Organic synthesis Publications

Electronnuclear double resonance (ENDOR) is a powerful tool for determining the spatial and electronic structure of paramagnetic systems. It often suffers from a limited signal-to-noise ratio (SNR), particularly for small hyperfine couplings, which correspond to long-range electronnuclear distances. We implement a Hadamard frequency multiplexing strategy to enhance the sensitivity in frequency-domain ENDOR spectroscopy. This method makes use of simultaneous or sequential excitation of multiple nuclear frequencies within a single pulse sequence, with spectral reconstruction via a Hadamard transform. Using fluorine ENDOR of fluorinated small molecules and spin-labeled proteins, we demonstrate up to 2-fold improvement in SNR. Approaches that mitigate the limitations of radiofrequency power and relaxation effects are presented, making this strategy useful for both organic radicals and paramagnetic metal complexes. Beyond ENDOR, Hadamard encoded acquisition also improves electron double resonance detected NMR sensitivity, suggesting broad applicability across EPR methods that rely on frequency sweeps.

Time-domain electronnuclear double resonance (ENDOR) was employed to determine the nuclear decoherence rate (1/T2n) of fluorine nuclei in four model Gd(III) chelates of varying structures, over the temperature range 3.710 K. These complexes are derivatives of Gd(III) spin labels used in 19F-ENDOR distance measurements, which emerged as an efficient method for measuring short-range distances in biomolecules. It was found that the 19F decoherence originates primarily from electron spin flips, following the relationship T2n ≈ 2T1e, where T1e is the Gd(III) spinlattice relaxation time. The obtained 19F decoherence rates (18 kHz) indicate that the intrinsic 19F-ENDOR line widths are small relative to other broadening contributions, and therefore do not significantly limit distance resolution of 19F ENDOR. Proton decoherence measurements were carried out for comparison, revealing two 1H populations with different relaxation rates; the faster component was sensitive to the matrix protonation and attributed to dipolar flip-flops among weakly coupled protons, a mechanism absent for 19F. These results elucidate key factors affecting ENDOR resolution and provide new insights into the nuclear spin relaxation mechanism in paramagnetic systems.

¹⁹F electron-nuclear double resonance (ENDOR) has emerged as an attractive method for determining distance distributions in biomolecules in the range of 0.7-2 nm, which is not easily accessible by pulsed electron dipolar spectroscopy. The ¹⁹F ENDOR approach relies on spin labeling, and in this work, we compare various labels performance. Four protein variants of GB1 and ubiquitin bearing fluorinated residues were labeled at the same site with nitroxide and trityl radicals and a Gd(iii) chelate. Additionally, a double-histidine variant of GB1 was labeled with a Cu(ii) nitrilotriacetic acid chelate. ENDOR measurements were carried out at W-band (95 GHz) where ¹⁹F signals are well separated from ¹H signals. Differences in sensitivity were observed, with Gd(iii) chelates providing the highest signal-to-noise ratio. The new trityl label, OXMA, devoid of methyl groups, exhibited a sufficiently long phase memory time to provide an acceptable sensitivity. However, the longer tether of this label effectively reduces the maximum accessible distance between the ¹⁹F and the C_α of the spin-labeling site. The nitroxide and Cu(ii) labels provide valuable additional geometric insights via orientation selection. Prediction of electron-nuclear distances based on the known structures of the proteins were the closest to the experimental values for Gd(iii) labels, and distances obtained for Cu(ii) labeled GB1 are in good agreement with previously published NMR results. Overall, our results offer valuable guidance for selecting optimal spin labels for ¹⁹F ENDOR distance measurement in proteins.

The lag phase is key in resuming bacterial growth, but it remains underexplored particularly in environmental bacteria. Here we use transcriptomics and 13C-labelled metabolomics to show that the lag phase of the model marine bacterium Phaeobacter inhibens is shortened by methylated compounds produced by the microalgal partner, Emiliania huxleyi. Methylated compounds are abundantly produced and released by microalgae, and we show that their methyl groups can be collected by bacteria and assimilated through the methionine cycle. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and highlight the adjustability of this growth phase. In addition, we show that methylated compounds, typical of photosynthetic organisms, prompt diverse reductions in lag times in bacteria associated with algae and plants, potentially favouring early growth in some bacteria. These findings suggest ways to accelerate bacterial growth and underscore the significance of studying bacteria within an environmental context.

