Exocyclic Group Research Articles

Determination of Perillic Acid in Bioconversion Supernatants by Gas Chromatography

Perillic acid can be obtained from microbial oxidation of the exocyclic methyl group of limonene. Due to the pharmacological potential of such a metabolite, the biotransformation processes leading to its synthesis have been approached in recent studies. A robust analytical method is needed to assess the performance of such studies. An analytical method was developed and validated to determine perillic acid in the supernatants of a yeast-induced bioconversion of limonene, involving gas chromatography (GC) and an acid-induced precipitation during the sample preparation. GC analysis was performed using a column with polyethylene glycol as stationary phase (HP-Innowax) which resulted in higher loads and better peak shape. The sample preparation involved the supernatant initial filtration and precipitation with 0.6 M HCl followed by centrifugation and dissolution in ethyl acetate. GC analysis conditions were oven from 50°C to 250°C at 20°C·min-1, and then held 5 min (total runtime 15 min). Injector was set at 280°C, and detector at 300°C. Helium was the carrier gas at 1 ml·min-1. Injections of 1.0 μl were at the split ratio 25:1. The method was validated: Linearity with R2 of 0.9992, Accuracy of 98.3% in the range 190 - 950 μg·ml-1; Limit of detection of 10.4 μg·ml-1; Repeatability of 2.1% RSD. Thus, a complete methodology to determine perillic acid in a bioconversion supernatant was developed and validated. This overall approach may be useful for bioconversions of monoterpenes by other microorganisms that metabolize limonene.

Synthesis and structure of a carbohydrate-fused [15]-macrodilactone

The design, synthesis and structural characterization of a new α-d-glucose fused [15]-macrodilactone is reported. The macrolide was synthesized by a route involving sequential acylations of glucose at the C4′ and C6′ hydroxyl groups followed by an intramolecular Stille reaction previously established for other [15]-macrodilactones. Analysis of the X-ray crystallographic structure of the macrolide revealed a unique conformation of this macrocycle that differs from earlier models for [13]- and [15]-macrodilactones. Organizing the three planar units and the pyranose moiety into a macrocyclic ring resulted in a cup-shaped structure with planar chirality. Further, the gt conformation of the exocyclic hydroxymethyl group in the glucose unit was found to be crucial for controlling the planar chirality and, hence, governing the molecular shape and overall topology of the compound.

Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity.

G-quadruplex (G4) with stacked G-tetrads structure is able to bind hemin (iron (III)-protoporphyrin IX) to form a unique type of DNAzyme/RNAzyme with peroxidase-mimicking activity, which has been widely employed in multidisciplinary fields. However, its further applications are hampered by its relatively weak activity compared with protein enzymes. Herein, we report a unique intramolecular enhancement effect of the adjacent adenine (EnEAA) at 3′ end of G4 core sequences that significantly improves the activity of G4 DNAzymes. Through detailed investigations of the EnEAA, the added 3′ adenine was proved to accelerate the compound I formation in catalytic cycle and thus improve the G4 DNAzyme activity. EnEAA was found to be highly dependent on the unprotonated state of the N1 of adenine, substantiating that adenine might function as a general acid–base catalyst. Further adenine analogs analysis supported that both N1 and exocyclic 6-amino groups in adenine played key role in the catalysis. Moreover, we proved that EnEAA was generally applicable for various parallel G-quadruplex structures and even G4 RNAzyme. Our studies implied that adenine might act analogously as the distal histidine in protein peroxidases, which shed light on the fundamental understanding and rational design of G4 DNAzyme/RNAzyme catalysts with enhanced functions.

Reactions of arylenedioxytrihalophosphoranes with acetylenes 14. Methoxyphenylacetylenes in the reaction with 2,2,2-trichlorobenzo-1,3,2-dioxaphosphole

Reactions of 2,2,2-trichlorobenzo-1,3,2-dioxaphosphole with 2-, 3-, 4-methoxyphenyl-, 3,4-dimethoxyphenyl- and 2,3,4-trimethoxyphenylacetylenes furnished 4-phenylbenzo-1,2-oxaphosphinine derivatives. The presence of one, two, or three donor methoxy groups in the aromatic ring of phenylacetylene does not change the general direction of the reaction which is characteristic of arylacetylenes and lead to 4-arylareno-1,2-oxaphosphinine derivatives. The presence of substituents in the exocyclic aryl group at ortho-position to the oxaphosphinine ring led to the appearance of atropoisomers.

