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Find video protocols related to scientific articles indexed in Pubmed.
Anisotropic shift of surface plasmon resonance of gold nanoparticles doped in nematic liquid crystal.
Opt Express
PUBLISHED: 10-17-2014
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Study of the liquid crystal (LC) director around nanoparticles has been an important topic of research very recently, since it allows design and fabrication of next-generation LC devices that are impossible in the past. In our experiment, alkanethiol-capped gold nanoparticles (GNPs) were dispersed in nematic LC. Analysis of the LC director around GNPs was performed by investigating the behavior of surface plasmon polariton (SPP) absorption peaks of the GNPs using spectrophotometry technique. It is found that the incident linearly polarized light orientated at 0°, 45°, and 90° angles with respect to the rubbing direction experiences varying interaction with the LC medium. The corresponding transmission of light reveals the anisotropic shift in wavelength of SPP peak. The anisotropic behavior of SPPs of the GNPs is in agreement with theoretical calculations.
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Advances in gold nanoparticle-liquid crystal composites.
Nanoscale
PUBLISHED: 06-14-2014
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We present the advancement in the research of the dispersion of gold nanoparticles (GNPs) in thermotropic calamitic liquid crystals. The formation/behavior of surface plasmon resonance (SPR) in GNPs is briefly described. The uniform dispersion of GNPs into liquid crystals along with two important aspects, i.e. tuning of GNP properties by liquid crystal and vice versa, are widely discussed. Overall, the article highlights the advances in the research into GNP-liquid crystal composites in terms of their scientific and technological aspects.
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n??* interactions engender chirality in carbonyl groups.
Org. Lett.
PUBLISHED: 06-13-2014
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An n??* interaction stems from the delocalization of the electron pair (n) of a donor group into the antibonding orbital (?*) of a carbonyl group. Crystallographic analyses of five pairs of diastereoisomers demonstrate that an n??* interaction can induce chirality in an otherwise planar, prochiral carbonyl group. Thus, a subtle delocalization of electrons can have stereochemical consequences.
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Targeting the pancreatic ?-cell to treat diabetes.
Nat Rev Drug Discov
PUBLISHED: 02-14-2014
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Diabetes is a leading cause of morbidity and mortality worldwide, and predicted to affect over 500 million people by 2030. However, this growing burden of disease has not been met with a comparable expansion in therapeutic options. The appreciation of the pancreatic ?-cell as a central player in the pathogenesis of both type 1 and type 2 diabetes has renewed focus on ways to improve glucose homeostasis by preserving, expanding and improving the function of this key cell type. Here, we provide an overview of the latest developments in this field, with an emphasis on the most promising strategies identified to date for treating diabetes by targeting the ?-cell.
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Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming.
PLoS ONE
PUBLISHED: 01-01-2014
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Type-1 diabetes (T1D) is an autoimmune disease in which insulin-secreting pancreatic beta cells are destroyed by the immune system. An emerging strategy to regenerate beta-cell mass is through transdifferentiation of pancreatic alpha cells to beta cells. We previously reported two small molecules, BRD7389 and GW8510, that induce insulin expression in a mouse alpha cell line and provide a glimpse into potential intermediate cell states in beta-cell reprogramming from alpha cells. These small-molecule studies suggested that inhibition of kinases in particular may induce the expression of several beta-cell markers in alpha cells. To identify potential lineage reprogramming protein targets, we compared the transcriptome, proteome, and phosphoproteome of alpha cells, beta cells, and compound-treated alpha cells. Our phosphoproteomic analysis indicated that two kinases, BRSK1 and CAMKK2, exhibit decreased phosphorylation in beta cells compared to alpha cells, and in compound-treated alpha cells compared to DMSO-treated alpha cells. Knock-down of these kinases in alpha cells resulted in expression of key beta-cell markers. These results provide evidence that perturbation of the kinome may be important for lineage reprogramming of alpha cells to beta cells.
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An n??* interaction reduces the electrophilicity of the acceptor carbonyl group.
Chem. Commun. (Camb.)