Fluorine electron-nuclear double resonance (¹⁹F ENDOR) has recently emerged as a valuable tool in structural biology for distance determination between F atoms and a paramagnetic center, either intrinsic or conjugated to a biomolecule via spin labeling. Such measurements allow access to distances too short to be measured by double electron-electron resonance (DEER). To further extend the accessible distance range, we exploit the high-spin properties of Gd(III) and focus on transitions other than the central transition (|−1/2⟩ ↔ |+1/2⟩), that become more populated at high magnetic fields and low temperatures. This increases the spectral resolution up to ca. 7 times, thus raising the long-distance limit of ¹⁹F ENDOR almost 2-fold. We first demonstrate this on a model fluorine-containing Gd(III) complex with a well-resolved ¹⁹F spectrum in conventional central transition measurements and show quantitative agreement between the experimental spectra and theoretical predictions. We then validate our approach on two proteins labeled with ¹⁹F and Gd(III), in which the Gd-F distance is too long to produce a well-resolved ¹⁹F ENDOR doublet when measured at the central transition. By focusing on the |−5/2⟩ ↔ |−3/2⟩ and |−7/2⟩ ↔ |−5/2⟩ EPR transitions, a resolution enhancement of 4.5- and 7-fold was obtained, respectively. We also present data analysis strategies to handle contributions of different electron spin manifolds to the ENDOR spectrum. Our new extended ¹⁹F ENDOR approach may be applicable to Gd-F distances as large as 20 Å, widening the current ENDOR distance window.

Studies of protein structure and dynamics are usually carried out in dilute buffer solutions, conditions that differ significantly from the crowded environment in the cell. The double electron-electron resonance (DEER) technique can track proteins conformations in the cell by providing distance distributions between two attached spin labels. This technique, however, cannot access distances below 1.8 nm. Here, we show that Gd ^III- ¹⁹F Mims electron-nuclear double resonance (ENDOR) measurements can cover part of this short range. Low temperature solution and in-cell ENDOR measurements, complemented with room temperature solution and in-cell Gd ^III- ¹⁹F PRE (paramagnetic relaxation enhancement) NMR measurements, were performed on fluorinated GB1 and ubiquitin (Ub), spin-labeled with rigid Gd ^III tags. The proteins were delivered into human cells via electroporation. The solution and in-cell derived Gd ^III- ¹⁹F distances were essentially identical and lie in the 11.5 nm range revealing that both, GB1 and Ub, retained their overall structure in the Gd ^III and ¹⁹F regions in the cell.

It is an open question whether the conformations of proteins sampled in dilute solutions are the same as in the cellular environment. Here we address this question by double electron-electron resonance (DEER) distance measurements with Gd(III) spin labels to probe the conformations of calmodulin (CaM) in vitro, in cell extract, and in human HeLa cells. Using the CaM mutants N53C/T110C and T34C/T117C labeled with maleimide-DOTA-Gd(III) in the N- and C-terminal domains, we observed broad and varied interdomain distance distributions. The in vitro distance distributions of apo-CaM and holo-CaM in the presence and absence of the IQ target peptide can be described by combinations of closed, open, and collapsed conformations. In cell extract, apo- and holo-CaM bind to target proteins in a similar way as apo- and holo-CaM bind to IQ peptide in vitro. In HeLa cells, however, in the presence or absence of elevated in-cell Ca2+ levels CaM unexpectedly produced more open conformations and very broad distance distributions indicative of many different interactions with in-cell components. These results show-case the importance of in-cell analyses of protein structures.

Chirp and shaped pulses have been recently shown to be highly advantageous for improving sensitivity in DEER (double electronelectron resonance, also called PELDOR) measurements due to their large excitation bandwidth. The implementation of such pulses for pulse EPR has become feasible due to the availability of arbitrary waveform generators (AWG) with high sampling rates to support pulse shaping for pulses with tens of nanoseconds duration. Here we present a setup for obtaining chirp pulses on our home-built W-band (95 GHz) spectrometer and demonstrate its performance on Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements. We carried out an extensive optimization procedure on two model systems, Gd(III)-PyMTAspacerGd(III)-PyMTA (Gd-PyMTA ruler; zero-field splitting parameter (ZFS) D ∼ 1150 MHz) as well as nitroxidespacernitroxide (nitroxide ruler) to evaluate the applicability of shaped pulses to Gd(III) complexes and nitroxides, which are two important classes of spin labels used in modern DEER/EPR experiments. We applied our findings to ubiquitin, doubly labeled with Gd-DOTA-monoamide (D ∼ 550 MHz) as a model for a system with a small ZFS. Our experiments were focused on the questions (i) what are the best conditions for positioning of the detection frequency, (ii) which pump pulse parameters (bandwidth, positioning in the spectrum, length) yield the best signal-to-noise ratio (SNR) improvements when compared to classical DEER, and (iii) how do the sample's spectral parameters influence the experiment. For the nitroxide ruler, we report an improvement of up to 1.9 in total SNR, while for the Gd-PyMTA ruler the improvement was 3.13.4 and for Gd-DOTA-monoamide labeled ubiquitin it was a factor of 1.8. Whereas for the Gd-PyMTA ruler the two setups pump on maximum and observe on maximum gave about the same improvement, for Gd-DOTA-monoamide a significant difference was found. In general the choice of the best set of parameters depends on the D parameter of the Gd(III) complex.