Synthesis, optical and electrochemical properties of substituted 2-cinnamoyl-1, 3-indandione O-methyl ethers

Seven new 2-cinnamoyl-1,3-indandione (2CID) O-methyl ethers with different substituents (R = –H, –CH3, –OCH3, –N(C6H5)2, –N(CH2CH2CN)2, julolidyl, –N(CH3)2) in 4-position of the cinnamoyl moiety were synthesized. The methylation with dimethylsulfate occurred at the oxygen atom of the exocyclic enol group with high selectivity.The synthesized compounds were characterized by 1H, 13C NMR, IR, UV–Vis and luminescence spectroscopy, their electrochemical properties were investigated by cyclic voltammetry. The obtained results indicates that introducing an electron donating substituents in the 4-position of cinnamoyl moiety facilitates electrochemical oxidation, remarkably shifts absorption and emission bands to longer wavelengths, simultaneously increases extinction coefficient (ε). O-methyl ethers with strong electron donating groups (R = –N(C6H5)2, –N(CH2CH2CN)2, julolidyl, –N(CH3)2) in molecule are characterized by luminescence with maximum in range from 547 to 647 nm and absolute photoluminescence quantum yields from 0.02 to 0.32. Quantum yield (QY) of chromophore containing julolidyl fragment is solvent dependent. It was 0.32 in chloroform and decreased in other polar (ethanol, acetone) solvents.

Structures of Xenopus Embryonic Epidermal Lectin Reveal a Conserved Mechanism of Microbial Glycan Recognition

Intelectins (X-type lectins), broadly distributed throughout chordates, have been implicated in innate immunity. Xenopus laevis embryonic epidermal lectin (XEEL), an intelectin secreted into environmental water by the X. laevis embryo, is postulated to function as a defense against microbes. XEEL is homologous (64% identical) to human intelectin-1 (hIntL-1), which is also implicated in innate immune defense. We showed previously that hIntL-1 binds microbial glycans bearing exocyclic vicinal diol groups. It is unknown whether XEEL has the same ligand specificity. Also unclear is whether XEEL and hIntL-1 have similar quaternary structures, as XEEL lacks the corresponding cysteine residues in hIntL-1 that stabilize the disulfide-linked trimer. These observations prompted us to further characterize XEEL. We found that hIntL-1 and XEEL have similar structural features. Even without the corresponding intermolecular disulfide bonds present in hIntL-1, the carbohydrate recognition domain of XEEL (XEELCRD) forms a stable trimer in solution. The structure of XEELCRD in complex with d-glycerol-1-phosphate, a residue present in microbe-specific glycans, indicated that the exocyclic vicinal diol coordinates to a protein-bound calcium ion. This ligand-binding mode is conserved between XEEL and hIntL-1. The domain architecture of full-length XEEL is reminiscent of a barbell, with two sets of three glycan-binding sites oriented in opposite directions. This orientation is consistent with our observation that XEEL can promote the agglutination of specific serotypes of Streptococcus pneumoniae. These data support a role for XEEL in innate immunity, and they highlight structural and functional conservation of X-type lectins among chordates.

Synthesis and properties of novel 2'-C,4'-C-ethyleneoxy-bridged 2'-deoxyribonucleic acids with exocyclic methylene groups.

Three 2'-C,4'-C-ethyleneoxy-bridged 2'-deoxyribonucleic acids possessing six-membered bridges with 6'-oxygen and 8'-exocyclic methylene groups (methylene-EoDNAs) were designed and synthesized in nine to ten steps from 5-methyluridine. The methylene-EoDNA-modified oligonucleotides showed excellent binding affinity with target ssRNA and extremely high nuclease resistance compared with natural oligonucleotides. These results proved the potential of methylene-EoDNAs for nucleic acid based technology.

