A 3 nm-sized cage-shaped Hg₆L₄ complex with large openings was quantitatively formed from trismonodentate ligand (L) and Hg²⁺ ions in a self-assembled manner. The cage complex shows reversible interconversion with a capsule-shaped Hg₆L₈ complex in response to the ratio of ligand to Hg²⁺. This structural switching is coupled with reversible ON/OFF switching of fluorescence between fluorescent Hg₆L₈ capsule and nonfluorescent Hg₆L₄ cage.

The transient titanium alkylidyne complex (PNP)Ti⋮C^tBu (PNP = N[2-P(CHMe₂)₂-4-methylphenyl]₂^-) can readily activate, in some cases regioselectively, the aromatic C−H bond of anisole and fluoro-substituted anisoles to generate titanium alkylidene complexes having a substituted aryl group. Intermolecular C−O bond activation occurs when perfluoroanisole reacts with (PNP)Ti⋮C^tBu to afford the disubstituted alkylidene methoxide (PNP)TiC[^tBu(C₆F₅)](OCH₃). Likewise, intermediate (PNP)Ti⋮C^tBu can also promote the intermolecular C−F activation of C₆F₆ and CF₃C₆F₅ to generate disubstituted alkylidene fluorides (PNP)Ti[^tBu(Ar_F)](F) (Ar_F = C₆F₅, C₆F₄CF₃). In the case of Ar = C₆F₄CF₃, the product resulting from para-aryl C−F activation was isolated. For the latter two C−F bond activation reactions, mixtures of alkylidene rotamers exist in solution. Complexes resulting from C−H, C−O, and C−F (including the rotamers for the latter reaction) activation have been characterized by single-crystal X-ray diffraction methods.

High-resolution solid-state NMR spectra of three full-length membrane proteins uniformly aligned in lipid bilayers between glass slides are observed at high magnetic field. The resolution of the specific amino acid labeled samples shows promise for large membrane protein structure determination utilizing aligned samples and shows resonance patterns known as PISA wheels. The tilt angles of the transmembrane helices are extracted from the resonance patterns in PISEMA spectra.

We report on the creation of films of end-grafted hyaluronan, based on solid-supported lipid membranes. We characterize the layer thickness, the grafting density, the mechanical properties and the permeability of these highly hydrated and up to several hundred nanometer-thick monomolecular layers by quartz crystal microbalance with dissipation monitoring, by colloidal probe triple-wavelength reflection interference contrast microscopy, and by reflectometry. The two-dimensional assemblies thus created are expected to serve as versatile platforms to study, in a well-controlled and quantitative manner, the effect of hyaluronan-binding proteins on the structure, properties, and biological function of this type of films.

Protein cation-π interactions are frequently found near the protein surface with their interacting residues partly solvent exposed. The structurally characterized α₃W model protein contains the W32/K36 cation-π interaction which has properties similar to those of naturally occurring protein cation-π interactions. α₃W was studied with the following results:  Cation-π interactions formed by a buried tryptophan and a partly solvated lysine, arginine, or histidine range from −0.8 to −0.5 kcal mol^-1 and rank as:  W32/K36 ≈ W32/R36 > W32/H36. The W32/K36 pair in α₃W represents the first W/K cation-π interaction for which both the structure and the bond energy have been experimentally determined. Upon increasing the solvent exposure of the cation-π pair, the W/K interaction energy drops from −0.73 to −0.06 and +0.15 kcal mol^-1. These results suggest that solvent exposure can tune the interaction energy between a tryptophan and a lysine by at least 0.9 kcal mol^-1.

A series of DNA polymerases were found to catalyze DNA-directed synthesis of 2‘-deoxy-2‘-fluoro-arabinonucleic acids (FANA) as well as FANA-directed DNA synthesis in vitro.

An iron(II) complex with ferrocenyl groups, [Fe(dppFc)₂](BF₄)₂·2Et₂O (1·2Et₂O, dppFc = 1-ferrocenyl-2-{(2,6-bis(pyrazolyl)pyridyl}ethylene), was prepared. X-ray crystallographic analyses revealed that 1·2Et₂O underwent a single-crystal-to-single-crystal transformation with the release of crystal solvent molecules. In magnetic susceptibility measurements, a reversible conversion between paramagnetism and spin-crossover induced by solvent molecules was observed.

Using the difference Fourier analysis of neutron powder diffraction data along with first-principles calculations, we reveal detailed structural information such as methyl group orientation, hydrogen adsorption sites, and binding energies within the nanopore structure of ZIF8 (Zn(MeIM)₂). Surprisingly, the two strongest adsorption sites that we identified are both directly associated with the organic linkers, instead of the ZnN₄ clusters, in strong contrast to classical MOFs, where the metal-oxide clusters are the primary adsorption sites. These observations are important and hold the key to optimizing this new class of ZIF materials for practical hydrogen storage applications. Finally, at high concentration H₂-loadings, ZIF8 structure is capable of holding up to 28 H₂ molecules (i.e., 4.2 wt %) in the form of highly symmetric novel three-dimensional interlinked H₂-nanoclusters with relatively short H₂−H₂ distances compared to solid H₂. Hence, ZIF compounds with robust chemical stability can be also an ideal template host-material to generate molecular nanostructures with novel properties.

We have synthesized BiNiX, a caged methylxanthine agonist for the ryanodine receptor (RyR)the major calcium channel that mediates Ca²⁺ release from intracellular Ca²⁺ stores in electrically excitable cells. BiNiX is easily loaded into living cells through incubation with its acetoxymethyl (AM) ester. Delivery of focused UV light pulses to the loaded cell releases paraxanthine focally and rapidly to activate RyRs to release Ca²⁺, thus elevating intracellular Ca²⁺ concentration to initiate Ca²⁺-dependent signaling cascades. We demonstrate the biological utility of BiNiX in heart muscle cells by showing that local intracellular photolysis of BiNiX triggers Ca²⁺ release and consequent muscle contraction.

Chemical shifts are fundamental to interpretation of NMR spectra and provide constraints for macromolecular structure determination, refinement, and validation, as well as details of active-site chemistry in enzymes. Insights into the origins of the chemical shift can be leveraged to improve chemical analysis, including conformation, bonding, and dynamics. To exploit this information fully, it is desirable to measure not only isotropic chemical shifts but also the full chemical-shift anisotropy (CSA) tensor. Until recently, most efforts to measure backbone amide and carbonyl CSAs have relied upon cross-correlated relaxation and residual anisotropic shifts in solution NMR. In solid-state NMR, analysis of sideband patterns has typically been reserved for site-specifically labeled samples or small peptides. Here we demonstrate that the Herzfeld−Berger method (Herzfeld, J.; Berger, A. E. J. Chem. Phys. 1980, 73, 6021−6030) can be applied to highly ¹³C,¹⁵N-enriched solid proteins, using 2D heteronuclear correlation in combination with high magnetic fields (750 MHz ¹H frequency) and pattern labeling of ¹³C sites. The experiments report on 42 pairs of amide and carbonyl tensors in the microcrystalline protein GB1.

Reversible phosphorylation of tyrosine residues serves as a biochemical “switch” that alters the functional properties of many proteins involved in cellular signal transduction processes. Protein tyrosine phosphatases (PTPs) catalyze the removal of phosphoryl groups from tyrosine residues in target proteins, thereby playing a central role in the regulation of diverse cellular processes including glucose metabolism, cell cycle control, and immune responses. Accordingly, small molecules capable of inactivating PTPs may find use as therapeutic agents and tools for the study of diverse signal transduction pathways. In the work reported here, peroxymonophosphate (^2-O₃POOH) was reported to be an exceptional inactivator of PTP1B, an archetypal member of the PTP enzyme family (K_I = 6.6 × 10^-7 M and k_inact = 0.043 s^-1). In this regard, peroxymonophosphate is over 7000 times more potent than hydrogen peroxide, the endogenous regulator of PTP1B. Inactivation of PTP1B by peroxymonophosphate is active site directed and, like that by hydrogen peroxide, is readily reversed by treatment with dithiothreitol (5 mM). Together the findings suggest that peroxymonophosphate oxidizes the active site cysteine residue of PTP1B to the sulfenic acid oxidation state. Importantly, peroxymonophosphate (100 nM) yields substantial inactivation of PTP1B even in the presence of physiologically relevant concentrations of the biological thiol glutathione (1 mM). Collectively, these properties may make peroxymonophosphate a useful tool for probing the role of cysteine-dependent PTPs in various signal transduction pathways. Finally, it is interesting to note that peroxymonophosphate may be biosynthetically accessible via the reaction of endogenous hydrogen peroxide with phosphoryl donors. Peroxymonophosphate possesses key properties expected for the endogenous signaling molecule involved in the redox regulation of PTP activity.

Oxathiocoraline, a member of the quinoxaline antibiotic family, has been synthesized on solid-phase. The depsipeptide exhibits high synthetic complexity owing to the presence of consecutive NMe amino acids, two ester moieties, a disulfide bridge, and two SMe Cys residues. Because of internal diketopiperazine formation, standard stepwise or convergent approaches failed to deliver the linear octadepsipeptide precursor. Therefore, an alternative methodology where an intermolecular disulfide dimer is formed on solid-phase was developed. Cleavage of the dimer from the solid-phase and subsequent bismacrolactamization followed by incorporation of the heterocyclic unit afforded the target compound. Oxathiocoraline showed antitumoral activity in three tumor cell lines.

The addition of p-perfluoro-ethylbenzoic acid as capping reagent yields stable size-selected MOF-5 colloids and suggests a general concept for controlled particle formation of carboxylic acid based MOFs in solution.

Si quantum dots, nanoparticles, nanowires, and ordered Si complex micro-/nanostructures can be obtained directly from silicon wafer by a polyoxometalate-assisted electrochemical method.

A 1,3- or a 1,4-cis axial tert-butyldimethylsilyloxy substituent on the pyranose derived chiral auxiliary for the allene ether Nazarov cyclization leads to products in high optical purity. α-Pyranose and β-pyranose derived auxiliaries lead to enantiomeric products.

Reactions with dianion nucleophiles were used to determine deuterium kinetic isotope effects (KIE's) in gas-phase E2 and S_N2 reactions. This approach allows for the direct identification of elimination and substitution products in the reactions of simple alkyl halides. In general, the E2 reactions give large KIE's (∼7) for perdeutero substrates; however, elimination isotope effects are attenuated in reactions that occur near the collision-controlled limit. In a very slow elimination, a large KIE (>20) is observed, presumably due to lifetime effects in the collision complex. The S_N2 reactions all give secondary deuterium isotope effects near unity, with the exception of one system, where suppression of the E2 channel in the perdeutero substrate leads to an enhancement of the S_N2 rate and causes a modest inverse isotope effect.