By providing accurate distance measurements between spin labels site-specifically attached to bio-macromolecules, double electron-electron resonance (DEER) spectroscopy provides a unique tool to probe the structural and conformational changes in these molecules. Gd³⁺-tags present an important family of spin-labels for such purposes, as they feature high chemical stability and high sensitivity in high-field DEER measurements. The high sensitivity of the Gd³⁺ ion is associated with its high spin (S = 7/2) and small zero field splitting (ZFS), resulting in a narrow spectral width of its central transition at high fields. However, under the conditions of short distances and exceptionally small ZFS, the weak coupling approximation, which is essential for straightforward DEER data analysis, becomes invalid and the pseudo-secular terms of the dipolar Hamiltonian can no longer be ignored. This work further explores the effects of pseudo-secular terms on Gd³⁺-Gd³⁺ DEER measurements using a specifically designed ruler molecule; a rigid bis-Gd³⁺-DOTA model compound with an expected Gd³⁺-Gd³⁺ distance of 2.35 nm and a very narrow central transition at the W-band (95 GHz). We show that the DEER dipolar modulations are damped under the standard W-band DEER measurement conditions with a frequency separation, Δν, of 100 MHz between the pump and observe pulses. Consequently, the DEER spectrum deviates considerably from the expected Pake pattern. We show that the Pake pattern and the associated dipolar modulations can be restored with the aid of a dual mode cavity by increasing Δν from 100 MHz to 1.09 GHz, allowing for a straightforward measurement of a Gd³⁺-Gd³⁺ distance of 2.35 nm. The increase in Δν increases the contribution of the -5/2〉 → -3/2〉 and -7/2〉 → -5/2〉 transitions to the signal at the expense of the -3/2 〉 → -1/2〉 transition, thus minimizing the effect of dipolar pseudo-secular terms and restoring the validity of the weak coupling approximation. We apply this approach to the A93C/N140C mutant of T4 lysozyme labeled with two different Gd³⁺ tags that have narrow central transitions and show that even for a distance of 4 nm there is still a significant (about two-fold) broadening that is removed by increasing Δν to 636 MHz and 898 MHz.

Methods based on pulse electron paramagnetic resonance allow measurement of the electron-electron dipolar coupling between two spin labels. Here we compare the most popular technique, Double Electron-Electron Resonance (DEER or PELDOR), with the dead-time free 5-pulse Relaxation-Induced Dipolar Modulation Enhancement (RIDME) method for Gd(iii)-Gd(iii) distance measurements at W-band (94.9 GHz, ≈3.5 T) using Gd(iii) tags with a small zero field splitting (ZFS). Such tags are important because of their high EPR sensitivity arising from their narrow central transition. Two systems were investigated: (i) a rigid model compound with an inter-spin distance of 2.35 nm, and (ii) two mutants of a homodimeric protein, both labeled with a DOTA-based Gd(iii) chelate and characterized by an inter-spin distance of around 6 nm, one having a narrow distance distribution and the other a broad distribution. Measurements on the model compound show that RIDME is less sensitive to the complications arising from the failure of the weak coupling approximation which affect DEER measurements on systems characterized by short inter-spin distances between Gd(iii) tags having a narrow central transition. Measurements on the protein samples, which are characterized by a long inter-spin distance, emphasize the complications due to the appearance of harmonics of the dipolar interaction frequency in the RIDME traces for S > 1/2 spin systems, as well as enhanced uncertainties in the background subtraction. In both cases the sensitivity of RIDME was found to be significantly better than DEER. The effects of the experimental parameters on the RIDME trace are discussed.

Although Gd³⁺-based spin labels have been shown to be an alternative to nitroxides for double electron-electron resonance (DEER) distance measurements at high fields, their ability to provide solvent accessibility information, as nitroxides do, has not been explored. In addition, the effect of the label type on the measured distance distribution has not been sufficiently characterized. In this work, we extended the applicability of Gd³⁺ spin labels to solvent accessibility measurements on a peptide in model membranes, namely, large unilamellar vesicles (LUVs) using W-band ²H Mims electron-nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) techniques and Gd³⁺-ADO3A-labeled melittin. In addition, we carried out Gd³⁺-Gd³⁺ DEER distance measurements to probe the peptide conformation in solution and when bound to LUVs. A comparison with earlier results reported for the same system with nitroxide labels shows that, although in both cases the peptide binds parallel to the membrane surface, the Gd³⁺-ADO3A label tends to protrude from the membrane into the solvent, whereas the nitroxide does the opposite. This can be explained on the basis of the hydrophilicity of the Gd³⁺-ADO3A labels in contrast with the hydrophobicity of nitroxides. The distance distributions obtained from different labels are accordingly different, with the Gd³⁺-ADO3A yielding consistently broader distributions. These discrepancies are most pronounced when the peptide termini are labeled, which implies that such labeling positions may be inadvisible.

