Intramolecular Proximity Research Articles

Theoretical and experimental studies on the effect of the 1,2-diketone group on geometry distortion for phenacene-type polycyclic aromatic compounds

Abstract This paper addresses the geometry distortion of orthoquinone-containing phenacene-type compounds by comparing the structures of phenanthrene-9,10-dione, chrysene-5,6-dione, and picene-13,14-dione. Interestingly, the calculated geometry of chrysene-5,6-dione under the isolated state was drastically different from the experimental one observed by single-crystal X-ray analysis. Theoretical calculations suggested that the molecular geometry of the o-quinone derivatives was sensitive not only to the sterically intramolecular proximity between the carbonyl oxygen and the hydrogen atoms of the benzene rings but also to intermolecular interactions. The twist distortion affects properties such as oscillator strength and 1-electron transitions, for low-lying excited states.

Biradical pincers involving two phenylene, biphenylene or terphenylene arms: Evidence for approach of two terminal nitroxides

Four new pincer-type bisnitroxides, o-C6H4{CH2O-(p-C6H4)n-N(O•)-But}2 (abbreviated as pBi and pTer for n = 2 and 3, respectively; pPh for n = 1 (known)), and o-C6H4{CH2O-(p-C6H4)n-1-(m-C6H4)–N(O•)-But}2 (mBi and mTer for n = 2 and 3, respectively) were prepared, where o-xylylenedioxy was chosen as a hinge and phenylene, biphenylene, and terphenylene were selected as an arm. The crystallographic analysis clarified the intramolecular proximity of the two radical groups was observed for mBi, whereas pBi and mTer possess an open V-shape. In toluene solution ESR, five hyperfine splitting lines were recorded for every compound at room temperature or higher. The antiferromagnetic exchange interaction is estimated as 2J/kB = −0.05 to −0.0002 K from ESR simulation. The orders of the exchange interactions are as follows: Ph > Bi > Ter regarding the arm lengths and m > p regarding the positional isomers. The temperature at which alternating linewidths appeared was found to be a convenient temperature scale in this study.

Aurora B SUMOylation Is Restricted to Centromeres in Early Mitosis and Requires RANBP2.

Conjugation with the small ubiquitin-like modifier (SUMO) modulates protein interactions and localisation. The kinase Aurora B, a key regulator of mitosis, was previously identified as a SUMOylation target in vitro and in assays with overexpressed components. However, where and when this modification genuinely occurs in human cells was not ascertained. Here, we have developed intramolecular Proximity Ligation Assays (PLA) to visualise SUMO-conjugated Aurora B in human cells in situ. We visualised Aurora B-SUMO products at centromeres in prometaphase and metaphase, which declined from anaphase onwards and became virtually undetectable at cytokinesis. In the mitotic window in which Aurora B/SUMO products are abundant, Aurora B co-localised and interacted with NUP358/RANBP2, a nucleoporin with SUMO ligase and SUMO-stabilising activity. Indeed, in addition to the requirement for the previously identified PIAS3 SUMO ligase, we found that NUP358/RANBP2 is also implicated in Aurora B-SUMO PLA product formation and centromere localisation. In summary, SUMOylation marks a distinctive window of Aurora B functions at centromeres in prometaphase and metaphase while being dispensable for functions exerted in cytokinesis, and RANBP2 contributes to this control, adding a novel layer to modulation of Aurora B functions during mitosis.

Epoxy-Rich Systems with Preference for Etherification over Amine-Epoxy Reactions for Tertiary Amine Accelerators

Epoxies are often cured using primary and secondary amines in an efficient reaction catalyzed by tertiary amines. Through coordination effects, tertiary amines lower the transition-state energy enough to allow the reaction to take place under ambient conditions. In this paper, we demonstrate how, under ambient conditions, tertiary amines bound in close intramolecular proximity to a primary amine are able to catalyze amine-epoxy reactions as well as promote etherifications in epoxy-rich systems. 13C nuclear magnetic resonance (NMR) was used to identify the sequence of curing reactions in a model reaction of benzyl glycidyl ether (BGE) with the amines 3-diethylaminopropylamine (DEAPA), 3-dimethylaminopropylamine (DMAPA), and hexylamine, respectively. The results clearly show that DMAPA favors etherification over amine-epoxy reactions, while DEAPA displays the expected trend toward amine-epoxy reactions. This experiment was repeated for a curing epoxy system based on bisphenol A diglycidylether (BADGE) with the same three amines, and differential scanning calorimetry (DSC) confirmed this preference of reactions via quantification of the curing exotherms. Finally, a novel DMA setup corroborated the observed rate of reaction for each catalyst by measuring gelation time and vitrification during isothermal curing.