The scope of heterocycle ortho-alkylation has been dramatically expanded to include pharmaceutically important pyridines and quinolines, which contain only a single nitrogen. The reactions, which are conducted at a high concentration (0.8 M), can be performed with catalyst loadings as low as 1% Rh. Substitution ortho to the heterocycle ring nitrogen is required for efficient alkylation and is consistent with the intermediacy of a Rh−carbene intermediate similar to those proposed in our earlier work.

N-Heterocyclic carbenes derived from N-mesityl benzimidazolium salts are effective catalysts for generating homoenolate species from α,β-unsaturated aldehydes. The nucleophilic intermediate adds to azomethine imines, and the resulting activated carbonyl unit undergoes an intramolecular acylation event. This formal [3 + 3] cycloaddition between α,β-unsaturated aldehydes and azomethine imines catalyzed by NHC has been developed to give substituted pyridazinones in good to excellent yields with high diastereoselectivity (>20:1). The NHC-catalyzed reaction accommodates aromatic and alkyl α,β-unsaturated aldehydes and various aromatic azomethine imines. The pyridazinones can undergo selective six-membered ring opening upon addition of alcohols or amines to give esters and amides.

A new type of C₂-symmetric chiral diene ligand bearing a simple bicyclic [3.3.0] backbone was discovered. (3aS,6aS)-3,6-diphenyl-1,3a,4,6a-tetrahydropentalene was applied successfully in the Rh-catalyzed asymmetric arylation of N-tosylarylimines with arylboronic acids. With the new chiral diene ligand, a broad range of highly enantiomerically enriched diarylmethylamines (98−99% ee) as well as 3-aryl substituted phthalimidines (99% ee) could be easily prepared.

A practical high tetravalent Zr⁴⁺ ion conducting solid, Zr_1-x/4TaP_3-xW_xO₁₂ (0.0 ≤ x ≤ 0.2), was successfully prepared by strictly selecting both a crystal structure and constituent ion species. By introducing the hexavalent W⁶⁺ as the constituent ion of NASICON-type structure, the tetravalent Zr⁴⁺ ion conductivity was greatly enhanced in comparison with that of ZrTa(PO₄)₃ because of the reduction of the electrostatic interactions between the mobile Zr⁴⁺ cations and surrounding O^2- anions as well as the expansion of the NASICON crystal lattice. Among the samples prepared, the Zr_39/40TaP_2.9W_0.1O₁₂ (x = 0.1) solid showed the highest Zr⁴⁺ ion conductivity of 4.7 × 10^-4 S·cm^-1 at 873 K which enters into the practical application range (>10^-4 S·cm^-1).

We demonstrate NMR spectral separation of enantiomers of dl-alanine in the chiral anisotropic medium of variably stretched gelatin. This is done in an apparatus that employs gelatin gel in an elastic silicone-rubber tube. There are two adjustable properties of the gels, their concentration and their extension factor. Concentration has a far larger effect in manifesting quadrupolar and dipolar splittings and fine-tuning, to a specified splitting-value or to overcome peak overlap, is achieved by varying the extension of the gel. We show that alanine enantiomers can be distinguished by ¹H, ²H, and ¹³C NMR. This valuable spectral outcome is not specific to alanine and is a general property of gelatin gels, so they constitute a notable advance on previous related methods using liquid crystals.

Direct coordination of the dye resorufin (Resf) to the ruthenium center photosensitizes the Ru−NO bond and improves NO photolability of the designed {Ru−NO}⁶ nitrosyl [(Me₂bpb)Ru(NO)(Resf)] under visible light.

We recently described the high-resolution X-ray structure of a helical bundle composed of eight copies of the β-peptide Zwit-1F. Like many proteins in Nature, the Zwit-1F octamer contains parallel and antiparallel helices, extensive inter-helical electrostatic interactions, and a solvent-excluded hydrophobic core. Here we explore the stability of the Zwit-1F octamer using circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AU), differential scanning calorimetry (DSC), and NMR. These studies demonstrate that the thermodynamic and kinetic properties of Zwit-1F closely resemble those of α-helical bundle proteins. Together these studies should provide a model for the design of β-peptide proteins with biological functions.

Hydrothermal reaction of (S)-1,1‘1‘ ‘-2,4,6-trimethylbenzene-1,3,5-triyl-tris(methylene)-tris-pyrrolidine-2-carboxylic acid (TBPLA) with Ni(ClO₄)₂·6H₂O gave pale green block crystals of 1. X-ray crystal structure analysis showed the complex to be a trinuclear descrete homochiral molecule with each Ni center sitting in distorted octahedron geometries. Anisotropic permittivity measurements reveal that 1 exhibits huge dielectric anisotropy along its three different crystal axes that is ca. 3.5 times of ε_r (E//c)/ε_r (E//b) with temperature and frequency independence.

The synthesis of clathrate-II germanium □₂₄Ge₁₃₆ in an ionic liquid was recently discovered.¹ The key step in this process, the controlled oxidation of reactive precursor phases by a protic acid, was successfully applied to silicides M₄Si₄ (M = Na, K). Through this method, clathrate-I compounds of composition M_8-xSi₄₆ were obtained as crystalline products. The synthetic method demonstrates a mild oxidative route to a large class of metastable intermetallic compounds.

The first 26R channel structure, NTHU-5, built up with two types of helical metal phosphite chains has been synthesized under mild hydrothermal conditions; this novel open framework is composed of both octahedral Al³⁺ and tetrahedral Zn²⁺ centers and represents the first example with participation of aluminum in a pore size over 20R; the 26R channel is truly a stack of 26-membered rings instead of just an opening; this study has successfully demonstrated that two differently charged metal ions can form M−O−P−O−M‘ bonded structure with ring size larger than any other existing inorganic open frameworks; in addition, varied metal analogues can be prepared using the same approach; the system of NTHU-5 has provided an intriguingly new chemical synthesis for inorganic microporous materials with interesting reaction conditions.

Modified His−His dipeptides have been reacted with copper(I) salts to model active-site Cu ions bound by contiguous His residues in certain oxygen-activating copper proteins, as well as amyloid β-peptide. Chelation of copper(I) by these ligands affords linear, two-coordinate complexes as studied structurally by X-ray absorption spectroscopy. The complexes are robust toward oxidation, showing limited to no reactivity with O₂, and they bind CO weakly. Reaction with a third ligand (N-methylimidazole) affords complexes with a markedly different structure (distorted T-shaped) and reactivity, binding CO and oxidizing rapidly upon exposure to dioxygen.

We found that the topology of cleavable polymer from linear to hyperbranched can be tuned simply by varying the polymerization temperature:  linear polymers were produced at temperatures ≤ 40 °C, hyperbranched polymers were obtained at elevated temperatures (≥ 48 °C); the degree of branching (DB) of hyperbranched polymers increased with the increase of temperature. Furthermore, the produced linear and hyperbranched polymers contain stimuli-sensitive disulfide bonds in the backbone that can be easily cleaved into small organic molecules in the presence of DTT.

Metal nanoparticles have received great attention due to their unique optical properties and wide range of applicability. In this context, controlling the particle−particle interaction is a major challenge to generate programmable assembly of nanoparticles for application in device fabrication and detection systems. In this communication, we report a versatile solid phase synthesis of gold nanoparticle dimers using commercially available organic reagents in an asymmetric functionalization approach. The method provides the opportunity to synthesize gold nanoparticle dimers for a wide size range. In addition, dimers consisting of two particles of different sizes also were prepared. The yield of the dimers varies from ∼30 to ∼65%, depending on the particle sizes. The process could be generalized to fabricate metal−semiconductor conjugates and to control interparticle spacing by changing the chain lengths of the linker molecules.

To better understand the origin of intrinsic membrane potential in cells, we have performed atomic-scale molecular dynamics simulations of an asymmetric lipid membrane comprised of zwitterionic (neutral) phosphatidylcholine (PC) and phosphatidylethanolamine (PE) leaflets in the absence of salt. It turns out that the asymmetry in distribution of zwitterionic lipids across the membrane gives rise to a nonzero intrinsic potential difference of about 100 mV between the two sides of the membrane. This potential arises from the difference in dipole moments of the two leaflets of the asymmetric PC/PE membrane. Our findings suggest that the transmembrane lipid asymmetry typical of most living cells can contribute to the membrane potential.

The complex [Nd(L‘){Ga(NArCH)₂}(N‘ ‘)(THF)], which exhibits the first f-element−gallium bond, is formed from the reaction between the N-heterocyclic carbene-supported neodymium complex [Nd(L‘)(N‘ ‘)(I)] (L‘ = Bu^tNCH₂CH₂{C(NCSiMe₃ CHNBu^t)}; N‘ ‘ = N(SiMe₃)₂) and the anionic gallium(I) heterocycle [Ga(NArCH)₂][K(tmeda)] (Ar = 2,6-Prⁱ₂C₆H₃). The Nd−Ga bond energy is calculated to be 386 kJ mol^-1.

A new type of polyion complex (PIC) micelle was prepared from lysozyme and the block copolymer, PEG-pAsp(EDA-Cit), that can switch the charge from anionic to cationic at the endosomal pH. The charge-conversion was due to the degradation of the citraconic amide side chain at pH 5.5. This abrupt charge-conversion can make the PIC micelles promptly release the internal protein in response to the endosomal pH. This pH-sensitive charge-conversion polymer is promising for the future design of nanocarriers for early endosomal release.

A novel catalyst system based on complexes of calcium which promote the catalytic asymmetric 1,4-addition reactions and [3+2] cycloaddition reactions of α-amino acid derivatives with α,β-unsaturated carbonyl compounds have been developed. The reactions proceeded smoothly in the presence of 5−10 mol % of the chiral calcium catalyst to afford the desired adducts in high yields with high diastereo- and enantioselectivities. A wide range of α,β-unsaturated esters and amides were applicable, and other glycine and even dl-alanine derivatives reacted with several α,β-unsaturated carbonyl compounds to afford the corresponding substituted pyrrolodine derivatives in high yields with excellent diastereo- and enantioselectivities. In the reactions with dl-alanine derivatives, quaternary asymmetric carbons were constructed efficiently.