High-frequency double electron-electron resonance (DEER) distance measurements using different Gd³⁺ tags (Gd-DOTA and Gd-C1) were carried out on transmembrane helical peptides (ca. 0.15-nmol; WALP peptides) in a model membrane. The ability to pick up small distance variations, the chemical flexibility of the tags, and the remarkable absolute sensitivity, make this approach attractive for studies of membrane proteins.

Deuterium magic angle spinning (MAS) NMR is used to study the dynamics of an organic molecule, N-[triethoxysilylpropyl]acetamide-d₃, grafted at the inner surface of the mesoporous silica material, MCM-41. The grafted molecule has a deuterated methyl group at its free terminus to monitor its local mobility through changes in its dynamic ²H-MAS NMR spectrum. Different spectra were recorded as a function of temperature from two different water containing samples. Observation shows that a major part of the grafted molecule remains static, irrespective of the temperature and hydration state of the sample, whereas the rest shows spectral changes indicative of a two-site jump motion of the methyl groups. Experimental observations were substantiated using molecular dynamic (MD) simulations of the grafted molecule. Subsequently, the MD results corroborate a model for the grafted molecules experiencing an exchange between two conformations consistent with the analysis of the ²H-MAS NMR spectra.

The potential for manipulation and control inherent in molecule-based motors holds great scientific and technological promise. Molecules containing the azobenzene group have been heavily studied in this context. While the effects of the cis-trans isomerization of the azo group in such molecules have been examined macroscopically by a number of techniques, modulations of the elastic modulus upon isomerization in self-assembled films were not yet measured directly. Here, we examine the mechanical response upon optical switching of bis[(1,1'-biphenyl)-4-yl]diazene organized in a self-assembled film on Au islands, using atomic force microscopy. Analysis of higher harmonics by means of a torsional harmonic cantilever allowed real-time extraction of mechanical data. Quantitative analysis of elastic modulus maps obtained simultaneously with topographic images show that the modulus of the cis-form is approximately twice that of the trans-isomer. Quantum mechanical and molecular dynamics studies show good agreement with this experimental result, and indicate that the stiffer response in the cis-form comprises contributions both from the individual molecular bonds and from intermolecular interactions in the film. These results demonstrate the power and insights gained from cutting-edge AFM technologies, and advanced computational methods.

Self-assembled organic monolayers serve for modifying the work function of inorganic substrates. We examine the role of the molecular backbone in determining monolayer-adsorbed work function, by considering the adsorption of dithiols with either a partially conjugated or a saturated backbone on the GaAs(001) surface. Using a combination of chemically resolved electrical measurements based on X-ray photo-electron spectroscopy and contact potential difference, together with first principles electronic structure calculations, we are able to distinguish quantitatively between the contributions of the band bending and surface dipole components. We find that the substrates coated by partially conjugated layers possess a larger band-bending, relative to that of the substrates coated by saturated layers. This is associated with an increased density of surface states, likely related to the presence of oxygen. At the same time, the samples coated by partially conjugated layers also possess a larger bond-dipole, with the difference found to result primarily from an extended charge rearrangement on the molecular backbone. The two effects are, in this case, of opposite sign, but a significant net change in work function is still found. Thus, design of the molecular backbone emerges as an additional and important degree of freedom in the design of potential profiles and charge injection barriers in monolayer-based structures and devices.

Self-assembly (SA) of amphophilic block copolymers (polyethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)) was investigated in dispersions of multi-walled carbon nanotubes (MWNT) as a function of temperature using spin probe electron paramagnetic resonance (EPR) spectroscopy. Nitroxidelabeled Pluronic with a short poly(ethylene oxide) block, L62-NO, and a small molecular probe, 4-hydroxy-TEMPO-benzoate, 4HTB, were used for probing the local dynamic and polarity of the polymer chains in the presence of the nanostructures. It was found that MWNT modify the temperature and the dynamic behavior of polymer SA and comparison between the MWNT and single-walled nanotube (SWNT) showed that the structure and dynamical behavior of the nanostructure-polymer hybrids formed depend on the size matching between the diameter of the native micelles and the additives. While SWNT induced the formation of hybrid polymer-SWNT micelles, MWNT (with a diameter of 20-40 nm) induced the assembly of polymer aggregates at the surface of the MWNT.

