How Can Proteins Enter the Interior of a MOF? Investigation of Cytochrome c Translocation into a MOF Consisting of Mesoporous Cages with Microporous Windows

It has been demonstrated for the first time that the heme protein cytochrome c (Cyt c) can enter the interior of a MOF despite the larger molecular dimension of the protein relative to the access pore sizes. Mechanistic studies suggest that the Cyt c molecules must undergo a significant conformational change during translocation into the MOF interior through the relatively small nanopores.     

Partial Molar Volumes of Hydrophobic Compounds—Insight into the Solvation Shell? Part I

A simple model for the interaction of the solute with the solvent is presented. The relation between the molecular volume, partial molar volume, and the volume of the solvation shell of the compound studied is expressed by the parameter, defined as the relative density of the solvation shell. The values of are calculated for many organic compounds in aqueous solutions. It is stated that in a given series of compounds, depends strongly on the number of CH₂ groups in the compound studied. The correlation of and the polarity (defined as the ratio of the surface area of polar groups and atoms exposed to the total molecular surface area of the molecule studied) was found.     

Mechanism of GTP: Can all of the available data be accommodated?

Group transfer polymerization (GTP)^a of acrylic monomers is a living system mediated by a trialkylsilyl capped growing chain end. The fact that it operates at temperatures as high as 100° C differentiates GTP from living anionic polymerization, which at best operates at 25° C for hindered methacrylates. To accommodate all of the mechanistic data available it appears that at least two mechanistic pathways are required: an associative process for mild nucleophilic catalysts and a dissociative process for strong nucleophilic catalysts.     

How Can Theory Predict the Selectivity of Palladium‐Catalyzed Cross‐Coupling of Pristine Aromatic Molecules?

The new approach for palladium‐catalyzed cross‐coupling of two non‐activated aromatic compounds (D. R. Stuart, K. Fagnou, Science 2007 , 316, 1172) was studied theoretically. The energetic span model (S. Kozuch, S. Shaik, Acc. Chem. Res. 2011 , 44, 101, and references therein) was employed to analyze the kinetic behavior of the catalytic cycle. The computed energy profile, combined with the energetic span model, accounts for the experimental selectivity, which favors the hetero‐coupling of benzene with indole. This selectivity is driven by a fine balance of the entropic contributions and the high ratio of concentrations used for benzene over indole. This analysis may allow future theoretical predictions of how different aromatic compounds can be effectively coupled.     

Can Low‐Valent Germanium Chemistry Be Practiced Under Ambient Conditions? A Tale of a Water‐Stable Yet Reactive Germylene Monochloride Complex

A germylene monochloride complex ((DPM)GeCl, 1 ) that is water stable was isolated for the first time. Interestingly, it reacts with cesium fluoride under ambient conditions (non‐inert atmosphere and water‐containing solvent) to afford water stable germylene monofluoride complex ((DPM)GeF, 2 ). Due to the usage of DPM (dipyrrinate) ligand, germylene monohalides 1 and 2 show fluorescence in the visible region at 555 and 538 nm, respectively. Compounds 1 and 2 are the first fluorescent germylene complexes and were characterized by multinuclear NMR spectroscopy. The structure of compound 1 was also proved by single crystal X‐ray diffraction studies.     

How Can a Carbene be Active in an Ionic Liquid?

The solvation of the carbene 1‐ethyl‐3‐methylimidazole‐2‐ylidene in the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate was investigated by ab initio molecular dynamics simulations in order to reveal the interaction between these two highly important classes of materials: N‐heterocyclic carbenes with superb catalytic activity and ionic liquids with advantageous properties as solvents and reaction media. In contrast to previously published data on analogous systems, no hydrogen bond is observed between the hypovalent carbon atom and the most acidic ring hydrogen atoms, as these interaction sites of the imidazolium ring are predominantly occupied by the acetate ions. Keeping the carbene away from the ring hydrogen atoms prevents stabilization of this reactive species, and hence any retarding effect on subsequent reactions, which explains the observed high reactivity of the carbene in acetate‐based ionic liquids. Instead, the carbene exhibits a weaker interaction with the methyl group of the imidazolium cation by forming a hitherto unprecedented kind of C???H?C hydrogen bond. This unexpected finding not only indicates a novel kind of hydrogen bond for carbenes, but also shows that such interaction sites of the imidazolium cation are not limited to the ring hydrogen atoms. Thus, the results give the solute–solvent interactions within ionic liquids a new perspective, and provide a further, albeit weak, site of interaction to tune in order to achieve the desired environment for any dissolved active ingredient.     

Can the nonadiabatic photodynamics of aminopyrimidine be a model for the ultrafast deactivation of adenine?