Protein tyrosine phosphatases (PTPs) are a large family of enzymes that catalyze the hydrolytic removal of the phosphoryl group from phosphotyrosyl (pY) proteins. To date, the in vivo substrates and physiological functions of PTPs remain poorly defined. In this work, we have developed a novel combinatorial library method to systematically determine the substrate specificity of PTPs. A one-bead-one-compound peptide library containing five randomized residues, Fmoc-XXXXXpYAA (where X is norleucine or 17 proteinogenic amino acids excluding Tyr, Cys, and Met), was chemically synthesized on 90-μm TentaGel resin by the split-and-pool method. Limited treatment of the library with a PTP removed the phosphoryl group from beads that carry the most preferred substrates. The exposed tyrosine side chain was selectively oxidized into an orthoquinone by the treatment with tyrosinase in the presence of atmospheric oxygen. The orthoquinone was then selectively derivatized with biotin-hydrazide, followed by on-bead colorimetric assay. The positive beads were isolated and individually sequenced by partial Edman degradation/mass spectrometry to give the most preferred substrates of the PTP. Screening of the pY library against PTP1B confirmed the previously reported PTP1B specificity, but also revealed a second class of previously unrecognized peptide substrates. Several selected peptides were individually synthesized and assayed against PTP1B and the kinetic data confirmed the screening results. This method is generally applicable to studying the substrate specificity of other PTPs.

X-shaped rigid methylthio arylethynes (MTA) have been demonstrated to mediate the assembly of gold nanoparticles. The structural attributes of MTAs include molecular rigidity, π-conjugation, and importantly the tunability in terms of size, shape, and binding strength. The size, kinetics, optical, and spectroscopic properties of the MTA mediated assembly are shown to be tunable by these structural attributes. This is the first example demonstrating an interparticle structurally tunable assembly in terms of size, shape, and binding properties, and an intriguing surface-enhanced Raman scattering effect as well. These findings could lead to unprecedented control of the interparticle spatial properties in nanoparticle assemblies for the exploitation of the unique optical and spectroscopic properties.

Azide-modified graphitic surfaces were prepared by reaction with iodine azide. The surface-attached azides undergo the “click” reaction with alkyne-terminated molecules ethynylferrocene and 1-ethynyl-4-(trifluoromethyl)benzene. Voltammetric and XPS analyses show the surface coverage of both the azide and the subsequent triazole of 2 × 10¹³ molecules/cm². The 1,2,3-triazole linker is stable in an aqueous 1 M HCl solution for at least 60 min at 55 °C.

The new tungsten allyl nitrosyl complex, Cp*W(NO)(η³-CH₂CHCHMe)(CH₂CMe₃) (1) (Cp* = η⁵-C₅Me₅; Me = CH₃), selectively activates the terminal C−H bonds of n-pentane at room temperature and forms the thermally stable compound, Cp*W(NO)(η³-CH₂CHCHMe)(CH₂CH₂CH₂CH₂Me) (2), from which the n-pentyl ligand may be selectively released as 1-iodopentane by treatment with I₂. Current experimental evidence suggests that the C−H activation chemistry derived from 1 proceeds via two distinct steps:  (1) formation of the intermediate η²-diene complex, Cp*W(NO)(η²-CH₂CHCHCH₂) (A) via intramolecular β-H elimination of neopentane from 1, and (2) incorporation of n-pentane into A via intermolecular β-H addition to produce 2. Intermediate A can be trapped by PMe₃ as the Cp*W(NO)(η²-CH₂CHCHCH₂)(PMe₃) adduct (3), and the solid-state molecular structures of 1, 2, and 3 have been established by single-crystal X-ray crystallographic analyses.

Since the cold denaturation of most proteins occurs well below 0 °C, full access to the cold denatured state is normally limited by water freezing. To circumvent this difficulty the temperature of cold denaturation is normally raised, destabilizing the protein by point mutations and using chemical or physical denaturation. The main drawback of these approaches is that it is not generally possible to extrapolate the results to physiological conditions. Following a different approach, we looked for a protein whose cold denaturation could be studied in a normal buffer at physiological pH without the need of destabilization, in a temperature range accessible to several techniques. Here we describe the cold and heat denaturation of yeast frataxin (Yfh1). Both NMR and CD data were fitted by the same equation, showing that the collapse of the hydrophobic core is exactly paralleled by a decrease of the secondary structure content.

Staring from readily available polysubstituted allylic chlorides, a range of polysubstituted allylic zinc chlorides were obtained using a LiCl-mediated zinc dust insertion in 55−84% yield. A highly diastereoselective synthesis of homoallylic alcohols bearing up to two adjacent quaternary centers was achieved using these polysubstituted allylic zinc reagents.

The apo crystal structure of CTX-M-9 β-lactamase has been determined to 0.88 Å at pH 8.8. This unusually clear picture of proton positions and residue interactions supports the role of Glu166 as the general base for the controversial acylation step of class A β-lactamase catalysis. The ability to distinguish low-energy conformations sampled by the enzyme allows us to link the two conformations of Lys73 to different protonation states of Glu166.

A convergent, enantioselective synthesis of the proposed structure of kedarcidin chromophore (1) is described. The route is 24 steps in the longest linear sequence (beginning with the commercial reagent 2,3-O-isopropylidene-d-erythronolactone) with an average yield of 75% per step (overall yield:  0.1%). Our ¹H NMR data for 1 do not coincide with the data reported for kedarcidin chromophore. We have re-analyzed the original data and here propose a stereochemical revision at position C10, the site of attachment of the l-mycarose carbohydrate residue to the chromophore core (structure 2).

The sequence-specific DNA alkylation by conjugates 4 and 5, which consist of N-methylpyrrole (Py)−N-methylimidazole (Im) polyamides and 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI) linked with an indole linker, was investigated in the absence or presence of partner Py−Im polyamide 6. High-resolution denaturing polyacrylamide gel electrophoresis revealed that conjugate 4 alkylates DNA at the sequences 5‘-(A/T)GCCTA-3‘ through hairpin formation, and alkylates 5‘-GGAAAGAAAA-3‘ through an extended binding mode. However, in the presence of partner Py−Im polyamide 6, conjugate 4 alkylates DNA at a completely different sequence, 5‘-AGGTTGTCCA-3‘. Alkylation of 4 in the presence of 6 was effectively inhibited by a competitor 7. Surface plasmon resonance (SPR) results indicated that conjugate 4 does not bind to 5‘-AGGTTGTCCA-3‘, whereas 6 binds tightly to this sequence. The results suggest that alkylation proceeds through heterodimer formation, indicating that this is a general way to expand the recognition sequence for DNA alkylation by Py−Im seco-CBI conjugates.

Concanavalin A is a member of the plant hemeagglutinin (or plant lectin) family that contains two metal binding sites; one, called S1, is occupied by Mn²⁺ and the other, S2, by Ca²⁺. ⁵⁵Mn electron−nuclear double resonance (ENDOR) measurements were performed on a single crystal of concanavalin A at W-band (95 GHz, ∼3.5 T) to determine the ⁵⁵Mn nuclear quadrupole interaction in a protein binding site and its relation to structural parameters. Such measurements are easier at a high field because of the high sensitivity for size-limited samples and the reduction of second-order effects on the spectrum which simplifies spectral analysis. The analysis of the ⁵⁵Mn ENDOR rotation patterns showed that two chemically inequivalent Mn²⁺ types are present at low temperatures, although the high-resolution X-ray structure reported only one site. Their quadrupole coupling constants, e²Qq/h, are significantly different; 10.7 ± 0.6 MHz for M and only −2.7 ± 0.6 MHz for M . The ENDOR data also refined the hyperfine coupling determined earlier by single-crystal EPR measurements, yielding a small but significant difference between the two:  −262.5 MHz for M and −263.5 MHz for M . The principal z-axis for M is not aligned with any of the Mn-ligand directions, but is 25° off the Mn-asp10 direction, and its orientation is different than that of the zero-field splitting (ZFS) interaction. Because of the small quadrupole interaction of M the orientation dependence was very mild, leading to larger uncertainties in the asymmetry parameter. Nonetheless, there too z is not along the Mn-ligand bonds and is rotated 90° with respect to Mn_A. These results show, that similar to the ZFS, the quadrupolar interaction is highly sensitive to small differences in the coordination sphere of the Mn²⁺, and the resolution of the two types is in agreement with the earlier observation of a two-site conformational dynamic detected through the ZFS interaction, which is frozen out at low temperatures and averaged at room temperature. To account for the structural origin of the different e²Qq/h values, the electric field gradient tensor was calculated using the point-charge model. The calculations showed that a relatively small displacement of the oxygen ligand of asp10 can lead to differences on the order observed experimentally.

Hydrogen−deuterium exchange experiments were carried out on the conjugate base of cysteine with four different deuterated alcohols. Three H/D exchanges are observed to take place in each case, and a relay mechanism which requires the SH and CO₂H groups to have similar acidities and subsequently proceeds through a zwitterionic intermediate is proposed. Gas-phase acidity measurements also were carried out in a quadrupole ion trap using the extended kinetic method and in a Fourier transform mass spectrometer by an equilibrium determination. The results are in excellent accord with each other and high-level ab initio and density functional theory calculations and indicate that the side-chain thiol in cysteine is more acidic than the carboxyl group by 3.1 kcal mol^-1. Deprotonated cysteine is thus predicted to be a thiolate ion. A zwitterionic species also was located on the potential energy surface, but it is energetically unfavorable (+10.1 kcal mol^-1).

Photoinduced proton transfer (PT) from cations 6-hydroxyquinolinium (6HQc) and 6-hydroxy-1-methylquinolinium (6MQc) to water and alcohols, and solvation of the zwitterionic conjugate base 1-methylquinolinium-6-olate (6MQz) were studied with stationary and transient absorption spectroscopy and by quantum chemical calculations. Transient emission spectra from 6MQz in acetonitrile and protic solvents shift dynamically to the red without changing their shape and intensity. The shift matches the solvation correlation function C(t) either measured with known solvatochromic probes coumarin 343 and coumarin 153 or derived from infrared/dielectric-loss data on neat solvents. This indicates that 6MQz monitors the solvation dynamics and that no intramolecular electron transfer occurs on a subpicosecond or longer time scale. The PT dynamics S(t) from 6HQc and 6MQc closely follows C(t), being initially 2−3 times slower. This allows for the conclusion that PT is controlled by solvation, with a barrier of 2 kJ/mol. In water, a pre-condition of this ultrafast reaction seems to be hydrogen-bonding between the negatively charged oxygen and two water molecules, resulting in a complex 6HQc:H₂O:H₂O. The complex is stable due to a high (47 kJ/mol) bonding energy between 6HQc and a water molecule. In acetonitrile, the reaction equilibrium is strongly shifted to the cation. There an intermediate PT state was detected, which may be ascribed to the cationic form 6HQc:H₂O due to residual water impurities. In water−acetonitrile mixtures, the ultrafast solvent-controlled PT is followed by a diffusion-controlled reaction; the measured rate k_D ≈ 10¹⁰ s^-1 M^-1 is characteristic for simple bimolecular diffusion. The dependence of the short-time PT signal on water concentration can be fitted with a Poisson distribution of water molecules around the cation. Altogether, the short-time and long-time behaviors provide strong evidence that diffusion of only one water molecule is sufficient to detach the proton. Subsequent solvent stabilization of the products completes the PT reaction.