We present a new approach to obtain details on the distribution and average structure and locations of membrane-associated peptides. The approach combines (i) pulse double electron-electron resonance (DEER) to determine intramolecular distances between residues in spin labeled peptides, (ii) electron spin echo envelope modulation (ESEEM) experiments to measure water exposure and the direct interaction of spin labeled peptides with deuterium nuclei on the phospholipid molecules, and (iii) Monte Carlo (MC) simulations to derive the peptide-membrane populations, energetics, and average conformation of the native peptide and mutants mimicking the spin labeling. To demonstrate the approach, we investigated the membrane-bound and solution state of the well-known antimicrobial peptide melittin, used as a model system. A good agreement was obtained between the experimental results and the MC simulations regarding the distribution of distances between the labeled amino acids, the side chain mobility, and the peptide's orientation. A good agreement in the extent of membrane penetration of amino acids in the peptide core was obtained as well, but the EPR data reported a somewhat deeper membrane penetration of the termini compared to the simulations. Overall, melittin adsorbed on the membrane surface, in a monomelic state, as an amphipatic helix with its hydrophobic residues in the hydrocarbon region of the membrane and its charged and polar residues in the lipid headgroup region.

Pulse double electron-electron spin resonance (DEER) measurements were applied to characterize the distribution and average number of guest-molecules (in the form of spin-probes) in Pluronic P123 micelles. Two types of spin-probes were used, one of which is a spin-labeled P123 (P123-NO), which is similar to the micelles constituent molecules, and the other is spin-labeled Brij56 (Brij56-NO) which is significantly different. Qualitative information regarding the relative location of the spin-labels within the micelles was obtained from the isotropic hyperfine coupling and the correlation times, determined from continuous wave EPR measurements. In addition, complementary small angle X-ray scattering (SAXS) measurements on the P123 micellar solutions, with and without the spin-probes, were carried out for an independent determination of the size of the core and corona of the micelles and to ensure that the spin-probes do not alter the size or shape of the micelles. Two approaches were used for the analysis of the DEER data. The first is model free, which is based on the determination of the leveling off value of the DEER kinetics. This provided good estimates of the number of radicals per micelle (low limit) which, together with the known concentration of the P123 molecules, gave the aggregation number of the P123 micelles. In addition, it provided an average distance between radicals which is within the range expected from the micelles size determined by SAXS. The second approach was to analyze the full kinetic form which is model dependent. This analysis showed that both spin-labels are not homogeneously distributed in either a sphere or a spherical shell, and that large distances are preferred. This analysis yielded a slightly larger occupation volume within the micelle for P123-NO than for Brij56-NO, consistent with their chemical character.

This study focuses on the formation mechanism of the bicontinuous cubic Ia3̄d mesoporous material KIT-6, both on the molecular and on the mesoscopic levels. KIT-6 is synthesized with Pluronic P123 (PEO ₂₀PPO₇₀PEO₂₀), low acid concentration, and n-butanol at 40°C. Through in situ EPR measurements on a series of spin-labeled Pluronic molecules introduced at minute quantities into the reaction mixture, changes in the hydrophobicity and the mobility of the polymer chains during the reaction were observed. In addition, to learn more on the functionality of the butanol in this synthesis, freeze-quench electron spin-echo envelope modulation (ESEEM) measurements on reaction mixtures in D₂O and in butanol-d₁₀ were preformed. The above experiments gave information on variations in the butanol location and content in the micellar structures during the formation of KIT-6. The evolution of the solution nanostructures was determined by cryo-TEM. Five main stages were resolved: the first two occurred during the first 140 min of the reaction, where condensation of the silica oligomers takes place at the micellar/water interface; this induces depletion of water and butanol molecules from the core - corona interface and reduces the mobility of the ends of the Pluronic chains located at the corona - water interface. This in turn leads to a transition from spheroidal micelles to threadlike micelles and to their aggregation toward the end of the second stage. During the third stage, precipitation (140-160 min), reorganization in the micellar structure, and a change in the relative sizes of core and corona take place. The fourth stage, that ends around 6 h, involves the formation of a hexagonal phase, through accelerated condensation of silica oligomers in the corona, accompanied by extensive depletion of water and butanol molecules. The presence of butanol in the micelle corona is essential in the last stage, 6-24 h, where the cubic phase is formed. We show that the addition of butanol to the reaction mixture of SBA-15 after the formation of the hexagonal phase leads to the formation of the cubic phase.

The isoflavones biochanin A (1a), genistein (1b), and daidzein (4) at concentrations >20 μM inhibit cell growth of various cancer cell lines. To enhance the antiproliferative activities of these compounds, we synthesized three analogs, 2-[3-carboxy-(6-tert-butoxycarbonylamino)-hexylamino-propyl]-7,5- dihydroxy-4-methoxyisoflavone (3a), 2-[3-[N-[6-(tert-butoxycarbonyl)- aminohexyl]]-caboxamidopropyl]-5,7,4-trihydroxyisoflavone (3b), and 5-{2-[3-(4-hydroxy-phenyl)-4-oxo-4H-chromen-7-yloxy]-acetylamino}-pentyl) -carbamic acid tert-butyl ester (6). When cancer cells expressing predominantly estrogen receptor mRNA of the β- relative to α-subtype were treated with 3a, 3b, or 6, DNA synthesis was inhibited in a dose-dependent manner, ranging from 15 to 3000 nmol/L, with little inhibitory effect in normal vascular smooth muscle cells. Compound 6 was the most potent one, and its antiproliferative effect in cancer cells was modulated by estrogen and by the apoptosis inhibitor Z-VADFK. When tested in vivo, compound 6 decreased tumor volume of ovarian xenografts by 50%, with no apparent toxicity. Compound 6 may be a promising agent for therapy of cancer either alone or in combination with chemotherapeutic agents.