ChemInform Abstract: Photocycloaddition and Rearrangement Reactions in a Putative Route to the Skeleton of Plicamine‐Type Alkaloids.

AbstractIntramolecular [2+2] photocycloaddition of isoquinolones (I) affords the corresponding cyclobutanes containing an exocyclic methylene group with high diastereoselectivity.

Chemistry of 1,5-diketones: V. Hydrazination of acyclic and heterocyclic (poly)carbonyl compounds

Reactions of 2-(1-aryl-3-oxo-3-phenylpropylidene)-3,4-dihydronaphthalen-1(2H)-ones, 3-(1-aryl-3-oxo-3-phenylpropyl)-3,4-dihydro-2H-chromene-2,4-diones, and 3,3'-(arylmethylene)bis(3,4-dihydro-2H-chromene-2,4-diones) with hydrazine hydrate have been studied. Depending on the substrate structure, these reactions involve intramolecular heterocyclization with participation of the exocyclic double bond and sidechain carbonyl group or both oxo groups to give new pyrazole, indazole, and diazepine derivatives, as well as hydrazones.

Synthesis of platencin core structures via twist-brendane

The formation of a twist-brendane via intramolecular enolate alkylation is described. Conversion of bicyclo[2.2.1]heptane scaffold present in this twist-brendane through a Grob-type fragmentation to unravel a functionalized bicyclo[2.2.2] system which contains all the necessary carbon atoms of the lipophilic core structure of nor -platencin, a platencin analogue is presented. Synthesis of core structure of platencin was also accomplished by extending this strategy to a starting material possessing a surrogate for the exocyclic methylene group.

Gaining insight into cell wall cellulose macrofibril organisation by simulating microfibril adsorption

One of the most important interactions within the paracrystalline matrix of the plant cell wall occurs between cellulose microfibrils to allow for the formation of larger diameter macrofibrils. Here, we have used computational techniques to investigate how different microfibril surfaces might adsorb onto one another. Molecular dynamics simulations show that limited direct adsorption occurs between non-polar surfaces and free energy of desorption calculations suggest this is due to a high energy barrier for the removal of a single layer of water between these surfaces. Further, it is predicted that when microfibril aggregation occurs, significant conformational changes take place at the surfaces of interaction involving O2 dihedral angles, exocyclic C6 conformation, and microfibril chain tilt. It is more likely that direct interactions initially take place between polar (110) surfaces, and that surface interactions occur between the same types of surface, such as 110 to 110, 1–10 to 1–10 or 200 to 100, where hydrogen bonds can be formed, to stabilise the aggregate. Additionally, we have identified that for the exocyclic group of a glucose residue to change conformation in origin layers, the O2 dihedral in residues before and adjacent to the glucose must rotate to a more cis-like conformation, compared to the trans-like conformation observed in crystalline cellulose. This change in exocyclic conformation occurs due to a slight shift in adjacent chains that preferentially stabilises the exocyclic conformation change in a specific glucose residue of each cellobiose repeat.

Mercury- and cadmium-assisted [2 + 2] cyclodimerization of tert-butylselenium diimide.