The reaction path for the ultrafast deactivation of 6-aminopyrimidine (6AP) has been investigated by means of ab initio surface-hopping dynamics. The electronic vertical excitation spectrum, excited-state S1 minima, and minima on the crossing seam of 6AP resemble well those found for adenine. The deactivation from the S1 to the S0 state takes place at the ultrafast time scale of 400 fs and involves the out-of-plane ring deformation of the C4 atom, a position that is sterically restricted in adenine by the imidazole ring. Mechanical restrictions have been used to simulate in a simple way the role of the imidazole group in adenine. As a result, deactivation via out-of-plane ring deformation of the C2 and N3 atoms are observed in good agreement with predictions for adenine. These dynamics results show that the previously suggested ring puckering deactivation paths really exist at a time scale, which is compatible with experimentally observed life times. The electronic structure of the crossing seam has been shown to have the same nature as those of simple biradicaloid systems, a feature which seems to be valid for any cyclic system.     

How could the program of aging be arranged?

Aging could be a consequence of the programmed partial dedifferentiation of brain neurons that is performed through nonrandom losses of chronomeres-short perichromosomal DNA molecules that also participate in maintenance of cellular differentiation state. Process of their sequential losses, implementing as the “relay-race partial dedifferentiations,” serves as a basis for the activity of the lifelong brain clock that regulates a physiological age of multicellular animals. These relay-race dedifferentiations are performed in a consecutive mode by different groups of neurons during the peaks of a so called T-rhythm, whose length of period is different in various animal species.     

DFT Methods to Study the Reaction Mechanism of Iridium‐Catalyzed Hydrogenation of Olefins: Which Functional Should be Chosen?

To enable the selection of more accurate computational methods for the future theoretical exploration of the reaction mechanism of Ir‐catalyzed olefin hydrogenation, we compared high‐level ab initio coupled cluster and DFT calculations with a simplified model of Pfaltz's Ir/P,N‐type catalyst for all four previously proposed Ir^I/Ir^III and Ir^III/Ir^V mechanisms. Through the systematic assessment of the DFT performances, the DFT empirical dispersion correction (DFT‐D3) is found to be indispensable for improving the accuracy of relative energies between the Ir^I/Ir^III and Ir^III/Ir^V mechanisms. After including the DFT‐D3 correction, the three best performing density functionals (DFs) are B2‐PLYP, BP86, and TPSSh. In these recommended DFs, the computationally more expensive double‐hybrid functional B2‐PLYP‐D3 has a balanced and outstanding performance for calculations of the reaction barriers, reaction energies, and energy gaps between different mechanisms, whereas the less costly BP86‐D3 and TPSSh‐D3 methods have outstanding, but relatively less uniform performances.     

Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C60 Cage? A Quantum Chemical Prospective

Based on an experimental observation, it has been controversially suggested in a study (Kurotobi et al., Science 2011 , 33, 613) that a single molecule of water can completely be localized within the subnano‐space inside the fullerene C₆₀ cage and, that neither the H atoms nor the O lone‐pairs are linked, either via hydrogen bonding or through dative bonding, with the interior C‐framework of the C₆₀ cage. To resolve the controversy, electronic structure calculations were performed by using the density functional theory, together with the quantum theory of atoms in molecules, the natural population and bond orbital analyses, and the results were analyzed by using varieties of recommended diagnostics often used to interpret noncovalent interactions. The present results reveal that the mechanically entrapped H₂O molecule is not electronically innocent of the presence of the cage; each H atom of H₂O is weakly O? H???C₆₀ bonded, whereas the O lone‐pairs are O???C₆₀ bonded regardless of the conformations investigated. Exploration of various featured properties suggests that H₂O@C₆₀ may be regarded as a unique system composed of both inter‐ and intramolecular interactions.     

Can mass dissociation patterns of transition‐metal complexes be predicted from electrochemical data?

The Cooks kinetic method has been very convenient to correlate the relative dissociation rates obtained by collision-induced fragmentation experiments with the energies of two related bonds in molecules and complexes in the gas phase. Reliable bond energy data are, however, not always available, particularly for polynuclear transition-metal complexes, such as the triruthenium acetate clusters of the general formula [Ru(3) (micro(3)-O)(micro-CH(3)COO)(6)(py)(2)(L)](+), where L = ring substituted N-heterocyclic ligands. Accordingly, their gas-phase collision-induced tandem mass spectrometry (CID MS/MS) dissociation patterns have been analyzed pursuing a relationship with the more easily accessible redox potentials (E(1/2)) and Lever's E(L) parameters. In fact, excellent linear correlations of ln(1/2A(L)/A(py)), where A(py) and A(L) are the abundance of the fragments retaining the pyridine (py) and L ligand, respectively, with E(1/2) and E(L) were found. This result shows that those electrochemical parameters are correlated with bond energies and can be used in the analysis of the dissociation data. Such modified Cooks method can be used, for example, to determine the electronic effects of substituents on the metal-ligand bonds for a series of transition-metal complexes.     

Can MM‐PBSA calculations predict the specificities of protein kinase inhibitors?

An application of the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction.     