We have developed a biochip platform technology suitable for controlled cell-free gene expression at the micrometer scale. A new hybrid molecule, "Daisy", was designed and synthesized to form in a single step a biocompatible lithographic interface on silicon dioxide. A protocol is described for the immobilization of linear DNA molecules thousands of base pairs long on Daisy-coated surfaces with submicrometer spatial resolution and up to high densities. On-chip protein synthesis can be obtained with a dynamic range of up to four orders of magnitude and minimal nonspecific activity. En route to on-chip artificial gene circuits, a simple two-stage gene cascade was built, in which the protein synthesized at the first location diffuses to regulate the synthesis of another protein at a second location. We demonstrate the capture of proteins from crude extract onto micrometer-scale designated traps, an important step for the formation of miniaturized self-assembled protein chips. Our biochip platform can be combined with elastomeric microfluidic devices, thereby opening possibilities for isolated and confined reaction chambers and artificial cells in which the transport of products and reagents is done by diffusion and flow. The Daisy molecule and described approach enables groups not proficient in surface chemistry to construct active biochips based on cellfree gene expression.

Solid-state NMR has been used to analyze the chemical environments of sodium sites in powdered crystalline samples of sodium nucleotide complexes. Three of the studied complexes have been previously characterized structurally by crystallography (disodium deoxycytidine-5-monophosphate heptahydrate, disodium deoxyuridine-5-monophosphate pentahydrate and disodium adenosine-5-triphosphate trihydrate). For these salts, the nuclear quadrupole coupling parameters measured by ²³Na multiple-quantum magic-angle-spinning NMR could be readily correlated with sodium ion coordination environments. Furthermore, two complexes that had not been previously characterized structurally, disodium uridine-3-monophosphate and a disodium uridine-3-monophosphate/disodium uridine-2- monophosphate mix, were identified by solid-state NMR. A spectroscopic assignment of the four sites of an additional salt, disodium adenosine-5-triphosphate trihydrate, is also presented and discussed within the context of creating a general approach for the spectroscopic assignment of multiple sites in sodium nucleotide complexes.

The local dynamics of aromatic cores was analyzed for a homologous series of polyamides in the solid phase incorporating phenyl, biphenyl and naphthyl groups. Preliminary wide-line and spin-relaxation variable-temperature ¹H NMR measurements revealed the presence of thermally activated molecular motions for each polymer studied. A number of ¹³C NMR experiments were then implemented to further clarify the nature and extent of such motions. These included ¹H-¹³C 2D separate-local-field measurements, whose line shapes revealed that motions involved for all cases a superposition of states. These could in principle be associated with rigid and mobile populations in these semi-crystalline aramides, a model that yielded a proper description of the spectra at all temperatures. To further probe this model the relaxation behavior of the aramides' ¹³C spins was monitored in the rotating frame as a function of temperature, in both the presence and absence of homonuclear ¹H- ¹H decoupling. The variations observed in these measurements evidenced a thermally activated, relatively broad distribution of motional rates in the polymers. Editing the 2D local-field data according to the ¹³C relaxation also supported this heterogeneous dynamic model. The mechanism underlying this behavior and implications towards the ¹³C analysis of motions in aramides in particular and complex polymers in general, is briefly discussed.

In this study we show how deuterium magic-angle spinning NMR spectroscopy can be used to investigate the adsorption-desorption kinetics of molecules in solution at surface-liquid interfaces. An aqueous solution of deuterium-labeled tetraalanine is inserted in the pores of MCM-41 mesoporous material, and its ²H MAS NMR spectrum is measured as a function of temperature and fraction of filling of the pores. Prior to this study, the different types of water in MCM-41 are characterized as a function of water loading of the pores. Analysis of ²H MAS sideband line shapes enabled the determination of the adsorption and desorption rates and the activation energies of desorption.