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each −NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin−bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.

A quite unexpected sevenfold coordination of the hydrated Hg(II) complex in aqueous solution is revealed by an extensive study combining X-ray absorption spectroscopy (XAS) and quantum mechanics/molecular dynamics (QM/MD) calculations. As a matter of fact, the generally accepted octahedral solvation of Hg(II) ion cannot be reconciled with XAS results. Next, refined QM computations point out the remarkable stability of a heptacoordinated structure with C ₂ symmetry, and long-time MD simulations by new interaction potentials including many-body effects reveal that the hydrated complex has a quite flexible structure, corresponding for most of the time to heptacoordinated species. This picture is fully consistent with X-ray absorption near-edge structure experimental data which unambiguously show the preference for a sevenfold instead of a sixfold coordination.

A nanogapped microelectrode-based biosensor array is fabricated for ultrasensitive electrical detection of microRNAs (miRNAs). After peptide nucleic acid (PNA) capture probes were immobilized in nanogaps of a pair of interdigitated microelectrodes and hybridization was performed with their complementary target miRNA, the deposition of conducting polymer nanowires, polyaniline (PAn) nanowires, is carried out by an enzymatically catalyzed method, where the electrostatic interaction between anionic phosphate groups in miRNA and cationic aniline molecules is exploited to guide the formation of the PAn nanowires onto the hybridized target miRNA. The conductance of the deposited PAn nanowires correlates directly to the amount of the hybridized miRNA. Under optimized conditions, the target miRNA can be quantified in a range from 10 fM to 20 pM with a detection limit of 5.0 fM. The biosensor array is applied to the direct detection of miRNA in total RNA extracted from cancer cell lines.

A series of m-phenyleneethynylene (mPE) oligomers modified with a dimethylaminopyridine (DMAP) unit were treated with methyl sulfonates of varying sizes and shapes, and the relative reactivities were measured by UV spectrophotometry. Using a small-molecule DMAP analogue as a reference, each of the methyl sulfonates was shown to react at nearly identical rate. In great contrast, oligomers that are long enough to fold, and hence capable of binding the methyl sulfonate, experience rate enhancements of 18−1600-fold relative to that of the small-molecule analogue, depending on the type of alkyl chain attached to the guest. Three different oligomer lengths were studied, with the longest oligomers exhibiting the fastest rate and greatest substrate specificity. Even large, bulky guests show slightly enhanced methylation rates compared to that with the reference DMAP, which suggests a dynamic nature to the oligomer's binding cavity. Several mechanistic models to describe this behavior are discussed.

A new and unnatural type of phospholipids with the head group attached to the 2-position of the glycerol backbone has been synthesized and shown to be a good substrate for secretory phospholipase A₂ (sPLA₂). To investigate the unexpected sPLA₂ activity, we have compared three different phospholipids by using fluorescence techniques and HPLC, namely:  (R)-1,2-dipalmitoyl-glycero-3-phosphocholine (hereafter referred to as 1R), (R)-1-O-hexadecyl-2-palmitoyl-glycero-3-phoshocholine (2R), and (S)-1-O-hexadecyl-3-palmitoyl-glycero-2-phosphocholine (3S). Furthermore, to understand the underlying mechanisms for the observed differences, we have performed molecular dynamics simulations to clarify on a structural level the substrate specificity of sPLA₂ toward phospholipid analogues with their head groups in the 2-position of the glycerol backbone. We have studied the lipids above 1R, 2R, and 3S as well as their enantiomers 1S, 2S, and 3R. In the simulations of sPLA₂−1S and sPLA₂−3R, structural distortion in the binding cleft induced by the phospholipids showed that these are not substrates for sPLA₂. In the case of the phospholipids 1R, 2R, and 3S, our simulations revealed that the difference observed experimentally in sPLA₂ activity might be caused by reduced access of water molecules to the active site. We have monitored the number of water molecules that enter the active site region for the different sPLA₂−phospholipid complexes and found that the probability of a water molecule reaching the correct position such that hydrolysis can occur is reduced for the unnatural lipids. The relative water count follows 1R > 2R > 3S. This is in good agreement with experimental data that indicate the same trend for sPLA₂ activity:  1R > 2R > 3S.

Molecular level analysis of cell-surface phenomena could benefit from model systems comprising structurally defined components. Here we present the first step toward bottom-up assembly of model cell surfacesthe synthesis of mucin mimetics and their incorporation into artificial membranes. Natural mucins are densely glycosylated O-linked glycoproteins that serve numerous functions on cell surfaces. Their large size and extensive glycosylation makes the synthesis of these biopolymers impractical. We designed synthetically tractable glycosylated polymers that possess rodlike extended conformations similar to natural mucins. The glycosylated polymers were end-functionalized with lipid groups and embedded into supported lipid bilayers where they interact with protein receptors in a structure-dependent manner. Furthermore, their dynamic behavior in synthetic membranes mirrored that of natural biomolecules. This system provides a unique framework with which to study the behavior of mucin-like macromolecules in a controlled, cell surface-mimetic environment.

Novel tetraazachlorin (TAC)−fullerene (C₆₀) conjugates (TAC−C₆₀) and their analogues (TAiBC−C₆₀ and TABC−C₆₀ where TAiBC = tetraazaisobacteriochlorin and TABC = tetraazabacteriochlorin) have been synthesized by condensing 1,2-dicyanofullerene (1) and phthalonitrile derivatives (2) in the presence of nickel chloride in quinoline, and fully characterized using mass spectrometry and ¹H and ¹³C NMR. By arranging the TAC and C₆₀ units at the minimum distance, and taking also into account the molecular symmetry, the resultant conjugates show on−off electronic communication behavior, depending on the push−pull properties of the peripheral substituents in the TAC moiety. Consequently, the UV−vis absorption spectrum of the electron-releasing butyloxy-substituted TAC−C₆₀ (3a) contains an unusual group of three absorption bands in the Q-band region (500−900 nm) as a result of a strong electronic communication between the two moieties. On the other hand, the absorption spectrum of the electron-withdrawing butylsulfonyl-substituted TAC−C₆₀ (3b) comprises a typically normal TAC spectrum with markedly split two-peak Q-bands. A similar phenomenon is observed between alkoxy-substituted TAiBC−C₆₀ (4a) and butylsulfonyl-substituted TAiBC−C₆₀ (4b). This study reveals that the electron-donating or -withdrawing nature of the peripheral substituents on an azachlorin moiety has an important effect on the electronic structures of our novel azachlorin−C₆₀ conjugates, although the linking carbon atoms are aliphatic sp³ carbon atoms which generally do not contribute to aromaticity. The electronic structures of the conjugates have been investigated in detail using spectroscopic and electrochemical techniques with the aid of DFT calculations.

This paper describes the control of the nucleation and growth of calcite crystals by a matrix composed of an agarose hydrogel on top of a carboxylate-terminated self-assembled monolayer (SAM). The design of this matrix is based upon examples from biomineralization in which hydrogels are coupled with functionalized, organic surfaces to control, simultaneously, crystal morphology and orientation. In the synthetic system, calcite crystals nucleate from the (012) plane (the same plane that is observed in solution growth). The aspect ratio (length/width) of the crystals decreases from 2.1 ± 0.22 in solution to 1.2 ± 0.04 in a 3 w/v % agarose gel. One possible explanation for the change in morphology is the incorporation of gel fibers inside of the crystals during the growth process. Etching of the gel-grown crystals with deionized water reveals an interpenetrating network of gel fibers and crystalline material. This work begins to provide insight into why organisms use hydrogels to control the growth of crystals.

A carbon-detected TROSY-optimized experiment correlating ¹H^N, ¹⁵N, and ¹³C‘ resonances, referred to as c-TROSY−HNCO is presented, in which the ¹H^N and ¹⁵N TROSY effects are maintained in both indirect dimensions, while the directly detected ¹³C‘ is doubly TROSY-optimized with respect to ¹H^N and ¹⁵N. A new strategy for sensitivity enhancement, the so-called double echo-antiecho (dEA), is described and implemented in the c-TROSY−HNCO experiment. dEA offers sensitivity enhancement of in both indirect dimensions and is generally applicable to many multidimensional experiments. A carbon-detected HNCO experiment, c-HNCO, without TROSY optimization and sensitivity enhancement is also designed for comparison purposes. Relaxation simulations show that for a protein with a rotational correlation time of 10 ns or larger, the c-TROSY−HNCO experiment displays comparable or higher signal-to-noise (S/N) ratios than the c-HNCO experiment, although the former selects only 1/4 of the initial magnetization relative to the later. The high resolution afforded in the directly detected carbon dimension allows direct measurement of the doublet splitting to extract ¹J_C^αC‘ scalar and ¹D_C^αC‘ residual dipolar couplings. Simulations indicate that the c-TROSY−HNCO experiment offers higher precision (lower uncertainty) compared to the c-HNCO experiment for larger proteins. The experiments are applied to ¹⁵N/¹³C/²H/[Leu,Val]-methyl-protonated IIB^Mannose, a protein of molecular mass 18.6 kDa with a correlation time of ∼10 ns at 30 °C. The experimental pairwise root-mean-square deviation for the measured ¹J_C^αC‘ couplings obtained from duplicate experiments is 0.77 Hz. By directly measuring the doublet splitting, the experiments described here are expected to be much more tolerant to nonuniform values of ¹J_C^αC‘ (or ¹J_C^αC‘ + ¹D_C^αC‘ for aligned samples) and pulse imperfections due to the smaller number of applied pulses in the “out-and-stay” coherence transfer in the c-HNCO−TROSY experiment relative to conventional ¹H-detected “out-and-back” quantitative J correlation experiments.

