Can super-excited molecules survive fragmentation?

An Auger event triggered by electron-capture (EC) decay of ⁵⁷ Co incorporated in a chelate molecule results in the loss of an average of 5 electrons. During subsequent charge neutralization, the molecule acquires >50 eV of excitation energy. Only molecules having a large -electron system were found to escape fragmentation. The fate of the molecule was followed by the 14.4 keV Mössbauer emission which occurs 10^-7 second after the EC event. For a conjugated molecule to survive fragmentation, it should be able to disperse its energy in a time interval shorter than the period of atomic vibrations. We had proposed earlier that p-electrons undergo collective excitation and that the plasmon decays in <10^-14 second accompanied by ejection of an electron leaving the molecule unscathed. Intermolecular energy transfer is not important and even an isolated molecule of ⁵⁷ Co(II) phthalocyanine encapsulated in a zeolite supercage escapes fragmentation following an Auger event. Our model for rapid disposal of large excitation energy receives additional support from recent reports of single or mulitphoton plasmon excitation (20 eV) in an isolated C₆₀ and C₇₀ fullerene molecule followed by ejection of a single energetic electron leaving the molecule intact.     

Can a synthetic thread act as an electrochemically switchable molecular device?

Here we report that at room temperature in acetonitrile after the reduction of the naphthalimide-site, a synthetic molecular thread undergoes a complete conformational change which makes possible an efficient conversion of chemical energy into mechanical work; such results point out the ability of the thread to act as a molecular device under electrochemical control.     

Should dithiophosphinate esters function as RAFT agents?

[graph: see text] High-level ab initio calculations indicate that *CH3 addition to the sulfur center of S=P(Z)(Z')SCH3 (Z,Z' = CH3, CN, OCH3, Ph) is considerably less exothermic than addition to the corresponding RAFT agents, S=C(Z)SCH3. This suggests that dithiophosphinate esters may have only limited use in controlling free-radical polymerization, but should make excellent radical chain carriers in organic synthesis. The results cast doubt on the notion that phosphoranyl radicals are more "intrinsically" stabilized than carbon-centered radicals.     

Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron-containing proteins to be accurately modeled, focussing on iron-sulfur, iron-heme, and iron-only hydrogenases. Data computed at the B3LYP/6-31G* level for a training set of 60 representative complexes have been employed. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure and energetics of molecules both within and outside the training set, and overcome the extensive deficiencies of a B3LYP/STO-3G model. Particularly encouraging is the success of the parameters in describing [4Fe-4S] cubanes. The derived parameter set provides a starting point should greater accuracy for a more restricted range of compounds be required.     

Can octupolar molecules be poled by an external electric field?

Octupolar molecules are generally believed to be of potential use in developing nonlinear optical materials owing to the fact that they do not easily form molecular aggregates. This is often put against the conjectured drawback that electric fields have no poling, or ordering, effect for this class of molecules because of the lack of a permanent ground state dipole moment. In this paper, we analyze this notion in some detail and present results from molecular dynamics computer simulations of an ensemble of a prototypical octupolar molecule, the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecule, dissolved in chloroform. It is found that TATB molecules indeed show rather significant dipole moments in solutions because of the dual action of the thermal motions of the atoms and the strong intermolecular interactions. Applied electric fields accordingly show significant effects on the orientations of the molecular dipole moments. We also find that TATB molecules can aggregate because of the strong hydrogen-bonding interactions between the molecules, though they lack a static permanent dipole moment. Thus, the simulation results for TATB molecules in solution present us with a totally different notion about the collective properties of octupolar molecules. Taking account of quantum chemistry results, we found that the collective molecular nonlinear optical (NLO) properties are enhanced after the onset of the electric field, showing significant anisotropic characteristics.     

Can stimulated Raman pumping cause large population transfers in isolated molecules?

When stimulated Raman pumping (SRP) is applied to a stream of isolated molecules, such as found in a supersonic molecular beam expansion, we show that SRP can neither saturate nor power broaden a molecular transition connecting two metastable levels that is resonant with the energy difference between the pump and Stokes laser pulses. Using the optical Bloch-Feynman equations, we discuss the pumping of the hydrogen molecule from H(2) (v = 0, J = 0, M = 0) to H(2) (v = 1, J = 2, M = 0) as an illustration of how coherent population return severely reduces the SRP pumping efficiency unless the pump and Stokes laser pulses are applied with an appropriate relative delay and ratio of intensities.     

Can random copolymers serve as effective polymeric compatibilizers?

