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The use of functionalized nanoparticles (NPs) and their aggregation in the presence of a targeted analyte is a well-established molecular detection strategy predicated on harnessing specific molecular interactions to the NP periphery. Molecules able to specifically interact with the functionalized NPs alter the unique optical and electrochemical properties of the NPs as a function of interparticle spacing. While many intermolecular interactions have been successfully exploited in this manner in conjunction with aqueous NP systems, the use of non-aqueous NPs in the same capacity is significantly less explored. A fundamental interaction that has not been previously investigated in NP schemes is halogen bonding (XB). XB is an orthogonal, electrostatic interaction between a region of positive electrostatic potential (δ+) on a halogen atom (i.e., XB donor) and a negative (δ-) Lewis base (XB acceptor) molecule. To couple XB with NP systems, ligands featuring a molecular structure that promotes XB interactions need to be identified, optimized, and synthesized for subsequent attachment to NPs. Herein, density functional theory (DFT) and NMR techniques are used to identify a strong XB-donor moiety (-C

Halogen bonding (XB) is a highly directional, non-covalent intermolecular interaction between a molecule (XB donor) presenting a halogen with an electron-deficient region or sigma hole (σ-hole) and an electron-rich or Lewis-base molecule (XB acceptor). A systematic, experimental, and theoretical study of solution-phase XB strength as a function of the molecular structure for both XB donor and acceptor molecules is presented. The impact of specific structural features is assessed using 19F and 1H nuclear magnetic resonance (NMR) titrations to determine association constants, density functional theory calculations for interaction energies and bond lengths, as well as 19F-1H HOESY NMR measurements of intermolecular cross-relaxation between the interacting XB donor-acceptor adducts. For XB donor molecules (perfluoro-halogenated benzenes), results indicate the critical importance of iodine coupled with electron-withdrawing entities. Prominent structural components of XB acceptor molecules include a central atom working in conjunction with a Lewis-base atom to present high electron density directed at the σ-hole (e.g., tributylphosphine oxide). Additionally, larger surrounding aliphatic R groups (e.g., butyl and octyl) were found to significantly stabilize strong XB, particularly in solvents that promote the interaction. With a more thorough understanding of structure-optimized XB, one can envision harnessing XB interactions more strategically for specific design of optimal materials and chemical applications.

Two stereoregular 2D polyesters were synthesized by using topochemical polymerization of symmetric four-armed monomers. The monomers contain reactive carbon–carbon double bond(s) on each arm. The critical assemblies with multiple preorganized reactive centers were characterized by powder and single crystal X-ray diffraction. The solvent-free polymerization could be carried out with sunlight or UV irradiation. The locally confined photopolymerization process dimerized all of the olefins within the 2D bricklayer packing, which led to the formation of 2D polymers in the solid state. The process was monitored by FT-IR, and the products were confirmed by solid state NMR. After hydrolysis of the 2D polyester, the newly formed carbon–carbon single bonds during the [2 + 2] photocyclization were directly revealed by the single crystal structure of the hydrolysis product. Ultrathin sheets of the 2D polymer were observed under SEM and TEM after exfoliation.

Consequences of nuclear spin are presented, moving from an isolated spin to an ensemble of spins. Detection of the nuclear magnetic resonance (NMR) signal is briefly touched upon, following by a presentation of the information content of the NMR signal, including chemical shift, signal intensity, spin-spin coupling, and dipolar coupling. A short list of commonly used NMR experiments is given, followed by a discussion of the methodology used to pair NMR signals and the molecular sites from whence they arise.

The NMR spectra of taxadiene are assigned in Section 4.1 . Section 4.2 presents the logical methodology by which the structure of the twenty-carbon-containing isooxacyclotaxane (isoOCT) is deduced.

Five molecules of considerable complexity are presented. The NMR spectra of these molecules are assigned, by pairing observed NMR signals with NMR-active molecular sites.

The 1 H and 13 C NMR spectra of several large molecules are presented. The molecular sites and NMR signals of these molecules are paired to one another.