PUBLISHED: 08-10-2013
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Carbonyl-carbonyl (C=O···C=O) interactions are ubiquitous in both small and large molecular systems. This interaction involves delocalization of a lone pair (n) of a donor oxygen into the antibonding orbital (?*) of an acceptor carbonyl group. Analyses of high-resolution protein structures suggest that these carbonyl-carbonyl interactions prefer to occur in pairs, that is, one donor per acceptor. Here, the reluctance of the acceptor carbonyl group (C=O) to engage in more than one n??* electron delocalization is probed using imidazolidine-based model systems with one acceptor carbonyl group and two equivalent donor carbonyl groups. The data indicate that the electrophilicity of the acceptor carbonyl group is reduced when it engages in n??* electron delocalization. This diminished electrophilicity discourages a second n??* interaction with the acceptor carbonyl group.
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Pyramidalization of a carbonyl C atom in (2S)-N-(seleno-acet-yl)proline methyl ester.
Acta Crystallogr Sect E Struct Rep Online
PUBLISHED: 05-01-2013
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The title compound, C8H13NO2Se, crystallizes as a non-merohedral twin with an approximate 9:1 component ratio with two symmetry-independent mol-ecules in the asymmetric unit. Our density-functional theory (DFT) computations indicate that the carb-oxy C atom is expected to be slightly pyramidal due to an n? ?* inter-action, wherein the lone pair (n) of the Se atom overlap with the anti-bonding orbital (?*) of the carbonyl group. Such pyramidalization is observed in one mol-ecule of the title compound but not the other.
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An n??* interaction in aspirin: implications for structure and reactivity.
J. Org. Chem.
PUBLISHED: 09-06-2011
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Stereoelectronic effects modulate molecular structure, reactivity, and conformation. We find that the interaction between the ester and carboxyl moieties of aspirin has a previously unappreciated quantum mechanical character that arises from the delocalization of an electron pair (n) of a donor group into the antibonding orbital (?*) of an acceptor group. This interaction affects the physicochemical attributes of aspirin and could have implications for its pharmacology.
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A conserved interaction with the chromophore of fluorescent proteins.
Protein Sci.
PUBLISHED: 08-23-2011
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The chromophore of fluorescent proteins, including the green fluorescent protein (GFP), contains a highly conjugated imidazolidinone ring. In many fluorescent proteins, the carbonyl group of the imidazolidinone ring engages in a hydrogen bond with the side chain of an arginine residue. Prior studies have indicated that such an electrophilic carbonyl group in a protein often accepts electron density from a main-chain oxygen. A survey of high-resolution structures of fluorescent proteins indicates that electron lone pairs of a main-chain oxygen-Thr62 in GFP-donate electron density into an antibonding orbital of the imidazolidinone carbonyl group. This n??* electron delocalization prevents structural distortion during chromophore excitation that could otherwise lead to fluorescence quenching. In addition, this interaction is present in on-pathway intermediates leading to the chromophore, and thus could direct its biogenesis. Accordingly, this n??* interaction merits inclusion in computational and photophysical analyses of the chromophore, and in speculations about the molecular evolution of fluorescent proteins.
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An evaluation of peptide-bond isosteres.
Chembiochem
PUBLISHED: 04-28-2011
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Peptide-bond isosteres can enable a deep interrogation of the structure and function of a peptide or protein by amplifying or attenuating particular chemical properties. In this Minireview, the electronic, structural, and conformational attributes of four such isosteres-thioamides, esters, alkenes, and fluoroalkenes-are examined in detail. In particular, the ability of these isosteres to partake in noncovalent interactions is compared with that of the peptide bond. The consequential perturbations provide a useful tool for chemical biologists to reveal new structure-function relationships, and to endow peptides and proteins with desirable attributes.
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Synthesis of conformationally constrained 5-fluoro- and 5-hydroxymethanopyrrolidines. Ring-puckered mimics of gauche- and anti-3-fluoro- and 3-hydroxypyrrolidines.
J. Org. Chem.
PUBLISHED: 04-18-2011
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N-acetylmethanopyrrolidine methyl ester and its four 5-syn/anti-fluoro and hydroxy derivatives have been synthesized from 2-azabicyclo[2.2.0]hex-5-ene, a 1,2-dihydropyridine photoproduct. These conformationally constrained mimics of idealized C(?)-gauche and C(?)-anti conformers of pyrrolidines were prepared in order to determine the inherent bridge bias and subsequent heteroatom substituent effects upon trans/cis amide preferences. The bridgehead position and also the presence of gauche(syn)/anti-5-fluoro or 5-hydroxy substituents have minimal influence upon the K(T/C) values of N-acetylamide conformers in both CDCl(3) (43-54% trans) and D(2)O (53-58% trans). O-Benzoylation enhances the trans amide preferences in CDCl(3) (65% for a syn-OBz, 61% for an anti-OBz) but has minimal effect in D(2)O. The synthetic methods developed for N-BOC-methanopyrrolidines should prove useful in the synthesis of more complex derivatives containing ?-ester substituents. The K(T/C) results obtained in this study establish baseline amide preferences that will enable determination of contributions of ?-ester substituents to trans-amide preferences in methanoprolines.