We investigate the compatibilizing performance of a random copolymer in the melt state, using transmission electron microscopy. Blends of polystyrene (PS) and poly(methyl methacrylate) (PMMA) are chosen as a model system, and a random copolymer of styrene and methyl methacrylate (SMMA) with 70 wt % styrene is used as a compatibilizer. From TEM photographs it is clear that SMMA moves to the interface between PS and PMMA domains during melt mixing, and forms encapsulating layers. However, the characteristic size of the dispersed phase increases gradually with annealing time for all blend systems studied. This demonstrates that the encapsulating layer of SMMA does not provide stability against static coalescence, which calls into question the effectiveness of random copolymers as practical compatibilizers. We interpret the encapsulation by random copolymers in terms of a simple model for ternary polymer blends. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2835–2842, 1997     

Activating multistep charge-transfer processes in fullerene-subphthalocyanine-ferrocene molecular hybrids as a function of π-π orbital overlap

We have synthesized two different fullerene-subphthalocyanine-ferrocene conjugates. The molecules were designed so that the ferrocene unit is linked at the subphthalocyanine axial position through a phenoxy spacer while the C(60) is rigidly held close to the concave face of the macrocycle via a 3-fold C(3)-symmetrical anchoring. The Bingel trisaddition reaction leading to the final products proceeded with very high regioselectivities and full diastereoselectivity. The only difference between both systems is the length of the triple tether employed, which finely regulates the regioselectivity of the trisaddition reaction and the distance between the subphthalocyanine and the C(60) complementary π-π surfaces. Thus, when the tether is connected to the subphthalocyanine through a direct C-C bond, a short π-π distance of 3.25-3.30 ? was calculated. In contrast, when it is connected through a slightly longer C-O-C bond, the distance increases to 3.5-3.6 ?. This π-π distance has a strong influence on the ground-state electronic interactions between the subphthalocyanine and the C(60), as determined from electronic absorption and cyclic voltammetry measurements. In addition, fluorescence and time-resolved transient absorption experiments demonstrated that different mechanisms operate in the two systems after photoexcitation. Despite the similar HOMO-LUMO gaps, only when the two complementary π-π surfaces of the subphthalocyanine and the C(60) are held at a close distance, therefore showing a high degree of orbital overlap, is a multistep electron transfer process triggered, ultimately leading to the long-lived, spatially separated C(60) radical anion and ferrocenium radical cation pair. A full account of the synthesis, characterization, and studies of the ground- and excited-state electronic interactions occurring in these conjugates, as well as in their reference C(60)-subphthalocyanine and subphthalocyanine-ferrocene dyads, is presented in this article.     

The atomic force microscope: Can it be used to study biological molecules?

The conditions necessary for studying biological molecules with the atomic force microscope are discussed. It is shown that in order to avoid large substrate deformations the microscope should be operated in its attractive mode where the van der Waals force between the tip and the substrate is ≈ 10⁻¹¹ N and where the tip-substrate separation is of the order of 4–5 Å.     

How carbo-benzenes fit molecules in their inner core as do biologic ion carriers?

Structural Chemistry - The present computational study complements experimental efforts to describe and characterize carbo-benzene derivatives as paradigms of aromatic carbo-mers. A long-lasting...     

Can a consecutive double turn conformation be considered as a peptide based molecular scaffold for supramolecular helix in the solid state?

Helices and sheets are ubiquitous in nature. However, there are also some examples of self-assembling molecules forming supramolecular helices and sheets in unnatural systems. Unlike supramolecular sheets there are a very few examples of peptide sub-units that can be used to construct supramolecular helical architectures using the backbone hydrogen bonding functionalities of peptides. In this report we describe the design and synthesis of two single turn/bend forming peptides (Boc-Phe-Aib-Ile-OMe 1 and Boc-Ala-Leu-Aib-OMe 2) (Aib: α-aminoisobutyric acid) and a series of double-turn forming peptides (Boc-Phe-Aib-Ile-Aib-OMe 3, Boc-Leu-Aib-Gly-Aib-OMe 4 and Boc-γ-Abu-Aib-Leu-Aib-OMe 5) (γ-Abu: γ-aminobutyric acid). It has been found that, in crystals, on self-assembly, single turn/bend forming peptides form either a supramolecular sheet (peptide 1) or a supramolecular helix (peptide 2), unlike self-associating double turn forming peptides, which have only the option of forming supramolecular helical assemblages.     

