How close to two dimensions does a Lennard-Jones system need to be to produce a hexatic phase?

We report on a computer simulation study of a Lennard-Jones liquid confined in a narrow slit pore with tunable attractive walls. In order to investigate how freezing in this system occurs, we perform an analysis using different order parameters. Although some of the parameters indicate that the system goes through a hexatic phase, other parameters do not. This shows that to be certain whether a system of a finite particle number has a hexatic phase, one needs to study not only a large system, but also several order parameters to check all necessary properties. We find that the Binder cumulant is the most reliable one to prove the existence of a hexatic phase. We observe an intermediate hexatic phase only in a monolayer of particles confined such that the fluctuations in the positions perpendicular to the walls are less than 0.15 particle diameters, i.e., if the system is practically perfectly 2D.     

How does a thin volatile film move?

When a water film evaporates from a mica substrate, an interface similar to a solidification front develops, separating two films of different thicknesses. We show experimentally that the evolution dynamics is controlled mainly by material diffusion through the vapor phase rather than by hydrodynamic flow through the film. Our results illustrate the role of different contributions to pattern formation of volatile liquid films.     

How does vanadium nitrogenase reduce CO to hydrocarbons?

Nitrogenase enzymes containing molybdenum normally reduce N(2) to NH(3), and are severely inhibited by CO, but vanadium-nitrogenase reduces CO to hydrocarbons C(2)H(4), C(2)H(6) and C(3)H(8). Aspects of the mechanism of this unexpected and unprecedented reaction have been investigated by density functional simulations of the iron-vanadium cofactor FeV-co [NFe(7)VS(9)(homocitrate)] protein-bound by cysteine and histidine. It is found that the intramolecular hydrogenating machinery previously proposed for N(2) reduction (including H-atom tunneling) can also effect reduction of CO. There are feasible steps for all of the requisite components of the overall reaction, namely (i) the binding of CO, (ii) the initial hydrogenation of CO to HCO, (iii) continued hydrogenations of CO at both C and O to HCOH and H(2)COH, (iv) eliminations of O as H(2)O, and (v) the C-C bond formation steps. Intermediate organic fragments can migrate around the active face of FeV-co, and hydrogen bonding between COH functions and S or SH components of FeV-co can occur and contribute to the stabilisation and orientation of intermediates. It is suggested that the difference between Mo-nitrogenase and V-nitrogenase occurs in the immediately surrounding protein, which facilitates (possibly via water associated with homocitrate bound to V) the exogenous protonation and dehydration of -COH intermediates.     

How large a 3JHCCH coupling can be? Prediction of giant vicinal couplings in quinonoid systems

Second-order polarization propagator approximation (SOPPA) and density functional theory (DFT) B3LYP computations revealed the presence of giant ³J_HCCH couplings, up to more than 60 Hz, in conjugated quinonoid systems, very far above the typical limit of ~15 Hz. Strong hyperconjugative interactions of the C–H σ orbitals with the quinonoid 8-e⁻ π system, which allows effective propagation of the spin polarization, seem to be responsible for those extraordinarily large couplings. Computation on several model systems showed the additive nature of the contributions from the available coupling paths to the total coupling.     

How does a hydrocarbon staple affect peptide hydrophobicity?

Water is essential for the proper folding of proteins and the assembly of protein–protein/ligand complexes. How water regulates complex formation depends on the chemical and topological details of the interface. The dynamics of water in the interdomain region between an E3 ubiquitin ligase (MDM2) and three different peptides derived from the tumor suppressor protein p53 are studied using molecular dynamics. The peptides show bimodal distributions of interdomain water densities across a range of distances. The addition of a hydrocarbon chain to rigidify the peptides (in a process known as stapling) results in an increase in average hydrophobicity of the peptide–protein interface. Additionally, the hydrophobic staple shields a network of water molecules, kinetically stabilizing a water chain hydrogen‐bonded between the peptide and MDM2. These properties could result in a decrease in the energy barrier associated with dehydrating the peptide–protein interface, thereby regulating the kinetics of peptide binding. © 2015 Wiley Periodicals, Inc.     

How many hydrogen atoms can be bound to a metal? Predicted MH12 species

Quantum chemical calculations predict the existence of new molecular species with general formula MH12, where M is a group 6 atom. The previous MHn species had n values up to 9. The new systems with n = 12 would be a new record for metal hydrides.     