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Signature of n??* interactions in ?-helices.
Protein Sci.
PUBLISHED: 02-11-2011
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The oxygen of a peptide bond has two lone pairs of electrons. One of these lone pairs is poised to interact with the electron-deficient carbon of the subsequent peptide bond in the chain. Any partial covalency that results from this n??* interaction should induce pyramidalization of the carbon (C(i)) toward the oxygen (O(i-1)). We searched for such pyramidalization in 14 peptides that contain both ?- and ?-amino acid residues and that assume a helical structure. We found that the ?-amino acid residues, which adopt the main chain dihedral angles of an ?-helix, display dramatic pyramidalization but the ?-amino acid residues do not. Thus, we conclude that O(i-1) and C(i) are linked by a partial covalent bond in ?-helices. This finding has important ramifications for the folding and conformational stability of ?-helices in isolation and in proteins.
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The aberrance of the 4S diastereomer of 4-hydroxyproline.
J. Am. Chem. Soc.
PUBLISHED: 08-05-2010
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Prolyl 4-hydroxylases install a hydroxyl group in the 4R configuration on the gamma-carbon atom of certain (2S)-proline (Pro) residues in tropocollagen, elastin, and other proteins to form (2S,4R)-4-hydroxyproline (Hyp). The gauche effect arising from this prevalent post-translational modification enforces a C(gamma)-exo ring pucker and stabilizes the collagen triple helix. The Hyp diastereomer (2S,4S)-4-hydroxyproline (hyp) has not been observed in a protein, despite the ability of electronegative 4S substituents to enforce the more common C(gamma)-endo ring pucker of Pro. Here, we use density functional theory, spectroscopy, crystallography, and calorimetry to explore the consequences of hyp incorporation on protein stability using a collagen model system. We find that the 4S-hydroxylation of Pro to form hyp does indeed enforce a C(gamma)-endo ring pucker but a transannular hydrogen bond between the hydroxyl moiety and the carbonyl of hyp distorts the main-chain torsion angles that typically accompany a C(gamma)-endo ring pucker. This same transannular hydrogen bond enhances an n-->pi* interaction that stabilizes the trans conformation of the peptide bond preceding hyp, endowing hyp with the unusual combination of a C(gamma)-endo ring pucker and high trans/cis ratio. O-Methylation of hyp to form (2S,4S)-4-methoxyproline (mop) eliminates the transannular hydrogen bond and restores a prototypical C(gamma)-endo pucker. mop residues endow the collagen triple helix with much more conformational stability than do hyp residues. These findings highlight the critical importance of the configuration of the hydroxyl group installed on C(gamma) of proline residues.
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A stereoelectronic effect in prebiotic nucleotide synthesis.
ACS Chem. Biol.
PUBLISHED: 05-27-2010
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A plausible route for the spontaneous synthesis of an activated ribonucleotide that is poised for polymerization has been put forth (Powner et al. (2009) Nature, 459, 239-242). A key step in this route necessitates the regioselective phosphorylation of the secondary alcohol on C(3) of an anhydroarabinonucleoside in the presence of the primary alcohol on C(5). Here, we propose that this regioselectivity relies on electron delocalization between a lone pair (n) of O(5) and an antibonding orbital (pi*) of C(2) horizontal lineN(3). This n-->pi* interaction modulates reactivity without the use of a protecting group. Thus, a stereoelectronic effect could have opened a gateway to the "RNA world", the chemical milieu from which the first forms of life are thought to have emerged on Earth some 4 billion years ago.
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n --> pi* Interaction and n)(pi Pauli repulsion are antagonistic for protein stability.