The complexes [MCl2{N,N'-(t)BuNSe(μ-N(t)Bu)2SeN(t)Bu}] [M = Cd (1), Hg (2)] were obtained in high yields by the reaction of tert-butylselenium diimide Se(IV)(N(t)Bu)2 with CdCl2 or HgCl2 in tetrahydrofuran. Recrystallization of 1 and 2 from acetonitrile (MeCN) afforded yellow crystals of 1·MeCN and 2·MeCN, respectively. Isomorphic 1·MeCN and 2·MeCN contain an unprecedented dimeric selenium diimide ligand, which is N,N'-chelated to the metal through exocyclic imido groups. In addition to the complexes 1 and 2, the (77)Se NMR spectra of acetonitrile solutions of 1·MeCN and 2·MeCN indicated the presence of the dimeric (t)BuNSe(μ-N(t)Bu)2SeN(t)Bu, monomeric Se(IV)(N(t)Bu)2, and cyclic selenium imides. Density functional theory calculations at the PBE0/def2-TZVPP level of theory were used to assign the (77)Se resonances of the dimer. A comparison of Gibbs energies of formation of some metal dichloride complexes [MCl2{N,N'-Se(IV)(N(t)Bu)2}] and [MCl2{N,N'-(t)BuNSe(μ-N(t)Bu)2SeN(t)Bu}] (M = Zn, Cd, Hg) indicated that the formation of complexes containing a dimeric selenium diimide ligand is favored over those containing a monomeric ligand for the group 12 metals. In the case of the group 10 metal halogenides (M = Ni, Pd, Pt), the Gibbs energies of the complexes with monomeric Se(IV)(N(t)Bu)2 ligands are close to those containing dimeric (t)BuNSe(μ-N(t)Bu)2SeN(t)Bu ligands. A plausible reaction pathway with a low activation energy involves the initial formation of [MCl2{N,N'-Se(IV)(N(t)Bu)2}] (M = Zn, Cd, Hg), which then reacts with another molecule of Se(N(t)Bu)2, leading to the final [MCl2{N,N'-(t)BuNSe(μ-N(t)Bu)2SeN(t)Bu}] complex. Without the presence of group 12 metal halogenides, the [2 + 2] cyclodimerization of Se(IV)(N(t)Bu)2 is virtually thermoneutral, but the activation energy is relatively high, which accounts for the kinetic stability of (t)BuNSe(μ-N(t)Bu)2SeN(t)Bu in solution. A minor byproduct, [Cd7Cl14{N,N'-Se(II)(NH(t)Bu)2}6]·4CH2Cl2, was identified by X-ray crystallography as a heptanuclear cluster with selenium(II) diamide ligands N,N'-chelated to the cadmium centers.

Solution structure of ligands involved in purine salvage pathway

Analogues of intermediates involved in the purine salvage pathway can be exploited as potential drug molecules against enzymes of protozoan parasites. To develop such analogues we need knowledge of the solution structures, predominant tautomer at physiological pH and protonation-state of the corresponding natural ligand. In this regard, we have employed ultraviolet resonance Raman spectroscopy (UVRR) in combination with density functional theory (DFT) to study the solution structures of two relatively unexplored intermediates, 6-phosphoryl IMP (6-pIMP) and succinyl adenosine-5′-monophosphate (sAMP), of purine salvage pathway. These molecules are intermediates in a two step enzymatic process that converts inosine-5′-monpophosphate (IMP) to adenosine-5′-monophosphate (AMP). Experimental data on the molecular structure of these ligands is lacking. We report UVRR spectra of these two ligands, obtained at an excitation wavelength of 260nm. Using isotope induced shifts and DFT calculations we assigned observed spectra to computed normal modes. We find that sAMP exists as neutral species at physiological pH and the predominant tautomer in solution bears proton at N10 position of purine ring. Though transient in solution, 6-pIMP is captured in the enzyme-bound form. This work provides the structural information of these ligands in solution state at physiological pH. We further compare these structures with the structures of AMP and IMP. Despite the presence of similar purine rings in AMP and sAMP, their UVRR spectra are found to be very different. Similarly, though the purine ring in 6-pIMP resembles that of IMP, UVRR spectra of the two molecules are distinct. These differences in the vibrational spectra provide direct information on the effects of exocyclic groups on the skeletal structures of these molecules. Our results identify key bands in the vibrational spectra of these ligands which may serve as markers of hydrogen bonding interactions upon binding to the active-sites of enzymes.