Hyaluronan, a high molecular weight, negatively charged polysaccharide, is a major constituent of the extracellular matrix. High molecular weight hyaluronan is antiangiogenic, but its degradation by hyaluronidase generates proangiogenic breakdown products. Thus, by expression of hyaluronidase, cancer cells can tilt the angiogenic balance of their microenvironment. Indeed, hyaluronidase-mediated breakdown of hyaluronan correlates with aggressiveness and invasiveness of ovarian cancer metastasis and with tumor angiogenesis. The goal of this work was to develop a novel smart contrast material for detection of hyaluronidase activity by magnetic resonance imaging (MRI). Gadolinium-diethylenetriaminepentaacetic acid (GdDTPA) covalently linked to hyaluronan on the surface of agarose beads showed attenuated relaxivity. Hyaluronidase, either purified from bovine testes or secreted by ES-2 and OVCAR-3 human epithelial ovarian carcinoma cells, activated the hyaluronan-GdDTPA-beads by rapidly altering the R₁ and R₂ relaxation rates. The change in relaxation rates was consistent with the different levels of biologically active hyaluronidase secreted by those cells. Hyaluronan-GdDTPA-beads were further used for demonstration of MRI detection of hyaluronidase activity in the proximity of s.c. ES-2 ovarian carcinoma tumors in nude mice. Thus, hyaluronan-GdDTPA-beads could allow noninvasive molecular imaging of hyaluronidase-mediated tilt of the peritumor angiogenic balance.

The properties of the silica layer during the formation of the mesoporous material MCM-41 were investigated by electron paramagnetic resonance (EPR) experiments carried out on a specifically designed, organo(trialkoxy)-silane spin probe, SL1SiEt. Minute amounts of the spin probe were co-condensed with the silica source, tetraethyl orthosilicate (TEOS), in the synthesis of MCM-41 with cetyltrimethylammonium bromide (CTAB) under basic conditions. The mobility and location of the spin probe were followed in the CTAB micellar solution before the reaction, in the reaction mixture and in the final ordered material. It was found that the EPR spectra of hydrolyzed SL1SiEt throughout the room temperature part of the reaction are characteristic of a fast tumbling species, indicating that the silica is highly fluid prior to drying. After filtering, a slow motion type spectrum was observed, showing that the spin-label experiences considerable motional hindrance. The liquidlike behavior could be restored upon stirring the material in water. When the reaction is performed with a hydrothermal stage, the spectrum of SL1SiEt in the final product is the same as that of the room temperature synthesized material, but the addition of water did not restore the high mobility, due to a higher degree of silica cross-linking. The location of SL1SiEt throughout the formation process was obtained from electron spin-echo envelope modulation (ESEEM) measurements on MCM-41 prepared with CTAB deuterated either at the N-methyl or the a position and in a reaction carried out in D₂O. Comparing the deuterium modulation depth, k(²H), induced by CTAB-α-d₂, CTAB-d₉, or D₂O in CTAB micellar solutions of a number of reference spin probes with those of SL1SiEt revealed that the hydrolyzed SL1SiEt is located near the polar heads of the surfactant in the absence of base and TEOS. This supports the postulation of charge matching at the interface as a driving force for the formation of the mesostructure. Similar experiments carried out on reaction mixtures containing SL1SiEt showed a decrease of k(²H) from CTAB-α-d₂ and CTAB-d₉ compared to the micellar solution, exhibiting practically no time dependence. This indicates that the spin probe is pulled away from the micelle-water interface into the loosely linked, forming silica network. After drying, the modulation depth induced by CTAB-α-d₂ and CTAB-d₉ increases, showing that, once the water is removed, the silica walls contract around the micelles, pushing the silica-linked spin probe into the organic phase within the mesopores.

Electrical conduction through molecules depends critically on the delocalization of the molecular electronic orbitals and their connection to the metallic contacts. Thiolated (-SH) conjugated organic molecules are therefore considered good candidates for molecular conductors: in such molecules, the orbitals are delocalized throughout the molecular backbone, with substantial weight on the sulphur-metal bonds. However, their relatively small size, typically ∼1 nm, calls for innovative approaches to realize a functioning single-molecule device. Here we report an approach for contacting a single molecule, and use it to study the effect of localizing groups within a conjugated molecule on the electrical conduction. Our method is based on synthesizing a dimer structure, consisting of two colloidal gold particles connected by a dithiolated short organic molecule, and electrostatically trapping it between two metal electrodes. We study the electrical conduction through three short organic molecules: 4,4-biphenyldithiol (BPD), a fully conjugated molecule; bis-(4-mercaptophenyl)-ether (BPE), in which the conjugation is broken at the centre by an oxygen atom; and 1,4- benzenedimethanethiol (BDMT), in which the conjugation is broken near the contacts by a methylene group. We find that the oxygen in BPE and the methylene groups in BDMT both suppress the electrical conduction relative to that in BPD.

The initial formation stages of the Mesoporous material SBA-15 by using spin-labeled block co-polymer templates was investigated. The formation of SBA-15 was discussed on the molecular level, with emphasis on the early stages of the reaction, when interaction between silica precursors and the Pluronic micelles occured. The combination of in situ X-band electron parmagnetic resonance (EPR) spectroscopy and electron spin-echo envelop modulation (ESEEM) experiments of Pluronic spin probes with different PEO and PPO chain lengths were used to achieve the mesoporous material. The result show that the silica polymerization propagated outward from the core/corona interface.