Photoalignment of nematic liquid crystals is demonstrated using a di-π-methane rearrangement of a designed polymer. The alignment mechanism makes use of the strong coupling of the liquid crystal directors to dibenzobarrelene groups. The large structural changes that accompany photoisomerization effectively passivate segments of the polymer, allowing the remaining dibenzobarrelene groups to dominate the director alignment. Photoisomerization requires triplet sensitization, and the polymer was designed to have a uniaxially fixed rigid structure and rapid triplet energy transfer from the proximate benzophenone units to the dibenzobarrelene groups. The isomerization was observed to be regiospecific, and thin films showed alignment.

Addition of ethylene to Mo(NAr)(CHCMe2Ph)(OHIPT)(Pyr) (NAr = N-2,6-i-Pr2C6H3, OHIPT = O-2,6-(2,4,6-i-Pr3C6H2)2C6H3, Pyr = NC4H4) led to the trigonal-bipyramidal metallacyclobutane complex Mo(NAr)(C...

Two diastereomers of the monoalkoxidepyrrolide (MAP) species, W(NAr)(CH(2))(Me(2)Pyr)(OR*) (1; Ar = 2,6-diisopropylphenyl, Me(2)Pyr = 2,5-dimethylpyrrolide, OR* = (R)-3,3'-dibromo-2'-(tert-butyldimethylsilyloxy)-5,5',6,6',7,7',8,8'-octahydro-1,1'-binaphthyl-2-olate), were generated through addition of R*OH to W(NAr)(CH(2))(Me(2)Pyr)(2). The unsubstituted tungstacyclobutane species, W(NAr)(C(3)H(6))(Me(2)Pyr)(OR*) (2), was isolated by treating the mixture of diastereomers of 1 with ethylene. An X-ray study revealed 2 to have a trigonal bipyramidal structure in which the imido and phenoxide ligands are in axial positions. A variety of NMR experiments were carried out on 1 and 2. The major findings are the following: (i) the methylidene ligands in the two diastereomers of 1 rotate readily about the W horizontal lineC bond (k = 2-7 s(-1) at 22 degrees C); (ii) NMR studies are consistent with 2 breaking up to give an intermediate alkylidene/ethylene complex, (R)- and (S)-W(CH(2))(C(2)H(4)); and (iii) the ethylene in the (R)-W(CH(2))(C(2)H(4)) intermediate can rotate about the W-ethylene bond axis at approximately the same rate as 2 re-forms or ethylene is lost to give 1. Compound 1 reacts with trimethylphosphine to yield (R)-1(PMe(3)). Two intermediate PMe(3) adducts were observed and found to convert to (R)-1(PMe(3)) in an intramolecular fashion with an average rate constant at 5 degrees C of approximately 1.4 x 10(-4) s(-1). Both neophylidene (4) and methylidene (5) MAP species containing 2,3,5,6-tetraphenylphenoxide ligand also were prepared. Compound 5 can be heated to 80 degrees C, where methylidene rotation about the W=C bond is facile and observable in a variable-temperature (1)H NMR spectrum. A (1)H-(1)H EXSY spectrum of 5 in benzene-d(6) at 20 degrees C showed that the methylidene protons are exchanging with k = 90 s(-1). A structure of 5(THF) showed it to be a square pyramid with the methylidene ligand in the apical position and THF coordinated trans to the imido ligand. Exposure of 5 to ethylene generated the tungstacyclobutane complex, W(NAr)(C(3)H(6))(Me(2)Pyr)(OR) (6), whose structure is analogous to that of 2. Treatment of 5 with PMe(3) yielded yellow 5(PMe(3)), an X-ray study of which revealed it to be a square pyramid with the methylidene ligand in the apical position and the phosphine trans to the pyrrolide. These studies suggest that metallacyclobutane intermediates in metathesis reactions with MAP species are likely to contain axial imido and phenoxide ligands, that metallacycles are formed when an olefin approaches the metal in a MAP species trans to the pyrrolide, and that the configuration at the metal inverts as a consequence of each forward metathesis step.