Improving molecular docking through eHiTS’ tunable scoring function

We present three complementary approaches for score-tuning that improve docking performance in pose prediction, virtual screening and binding affinity assessment. The methodology utilizes experimental data to customize the scoring function for the system of interest considering the specific docking scenario. The tuning approach, which has been implemented as an automated utility in eHiTS, is introduced as a solution to one of the conundrums of the molecular docking paradigm, namely, the lack of a universally well performing scoring function. The accuracy of scoring functions has been shown to be generally system-dependent, and particularly lacking for binding energy and bio-activity predictions. In the proposed approach, pose and energy predictions are enhanced by adjusting the relative weights of the eHiTS energy terms to improve score-RMSD or score-affinity correlations. In a virtual screening context ligand-based similarity is used to rescale the docking score such that better enrichment factors are achieved. We discuss the algorithmic details of the methods, and demonstrate the effects of score tuning on a variety of targets, including CDK2, BACE1 and neuraminidase, as well as on the popular benchmarks—the Directory of Useful Decoys and the PDBBind database.     

Can prenylcysteines be exploited as ligands for mammalian multidrug-resistance transporters?

The overexpression of specific transport proteins in the membrane of many cancer cells renders these cells resistant to many therapeutic drugs. Some lipid-modified cysteine compounds inhibit one drug-transporting protein, indicating the potential of developing such compounds as therapeutic agents.     

Are metals made from molecules?

In the traditional view, covalently bound materials differ in a fundamental way from metallic substances. Though both are built from more basic units that are, in turn, constructed from a small number of atoms, for these two materials classes the nature of these units is thought to be quite different. For covalent solids and liquids, these units are considered to be molecular, meaning that they possess properties and bonding that are retained in the condensed phase and thus they continue to be identifiable within the larger system. For metallic materials, these basic units are considered to be mere constructs that are not observable against the delocalized bonding of metals or alloys. The perceived dissimilarity of metallic and covalently bound materials has fostered distinctly different approaches to their design and improvement. Here, the delocalized view of metallic bonding is examined. This examination suggests that much of the rationale used in the design of molecular materials my be applied to metals and alloys as well.     

Can chiral single walled carbon nanotubes be used as enantiospecific adsorbents?

Single-walled carbon nanotubes can exist in chiral forms and can adsorb a range of molecules. We use atomistic simulations to consider whether enantiopure carbon nanotubes might be effective enantiospecific adsorbents for chiral molecules. We examine the adsorption of both enantiomers of trans-1,2-dimethylcyclopropane and trans-1,2-dimethylcyclohexane in a range of chiral nanotubes. Our simulations indicate that these molecules are strongly adsorbed in nanotubes, that is, they have large heats of adsorption, but the energy differences between adsorbed enantiomers are negligible. We argue that this result is generic for chiral organic molecules adsorbed in carbon nanotubes, suggesting that these materials will not be effective enantiospecific adsorbents.     

Can a catanionic surfactant mixture act as a drug delivery vehicle?

Surfactants can self-assemble in dilute aqueous solutions into a variety of microstructures, including micelles, vesicles, and bilayers. Recently, there has been an increasing interest in unilamellar vesicles, which are composed of a closed bilayer that separates an inner aqueous compartment from the outer aqueous environment. This interest is motivated by their potential to be applied as vehicles for active agents in drug delivery via several routes of administration. Active drug molecules can be encapsulated in the bilayer membrane if they are lipophilic or in the core of the vesicle if they are hydrophilic. Furthermore vesicles formed by mixing of cationic and anionic surfactants (so called ‘catanionic’ systems) can be used as models for biological membranes as they have low critical micelle concentration (cmc) and are highly biocompatible. In this work the formation of amino acid based mixed surfactant vesicles and their stabilization and biocompatibility were studied systematically using several instrumental techniques.     

Aβ-binding molecules: Possible application as imaging probes and as anti-aggregation agents

As amyloid β (Aβ) is at the centre of pathogenesis of Alzheimer's disease (AD), Aβ aggregate-specific probes for in vivo studies of Aβ are potentially important for the early diagnosis and the assessment of new treatment strategies in the AD brain by noninvasive imaging. Several series of compounds derived from Congo red (CR) and Thioflavin T (ThT) have been evaluated as potential probes for the Aβ imaging. They include a diversity of core structures contributing to their affinities to Aβ. Small-molecule inhibi- tors were known to inhibit the formation of Aβ oligomers and fibrils. This inhibition has to be performed in such a way that these inhibitors bind to Aβ in the binding channel where Aβ-binding probes should sit. Therefore, several of them were used as novel core structures to develop Aβ probes, with their de- rivatives exhibiting good Aβ affinities. This approach will facilitate the design of a variety of candidates for Aβ probe molecules and anti-aggregation-therapeutic drugs. Moreover, the finding of Aβ probes with diverse core structures recognized by binding sites on Aβs will likely provide a promising per- spective for the design of 99mTc-labeled probe-derived molecules.