A molecular origin of the striking rate increase observed in a reaction on water is studied theoretically. A key aspect of the on-water rate phenomenon is the chemistry between water and reactants that occurs at an oil−water phase boundary. In particular, the structure of water at the oil−water interface of an oil emulsion, in which approximately one in every four interfacial water molecules has a free (“dangling”) OH group that protrudes into the organic phase, plays a key role in catalyzing reactions via the formation of hydrogen bonds. Catalysis is expected when these OH's form stronger hydrogen bonds with the transition state than with the reactants. In experiments more than a 5 orders of magnitude enhancement in rate constant was found in a chosen reaction. The structural arrangement at the “oil−water” interface is in contrast to the structure of water molecules around a small hydrophobic solute in homogeneous solution, where the water molecules are tangentially oriented. The latter implies that a breaking of an existing hydrogen-bond network in homogeneous solution is needed in order to permit a catalytic effect of hydrogen bonds, but not for the on-water reaction. Thereby, the reaction in homogeneous aqueous solution is intrinsically slower than the surface reaction, as observed experimentally. The proposed mechanism of rate acceleration is discussed in light of other on-water reactions that showed smaller accelerations in rates. To interpret the results in different media, a method is given for comparing the rate constants of different rate processes, homogeneous, neat and on-water, all of which have different units, by introducing models that reduce them to the same units. The observed deuterium kinetic isotope effect is discussed briefly, and some experiments are suggested that can test the present interpretation and increase our understanding of the on-water catalysis.

S-Nitrosothiols (RSNOs) are important exogenous and endogenous sources of nitric oxide (NO) in biological systems. A series of 4-aryl-1,3,2-oxathiazolylium-5-olates derivatives with varying aryl para-substituents (−CF₃, −H, −Cl, and −OCH₃) were synthesized. These compounds were found to release NO under acidic condition (pH = 5). The decomposition pathway of the aryloxathiazolyliumolates proceeded via an acid-catalyzed ring-opening mechanism after which NO was released and an S-centered radical was generated. Electron paramagnetic resonance (EPR) spin trapping studies were performed to detect NO and the S-centered radical using the spin traps of iron(II) N-methyl-d-glucamine dithiocarbamate [(MGD)₂−Fe^II] and 5,5-dimethyl-1-pyrroline N-oxide (DMPO). Also, EPR spin trapping and UV−vis spectrophotometry were used to analyze the effect of aryl para substitution on the NO-releasing property of aryloxathiazolyliumolates. The results showed that the presence of an electron-withdrawing substituent such as −CF₃ enhanced the NO-releasing capability of the aryloxathiazolyliumolates, whereas an electron-donating substituent like methoxy (−OCH₃) diminished it. Computational studies using density functional theory (DFT) at the PCM/B3LYP/6-31+G**//B3LYP/6-31G* level were used to rationalize the experimental observations. The aryloxathiazolyliumolates diminished susceptibility to reduction by ascorbate or gluthathione, and their capacity to cause vasodilation as compared to other S-nitrosothiols suggests potential application in biological systems.

In this paper we present the synthesis as well as a detailed study of the electrochemical and photophysical properties of a series of neutral organic mixed-valence (MV) compounds, 1−7, in which different amine donor centers are connected to perchlorinated triarylmethyl radical units by various spacers. We show that this new class of compounds are excellent model systems for the investigation of electron transfer due to their uncharged character and, consequently, their excellent solubility, particularly in nonpolar solvents. A detailed band shape analysis of the intervalence charge-transfer (IV-CT) bands in the context of Jortner's theory allowed the electron-transfer parameters (inner vibrational reorganization energy λ_v, outer solvent reorganization energy λ_o, and the difference in the free energy between the diabatic ground and excited states, ΔG°°, as well as the averaged molecular vibrational mode ν̃_v) to be extracted independently. In this way we were able to analyze the solvatochromic behavior of the IV-CT bands by evaluating the contribution of each parameter. By comparison of different compounds, we were also able to assign specific molecular moieties to changes in ν̃_v. For this class of molecules, we also demonstrate that the adiabatic dipole moment difference Δμ_ab and, consequently, the electronic coupling V₁₂ can be evaluated directly from the absorption spectra by a new variant of the solvatochromic method. Furthermore, an investigation of the electrochemistry of compounds 1−7 by cyclic voltammetry as well as spectroelectrochemistry shows that, not only in the neutral MV compounds but also in their oxidized forms, a charge transfer can be optically induced but with exchanged donor−acceptor functionalities of the redox centers.

Despite the similarity in the active site pockets of carbonic anhydrase (CA) isozymes I and II, the binding affinities of benzenesulfonamide inhibitors are invariably higher with CA II as compared to CA I. To explore the structural basis of this molecular recognition phenomenon, we have designed and synthesized simple benzenesulfonamide inhibitors substituted at the para position with positively charged, negatively charged, and neutral functional groups, and we have determined the affinities and X-ray crystal structures of their enzyme complexes. The para-substituents are designed to bind in the midsection of the 15 Å deep active site cleft, where interactions with enzyme residues and solvent molecules are possible. We find that a para-substituted positively charged amino group is more poorly tolerated in the active site of CA I compared with CA II. In contrast, a para-substituted negatively charged carboxylate substituent is tolerated equally well in the active sites of both CA isozymes. Notably, enzyme−inhibitor affinity increases upon neutralization of inhibitor charged groups by amidation or esterification. These results inform the design of short molecular linkers connecting the benzenesulfonamide group and a para-substituted tail group in “two-prong” CA inhibitors:  an optimal linker segment will be electronically neutral, yet capable of engaging in at least some hydrogen bond interactions with protein residues and/or solvent. Microcalorimetric data reveal that inhibitor binding to CA I is enthalpically less favorable and entropically more favorable than inhibitor binding to CA II. This contrasting behavior may arise in part from differences in active site desolvation and the conformational entropy of inhibitor binding to each isozyme active site.

There has been a great interest in developing photoswitchable magnetic materials because of their possible applications for future high-density information storage media. In fact, however, the examples reported so far did not show ferromagnetic behavior at room temperature. From the viewpoint of their practical application to magnetic recording systems, the ability to fix their magnetic moments such that they still exhibit room-temperature ferromagnetism is an absolute requirement. Here, we have designed reversible photoswitchable ferromagnetic FePt nanoparticles whose surfaces were coated with azobenzene-derivatized ligands. On the surfaces of core particles, reversible photoisomerization of azobenzene in the solid state was realized by using spacer ligands that provide sufficient free volume. These photoisomerizations brought about changes in the electrostatic field around the core-FePt nanoparticles. As a result, we have succeeded in controlling the magnetic properties of these ferromagnetic composite nanoparticles by alternating the photoillumination in the solid state at room temperature.

Ricin Toxin A-chain (RTA) catalyzes the hydrolytic depurination of A₄₃₂₄, the first adenosine of the GAGA tetra-loop portion of 28S eukaryotic ribosomal RNA. Truncated stem-loop versions of the 28S rRNA are RTA substrates. Here, we investigate circular DNA and DNA/RNA hybrid GAGA sequence oligonucleotides as minimal substrates and inhibitor scaffolds for RTA catalysis. Closing the 5‘- and 3‘-ends of a d(GAGA) tetraloop creates a substrate with 92-fold more activity with RTA (k_cat/K_m) than that for the d(GAGA) linear form. Circular substrates have catalytic rates (k_cat) comparable to and exceeding those of RNA and DNA stem-loop substrates, respectively. RTA inhibition into the nanomolar range has been achieved by introducing an N-benzyl-hydroxypyrrolidine (N-Bn) transition state analogue at the RTA depurination site in a circular GAGA motif. The RNA/DNA hybrid oligonucleotide cyclic GdAGA provides a new scaffold for RTA inhibitor design, and cyclic G(N-Bn)GA is the smallest tight-binding RTA inhibitor (K_i = 70 nM). The design of such molecules that lack the base-paired stem-loop architecture opens new chemical synthetic approaches to RTA inhibition.

As part of an effort to expand the genetic alphabet, we examined the synthesis of DNA with six different unnatural nucleotides bearing methoxy-derivatized nucleobase analogues. Different nucleobase substitution patterns were used to systematically alter the nucleobase electronics, sterics, and hydrogen-bonding potential. We determined the ability of the Klenow fragment of E. coli DNA polymerase I to synthesize and extend the different unnatural base pairs and mispairs under steady-state conditions. Unlike other hydrogen-bond acceptors examined in the past, the methoxy groups do not facilitate mispairing, implying that they are not recognized by any of the hydrogen-bond donors of the natural nucleobases; however, they do facilitate replication. The more efficient replication results largely from an increase in the rate of extension of primers terminating at the unnatural base pair and, interestingly, requires that the methoxy group be at the ortho position where it is positioned in the developing minor groove and can form a functionally important hydrogen bond with the polymerase. Thus, ortho methoxy groups should be generally useful for the effort to expand the genetic alphabet.

This paper reports the design, synthesis, and characterization of a family of cyclic peptides that mimic protein quaternary structure through β-sheet interactions. These peptides are 54-membered-ring macrocycles comprising an extended heptapeptide β-strand, two Hao β-strand mimics [JACS 2000, 122, 7654] joined by one additional α-amino acid, and two δ-linked ornithine β-turn mimics [JACS 2003, 125, 876]. Peptide 3a, as the representative of these cyclic peptides, contains a heptapeptide sequence (TSFTYTS) adapted from the dimerization interface of protein NuG2 [PDB ID:  1mio]. ¹H NMR studies of aqueous solutions of peptide 3a show a partially folded monomer in slow exchange with a strongly folded oligomer. NOE studies clearly show that the peptide self-associates through edge-to-edge β-sheet dimerization. Pulsed-field gradient (PFG) NMR diffusion coefficient measurements and analytical ultracentrifugation (AUC) studies establish that the oligomer is a tetramer. Collectively, these experiments suggest a model in which cyclic peptide 3a oligomerizes to form a dimer of β-sheet dimers. In this tetrameric β-sheet sandwich, the macrocyclic peptide 3a is folded to form a β-sheet, the β-sheet is dimerized through edge-to-edge interactions, and this dimer is further dimerized through hydrophobic face-to-face interactions involving the Phe and Tyr groups. Further studies of peptides 3b−3n, which are homologues of peptide 3a with 1−6 variations in the heptapeptide sequence, elucidate the importance of the heptapeptide sequence in the folding and oligomerization of this family of cyclic peptides. Studies of peptides 3b−3g show that aromatic residues across from Hao improve folding of the peptide, while studies of peptides 3h−3n indicate that hydrophobic residues at positions R₃ and R₅ of the heptapeptide sequence are important in oligomerization.