How Does CuII Convert into CuI? An Unexpected Ring‐Mediated Single‐Electron Reduction

Cu(x)O (x=1,2) nanomaterials with tailored composition and properties-a hot topic in sustainable technologies-may be fabricated from molecular sources through bottom-up processes that involve unexpected changes in the metal oxidation state and open intriguing challenges on the copper redox chemistry. How copper(II) sources may lead to copper(I) species in spite of the absence of any explicit reducing agent, and even in the presence of oxygen, is one such question-to date unanswered. Herein, we study copper "reduction without reductants" within one molecule and reveal that the actual reducing agent is abstracted atomic hydrogen. By investigating the fragmentation of a copper(II) precursor for copper oxide nanostructures by combined ESI-MS with multiple collisional experiments (ESI/MS(n)) and theoretical calculations, we highlight a copper-promoted C-H bond activation, leading to reduction of the metal center and formation of a Cu(I)-C-NCCN six-membered ring. Such a novel ring system is the structural motif for a new family of cyclic copper(I) adducts, which show a bonding scheme, herein reported for the first time, that may shed unprecedented light on copper chemistry. Beyond the relevance for the preparation of copper oxide nanostructures, the hydrogen-abstraction/proton-delivery/electron-gain mechanism of copper(II) reduction disclosed herein appears to be a general property of copper and might help to understand its redox reactivity.     

Electrochemical Nanoparticle Sizing Via Nano-Impacts: How Large a Nanoparticle Can be Measured?

The field of nanoparticle (NP) sizing encompasses a wide array of techniques, with electron microscopy and dynamic light scattering (DLS) having become the established methods for NP quantification; however, these techniques are not always applicable. A new and rapidly developing method that addresses the limitations of these techniques is the electrochemical detection of NPs in solution. The ‘nano-impacts’ technique is an excellent and qualitative in situ method for nanoparticle characterization. Two complementary studies on silver and silver bromide nanoparticles (NPs) were used to assess the large radius limit of the nano-impact method for NP sizing. Noting that by definition a NP cannot be larger than 100 nm in diameter, we have shown that the method quantitatively sizes at the largest limit, the lower limit having been previously reported as ∼6 nm.¹     

On the mechanism of conversion of N-acyl-4-acyloxy-beta-lactams into 2-substituted 1,3-oxazin-6-ones. Can a low-barrier transition state be antiaromatic?

The mechanism of the conversion of N-acyl-4-acyloxy-beta-lactams into 1,3-oxazin-6-ones has been investigated using ab initio and density functional theories. It has been found that two pseudopericyclic reactions are involved in the whole process. The first key reaction is a retro-[4-exo-dig] cyclization instead of a thermal conrotatory electrocyclic ring opening. Magnetic characterization of the corresponding transition structure shows antiaromatic character, despite the low activation energy associated with this process. The second step is very exothermic and has no activation barrier. It corresponds to another pseudopericyclic reaction instead of a six-electron disrotatory electrocyclization. These results confirm that there is no correlation between aromaticity and pseudopericyclic reactions. In contrast, thermal-symmetry-allowed pericyclic reactions are always aromatic. Therefore, magnetic analysis of the corresponding transition structures constitutes a useful tool to distinguish between both kinds of processes.     

New Insight into the Source of Biomolecular Homochirality: An Extraterrestrial Origin for Molecules of Life?

Circular polarized light in space might be responsible for the fact that amino acids isolated from meteorites are not racemic. For example, 1 has been found with an enantiomeric excess of up to 10.4%. Such radiation has now been observed for the first time.     

Can a C-H···O interaction be a determinant of conformation?

Whether nonconventional hydrogen bonds, such as the C-H···O interaction, are a consequence or a determinant of conformation is a long-running and unresolved issue. Here we outline a solid-state and quantum mechanical study designed to investigate whether a C-H···O interaction can override the significant trans-planar conformational preferences of α-fluoroamide substituents. A profound change in dihedral angle from trans-planar((OCCF)) to cis-planar((OCCF)) observed on introducing an acceptor group for a C-H···O hydrogen bond is consistent with this interaction functioning as a determinant of conformation in certain systems. This testifies to the potential influence of the C-H···O hydrogen bond and is consistent with the assignment of this interaction as a contributor to overall conformation in both model and natural systems.     

Can coil-to-globule transition of a single chain be treated as a phase transition?

The effects of the concentration (C) and heating rate on the collapse and association of poly(N-isopropylacrylamide) chains in water have been investigated by use of ultrasensitive differential scanning calorimetry. In the dilute solutions, both the phase transition temperature (Tp) and enthalpy change (DeltaH) increase with the heating rate but decrease with concentration. By extrapolation to zero heating rate and zero concentration, Tp and DeltaH for coil-to-globule transition of a single chain in thermodynamic equilibrium can be obtained. In semidilute solutions, both Tp and DeltaH increase with the heating rate but slightly vary with the concentration. Tp and DeltaH for pure interchain association in equilibrium are obtained by extrapolation to zero heating rate. Our experiments reveal that only intrachain contraction occurs when the concentration is infinitely close to zero. When the concentration is above the overlap concentration (C*), only interchain association exists. In the range 0相似文献