Trends in trigonal prismatic Ln-[1]ferrocenophane complexes and discovery of a Ho3+ single-molecule magnet.

Lanthanide metallocenophanes are an intriguing class of organometallic complexes that feature rare six-coordinate trigonal prismatic coordination environments of 4f elements with close intramolecular proximity to transition metal ions. Herein, we present a systematic study of the structural and magnetic properties of the ferrocenophanes, [LnFc3(THF)2Li2]−, of the late trivalent lanthanide ions (Ln = Gd (1), Ho (2), Er (3), Tm (4), Yb (5), Lu (6)). One major structural trend within this class of complexes is the increasing diferrocenyl (Fc2−) average twist angle with decreasing ionic radius (rion) of the central Ln ion, resulting in the largest average Fc2− twist angles for the Lu3+ compound 6. Such high sensitivity of the twist angle to changes in rion is unique to the here presented ferrocenophane complexes and likely due to the large trigonal plane separation enforced by the ligand (>3.2 Å). This geometry also allows the non-Kramers ion Ho3+ to exhibit slow magnetic relaxation in the absence of applied dc fields, rendering compound 2 a rare example of a Ho-based single-molecule magnet (SMM) with barriers to magnetization reversal (U) of 110–131 cm−1. In contrast, compounds featuring Ln ions with prolate electron density (3–5) don't show slow magnetization dynamics under the same conditions. The observed trends in magnetic properties of 2–5 are supported by state-of-the-art ab initio calculations. Finally, the magneto-structural relationship of the trigonal prismatic Ho-[1]ferrocenophane motif was further investigated by axial ligand (THF in 2) exchange to yield [HoFc3(THF*)2Li2]− (2-THF*) and [HoFc3(py)2Li2]− (2-py) motifs. We find that larger average Fc2− twist angles (in 2-THF* and 2-py as compared to in 2) result in faster magnetic relaxation times at a given temperature.

How to Measure Separations and Angles Between Intramolecular Fluorescent Markers.

Structure and function of an individual biomolecule can be explored with minimum two fluorescent markers of different colors. Since the light of such markers can be spectrally separated and imaged simultaneously, the markers can be colocalized. Here, we describe the method used for such two-color colocalization microscopy. Then we extend it to fluorescent markers with fixed orientations and in intramolecular proximity. Our benchmarking of this extension produced two extra results: (a) we established short double-labeled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly; (b) we established how to map with super-resolution between color-separated channels, which should be useful for all dual-color colocalization measurements with either fixed or freely rotating fluorescent molecules. Throughout, we use only simple means: from each color-separated microscope image in a time-lapse movie, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space, both with accuracy and precision. The relative positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA (dsDNA) molecules internally labeled with two fixed fluorophores, we (i) demonstrate the accuracy and precision of our localization- and mapping-methods, using the known structure of dsDNA as benchmark; (ii) resolve 10 base pair differences in fluorophore separations; (iii) determine the unique 3D orientation of each DNA molecule.

Optimized measurements of separations and angles between intra-molecular fluorescent markers.

We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly.