Nanostructured host−guest materials are important for various applications in nanoscience, and therefore, a thorough understanding of the dynamics of the guest molecules within the host matrix is needed. To this aim we used single-molecule fluorescence techniques to simultaneously examine the spectral and the orientational behavior of single molecules in nanostructured porous host materials. Two types of host−guest systems have been investigated. First, oxazine-1 dye molecules were fixed rigidly in the channels of microporous AlPO₄-5 crystals. Second, it was shown that terrylenediimide (TDI) dye molecules move in the mesoporous network of an uncalcined M41S thin film. In the first sample both spectral fluctuations (∼5 nm) and rare spectral jumps (>10 nm) of the emission maximum were observed. However, the orientation of the emission dipole of the dye molecules remained constant. In contrast, the second system showed orientational dynamics as well as substantially more spectral dynamics. In this system the molecules were found to move between different regions in the host. The typical motion of the TDI molecules in the pores of M41S was not continuous but characterized by jumps between specific sites. Moreover, the spectral and orientational dynamics were correlated and arose directly from the different environments that were being explored by the mobile molecule.

We demonstrate the creation and observation of para-hydrogen-induced polarization in heterogeneous hydrogenation reactions. Wilkinson's catalyst, RhCl(PPh₃)₃, supported on either modified silica gel or a polymer, is shown to hydrogenate styrene into ethylbenzene and to produce enhanced spin polarizations, observed through NMR, when the reaction was performed with H₂ gas enriched in the para spin isomer. Furthermore, gaseous phase para-hydrogenation of propylene to propane with two catalysts, the Wilkinson's catalyst supported on modified silica gel and Rh(cod)(sulfos) (cod = cycloocta-1,5-diene; sulfos = ^-O₃S(C₆H₄)CH₂C(CH₂PPh₂)₃) supported on silica gel, demonstrates heterogeneous catalytic conversion resulting in large spin polarizations. These experiments serve as a direct verification of the mechanism of heterogeneous hydrogenation reactions involving immobilized metal complexes and can be potentially developed into a practical tool for producing catalyst-free fluids with highly polarized nuclear spins for a broad range of hyperpolarized NMR and MRI applications.

The highly electrophilic, coordinatively unsaturated, 16-electron [Ru(P(OH)₃)(dppe)₂][OTf]₂ (dppe = Ph₂PCH₂CH₂PPh₂) complex 1 activates the H−H, the Si−H, and the B−H bonds, in H₂(g), EtMe₂SiH and Et₃SiH, and H₃B·L (L = PMe₃, PPh₃), respectively, in a heterolytic fashion. The heterolysis of H₂ involves an η²-H₂ complex (observable at low temperatures), whereas the computations indicate that those of the Si−H and the B−H bonds proceed through unobserved η¹-species. The common ruthenium-containing product in these reactions is trans-[Ru(H)(P(OH)₃)(dppe)₂][OTf], 2. The [Ru(P(OH)₃)(dppe)₂][OTf]₂ complex is unique with regard to activating the H−H, the Si−H, and the B−H bonds in a heterolytic manner. These reactions and the heterolytic activation of the C−H bond in methane by the model complex [Ru(POH)₃)(H₂PCH₂CH₂PH₂)₂][Cl][OTf], 4, have been investigated using computational methods as well, at the B3LYP/LANL2DZ level. While the model complex activates the H−H, the Si−H, and the B−H bonds in H₂, SiH₄, and H₃B·L (L = PMe₃, PPh₃), respectively, with a low barrier, activation of the C−H bond in CH₄ involves a transition state of 57.5 kcal/mol high in energy. The inability of the ruthenium complex to activate CH₄ is due to the undue stretching of the C−H bond needed at the transition state, in comparison to the other substrates.

We systematically examined the mechanism of the solvent polarity dependence of the fluorescence ON/OFF threshold of the BODIPY (boron dipyrromethene) fluorophore and the role of photoinduced electron transfer (PeT). In a series of BODIPY derivatives with variously substituted benzene moieties at the 8-position, the oxidation potential of the benzene moiety became more positive and the reduction potential of the BODIPY fluorophore became more negative as the solvent polarity was decreased; consequently, the free energy change of PeT from the benzene moiety becomes larger in a more nonpolar environment. Utilizing this finding, we designed and synthesized a library of probes in which the threshold of fluorescence ON/OFF switching corresponds to different levels of solvent polarity. These environment-sensitive probes were used to examine bovine serum albumin (BSA) and living cells. The polarity at the surface of albumin was concluded to be similar to that of acetone, while the polarity of the internal membranes of HeLa cells was similar to that of dichloromethane.

The photochemistry of isomeric methoxyphenyl chlorides and phosphates has been examined in different solvents (and in the presence of benzene) and found to involve the triplet state. With the chlorides, C−Cl bond homolysis occurs in cyclohexane and is superseded by heterolysis in polar media, while the phosphate group is detached (heterolytically) only in polar solvents. Under such conditions, the isomeric triplet methoxyphenyl cations are the first formed intermediates from both precursors, but intersystem crossing (isc) to the singlets can take place. Solvent addition (forming the acetanilide in MeCN, the ethers in alcohols, overall a S_N1 solvolysis) is a diagnostic reaction for the singlet cation, as reduction and trapping by benzene are for the corresponding triplet. Solvolysis is most important with the meta isomer, for which the singlet is calculated (UB3LYP/6-31g(d)) to be the ground state of the cation (ΔE = 4 kcal/mol) and isc is efficient (k_isc ca. 1 × 10⁸ s^-1), and occurs to some extent with the para isomer (isoenergetic spin states, k_isc ca. 1.7 × 10⁶ s^-1). The triplet is the ground state with the ortho isomer, and in that case isc does not compete, although trapping by benzene is slow because of the hindering of C₁ by the substituent. The position of the substituent thus determines the energetic order of the cation spin states, in particular through the selective stabilization of the singlet by the m-methoxy group, a novel case of “meta effect”.

Cytosine methylation is one of the most important epigenetic events, and much effort has been directed to develop a simple reaction for methylcytosine detection. In this paper, we describe the design of tag-attachable ligands for direct methylcytosine labeling and their application to fluorescent and electrochemical assays. The effect of the location of bipyridine substituents on the efficiency of osmium complexation at methylcytosine was initially investigated. As a result, a bipyridine derivative with a substituent at the C4 position showed efficient complexation at the methylcytosine residue of single-stranded DNA in a reaction mixture containing potassium osmate and potassium hexacyanoferrate(III). On the basis of this result, a bipyridine derivative with a tag-attachable amino linker at the C4 position was synthesized. The efficiency of metal complex formation in the presence of the osmate and the synthetic ligand was clearly changed by the presence/absence of a methyl group at the C5 position of cytosine. The succinimidyl esters of functional labeling units were then attached to the bipyridine ligand fixed on the methylcytosine. These labels attached to methylcytosine enabled us to detect the target methylcytosine in DNA both fluorometrically and electrochemically. For example, we were able to fluorometrically obtain information on the methylation status at a specific site by means of fluorescence resonance energy transfer from a hybridized fluorescent DNA probe to a fluorescent label on methylcytosine. In addition, by the combination of electrochemically labeled methylcytosine and an electrode modified by probe DNAs, a methylcytosine-selective characteristic current signal was observed. This direct labeling of methylcytosine is a conceptually new methylation detection assay with many merits different from conventional assays.

Intraprotein interdomain electron transfer (IET) from flavin mononucleotide (FMN) to heme is essential in nitric oxide (NO) synthesis by NO synthase (NOS). Our previous laser flash photolysis studies have provided a direct determination of the kinetics of IET between the FMN and heme domains in truncated oxyFMN constructs of rat neuronal NOS (nNOS) and murine inducible NOS (iNOS), in which only the oxygenase and FMN domains along with the calmodulin (CaM) binding site are present [Feng, C. J.; Tollin, G.; Holliday, M. A.; Thomas, C.; Salerno, J. C.; Enemark, J. H.; Ghosh, D. K. Biochemistry 2006, 45, 6354−6362. Feng, C. J.; Thomas, C.; Holliday, M. A.; Tollin, G.; Salerno, J. C.; Ghosh, D. K.; Enemark, J. H. J. Am. Chem. Soc. 2006, 128, 3808−3811]. Here, we report the kinetics of IET between the FMN and heme domains in a rat nNOS holoenzyme in the presence and absence of added CaM using laser flash photolysis of CO dissociation in comparative studies on partially reduced NOS and a single domain NOS oxygenase construct. The IET rate constant in the presence of CaM is 36 s^-1, whereas no IET was observed in the absence of CaM. The kinetics reported here are about an order of magnitude slower than the kinetics in a rat nNOS oxyFMN construct with added CaM (262 s^-1). We attribute the slower IET between FMN and heme in the holoenzyme to the additional step of dissociation of the FMN domain from the reductase complex before reassociation with the oxygenase domain to form the electron-transfer competent output state complex. This work provides the first direct measurement of CaM-controlled electron transfer between catalytically significant redox couples of FMN and heme in a nNOS holoenzyme.

We report the creation and properties of colloidally stable shell-cross-linked cylindrical organometallic block copolymer micelles with adjustable length and swellability. The one-dimensional (1D) structures with semicrystalline polyferrocenylsilane (PFS) cores and polyisoprene (PI) coronas were initially self-assembled from PI-b-PFS block copolymers in a PI-selective solvent such as hexane. The length of the cylinders could be varied from hundreds of nanometers to several tens of micrometers by adjusting solution conditions, using various solvents such as hexane, decane, or hexane/THF (or toluene) mixtures. The cylindrical micelles with vinyl groups in the PI corona were cross-linked through a Pt(0)-catalyzed hydrosilylation reaction using 1,1,3,3-tetramethyl disiloxane as a cross-linker at room temperature. The shell cross-linking significantly increased the stability of the micelles relative to the un-cross-linked precursors as no fragmentation was observed upon sonication in solution. In addition, the structural integrity of the micelles was also enhanced after solvent removal; a solid sample was successfully microtomed and then examined using TEM, which revealed circular cross-sections for the PI-b-PFS micelles with an average diameter of ca. 15 nm. We also discovered that shell cross-linking is a prerequisite for generating ceramic replicas through the pyrolysis of PI-b-PFS aggregates. Moreover, we were able to pattern the cross-linked micelles on a flat substrate by microfluidic techniques, generating perpendicularly crossed lines of aligned micelles. In short, the shell-cross-linked PI-b-PFS 1D organometallic aggregates are a promising new type of nanomaterial with intriguing potential applications.

The gas sensing behaviors of cobalt phthalocyanine (CoPc) and metal-free phthalocyanine (H₂Pc) thin films were investigated with respect to analyte basicity. Chemiresistive sensors were fabricated by deposition of 50 nm thick films on interdigitated gold electrodes via organic molecular beam epitaxy (OMBE). Time-dependent current responses of the films were measured at constant voltage during exposure to analyte vapor doses. The analytes spanned a range of electron donor and hydrogen-bonding strengths. It was found that, when the analyte exceeded a critical base strength, the device responses for CoPc correlated with Lewis basicity, and device responses for H₂Pc correlated with hydrogen-bond basicity. This suggests that the analyte−phthalocyanine interaction is dominated by binding to the central cavity of the phthalocyanine with analyte coordination strength governing CoPc sensor responses and analyte hydrogen-bonding ability governing H₂Pc sensor responses. The interactions between the phthalocyanine films and analytes were found to follow first-order kinetics. The influence of O₂ on the film response was found to significantly affect sensor response and recovery. The increase of resistance generally observed for analyte binding can be attributed to hole destruction in the semiconductor film by oxygen displacement, as well as hole trapping by electron donor ligands.