SBA-15 is an hexagonal mesoporous material which is synthesized with nonionic poly(ethylene oxide)-poly-(propylene oxide)-poly(ethylene oxide) block copolymers (Pluronics, EO_yPO_xEO_y), templates. Pore diameters in the range of 2-30 nm can be obtained with a relatively thick silica wall (up to 6 nm). This material possesses both large, uniform, and ordered channels, along with a complementary net of micropores which provides connectivity between the ordered channels through the silica. This study focuses on the investigation of the formation mechanism of SBA-15 with emphasis on the PEO interactions with the silica and the initiation of the micropores. This was achieved using in situ X-band EPR spectroscopy in combination with electron spin-echo envelope modulation (ESEEM) experiments. The paramagnetic centers were introduced as spin-labeled Pluronic L62 (EO₆PO₃₀EO₆) where nitroxides replace the OH groups at the end of the polypropylene oxide (PEO) blocks (L62-NO). Initially, the acidic reaction conditions were adjusted to prevent the decomposition of the nitroxide radical, while still producing highly ordered SBA-15. Then, the locations of the nitroxides of L62-NO within the micelles of Pluronic P123 (y = 20, x = 70) and L64 (y = 13, x = 30) were determined through three-pulse ESEEM experiments on solutions prepared in D₂O. In these experiments, the ²H modulation induced by D₂O was compared with that of a series of small spin-probes with known hydrophilic and hydrophobic characters that were introduced into the micelles. The NO group of L62-NO was found to be close to the core-corona interface in both types of Pluronics. The temporal evolution of the EPR spectrum during the reaction showed that for SBA-15 made with P123 the most significant changes in the L62-NO spectrum occur within the first 100 min. Furthermore, X-ray diffraction measurements of dried materials showed that the hexagonal structure of SBA-15 is also created within the first 2 h. A partitioning of the L62-NO between the precursors of the mesopores and micropores of the SBA-15 structure takes place at the very early stages of the reaction, and a continuous depletion of water within the corona-core interface was observed. In the final product obtained without a thermal stage, the majority of the PEO chains are located in the micropores. The extent of the PEO chains located within the silica micropores depends on the thermal stage temperature and on the Si/P123 molar ratio. In the L64 synthesis, practically all of the NO groups of L62-NO are located within the silica network and experience a single environment.

The local ordering, morphology, and dynamics of aromatic cores and flexible alkyl spacers were analyzed for a homologous series of main-chain polymeric liquid crystals. ¹³C NMR experiments showed that the nematic ordering achieved by these synthetic polymers was retained into the solid state if their quenchings occur while remaining within the strong NMR magnetic field. The degree of orientation in the resulting glasses was investigated by variable-angle NMR experiments and found to differ between polymers with an even number of methylene units in the flexible spacer vs those with an odd number. To further discern at a molecular level the nature of these differences, the structures of these polyesters were examined by high-resolution solid-state ¹³C NMR. It was found that while the odd-chained series displayed a conformational annealing upon aligning, even-chained polymers were generally in all-trans conformations both for as-synthesized and for aligned samples. Variable-temperature 1D and 2D NMR experiments also illustrated substantial differences in the degree of motional dynamics between the odd and even polymer series: whereas considerable rigidity was exhibited by the even-numbered series all the way up to 150 °C, a relatively high flexibility displayed by the odd-methylene polymers. In unison, these measurements provide insight into the significant changes that can be imparted into the structure and dynamics of main-chain thermotropic polymers by subtle manipulations of their monomeric structures.

Although magnesium fulfills several essential biochemical roles, direct studies on this ion are complicated by its unfavorable spectroscopic characteristics. This contribution explores the possibility of monitoring magnesium-nucleic acid binding via a combination of [Co(NH₃)₆]³⁺ as surrogate for [Mg(H₂O)₆]²⁺, and of high-resolution solid-state ⁵⁹Co NMR as a spectroscopic probe. Such strategy quenches fast cationic exchanges between bound and free states, while exploiting the superior NMR properties of the ⁵⁹Co spin. Experiments on relatively small amounts of tRNA can then discern resonances corresponding to different metal binding environments. These characterizations were assisted by studies on model compounds and by multinuclear ³¹P-⁵⁹Co recoupling experiments.

A general treatment of the residual 1-S dipolar couplings that arise when heteronuclear quadrupolar spin pairs are subjected to MAS is presented. The resulting model yields analytical expressions for the multiplet structure of 1D S-spin spectra.

The order and dynamics of two lyotropic aromatic polyamides were studied by variable-director nuclear magnetic resonance (NMR). The spectra showed peaks shifting as well as broadening as a function of the director's orientation which are accounted on the basis of an exchange model involving molecular reorientations of the polymer chains that are happening in the intermediate NMR time scale. The description of the macromolecular order and dynamics in these fluids was extracted from the experimental line shapes.