How large does a compound screening collection need to be?

Increasingly, chemical libraries are being produced which are focused on a biological target or group of related targets, rather than simply being constructed in a combinatorial fashion. A screening collection compiled from such libraries will contain multiple analogues of a number of discrete series of compounds. The question arises as to how many analogues are necessary to represent each series in order to ensure that an active series will be identified. Based on a simple probabilistic argument and supported by in-house screening data, guidelines are given for the number of compounds necessary to achieve a "hit", or series of hits, at various levels of certainty. Obtaining more than one hit from the same series is useful since this gives early acquisition of SAR (structure-activity relationship) and confirms a hit is not a singleton. We show that screening collections composed of only small numbers of analogues of each series are sub-optimal for SAR acquisition. Based on these studies, we recommend a minimum series size of about 200 compounds. This gives a high probability of confirmatory SAR (i.e. at least two hits from the same series). More substantial early SAR (at least 5 hits from the same series) can be gained by using series of about 650 compounds each. With this level of information being generated, more accurate assessment of the likely success of the series in hit-to-lead and later stage development becomes possible.     

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 many dimensions are required to approximate the potential energy landscape of a model protein?

A scheme to approximate the multidimensional potential energy landscape in terms of a minimal number of degrees of freedom is proposed using a linear transformation of the original atomic Cartesian coordinates. For one particular off-lattice model protein the inherent frustration can only be reproduced satisfactorily when a relatively large number of coordinates are employed. However, when this frustration is removed in a Go-type model, the number of coordinates required is significantly lower, especially around the global potential energy minimum. To aid our interpretation of the results we consider modified disconnectivity graphs where a measure of the structural diversity and a metric relation between the stationary points are incorporated.     

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 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.     

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   

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 does γ-irradiation affect the properties of a microfiltration membrane constituted of two polymers with different radiolytic behavior?

The objective of this work is to present the behavior of a fluorinated microporous membrane composed of poly(vinylidene fluoride) (PVDF) mechanically reinforced by a polyamide-66 (PA-66) fabric under γ-irradiation with dose ranging between 0 and 100 kGy, in inert atmosphere and at room temperature. Particular attention was paid to the evolution of mechanical properties, the surface morphology and pores size distribution of this membrane, in order to study the filtration capacity and selectivity with increasing radiation dose. Moreover, the repartition of the generated radicals onto the two components of the membrane was achieved by electron spin resonance (ESR) spectroscopy. Two different regimes are observed depending on the dose range, and a correlation between the mechanical behavior of the membrane and the evolution of the concentration of the radicals in the PA fabric is observed. Globally, the porosity of the surface membrane does not vary whatever the dose may be, but the mechanical properties of the membrane as well as the permeability are strongly affected, even for low radiation dose such as 10 kGy. These results are related to chain scissions on the PA fabric, which occurred preferentially, compared to cross-linking, in the investigated dose range.     

Direct dynamics trajectory study of vibrational effects: can polanyi rules be generalized to a polyatomic system?

We present an ab initio direct dynamics trajectory study of the hydrogen abstraction reaction: H2CO+ + CD4 --> H2COD+ + CD3, with methane excited in two different distortion modes (nu4 and nu2). The trajectory simulations were able to reproduce experimental results and for the first time show how vibrational enhancement originates in reaction of small polyatomic species. Roughly equal contributions from two vibrational enhancement mechanisms were found. The "distortion" mechanism correlates the vibrational effects with vibration-induced reactant distortions, and the "velocity" mechanism correlates vibrational effects with vibrational velocities of the constituent atoms. This reaction has a reactant-like transition state and, thus, would correspond to an "early" barrier system in the context of the well-known Polanyi rules for predicting effects of vibration and collision energy. Straightforward application of these rules would predict that vibration should be ineffective in driving reaction, in disagreement with both experiment and trajectory results. Using the trajectories for guidance, we were able to construct a two-dimensional cut through the reaction potential energy surface that does suggest a predictive, Polanyi-type rule.     