Raw, micrometric HiPCO single wall carbon nanotube (SWNT) material was submitted to harsh acid oxidative treatment with a 3:1 H₂SO₄/HNO₃ mixture to give short residues of SWNT (s-SWNT, <200 nm length measured by TEM). s-SWNT was functionalized through the tip carboxylic groups by peptide bonds using 3-mercatopropanamine linkers that subsequently were reacted with 2,6-diphenyl-4-(4-vinylbiphenyl)pyrylium using azobis(isobutyronitrile) as a radical initiator. After purification by dialysis, the resulting s-SWNT having covalently linked through an ethylthiopropylamide tether the strong electron-transfer pyrylium photosensitizer (Py-sSWNT) was characterized by solution ¹H NMR spectroscopy (observation of specific signals due to the heterocyclic protons). Emission spectroscopy shows that the fluorescence of 2,6-diphenyl-4-(4-dodecylthiobiphenyl)pyrylium (Py-SC₁₂) tetrafluoroborate (a model compound to the tethered pyrylium moiety in Py-sSWNT) (λ_em 533 nm) is quenched by s-SWNT and vice versa that the emission of s-SWNT (λ_em 330 nm) is quenched by Py-SC₁₂. Depending on the excitation wavelength, Py-sSWNT exhibits dual emission corresponding to each of the two moieties, but with much less intensity than each of the model components independently. Laser flash photolysis of model Py-SC₁₂ allows detection of the triplet (λ_T-T 750 nm, τ 11.7 μs) and the much longer-lived pyrylium centered radical (λ_max 525 nm, τ 147 μs). The latter species arises from photoinduced electron transfer from the sulfur atom, as the donor, to the pyrylium heterocycle in its electronic excited-state, as the electron acceptor. Laser flash photolysis (355 nm) of Py-sSWNT also allows detection of the pyrylium centered radical together with a broad absorption spanning from 200 to 500 nm and peaking at 280 nm. The latter band is absent in the laser flash photolysis of the model s-SWNT and was attributed to the electron hole localized on the nanotube moiety of Py-SWNT. The most remarkable effect of the steady-state irradiation is a 1 order of magnitude increase in the solubility of Py-sSWNT. According to TEM images this photoinduced solubility can be attributed to the debundling of the nanotubes due to photoinduced charge separation through the nanotube walls. In addition to exemplify how molecular compounds with photoresponsive properties can be derived from SWNT materials, the observation of photoinduced solubility can serve to develop SWNT layers suitable for photolithography patterning.

Structural analysis of flexible macromolecular systems such as intrinsically disordered or multidomain proteins with flexible linkers is a difficult task as high-resolution techniques are barely applicable. A new approach, ensemble optimization method (EOM), is proposed to quantitatively characterize flexible proteins in solution using small-angle X-ray scattering (SAXS). The flexibility is taken into account by allowing for the coexistence of different conformations of the protein contributing to the experimental scattering pattern. These conformers are selected using a genetic algorithm from a pool containing a large number of randomly generated models covering the protein configurational space. Quantitative criteria are developed to analyze the EOM selected models and to determine the optimum number of conformers in the ensemble. Simultaneous fitting of multiple scattering patterns from deletion mutants, if available, provides yet more detailed local information about the structure. The efficiency of EOM is demonstrated in model and practical examples on completely or partially unfolded proteins and on multidomain proteins interconnected by linkers. In the latter case, EOM is able to distinguish between rigid and flexible proteins and to directly assess the interdomain contacts.

Two novel series of polyfluorinated amino acids (PFAs) were designed and synthesized according to a very short and scalable synthetic sequence. The advantages and limitations of these moieties for screening purposes are presented and discussed. The potential applications of these PFAs were tested with their incorporation into small arginine-containing peptides that represent suitable substrates for the enzyme trypsin. The enzymatic reactions were monitored by ¹⁹F NMR spectroscopy, using the 3-FABS (three fluorine atoms for biochemical screening) technique. The high sensitivity achieved with these PFAs permits a reduction in substrate concentration required for 3-FABS. This is relevant in the utilization of 3-FABS in fragment-based screening for identification of small scaffolds that bind weakly to the receptor of interest. The large dispersion of ¹⁹F isotropic chemical shifts allows the simultaneous measurement of the efficiency of the different substrates, thus identifying the best substrate for screening purposes. Furthermore, the knowledge of K_M and K_cat for the different substrates allows the identification of the structural motifs responsible for the binding affinity to the receptor and those affecting the chemical steps in enzymatic catalysis. This enables the construction of suitable pharmacophores that can be used for designing nonpeptidic inhibitors with high affinity for the enzyme or molecules that mimic the transition state. The novel PFAs can also find useful application in the FAXS (fluorine chemical shift anisotropy and exchange for screening) experiment, a ¹⁹F-based competition binding assay for the detection of molecules that inhibit the interaction between two proteins.

Recent experimental work on fast protein folding brings about an intriguing paradox. Microsecond-folding proteins are supposed to fold near or at the folding speed limit (downhill folding), but yet their folding behavior seems to comply with classical two-state analyses, which imply the crossing of high free energy barriers. However, close inspection of chemical and thermal denaturation kinetic experiments in fast-folding proteins reveals systematic deviations from two-state behavior. Using a simple one-dimensional free energy surface approach we find that such deviations are indeed diagnostic of marginal folding barriers. Furthermore, the quantitative analysis of available fast-kinetic data indicates that many microsecond-folding proteins fold downhill in native conditions. All of these proteins are then promising candidates for an atom-by-atom analysis of protein folding using nuclear magnetic resonance.¹ We also find that the diffusion coefficient for protein folding is strongly temperature dependent, corresponding to an activation energy of ∼1 kJ·mol^-1 per protein residue. As a consequence, the folding speed limit at room temperature is about an order of magnitude slower than the ∼ 1 μs estimates from high-temperature T-jump experiments. Our analysis is quantitatively consistent with the available thermodynamic and kinetic data on slow two-state folding proteins and provides a straightforward explanation for the apparent fast-folding paradox.

Single wall carbon nanotubes (SWNTs) bind strongly to sapphyrins, quintessential pentapyrrolic “expanded porphyrin” macrocycles, through donor−acceptor stacking interactions. The specific use of a functionalized sapphyrin diol yields stable water-suspendable nanotubes and also permits the formation of well-defined assemblies in ionic liquids. The absorption and steady-state fluorescence spectra of the resulting noncovalently functionalized nanotube complexes have been analyzed in aqueous media and ionic liquids, yielding a description of the photophysical properties of the nanotube−sapphyrin complexes as donor−acceptor species for light-harvesting.

To better understand the molecular basis for recognition of the DNA minor groove by heterocyclic cations, a series of “reversed amidine” substituted heterocycles has been prepared. Amidine derivatives for targeting the minor groove have the amidine carbon linked to a central heterocyclic system, whereas in the reverse orientation, an amidine nitrogen provides the link. The reverse system has a larger dihedral angle as well as a modified spatial relationship with the groove relative to amidines. Because of the large dihedral, the reversed amidines should have reduced binding to DNA relative to similar amidines. Such a reduction is observed in footprinting, circular dichroism (CD), biosensor-surface plasmon resonance (SPR), and isothermal titration calorimetric (ITC) experiments with DB613, which has a central phenyl-furan-phenyl heterocyclic system. The reduction is not seen when a pyrrole (DB884) is substituted for the furan. Analysis of a number of derivatives defines the pyrrole and a terminal phenyl substituent on the reversed amidine groups as critical components in the strong binding of DB884. ITC and SPR comparisons showed that the better binding of DB884 was due to a more favorable binding enthalpy and that it had exceptionally slow dissociation from DNA. Crystallographic analysis of DB884 bound to an AATT site shows that the compound was bound in the minor groove in a 1:1 complex as suggested by CD solution studies. Surprisingly, unlike the amidine derivative, the pyrrole −NH of DB884 formed an H-bond with a central T of the AATT site and this accounts for the enthalpy-driven strong binding. The structural results and molecular modeling studies provide an explanation for the differences in binding affinities for related amidine and reversed amidine analogues.

The threading behavior of a zinc analogue of a previously reported processive manganese porphyrin catalyst onto a series of polymers of different lengths is reported. It is demonstrated that the speed of the threading process is determined by the opening of the cavity of the toroidal porphyrin host, which can be tuned with the help of axial ligands that coordinate to the metal center in the porphyrin.

Lamellar structure of poly(Ala-Gly) or (AG)_n in the solid was examined using ¹³C solid-state NMR and statistical mechanical approaches. Two doubly labeled versions, [1-¹³C]Gly¹⁴[1-¹³C]Ala¹⁵- and [1-¹³C]Gly¹⁸[1-¹³C]Ala¹⁹ of (AG)₁₅ were examined by two-dimensional (2D) ¹³C spin diffusion NMR in the solid state. In addition five doubly labeled [¹⁵N,¹³C]-versions of the same peptide, (AG) ₁₅ and 15 versions labeled [3-¹³C] in each of the successive Ala residues were utilized for REDOR and ¹³C CP/MAS NMR measurements, respectively. The observed spin diffusion NMR spectra were consistent with a structure containing a combination of distorted β-turns with a large distribution of the torsion angles and antiparallel β-sheets. The relative proportion of the distorted β-turn form was evaluated by examination of ¹³C CP/MAS NMR spectra of [3-¹³C]Ala-(AG)₁₅. In addition, REDOR determinations showed five kinds of atomic distances between doubly labeled ¹³C and ¹⁵N nuclei which were also interpreted in terms of a combination of β-sheets and β-turns. Our statistical mechanical analysis is in excellent agreement with our Ala Cβ ¹³C CP/MAS NMR data strongly suggesting that (AG)₁₅ has a lamellar structure.