The anticancer molecule taxol (Paclitaxel) stands as one of the most medically and economically important natural products. However, despite decades of extensive study, its biosynthesis remains poorly understood. Unpredictable behavior of the first oxygenation enzyme, taxadiene-5α-hydroxylase, which produces a range of undesired products, currently stands as a key bottleneck to improved taxol production. We herein present chemical and biological evidence of an unreported epoxidase activity of taxadiene-5α-hydroxylase that puts into question the previously proposed radical-rebound mechanism. We demonstrate that the poor selectivity of taxadiene-5α-hydroxylase arises from nonselective degradation of an epoxide intermediate produced via a selective oxidation step, rather than from promiscuous oxidation, as previously proposed. We support these conclusions by demonstrating variable enzyme behavior in differing hosts and conditions, similarity of products and product ratios generated from chemical epoxidation, and taxadiene-5α-hydroxylase, and differing enzymatic activity on alternative taxadiene isomers. Additionally, we use directed mutagenesis to describe the oxidizing species of the P450, demonstrate that further in vivo functionalization of oxidized taxadiene is unable to improve selectivity of the oxidation, and show that multiple products are produced in the Taxus cuspidata and are not simply an artifact of heterologous expression. Our results highlight an important, and previously unknown, obstacle to improved taxol production. We further offer insights to overcome the challenges posed by an epoxide-mediated reaction, which sets the basis for further engineering of taxol biosynthesis.

Viral lethal mutagenesis is a strategy whereby the innate immune system or mutagenic pool nucleotides increase the error rate of viral replication above the error catastrophe limit. Lethal mutagenesis has been proposed as a mechanism for several antiviral compounds, including the drug candidate 5-aza-5,6-dihydro-2'-deoxycytidine (KP1212), which causes A-to-G and G-to-A mutations in the HIV genome, both in tissue culture and in HIV positive patients undergoing KP1212 monotherapy. This work explored the molecular mechanism(s) underlying the mutagenicity of KP1212, and specifically whether tautomerism, a previously proposed hypothesis, could explain the biological consequences of this nucleoside analog. Establishing tautomerism of nucleic acid bases under physiological conditions has been challenging because of the lack of sensitive methods. This study investigated tautomerism using an array of spectroscopic, theoretical, and chemical biology approaches. Variable temperature NMR and 2D infrared spectroscopic methods demonstrated that KP1212 existed as a broad ensemble of interconverting tautomers, among which enolic forms dominated. The mutagenic properties of KP1212 were determined empirically by in vitro and in vivo replication of a single-stranded vector containing a single KP1212. It was found that KP1212 paired with both A (10%) and G (90%), which is in accord with clinical observations. Moreover, this mutation frequency is sufficient for pushing a viral population over its error catastrophe limit, as observed before in cell culture studies. Finally, a model is proposed that correlates the mutagenicity of KP1212 with its tautomeric distribution in solution.

We report here the polymerization of several 7-isopropylidene-2,3-disubstituted norbornadienes, 7-oxa-2,3-dicarboalkoxynorbornadienes, and 11-oxa-benzonorbornadienes with a single tungsten oxo alkylidene catalyst, W(O)(CH-t-Bu)(OHMT)(Me2Pyr) (OHMT = 2,6-dimesitylphenoxide; Me2Pyr = 2,5-dimethylpyrrolide) to give cis, stereoregular polymers. The tacticities of the menthyl ester derivatives of two polymers were determined for two types. For poly(7-isopropylidene-2,3-dicarbomenthoxynorbornadiene) the structure was shown to be cis,isotactic, while for poly(7-oxa-2,3-dicarbomenthoxynorbornadiene) the structure was shown to be cis,syndiotactic. A bis-trifluoromethyl-7-isopropylidene norbornadiene was not polymerized stereoregularly with W(O)(CHCMe2Ph)(Me2Pyr)(OHMT) alone, but a cis, stereoregular polymer was formed in the presence of 1 equiv of B(C6F5)3.