Photocycloaddition and Rearrangement Reactions in a Putative Route to the Skeleton of Plicamine-Type Alkaloids

Two isoquinolones were prepared, to which an allenyl side chain was linked at position C4 via a stereogenic silyloxy-substituted carbon atom. Intramolecular [2+2] photocycloaddition reactions of these substrates proceeded with high diastereoselectivity and delivered the respective cyclobutanes with an exocyclic methylene group (83% and 49% yield). With the 5,6-dioxoloisoquinolone precursor an unprecedented meta-photocycloaddition was observed as a significant side reaction, which occurred at positions C4 and C8a of the isoquinolone skeleton. The cyclobutane products were, after N-alkylation and transformation into the respective cyclobutanones (22–57%), subjected to various rearrangement reactions. In detail, a direct photochemical rearrangement, thermal and photochemical Beckmann rearrangements, and Baeyer–Villiger oxidation reactions were studied. In all cases, products were found, which resulted from cleavage of the amino-substituted cyclobutane bond, but not from the desired cleavage of the alternative alkyl-substituted cyclobutane bond.

New cyclized 9,11-secosterols enol-ether from soft coral Psendopterogorgia americana

Chemical investigation of the MeOH extract from the gorgonian Pseudopterogorgia americana afforded two rare sterols, ameristerenol A (1) and B (2), both 9,11-secosterols containing a seven-membered cyclic enol-ether in ring C, and ameristerol A (3), the first 9,11-secosterol containing a gorgosterol side chain containing an exocyclic methylene group at C-24, along with three related known analogues. Ameristerenol A (1) was converted to semi-synthetic sterols 4-6. The structures of compounds 1-6 were determined on the basis of extensive spectroscopic analysis and by comparison with literature data.

How to find the optimal partner—studies of snurportin 1 interactions with U snRNA 5′ TMG-cap analogues containing modified 2-amino group of 7-methylguanosine

Snurportin 1 is an adaptor protein that mediates the active nuclear import of uridine-rich small nuclear RNAs (U snRNA) by the importin-β receptor pathway. Its cellular activity influences the overall transport yield of small ribonucleoprotein complexes containing N2,N2,7-trimethylguanosine (TMG) capped U snRNA. So far little is still known about structural requirements related to molecular recognition of the trimethylguanosine moiety by snurportin in solution. Since these interactions are of a great biomedical importance, we synthesized a series of new 7-methylguanosine cap analogues with extended substituents at the exocyclic 2-amino group to gain a deeper insight into how the TMG-cap is adapted into the snurportin cap-binding pocket. Prepared chemical tools were applied in binding assays using emission spectroscopy. Surprisingly, our results revealed strict selectivity of snurportin towards the TMG-cap structure that relied mainly on its structural stiffness and compactness.

Comparative Study of Conjugational Effects in 3,4,5-Triaryl-1-R-1,2-Diphospholes and 3,4,5-Triaryl-1,2-Diphosphacyclopentadienide-Anions

GRAPHICAL ABSTRACT

Reactivity Diversification – Synthesis and Exchange Reactions of Cobalt and Iron 2‐Alkenylpyridine/‐pyrazine Complexes Obtained by Vinylic C(sp2)–H Activation