Unsymmetrical cyanine dyes are widely used in biomolecular detection due to their fluorogenic behavior, whereby fluorescence quantum yields can be very low in fluid solution but are significantly enhanced in conformationally restricted environments. Herein we describe a series of fluorinated analogues of the dye thiazole orange that exhibit improved fluorescence quantum yields and photostabilities. In addition, computational studies on these dyes revealed that twisting about the monomethine bridge beyond an interplanar angle of 60° leads to a dark state that decays nonradiatively to the ground state, accounting for the observed fluorogenic behavior. The effects of position and number of fluorine substituents correlate with both observed quantum yield and calculated activation energy for twisting beyond this critical angle.

Membrane protein orientation has traditionally been determined by NMR using mechanically or magnetically aligned samples. Here we show a new NMR approach that abolishes the need for preparing macroscopically aligned membranes. When the protein undergoes fast uniaxial rotation around the bilayer normal, the 0°-frequency of the motionally averaged powder spectrum is identical to the frequency of the aligned protein whose alignment axis is along the magnetic field. Thus, one can use unoriented membranes to determine the orientation of the protein relative to the bilayer normal. We demonstrate this approach on the M2 transmembrane peptide (M2TMP) of influenza A virus, which is known to assemble into a proton-conducting tetrameric helical bundle. The fast uniaxial rotational diffusion of the M2TMP helical bundle around the membrane normal is characterized via ²H quadrupolar couplings, C−H and N−H dipolar couplings, ¹³C chemical shift anisotropies, and ¹H T_1ρ relaxation times. We then show that ¹⁵N chemical shift anisotropy and N−H dipolar coupling measured on these powder samples can be analyzed to yield precise tilt angles and rotation angles of the helices. The data show that the tilt angle of the M2TMP helices depends on the membrane thickness to reduce the hydrophobic mismatch. Moreover, the orientation of a longer M2 peptide containing both the transmembrane domain and cytoplasmic residues is similar to the orientation of the transmembrane domain alone, suggesting that the transmembrane domain regulates the orientation of this protein and that structural information obtained from M2TMP may be extrapolated to the longer peptide. This powder-NMR approach for orientation determination is generally applicable and can be extended to larger membrane proteins.

Dome-shaped gold nanoparticles (with an average diameter of 10.5 nm) are grown on H-terminated Si(100) substrates by simple techniques involving electro- and electroless deposition from a 0.05 mM AuCl₃ and 0.1 M NaClO₄ solution. XPS depth profiling data (involving Au 4f core-level and valence band spectra) reveal for the first time the formation of gold silicide at the interface between the Au nanoparticles and Si substrate. UV−visible diffuse reflectance spectra indicate that both samples have surface plasmon resonance maxima at 558 nm, characteristic of an uniform distribution of Au nanoscale particles of sufficiently small size. Glancing-incidence XRD patterns clearly show that the deposited Au nanoparticles belong to the fcc phase, with the relative intensity of the (220) plane for Au nanoparticles obtained by electroless deposition found to be notably larger than that by electrodeposition.

Helical rosette nanotubes (RNTs) are obtained through the self-assembly of the G∧C motif, a self-complementary DNA base analogue featuring the complementary hydrogen bonding arrays of both guanine and cytosine. The first step of this process is the formation of a 6-membered supermacrocycle (rosette) maintained by 18 hydrogen bonds, which then self-organizes into a helical stack defining a supramolecular sextuple helix whose chirality and three-dimensional organization arise from the chirality, chemical structure, and conformational organization of the G∧C motif. Because a chiral G∧C motif is predisposed to express itself asymmetrically upon self-assembly, there is a natural tendency for it to form one chiral RNT over its mirror image. Here we describe the synthesis and characterization of a chiral G∧C motif that self-assembles into helical RNTs in methanol, but undergoes mirror image supramolecular chirality inversion upon the addition of very small amounts of water (<1% v/v). Extensive physical and computational studies established that the mirror-image RNTs obtained, referred to as chiromers, result from thermodynamic (in water) and kinetic (in methanol) self-assembly processes involving two conformational isomers of the parent G∧C motif. Although derived from conformational states, the chiromers are thermodynamically stable supramolecular species, they display dominant/recessive behavior, they memorize and amplify their chirality in an achiral environment, they change their chirality in response to solvent and temperature, and they catalytically transfer their chirality. On the basis of these studies, a detailed mechanism for supramolecular chirality inversion triggered by specific molecular interactions between water molecules and the G∧C motif is proposed.

A combined kinetic and DFT study of the uncatalyzed isomerization of cationic solvent complexes of the type cis-[Pt(R‘)(S)(PR₃)₂]⁺ (R‘ = linear and branched alkyls or aryls and S = solvents) to their trans isomers has shown that the reaction goes through the rate-determining dissociative loss of the weakly bonded molecule of the solvent and the interconversion of two geometrically distinct T-shaped 14-electron three-coordinate intermediates. The Pt−S dissociation energy is strongly dependent on the coordinating properties of S and independent of the nature of R‘. The energy barrier for the fluxional motion of [Pt(R‘)(PR₃)₂]⁺ is comparatively much lower (≈8−21 kJ mol^-1). The presence of β-hydrogens on the alkyl chain (R‘ = Et, Prⁿ, and Buⁿ) produces a great acceleration of the reaction rate. This accelerating effect has been defined as the β-hydrogen kinetic effect, and it is a consequence of the stabilization of the transition state and of the cis-like three-coordinate [Pt(R‘)(PR₃)₂]⁺ intermediate through an incipient agostic interaction. The DFT optimization of [Pt(R‘)(PMe₃)₂]⁺ (R‘ = Et, Prⁿ, and Buⁿ) reproduces a classical dihapto Pt····η²-HC agostic mode between the unsaturated metal and a dangling C−H bond. The value of the agostic stabilization energy (in the range of ≈21−33 kJ mol^-1) was estimated by both kinetic and computational data and resulted in being independent of the length of the hydrocarbon chain of the organic moiety. A better understanding of such interactions in elusive reaction intermediates is of primary importance in the control of reaction pathways, especially for alkane activation by metal complexes.

This paper introduces a fundamentally new concept in adsorbents, whereby the sorption of an aqueous solute by a cross-linked polymer is controlled by a gel to liquid-crystalline phase transition. To demonstrate proof of principle, a bilayer forming surfactant, N,N-dioctadecyl,N,N-dimethylammonium bromide (DODAB) has been immobilized onto a cation exchange resin, Dowex 50WX2, and its thermotropic phase behavior and solute-adsorption properties have been investigated. Examination by a combination of differential scanning calorimetry and X-ray scattering has confirmed the retention of a gel to liquid-crystalline phase transition of the surfactant, occurring between 296 and 318 K. Adsorption measurements that were made for 4-chlorotetrahydropyran, 1,2-dichloroethane, and benzyl alcohol have also confirmed uptake by the resin in the liquid-crystalline phase and release in the gel phase.

The catalytic promiscuity of E. coli alkaline phosphatase (AP) and many other enzymes provides a unique opportunity to dissect the origin of enzymatic rate enhancements via a comparative approach. Here, we use kinetic isotope effects (KIEs) to explore the origin of the 10⁹-fold greater catalytic proficiency by AP for phosphate monoester hydrolysis relative to sulfate monoester hydrolysis. The primary ¹⁸O KIEs for the leaving group oxygen atoms in the AP-catalyzed hydrolysis of p-nitrophenyl phosphate (pNPP) and p-nitrophenylsulfate (pNPS) decrease relative to the values observed for nonenzymatic hydrolysis reactions. Prior linear free energy relationship results suggest that the transition states for AP-catalyzed reactions of phosphate and sulfate esters are “loose” and indistinguishable from that in solution, suggesting that the decreased primary KIEs do not reflect a change in the nature of the transition state but rather a strong interaction of the leaving group oxygen atom with an active site Zn²⁺ ion. Furthermore, the primary KIEs for the two reactions are identical within error, suggesting that the differential catalysis of these reactions cannot be attributed to differential stabilization of the leaving group. In contrast, AP perturbs the KIE for the nonbridging oxygen atoms in the reaction of pNPP but not pNPS, suggesting a differential interaction with the transferred group in the transition state. These and prior results are consistent with a strong electrostatic interaction between the active site bimetallo Zn²⁺ cluster and one of the nonbridging oxygen atoms on the transferred group. We suggest that the lower charge density of this oxygen atom on a transferred sulfuryl group accounts for a large fraction of the decreased stabilization of the transition state for its reaction relative to phosphoryl transfer.

The Rh-catalyzed reaction of alkynes with 2-bromophenylboronic acids involves carbonylative cyclization to give indenones. The key steps in the reaction involve the addition of an arylrhodium(I) species to an alkyne and the oxidative addition of C−Br bonds on the adjacent phenyl ring to give vinylrhodium(I) species II. The regioselectivity depends on both the electronic and the steric nature of the substituents on the alkynes. A bulky group and an electron-withdrawing group favor the α-position of indenones. In the case of silyl- or ester-substituted alkynes, the regioselectivity is extremely high. The selectivity increases in the order SiMe₃ > COOR ≫ aryl ≫ alkyl. The reaction of norbornene with 2-bromophenylboronic acids under 1 atm of CO gives the corresponding indanone derivative. The reaction of alkynes with 2-bromophenylboronic acids under nitrogen gives naphthalene derivatives, in which two molecules of alkynes are incorporated. A vinylrhodium complex similar to II can also be generated by a different route by employing 2-bromophenyl(trimethylsilyl)acetylene and arylboronic acids in the presence of Rh(I) complex as the catalyst, resulting in the formation of indenones. The reaction of 1-(2-bromophenyl)-hept-2-yn-1-one with PhB(OH)₂ in the presence of Rh(I) complex also resulted in carbonylative cyclization to give an indan-1,3-dione derivative.

The first organocatalytic enantioselective 1,6-addition of β-ketoesters and benzophenone imine to electron-poor δ-unsubstituted dienes using cinchona alkaloids under phase-transfer conditions is demonstrated. The scope of the reaction for the β-ketoesters is outlined for reactions with different δ-unsubstituted dienes having ketones, esters, and sulfones as electron-withdrawing substituents giving the corresponding optically active products in good yields and enantioselectivities in the range of 90−99% ee. The 1,6-addition also proceeds with a number of cyclic β-ketoesters having different ring sizes, ring systems and substituents in high yields and enantioselectivities. The potential of this new organocatalytic 1,6-addition for β-ketoesters is demonstrated by a two-step synthesis of the bicyclo[3.2.1]octan-8-one structure, a bicyclic bridged skeleton occurring in a variety of natural compounds. Benzophenone imines also undergo the organocatalytic asymmetric 1,6-addition to the activated dienes in high yields and with enantioselectivities from 92% to 98% ee, except in one case. The synthetic utility of this asymmetric reaction is demonstrated by the two-step transformation of the allylated α-amino acid derivative to highly attractive optically active pyrrolidines.