A new experimental approach for measuring diffusion coefficients of sorbed gas in polymers has been developed based on a combination of NMR spectroscopy and the use of polymer microspheres. The system chosen to demonstrate the technique is xenon gas sorbed into polystyrene beads of micron size. Pressures in the range of 10-15 atm are sealed in NMR tubes containing a gram or so of polymer. Chemical shift exchange of the xenon gas is easily monitored in either one or two dimensions through the xenon-129 resonances since well-separated signals are observed for the sorbed and free gas. To quantitatively determine diffusion coefficients, selective saturation of the gas phase resonance is used to reduced that signal to zero. Then the decay of the sorbed signal is monitored as a function of saturation time to determine the rate of diffusion of gas out of the polymer microsphere. Diffusion in this case is simply described mathematically by diffusion out of a sphere. A model has been developed to take into account the effects of diffusion in combination with spin-lattice relaxation of the xenon-129 sorbed in the polymer. The diffusion coefficient of xenon in polystyrene at 25 °C is (1.9 ± 0.4) x 10 -9 cm 2 /s. Measurements were made up to 115 °C and an apparent activation energy of 36 kJ/mol was found for diffusion in glassy polystyrene with a sharp increase in the diffusion coefficient when the glass transition region was reached.

A sample of polystyrene beads, 18 μm in diameter, has been sealed in an NMR tube under 10 atm of xenon gas. Two dimensional,129Xe NMR spectra show cross peaks between the resonances corresponding to xenon in the free gas and the sorbed state, indicating that appreciable exchange occurs during the mixing time of the NMR experiment. Selective saturation of the free gas resonance attenuates the integrated intensity of the sorbed xenon resonance as a function of saturation time, thus allowing the accurate measurement of the exchange rates between the gas and the sorbed states. A model has been developed using a slightly modified form of Crank’s treatment of diffusion in a sphere which allows for the accurate determination of the diffusion coefficient for xenon in the sorbed state. The diffusion coefficient for xenon in polystyrene at 25°C is determined to be 2.9·10−9 cm2/s.

Hydroxylated glycerol dialkyl glycerol tetraethers (hydroxy-GDGTs) were detected in marine sediments of diverse depositional regimes and ages. Mass spectrometric evidence, complemented by information gleaned from two-dimensional (2D) 1H–13C nuclear magnetic resonance (NMR) spectroscopy on minute quantities of target analyte isolated from marine sediment, allowed us to identify one major compound as a monohydroxy-GDGT with acyclic biphytanyl moieties (OH-GDGT-0). NMR spectroscopic and mass spectrometric data indicate the presence of a tertiary hydroxyl group suggesting the compounds are the tetraether analogues of the widespread hydroxylated archaeol derivatives that have received great attention in geochemical studies of the last two decades. Three other related compounds were assigned as acyclic dihydroxy-GDGT (2OH-GDGT-0) and monohydroxy-GDGT with one (OH-GDGT-1) and two cyclopentane rings (OH-GDGT-2). Based on the identification of hydroxy-GDGT core lipids, a group of previously reported unknown intact polar lipids (IPLs), including the ubiquitously distributed H341-GDGT (Lipp J. S. and Hinrichs K. -U. (2009) Structural diversity and fate of intact polar lipids in marine sediments. Geochim. Cosmochim. Acta 73, 6816–6833), and its analogues were tentatively identified as glycosidic hydroxy-GDGTs. In addition to marine sediments, we also detected hydroxy-GDGTs in a culture of Methanothermococcus thermolithotrophicus. Given the previous finding of the putative polar precursor H341-GDGT in the planktonic marine crenarchaeon Nitrosopumilus maritimus, these compounds are synthesized by representatives of both cren- and euryarchaeota. The ubiquitous distribution and apparent substantial abundance of hydroxy-GDGT core lipids in marine sediments (up to 8% of total isoprenoid core GDGTs) point to their potential as proxies.

Dopant uptake in sodium-doped poly( p -phenylene vinylene) (PPV) has been measured, and e.s.r. spectroscopy has been used to follow the changes in unpaired spin concentration as the doping reaction proceeds. 2 H n.m.r. line shapes of sodium-doped, ring-deuterated PPV (PPV-d 4 ) have also been studied to observe the effects of doping. They contain two distinct components, one of which is attributed to hydride formation. The overall pattern is insensitive to temperature changes.