AbstractThe reactivity of 2‐alkenylpyridine derivatives with trimethylphosphane‐supported iron– and cobalt–methyl adducts were investigated and provided a series of C,N‐cyclometalated complexes through smooth vinyl C(sp2)–H activation. The reactions of Co(CH3)(PMe3)4 with 2‐vinylpyridine, 2‐(1‐phenylvinyl)pyridine, and 2‐vinylpyrazine provided dark green crystals of the five‐membered metallacycles (κ2‐C,N‐R1R2C=CH)Co(PMe3)3 (1: R1 = C5H4N, R2 = H; 2: R1 = C5H4N, R2 = Ph; 3: R1 = C4H3N2,R2 = H). The oxidative addition of 1–3 with iodomethane afforded the mer‐trans trivalent cobalt complexes (κ2‐C,N‐R1R2C=CH)Co(CH3)I(PMe3)2 (4: R1 = C5H4N, R2 = H; 5: R1 = C5H4N, R2 = Ph; 6: R1 = C4H3N2, R2 = H) in modest yields. The reaction of 2 with an additional equivalent of 2‐(1‐phenylvinyl)pyridine incorporated a second C,N metallacycle with an η2‐bonded alkenyl moiety to provide (κ2‐C,N‐C5H4N–CH=CH)(κ3,η2‐C,C,N‐C5H4N–CH=CH2)Co(PMe3) (7). No cyclometalation was observed with 8‐vinylquinoline and Co(CH3)(PMe3)4, which afforded (κ3,η2‐C,C,N‐C9H6N–CH=CH2)Co(CH3)(PMe3)2 (8) with retention of the Co–CH3 group; therefore, a suitable bite angle is required for C–H activation. No N coordination was observed with Fe(CH3)2(PMe3)4 and 8‐vinylquinoline (reductive elimination of C2H6), which afforded a low‐valent Fe(PMe3)3 moiety bound in an η4‐fashion with the exocyclic vinyl group and the ortho‐carbon atoms to give (κ4,η4‐C,C,C,C‐C9H6N–CH=CH2)Fe(PMe3)3 (9). In polar solvents, an equilibrium of cyclometalated 7,8‐benzoquinoline exists between the mer‐trans (90 %) and mer‐cis (10 %) configurations of (κ2‐C,N‐C13H6N)Fe(CH3)(PMe3)3 (10). At variance with the previously reported bicyclometalation of 2‐(2‐naphthalene‐1‐ylvinyl)pyridine with iron adducts, similar reactions with methylcobalt species provided the monocyclometalated η2,σ1‐bound coordination motif (κ3,η2‐C,C,N‐C5H4N–CH=CH–C10H6)Co(PMe3)2 (11). The reaction of 11 with carbon monoxide provided the monocarbonyl complex (κ3,η2‐C,C,C‐C5H4N–CH=CH–C10H6)Co(CO)(PMe3)2 (12), accompanied by the release of the N‐coordination site. The carbonylation of (κ3‐C,C,N‐C5H4N–CH=C–C10H6)Fe(PMe3)3 resulted in the exchange of one PMe3 ligand with the retention of the coordination sites to generate (κ3‐C,C,N‐C5H4N–CH=C–C10H6)Fe(CO)(PMe3)2 (13). All new compounds were identified by NMR spectroscopy and structurally characterized by single‐crystal X‐ray crystallography (with the exception of 10 and 13).

Was a Pyrimidine‐Pyrimidine Base Pair the Ancestor of Watson‐Crick Base Pairs? Insights from a Systematic Approach to the Origin of RNA

AbstractUncovering the origin of RNA is essential for understanding the origins of life. The persistent inability of chemists to identify a plausible prebiotic route to RNA polymers, along with the seemingly optimal structure of RNA for its functions in extant life, argue in favor of the hypothesis that RNA is a product of chemical or biological evolution. To understand the origin of RNA, we must consider which molecules could have originally acted in place of RNA’s substructures (i.e., nucleobases (the recognition units), ribose (a trifunctional connector), and phosphate (an ionized linker)) in the oldest ancestor of RNA (or proto‐RNA). Major challenges to uncovering the chemical structure of proto‐RNA include finding molecules that would have spontaneously undergone molecular selection and covalent assembly into an RNA‐like polymer, within the complex mixture of the “prebiotic soup” and without the aid of enzymes. In this review, we discuss progress towards identifying the recognition units of proto‐RNA and mechanisms by which the ancestral nucleobases might have been originally selected and incorporated into polymers. We consider possible proto‐nucleobases within the chemical space of the heterocycles defined by the purines and pyrimidines that have H, NH2, or O as exocyclic groups (which includes the extant nucleobases). Taking into account the results of numerous experiments that have explored nucleic acids with alternative backbones and noncanonical nucleobases, we are able to remove about half of these 81 molecules from candidacy as ancestral nucleobases. A particularly encouraging result of this approach is the identification of two molecules, 2,4,6‐triaminopyrimidine and barbituric acid, which look very promising as possible nucleobases of proto‐RNA.

2-Aminopurine as a fluorescent probe of DNA conformation and the DNA-enzyme interface.

Nearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.