Polyglutamine domain flexibility mediates the proximity between flanking sequences in huntingtin

Huntington disease (HD) is a neurodegenerative disorder caused by a CAG expansion within the huntingtin gene that encodes a polymorphic glutamine tract at the amino terminus of the huntingtin protein. HD is one of nine polyglutamine expansion diseases. The clinical threshold of polyglutamine expansion for HD is near 37 repeats, but the mechanism of this pathogenic length is poorly understood. Using Förster resonance energy transfer, we describe an intramolecular proximity between the N17 domain and the downstream polyproline region that flanks the polyglutamine tract of huntingtin. Our data support the hypothesis that the polyglutamine tract can act as a flexible domain, allowing the flanking domains to come into close spatial proximity. This flexibility is impaired with expanded polyglutamine tracts, and we can detect changes in huntingtin conformation at the pathogenic threshold for HD. Altering the structure of N17, either via phosphomimicry or with small molecules, also affects the proximity between the flanking domains. The structural capacity of N17 to fold back toward distal regions within huntingtin requires an interacting protein, protein kinase C and casein kinase 2 substrate in neurons 1 (PACSIN1). This protein has the ability to bind both N17 and the polyproline region, stabilizing the interaction between these two domains. We also developed an antibody-based FRET assay that can detect conformational changes within endogenous huntingtin in wild-type versus HD fibroblasts. Therefore, we hypothesize that wild-type length polyglutamine tracts within huntingtin can form a flexible domain that is essential for proper functional intramolecular proximity, conformations, and dynamics.

New Chelating Ligands Based on S-Organosulfurdiimides: Synthesis and Single Crystal X-ray Structures of their Lithium Complexes

Three new diimidosulfinates, [TMSCH(2)S(N(t)Bu)(2)Li](2) (1), [2-PyCH(2)S(N(t)Bu)(2)Li](2) (2), and [{PhCH(2)S(N(t)Bu)(2)Li}(2) x THF] (3) (TMS = trimethylsilyl; Py = 2-pyridyl), have been synthesized by the reaction of functionalized alpha-CH(2)-organolithium compounds with bis-tert-butylsulfurdiimide. These new organolithium chelates are characterized by NMR ((1)H, (13)C, (7)Li, and (29)Si) spectroscopy and single-crystal X-ray diffraction analyses. Compounds 1 and 2 crystallize as dimers without donor molecules, whereas one of the lithium atoms in 3 is coordinated by a single THF molecule. The crystal structure of 1 shows significant intramolecular proximity between one methyl group of the trimethylsilyl (TMS) and one lithium atom, which could be described as an electrostatic Li...C interaction. The coordination sphere of each lithium atom in 2 is completed by donation from the nitrogen atom of the pyridyl ring; however, one of the lithium atoms in 3 is coordinated by a THF molecule. In addition, the first mixed sulfurdiimide species containing a diimidosulfinate and a diimidosulfite fragment, [{PhCHS(N(t)Bu)(2)Li(2)(THF)(2)}{MeS(N(t)Bu)(2)Li(THF)}] (4), was isolated by deprotonation of the alpha-CH(2) group in 3. The single-crystal X-ray structure of 4 revealed two different S-bound substituents coexisting in one dimer and two asymmetrically coordinated lithium atoms.

Contacted Ion-Pair Lithium Alkylamidoaluminates: Intramolecular Alumination (Al−H Exchange) Traps for TMEDA and PMDETA

Exploring the reactivity of mixed-metal synergic bases, it is found that the lithium TMP aluminate iBu3Al(TMP)Li functions as a dual TMP/alkyl base, exhibiting 2-fold AMMAl (alkali-metal-mediated alumination) toward TMEDA to yield the heterobimetallic bis-(deprotonated TMEDA) derivative [Li{Me2NCH2CH2N(Me)CH2}2Al(iBu)2] (2). In contrast, the amide enriched aluminate iBu2Al(TMP)2Li acts as only a single-fold amido base toward TMEDA or PMDETA to afford the amine-deprotonated derivatives [Li{Me2NCH2CH2N(Me)CH2}(TMP)Al(iBu)2] (4) and [Li{Me2NCH2CH2N(Me)CH2CH2N(Me)CH2}(TMP)Al(iBu)2] (5), respectively. On their own, the aluminum compounds iBu3Al or iBu2Al(TMP) are not sufficiently strong bases to metalate TMEDA or PMDETA, so in 2, 4, and 5, the α-deprotonations of TMEDA and PMDETA are synergic in origin, as the intramolecular communication between Li and Al appears to activate the TMP and iBu bases. This special behavior can be attributed to intramolecular proximity effects between the active base component (TMP or iBu) and the ligating TMEDA or PMDETA molecule. X-ray crystallography studies reveal 2 is a contacted ion-pair ate containing two α-aluminated TMEDA ligands, which chelate the lithium cation which is linked to the distorted tetrahedral Al center by two N bridges from the metalated junction of the TMEDA molecules. In contrast, 4 and 5 have a mixed NCH2-TMP bridging ligand set, completed by two terminal iBu ligands on Al and a chelating metalated TMEDA or PMDETA ligand attached to Li, respectively. In addition, the 1H, 7Li, and 13C{1H} spectra of 2 (recorded in C6D6 solutions), 4, and 5 (recorded in cyclohexane solutions-d12) are disclosed.