How does consensus scoring work for virtual library screening? An idealized computer experiment

It has been reported recently that consensus scoring, which combines multiple scoring functions in binding affinity estimation, leads to higher hit-rates in virtual library screening studies. This method seems quite independent to the target receptor, the docking program, or even the scoring functions under investigation. Here we present an idealized computer experiment to explore how consensus scoring works. A hypothetical set of 5000 compounds is used to represent a chemical library under screening. The binding affinities of all its member compounds are assigned by mimicking a real situation. Based on the assumption that the error of a scoring function is a random number in a normal distribution, the predicted binding affinities were generated by adding such a random number to the "observed" binding affinities. The relationship between the hit-rates and the number of scoring functions employed in scoring was then investigated. The performance of several typical ranking strategies for a consensus scoring procedure was also explored. Our results demonstrate that consensus scoring outperforms any single scoring for a simple statistical reason: the mean value of repeated samplings tends to be closer to the true value. Our results also suggest that a moderate number of scoring functions, three or four, are sufficient for the purpose of consensus scoring. As for the ranking strategy, both the rank-by-number and the rank-by-rank strategy work more effectively than the rank-by-vote strategy.     

How does a drug molecule find its target binding site?

Although the thermodynamic principles that control the binding of drug molecules to their protein targets are well understood, detailed experimental characterization of the process by which such binding occurs has proven challenging. We conducted relatively long, unguided molecular dynamics simulations in which a ligand (the cancer drug dasatinib or the kinase inhibitor PP1) was initially placed at a random location within a box that also contained a protein (Src kinase) to which that ligand was known to bind. In several of these simulations, the ligand correctly identified its target binding site, forming a complex virtually identical to the crystallographically determined bound structure. The simulated trajectories provide a continuous, atomic-level view of the entire binding process, revealing persistent and noteworthy intermediate conformations and shedding light on the role of water molecules. The technique we employed, which does not assume any prior knowledge of the binding site's location, may prove particularly useful in the development of allosteric inhibitors that target previously undiscovered binding sites.     

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.     

How do aryl groups attach to a graphene sheet?

How aryl groups attach to a graphene sheet is an experimentally unanswered question. Using first principles density functional theory methods, we shed light on this problem. For the basal plane, isolated phenyl groups are predicted to be weakly bonded to the graphene sheet, even though a new single C-C bond is formed between the phenyl group and the basal plane by converting a sp2-carbon in the graphene sheet to sp3. However, the interaction can be strengthened significantly with two phenyl groups attached to the para positions of the same six-membered ring to form a pair on the basal plane. The strongest bonding is found at the graphene edges. A 1,2-addition pair is predicted to be most stable for the armchair edge, whereas the zigzag edge possesses a unique localized state near the Fermi level that shows a high affinity for the phenyl group.     

How to Polymerize Ethylene in a Highly Controlled Fashion?

Very fast, reversible, polyethylene (PE) chain transfer or complex-catalysed "Aufbaureaktion" describes a "living" chain-growing process on a main-group metal or zinc atom; this process is catalysed by an organo-transition-metal or lanthanide complex. PE chains are transferred very fast between the two metal sites and chain growth takes place through ethylene insertion into the transition-metal- or lanthanide-carbon bond-coordinative chain-transfer polymerisation (CCTP). The transferred chains "rest" at the main-group or zinc centre, at which chain-termination processes like beta-H transfer/elimination are of low significance. Such protocols can be used to synthesise very narrowly distributed PE materials (M(w)/M(n)<1.1 up to a molecular weight of about 4000 g mol(-1)) with differently functionalised end groups. Higher molecular-weight polymers can be obtained with a slightly increased M(w)/M(n), since diffusion control and precipitation of the polymers influences the chain-transfer process. Recently, a few transition-metal- or lanthanide-based catalyst systems that catalyse such a highly reversible chain-growing process have been described. They are summarised and compared within this contribution.     

Can gas chromatography combustion isotope ratio mass spectrometry be used to quantify organic compound abundance?

Quantifying the concentrations of organics such as phospholipid fatty acids (PLFAs) and n‐alkanes and measuring their corresponding ¹³ C/¹² C isotope ratios often involves two separate analyses; (1) quantification by gas chromatography flame ionisation detection (GC‐FID) or gas chromatography/mass spectrometry (GC/MS), and (2) ¹³ C‐isotope abundance analysis by gas chromatography/combustion/isotope ratio mass spectrometry (GC‐C‐IRMS). This requirement for two separate analyses has obvious disadvantages in terms of cost and time. However, there is a history of using the data output of isotope ratio mass spectrometers to quantify various components; including the N and C concentrations of solid materials and CO₂ concentrations in gaseous samples. Here we explore the possibility of quantifying n‐alkanes extracted from sheeps' faeces and fatty acid methyl esters (FAMEs) derivatised from PLFAs extracted from grassland soil, using GC‐C‐IRMS. The results were compared with those from GC‐FID analysis of the same extracts. For GC‐C‐IRMS the combined area of the masses for all the ions (m/z 44, 45 and 46) was collected, referred to as 'area all', while for the GC‐FID analysis the peak area data were collected. Following normalisation to a common value for added internal standards, the GC‐C‐IRMS 'area all' values and the GC‐FID peak area data were directly compared. Strong linear relationships were found for both n‐alkanes and FAMEs. For the n‐alkanes the relationships were 1:1 while, for the FAMEs, GC‐C‐IRMS overestimated the areas relative to the GC‐FID results. However, with suitable reference material 1:1 relationships were established. The output of a GC‐C‐IRMS system can form the basis for the quantification of certain organics including FAMEs and n‐alkanes. Copyright © 2011 John Wiley & Sons, Ltd.     