J. Am. Chem. Soc.
PUBLISHED: 04-28-2010
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In many common protein secondary structures, such as alpha-, 3(10), and polyproline II helices, an n --> pi* interaction places the adjacent backbone amide carbonyl groups in close proximity to each other. This interaction, which is reminiscent of the Burgi-Dunitz trajectory, involves delocalization of the lone pairs (n) of the oxygen (O(i-1)) of a peptide bond over the antibonding orbital (pi*) of C(i)=O(i) of the subsequent peptide bond. Such a proximal arrangement of the amide carbonyl groups should be opposed by the Pauli repulsion between the lone pairs (n) of O(i-1) and the bonding orbital (pi) of C(i)=O(i). We explored the conformational effects of this Pauli repulsion by employing common peptidomimetics, wherein the n --> pi* interaction is attenuated while the Pauli repulsion is retained. Our results indicate that this Pauli repulsion prevents the attainment of such proximal arrangement of the carbonyl groups in the absence of the n --> pi* interaction. This finding indicates that the poor mimicry of the amide bond by many peptidomimetics stems from their inability to partake in the n --> pi* interaction and emphasizes the quantum-mechanical nature of the interaction between adjacent amide carbonyl groups in proteins.
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n-->pi* interactions in proteins.
Nat. Chem. Biol.
PUBLISHED: 02-08-2010
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Hydrogen bonds between backbone amides are common in folded proteins. Here, we show that an intimate interaction between backbone amides also arises from the delocalization of a lone pair of electrons (n) from an oxygen atom to the antibonding orbital (pi*) of the subsequent carbonyl group. Natural bond orbital analysis predicted significant n-->pi* interactions in certain regions of the Ramachandran plot. These predictions were validated by a statistical analysis of a large, non-redundant subset of protein structures determined to high resolution. The correlation between these two independent studies is striking. Moreover, the n-->pi* interactions are abundant and especially prevalent in common secondary structures such as alpha-, 3(10)- and polyproline II helices and twisted beta-sheets. In addition to their evident effects on protein structure and stability, n-->pi* interactions could have important roles in protein folding and function, and merit inclusion in computational force fields.
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Quantum mechanical origin of the conformational preferences of 4-thiaproline and its S-oxides.
Amino Acids
PUBLISHED: 01-25-2010
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The saturated ring and secondary amine of proline spawn equilibria between pyrrolidine ring puckers as well as peptide bond isomers. These conformational equilibria can be modulated by alterations to the chemical architecture of proline. For example, C(?) in the pyrrolidine ring can be replaced with sulfur, which can be oxidized either stereoselectively to yield diastereomeric S-oxides or completely to yield a sulfone. Here, the thiazolidine ring and peptide bond conformations of 4-thiaproline and its S-oxides were analyzed in an Ac-Xaa-OMe system using NMR spectroscopy, X-ray crystallography, and hybrid density functional theory. The results indicate that the ring pucker of the S-oxides is governed by the gauche effect, and the prolyl peptide bond conformation is determined by the strength of the n ? ?* interaction between the amide oxygen and the ester carbonyl group. These findings, which are consistent with those of isologous 4-hydroxyprolines and 4-fluoroprolines, substantiate the importance of electron delocalization in amino acid conformation.
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5(6)-anti-Substituted-2-azabicyclo[2.1.1]hexanes: a nucleophilic displacement route.
J. Org. Chem.
PUBLISHED: 10-06-2009
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Nucleophilic displacements of 5(6)-anti-bromo substituents in 2-azabicyclo[2.1.1]hexanes (methanopyrrolidines) have been accomplished. These displacements have produced 5-anti-X-6-anti-Y-difunctionalized-2-azabicyclo[2.1.1]hexanes containing bromo, fluoro, acetoxy, hydroxy, azido, imidazole, thiophenyl, and iodo substituents. Such displacements of anti-bromide ions require an amine nitrogen and are a function of the solvent and the choice of metal salt. Reaction rates were faster and product yields were higher in DMSO when compared to DMF and with CsOAc compared to NaOAc. Sodium or lithium salts gave products, except with NaF, where silver fluoride in nitromethane was best for substitution by fluoride. The presence of electron-withdrawing F, OAc, N(3), Br, or SPh substituents in the 6-anti-position slows bromide displacements at the 5-anti-position.
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Nature of amide carbonyl--carbonyl interactions in proteins.