The deoxycytidine analog KP1212, and its prodrug KP1461, are prototypes of a new class of antiretroviral drugs designed to increase viral mutation rates, with the goal of eventually causing the collapse of the viral population. Here we present an extensive analysis of viral sequences from HIV-1 infected volunteers from the first “mechanism validation” phase II clinical trial of a mutagenic base analog in which individuals previously treated with antiviral drugs received 1600 mg of KP1461 twice per day for 124 days. Plasma viral loads were not reduced, and overall levels of viral mutation were not increased during this short-term study, however, the mutation spectrum of HIV was altered. A large number (N = 105 per sample) of sequences were analyzed, each derived from individual HIV-1 RNA templates, after 0, 56 and 124 days of therapy from 10 treated and 10 untreated control individuals (>7.1 million base pairs of unique viral templates were sequenced). We found that private mutations, those not found in more than one viral sequence and likely to have occurred in the most recent rounds of replication, increased in treated individuals relative to controls after 56 (p = 0.038) and 124 (p = 0.002) days of drug treatment. The spectrum of mutations observed in the treated group showed an excess of A to G and G to A mutations (p = 0.01), and to a lesser extent T to C and C to T mutations (p = 0.09), as predicted by the mechanism of action of the drug. These results validate the proposed mechanism of action in humans and should spur development of this novel antiretroviral approach., Koronis Pharmaceuticals

2H quadrupole echo NMR spectra have been obtained from stacked films of stretched vinylene-deuterated poly(p-phenylenevinylene) with their draw axes ligned relative to the NMR magnetic field. The 2 H spectra show that the orientation of the vinylene C-D bonds of PPV-d 2 is similar to that of a structure based on trans-stilbene. Spectra obtained at high temperature reveal substantial chain motion and are consistent with a 180° rotational jump of portions of the PPV chain about the crystallographic c axis. Inversion-recovery quadrupole echo spectra were obtained for these films to determine tha anisotropy and magnitude of T 1 .

Phenylene ring-deuterated poly(p-phenylenevinylene) films were prepared from water-cast films of the precursor polymer and were heated and stretched to effect simultaneous orientation and elimination. 2 H quadrupole echo NMR spectra have been obtained from these films, aligned at an angle in the NMR magnetic field, for various draw ratios. The experimental data from 2 H spectra have been simulated with excellent agreement and thereby have yielded the chain orientation distribution in these films

All phenylene rings of an annealed poly(phenylene vinylene) (PPV) film are shown to be capable of undergoing 180° rotation jumps about the 1,4-phenylene ring axis. The dependence of the median jump rate on temperature can be described by an Arrhenius equation with an activation energy of 15kcal/mol. The phenylene rings of PPV show relatively homogeneous behavior and the observed distribution of ring flip rates could be caused by a maximum distribution of activation energies of ±2 kcal/mol.

Ring-deuterated poly( p -phenylene vinylene) has been doped with concentrated sulphuric acid and examined with 2 H quadrupole echo nuclear magnetic resonance spectroscopy. Doping is observed to change the relative population of fast versus slow flipping p -phenylene rings. This relationship has been investigated over a range of temperatures. Modelling this system as a two-site chemical exchange shows that the change in the relative populations of fast versus slow ‘flippers’ corresponds to an increase in the activation energy for the 180° ring flip. The width of the distribution of flip rates is also observed to increase upon doping. At elevated temperatures the samples studied undergo a significant loss of mass which corresponds to a loss of dopant. The chemistry of this process is examined.

Solid-state 13C cross-polarization magic-angle spinning (CPMAS) nuclear magnetic resonance (NMR) spectra have been obtained for annealed films of poly (p-phenylene vinylene) (PPV), prepared through the precursor route and for a deuterated PPV-d4, poly (p-2,3,5,6 tetradeuterophenylene vinylene). 13C CPMAS spectra of PPV are of high resolution, typically characteristic of a nearly fully crystalline structure. All four phenylene and vinylene resonances have been assigned, and for stretched films the 13C CPMAS linewidth and the quality of crystallinity are independent of the draw ratio. 13C CPMAS resolution and crystallite size (as determined by transmission electron microscopy, TEM) depend upon final annealing temperature. The greatest NMR resolution and largest crystallite size are obtained for films annealed at 300°C. The 13C CPMAS NMR spectra show the presence of phenylene ring 180° rotational jumps, and 13C CPMAS resolution is affected by rotational disorder about phenylene-vinylene bonds. NMR data show that PPV films possess molecular motion at elevated temperatures. Enhancement of this motion during annealing may provide a means for improving the quality of PPV crystallinity.