How can enzymes be so efficient?

Dudley Williams and his colleagues discuss how ligands can gain binding energy to their receptors, and substrate transition states to their enzymes, by tightening the protein structures, with a decrease in their dynamic behaviour.     

How large is the conjugative stabilization of diynes?

The conjugation stabilization energies of dienes and diynes are considerably larger than estimates based on heat of hydrogenation differences between 1,3-butadiyne and 1-butyne as well as between 1,3-butadiene and 1-butene. Such comparisons do not take into account the counterbalancing hyperconjugative stabilization of the partially hydrogenated products by their ethyl groups. When alkyl hyperconjugation is considered, the conjugation stabilization of diynes ( approximately 9.3 kcal/mol) is found by two methods (involving isomerization of nonconjugated into conjugated isomers and heats of hydrogenation) to be larger than that of dienes ( approximately 8.2 kcal/mol).     

How does a non-ionic hydrophobically modified telechelic polymer interact with a non-ionic vesicle? Rheological aspects

The association between hydrophobically modified polyethylene glycol, HM-PEG, and non-ionic vesicles of tetraethylene glycol monododecyl ether, C₁₂E₄, was investigated. HM-PEG is in a triblock form, with an alkyl chain attached to each hydrophilic polymer-end. Such polymer structure is denoted as telechelic. The vesicle average radius was measured by self-diffusion measurements. The system exhibits both a monophasic gel and biphasic regions. The monophasic region was characterized from a rheological point of view. We argue that the gel formation is due to the presence of polymer crosslinks between different surfactant aggregates, once the polymer's hydrophobic moieties may adsorb into the vesicle bilayer. This association is strongly concentration dependent which is reflected in the monotonic increase of the storage modulus, relaxation time and shear viscosity with the addition of surfactant and/or polymer.     

Is fullerene C60 large enough to host a multiply bonded dimetal?

Some dimetal fullerenes M 2@C 60 (M = Cr, Mo, W) have been studied with computational quantum chemistry methods. The transition metal diatomic molecules Cr 2, Mo 2, W 2 form exohedral complexes with C 60, while U 2 forms a highly symmetric endohedral compound and it is placed in the center of the C 60 cavity. This highly symmetric structure is an artifact due to the small size of the C 60 cavity, which constrains U 2 at the center. If a larger cavity is used, like C 70 or C 84, U 2 preferentially binds the internal walls of the cavity and the U-U bond no longer exists.     

How long does it take to melt a gold nanorod?: A femtosecond pump–probe absorption spectroscopic study

Using pump–probe femtosecond transient absorption spectroscopy, we determined the rate of the bleach of absorption around 700–800 nm due to the longitudinal surface plasmon band of gold nanorods. Using TEM of the spotted, completely irradiated solutions suggest that the dominant products of the photothermal conformation of the rods are spheres of comparable volume. This lead to the conclusion that the melting of the rods is at least 30–35 ps, independent of the power used (5–20 μJ) or the nanorod aspect ratio (1.9–3.7).     

Why does cyanide pretend to be a weak field ligand in [Cr(CN)5]3-?

Chemical reasoning based on ligand-field theory suggests that homoleptic cyano complexes should exhibit low-spin configurations, particularly when the coordination sphere is nearly saturated. Recently, the well-known chromium hexacyano complex anion [Cr(CN)6](4-) was shown to lose cyanide to afford [Cr(CN)5](3-) in the absence of coordinating cations. Furthermore, (NEt 4)3[Cr(CN)5] was found to be in a high-spin (S=2) ground state, which challenges the common notion that cyanide is a strong field ligand and should always enforce low-spin configurations. Using density functional theory coupled to a continuum solvation model, we examined both the instability of the hexacyanochromate(II) anion and the relative energies of the different spin states of the pentacyanochromate(II) anion. By making direct comparisons to the analogous Fe (II) complex, we found that cyanide electronically behaves as a strong-field ligand for both metals because the orbital interaction is energetically more favorable in the low-spin configuration than in the corresponding high-spin configuration. The Coulombic repulsion between the anionic cyanide ligands, however, dominates the overall energetics and ultimately gives preference to the high-spin complex, where the ligand-ligand separation is larger. Our calculations highlight that for a quantitative understanding of spin-state energetic ordering in a transition metal complex, ligand-ligand electrostatic interactions must be taken into account in addition to classical ligand-field arguments based on M-L orbital interaction energies.