Microscopic Protonation/Deprotonation Equilibria of the Anti‐Inflammatory Agent Piroxicam

AbstractThe microscopic ionization behavior of piroxicam was investigated using two different approaches, i.e., direct UV spectroscopy and an indirect analogue approach (deductive method). The best microscopic pKa values (pKa12 = 4.60, pKa21 = 5.40, pKa22 = 2.72, and pKa11 = 1.92) were obtained by the deductive method using as pKa22 the pKa of the enolic O‐methylated piroxicam 2. The results show remarkable electrostatic effects in the protonation/deprotonation equilibria, a marked increase in the acidity of the enolic function (2.68 pKa units) being caused by the pyridinium group. The electronic structure of piroxicam was studied based on 1H‐NMR chemical shifts at various ionization states, indicating an extended electron conjugation through the molecule. The partition measurements in octan‐1‐ol/H2O of zwitterionic compound 3 (the pyridyl N‐methyl derivative of piroxicam (1)) suggest that the two opposite charges in zwitterionic piroxicam are indeed in a close intramolecular proximity.

Polyadenylated Virus-specific RNA in Baby Hamster Kidney Cells, Transformed by Polyoma Virus

RNA from a clone of polyoma virus-transformed hamster cells was fractionated by chromatography on oligo(dT)-cellulose. The proportion of virus-specific RNA in the polyadenylated and non-polyadenylated fractions was determined by hybridization of the labelled RNA with excess purified polyoma DNA, immobilized on filters. Seventy to 80% of the virus-specific RNA in both polysomal and total cell RNA was found in the polyadenylated fraction. Since it has been shown previously that more than 65% of the total virus-specific RNA is restricted to the nucleus in this cell line, these results indicate that a high proportion (at least 53%) of the nuclear virus-specific RNA is polyadenylated. The sedimentation profile of total polyadenylated virus-specific RNA in dimethyl sulphoxide was comprised mainly of a broad band with a median sedimentation coefficient about 26S (relative to 28S rRNA). This profile was similar to that of total nuclear, and not cytoplasmic, virus-specific RNA. To estimate the intramolecular proximity of virus-specific sequences to poly(A), total RNA was subjected to limited thermal scission to an average mol. wt. similar to that of mRNA. The RNA remaining attached to poly(A) was then isolated, using oligo(dT)-cellulose. It was found that 65% of the virus-specific RNA that was originally attached to poly(A) was released by the thermal scission. Most of the virus-specific sequence within polyadenylated RNA molecules therefore must have been located at some distance from the polyadenylated 3'-terminus. This observation, together with the results of sedimentation analysis, can most simply be explained by postulating the existence of 'hybrid' RNA molecules containing a host-specified sequence located between a virus-specific sequence and the 3'-terminal poly(A).

Sesquiterpene lactones from Artemisia: Arbusculin-C, rothin-A and rothin-B

Three new santanolides, arbusculin-C (III), rothin-A (VIII), and rothin-B (XII), were isolated from species of the section Tridentatae Rydb. of the genus Artemisia. Their structural details were revealed by means of NMR spectroscopy, and diagnostically useful examples of intramolecular proximity deshielding by oxygen were observed. Biosyntheses of these and other eudesmanolides from A. arbuscula Nutt. ssp. arbuscula and A. rothrockii Gray were rationalized in two analogous pathways from assumed germacranolide precursors.