J. Am. Chem. Soc.
PUBLISHED: 05-28-2009
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Noncovalent interactions define and modulate biomolecular structure, function, and dynamics. In many protein secondary structures, an intimate interaction exists between adjacent carbonyl groups of the main-chain amide bonds. As this short contact contributes to the energetics of protein conformational stability as well as protein-ligand interactions, understanding its nature is crucial. The intimacy of the carbonyl groups could arise from a charge-charge or dipole-dipole interaction, or n-->pi * electronic delocalization. This last putative origin, which is reminiscent of the Burgi-Dunitz trajectory, involves delocalization of the lone pairs (n) of the oxygen (O(i-1)) of a peptide bond over the antibonding orbital (pi*) of the carbonyl group (C(i)=O(i)) of the subsequent peptide bond. By installing isosteric chemical substituents in a peptidic model system and using NMR spectroscopy, X-ray diffraction analysis, and ab initio calculations to analyze the consequences, the intimate interaction between adjacent carbonyl groups is shown to arise primarily from n-->pi* electronic delocalization. This finding has implications for organic, biological, and medicinal chemistry.
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Intimate interactions with carbonyl groups: dipole-dipole or n??*?
J. Org. Chem.
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Amide carbonyl groups in proteins can engage in C?O···C?O and C-X···C?O interactions, where X is a halogen. The putative involvement of four poles suggests that these interactions are primarily dipolar. Our survey of crystal structures with a C-X···C?O contact that is short (i.e., within the sum of the X and C van der Waals radii) revealed no preferred C-X···C?O dihedral angle. Moreover, we found that structures with a short X(-)···C?O contact display the signatures of an n??* interaction. We conclude that intimate interactions with carbonyl groups do not require a dipole.
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Mechanistic investigation of the sonochemical synthesis of zinc ferrite.
Ultrason Sonochem
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In this investigation, an attempt has been made to establish the physical mechanism of sonochemical synthesis of zinc ferrite with concurrent analysis of experimental results and simulations of cavitation bubble dynamics. Experiments have been conducted with mechanical stirring as well as under ultrasound irradiation with variation of pH and the static pressure of the reaction medium. Results of this study reveal that physical effects produced by transient cavitation bubbles play a crucial role in the chemical synthesis. Generation of high amplitude shock waves by transient cavitation bubbles manifest their effect through in situ micro-calcination of metal oxide particles (which are generated through thermal hydrolysis of metal acetates) due to energetic collisions between them. Micro-calcination of oxide particles can also occur in the thin liquid shell surrounding bubble interface, which gets heated up during transient collapse of bubbles. The sonochemical effect of production of OH radicals and H(2)O(2), in itself, is not able to yield ferrite. Moreover, as the in situ micro-calcination involves very small number of particles or even individual particles (as in intra-particle collisions), the agglomeration between resulting ferrite particles is negligible (as compared to external calcination in convention route), leading to ferrite particles of smaller size (6 nm).
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Synthesis of 5-fluoro- and 5-hydroxymethanoprolines via lithiation of N-BOC-methanopyrrolidines. Constrained C?-exo and C?-endo Flp and Hyp conformer mimics.
J. Org. Chem.
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Proline derivatives with a C(?)-exo pucker typically display a high amide bond trans/cis (K(T/C)) ratio. This pucker enhances n??* overlap of the amide oxygen and ester carbonyl carbon, which favors a trans amide bond. If there were no difference in n??* interaction between the ring puckers, then the correlation between ring pucker and K(T/C) might be broken. To explore this possibility, proline conformations were constrained using a methylene bridge. We synthesized discrete gauche and anti 5-fluoro- and 5-hydroxy-N-acetylmethanoproline methyl esters from 3-syn and 3-anti fluoro- and hydroxymethanopyrrolidines using directed ?-metalation to introduce the ?-ester group. NBO calculations reveal minimal n??* orbital interactions, so contributions from other forces might be of greater importance in determining K(T/C) for the methanoprolines. Consistent with this hypothesis, greater trans amide preferences were found in CDCl(3) for anti isomers en-MetFlp and en-MetHyp (72-78% trans) than for the syn stereoisomers ex-MetFlp and ex-MetHyp (54-67% trans). These, and other, K(T/C) results that we report here indicate how substituents on proline analogues can affect amide preferences by pathways other than ring puckering and n??* overlap and suggest that caution should be exercised in assigning enhanced pyrrolidine C(?)-exo ring puckering based solely on enhanced trans amide preference.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.