFOC) has been fabricated. A serpentine channel has been patterned with a sol-gel film that incorporates a cyclodextrin supramolecule modified with a Tb(3+) macrocycle. Bright emission from the Tb(3+) ion is observed upon exposure of the (mu)FOC to biphenyl in aqueous solution. The signal transduction mechanism was elucidated by undertaking steady-state and time-resolved spectroscopic measurements directly on the optical chemosensor patterned within the microfluidic network. The presence of biphenyl in the cyclodextrin receptor site triggers Tb(3+) emission by an absorption-energy transfer-emission process. These results demonstrate that the intricate signal transduction mechanisms of supramolecular optical chemosensors are successfully preserved in microfluidic environments.     

Ab Initio High Pressure Investigations of InI

The high pressure behaviour of InI is studied by DFT‐calculations and compared with experimental data. The existence of a 5s² electron pair in In⁺ represents an unfavourable bonding situation for high symmetry structures because of effective closed shell repulsion. Since cations with a ns² electron pair are highly polarizable and the electronic situation is more favourable in the low symmetry structure InI prefers a TlI‐type structure at ambient pressure. A pressure induced transition to the more densely packed high symmetry CsCl‐type structure takes place at about 19 GPa according to our calculations. At ambient pressure the interactions are predominantly ionic. However with increasing pressure the distances between In⁺ cations in the TlI‐type structure diminish drastically, mainly due to the changing space requirement of the lone electron pair. Apart from ionic interactions further bonding interactions between the In⁺ cations occur. At elevated pressure the electron localization function (ELF) as well as the band structure diagrams suggest metallic bonding between the In⁺ within the zigzag chain, i. e. increasing bonding interactions between the In⁺ cations due to the electron pair and its s‐p‐mixing. At ambient pressure In‐In interactions are rather weak and the space requirement of the lone electron pair mainly determines the characteristic arrangement of the ions. At elevated pressure the In‐In interactions become stronger and stabilise themselves additionally the specific structural arrangement.