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.     

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.     

How does a CC double bond cleave in the gas phase? Fragmentation of protonated ketotifen in mass spectrometry

In the literature, it is reported that the protonated ketotifen mainly undergoes C?C double bond cleavage in electrospray ionization tandem mass spectrometry (ESI‐MS/MS); however, there is no explanation on the mechanism of this fragmentation reaction. Therefore, we carried out a combined experimental and theoretical study on this interesting fragmentation reaction. The fragmentation of protonated ketotifen (m/z 310) always generated a dominant fragment ion at m/z 96 in different electrospray ionization mass spectrometers (ion trap, triple quadrupole and linear trap quadrupole (LTQ)‐orbitrap). The mechanism of the generation of this product ion (m/z 96) through the C?C double bond cleavage was proposed to be a sequential hydrogen migration process (including proton transfer, continuous two‐step 1,2‐hydride transfer and ion‐neutral complex‐mediated hydride transfer). This mechanism was supported by density functional theory (DFT) calculations and a deuterium labeling experiment. DFT calculations also showed that the formation of the product ion m/z 96 was most favorable in terms of energy. This study provides a reasonable explanation for the fragmentation of protonated ketotifen in ESI‐MS/MS, and the fragmentation mechanism is suitable to explain other C?C double bond cleavage reactions in mass spectrometry. Copyright © 2016 John Wiley & Sons, Ltd.     

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.     

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     

How does the nickel pincer complex catalyze the conversion of CO2 to a methanol derivative? A computational mechanistic study

The mechanistic details of nickel-catalyzed reduction of CO(2) with catecholborane (HBcat) have been studied by DFT calculations. The nickel pincer hydride complex ({2,6-C(6)H(3)(OP(t)Bu(2))(2)}NiH = [Ni]H) has been shown to catalyze the sequential reduction from CO(2) to HCOOBcat, then to CH(2)O, and finally to CH(3)OBcat. Each process is accomplished by a two-step sequence at the nickel center: the insertion of a C═O bond into [Ni]H, followed by the reaction of the insertion product with HBcat. Calculations have predicted the difficulties of observing the possible intermediates such as [Ni]OCH(2)OBcat, [Ni]OBcat, and [Ni]OCH(3), based on the low kinetic barriers and favorable thermodynamics for the decomposition of [Ni]OCH(2)OBcat, as well as the reactions of [Ni]OBcat and [Ni]OCH(3) with HBcat. Compared to the uncatalyzed reactions of HBcat with CO(2), HCOOBcat, and CH(2)O, the nickel hydride catalyst accelerates the H(δ-) transfer by lowering the barriers by 30.1, 12.4, and 19.6 kcal/mol, respectively. In general, the catalytic role of the nickel hydride is similar to that of N-heterocyclic carbene (NHC) catalyst in the hydrosilylation of CO(2). However, the H(δ-) transfer mechanisms used by the two catalysts are completely different. The H(δ-) transfer catalyzed by [Ni]H can be described as hydrogen being shuttled from HBcat to nickel center and then to the C═O bond, and the catalyst changes its integrity during catalysis. In contrast, the NHC catalyst simply exerts an electronic influence to activate either the silane or CO(2), and the integrity of the catalyst remains intact throughout the catalytic cycle. The comparison between [Ni]H and Cp(2)Zr(H)Cl in the stoichiometric reduction of CO(2) has suggested that ligand sterics and metal electronic properties play critical roles in controlling the outcome of the reaction. A bridging methylene diolate complex has been previously observed in the zirconium system, whereas the analogous [Ni]OCH(2)O[Ni] is not a viable intermediate, both kinetically and thermodynamically. Replacing HBcat with PhSiH(3) in the nickel-catalyzed reduction of CO(2) results in a high kinetic barrier for the reaction of [Ni]OOCH with PhSiH(3). Switching silanes to HBcat in NHC-catalyzed reduction of CO(2) generates a very stable NHC adduct of HCOOBcat, which makes the release of NHC less favorable.