The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.

It has been proposed that AlF4- can serve as a tetrahedral pseudophosphate bound to guanosine diphosphate (GDP) [or other nucleoside diphosphates (NDP)] in G-protein systems. In a previous paper [D. J. Nelson and R. B. Martin, J. Inorg. Biochem. 43, 37 (1991)], 19F and 1H NMR were used to analyze the ternary system Al(3+)-NDP-F- in aqueous solutions. Ternary complexes (NDP)AlFx (with x = 1-3) were identified, but no (NDP)AlF4 was found. In this paper, the equilibrium constants for ternary complex formation that were obtained in the previous paper were further tested in a more extensive 1H and 31P NMR study of speciation in systems that contained Al3+, F-, and adenosine 5'-diphosphate (ADP). The results of the study are in general support of previously derived constants for ternary complexes and also provide support for the existence at relatively high ADP concentration (approximately 10 mM) of a base-stacked intermolecular dihydroxy-di-Al3+ bridged ADP dimeric structure at an ADP to Al3+ molar ratio of 1:1. 31P NMR of the dimer reveals that each of the two Al3+ ions is bidentately coordinated to the alpha and beta phosphates of a single (but different) ADP molecule. Evidence is also presented for the existence at relatively low ADP concentration (approximately 0.5 mM) of a monomeric species in which a single Al3+ ion is coordinated to alpha and beta phosphates of a single ADP molecule. 1H NMR of the monomeric species reveals the expected "wrong-way chemical shift" of the adenine C8 proton upon Al3+ ion complexation to the phosphate chain.

Background The deoxycytidine analog KP1212, and its prodrug KP1461, are prototypes of a new class of antiretroviral drugs designed to increase viral mutation rates, with the goal of eventually causing the collapse of the viral population. KP1212 will diminish or extinguish HIV-1 replication in cell culture, and has had very good safety profiles in clinical trials. Here we present an extensive analysis of viral sequences from patients from the first “mechanism validation” phase II clinical trial in which “salvage” patients received 1600 mg of drug twice per day for 124 days. The Phase IIa study did not demonstrate significant diminution of viral load. This was not unexpected as prior cell culture studies showed little change in viral titer prior to population collapse [1]. In the present work we sought to identify a subclinical impact of KP1461 therapy [2]. Materials and methods We performed direct gene sequencing of a very large number (>100) of sequences derived from individual HIV-1 RNA templates, after 0, 56 and 124 days of therapy from 10 treated and 10 untreated individuals. NMR studies were performed to identify tautomeric forms of the drug. Results Private mutations, those not found in multiple viruses, were similar in treated and control individuals at day 0 (p=0.28), but were increased in treated individuals after 56 (p=0.02) and 124 (p=0.001) days of drug treatment. Furthermore, the spectrum of mutations observed in the treated group was distinct from that of the controls, with an excess of A to G and G to A mutations (p=0.01), and to a lesser extent T to C and C to T mutations (p=0.09), in the treated group. Tautomeric forms of the drug were detected that are predicted to result in a substantial number of misincorporation events during DNA synthesis. Conclusions The predicted mechanism of action of the drug (transition mutations with a bias toward A G) was demonstrated in vivo. The observed increase in mutations in treated patients and the chemical properties of the new drug support a new mechanism of action by a novel antiretroviral therapy in humans.

High resolution fluorescence and fluorescence excitation spectra of all‐trans‐2,4,6,8,10,12,14‐hexadecaheptaene have been obtained in n pentadecane at 10 K. The most prominent vibronic features, like those in spectra of shorter polyene hydrocarbons, are due to combinations of symmetric carbon–carbon stretching vibrations. These in turn are dominated by a double bond mode whose frequency increases from 1555 to 1782 cm−1 upon electronic excitation (1 1Ag→2 1Ag). This 227 cm−1 increase, the largest yet observed in polyene spectroscopy, can be explained by vibronic coupling between the ground and first excited singlets. The possible role of vibrational mixing due to mutual polarizibilities between carbon–carbon bonds also is discussed.