The formation and reactivity of sulfito complexes of tetraethylenepentamine-cobalt(III): X-ray structure of αα-[co(tetren)SO3]ClO4

The synthesis of complexes of the type Co(tetren)-OH₂³⁺ (tetren = tetraethylenepentamine) and their reactions with sulfite to produce O- and S-bonded isomers were studied in detail. The linkage isomerization reaction of αβS-Co(tetren)OSO₂⁺ to αβS-Co(tetren)SO₃⁺ is accompanied by a geometrical isomerization to αα-Co(tetren)SO₃⁺. The latter species was isolated as pure crystals and an X-ray structure was determined. The structure data clearly show the strong trans effect of the sulfito ligand, which may account for the geometrical isomerization process.     

A comparison of vanadyl acetylacetonate complexes of N2O heteroscorpionate ligands that vary systematically in donor set

We have successfully prepared a series of vanadyl complexes with N₂O heteroscorpionate ligands and have characterized their cis and trans geometrical isomers both in solution and the solid state. The major difference between the isomers, and between the various oxygen atom donors of the N₂O scorpionate ligands, is in their redox potentials which can span almost a volt for this ostensively similar set of compounds. Such data may be useful in screening vanadium complexes for potential biological activity.     

Syntheses and NMR Analyses of Eight Geometrical Isomers of 10,12,14-Hexadecatrienyl Acetate,Sex Pheromone Candidates of the Mulberry Pyralid

Eight geometrical isomers of 10,12,14-hexadecatrienyl acetate, female sex pheromone candidates of the mulberry pyralid (Glyphodes pyloalis Walker), were synthesized by six routes. Each route consisted of reactions by which two of three double bonds were introduced stereospecifically and another rather nonspecifically, giving mainly two geometrical isomers, which were analyzed by 2D-NMR after separating by reversed-phase HPLC or by a reaction with tetracyanoethylene. The signals of the olefinic protons and carbons of each geometrical isomer were assigned by COSY spectra and by C-H COSY spectra, respectively, in addition to the signals of the allylic protons and carbons, and its chemical structure was revealed by the values of their chemical shifts and coupling constants. Furthermore, a new empirical rule concerning the chemical shift changes of these carbons by converting the configuration of the conjugated triene system is suggested.     

La Préparation et l’isomérisme géometrique des Acides Cinnamiques Méthylthio-α Substitués

An improved method of preparation and the separation of geometrical isomers of cis and trans α-methylthio-cinnamic acid derivatives are described. The observation on the NMR spectra and the determination of geometrical structure of these compounds by various spectrometric methods are also included.     

Re-characterization of three conjugated linolenic acid isomers by GC-MS and NMR

Conjugated linolenic acids (CLN) refer to a group of octadecatrienoic acids with three conjugated double bonds. Minor positional and geometrical differences among CLN isomers make their separation and identification difficult. We have used GC-MS and NMR to study three common CLN isomers namely alpha-eleostearic acid, beta-eleostearic acid and punicic acid, finding that some signals of olefinic carbon atoms in NMR spectra were mistakenly assigned in the literature. The present study was therefore undertaken to re-characterize the location of CC double bonds and assign the chemical signals of proton and carbon atoms using (1)H NMR, (13)C NMR, (1)H-(1)H two-dimensional correlation spectra ((1)H-(1)H COSY) and (13)C-(1)H two-dimensional correlation spectra ((13)C-(1)H COSY). The geometrical structure of double bonds in these three CLN isomers was identified using homonuclear decoupling technique.     

Specificity of Enzyme System Producing C6-Aldehyde in Tea Chloroplasts

The substrate specificity of enzyme system producing C₆-aldehyde in Thea chloroplasts was clarified with an entire series of synthesized positional isomers, in which the position of cis-1, cis-4-pentadiene system varies from C-3 to C-13 in C₁₈ fatty acid and geometrical isomers of linoleic acid. The structural requirement for the substrate of enzyme system producing C₆-aldehyde is the presence of cis-1, cis-4-pentadiene system between ω-6 and ω-10.     

Geometrical and optical isomers of diethylenetriaminemonoacetato(ethylene-diamine)cobalt(III) ion and their isomerism

Two isomers of the complex ion in the title were obtained and each isomer was resolved chromatographically into its antipodes. The two isomers with their isomer proportion of 27.9 and 72.1% in the equilibrium mixture were assigned to α and β(mer-N) isomers, respectively, of three possible geometrical isomers, from the measurements of their absorption, circular dichroism, and NMR spectra.Preference of the β(mer-N) to the isomer and very poor yield of an expected β(fac-N) isomer were confirmed by conformational analyses carried out for each structure of the isomers of Λ configuration, with possible configurations around nitrogen atoms and conformations of chelate rings. They gave minimized total strain energies of 43.13, 44.24, and 52.63 kJ/mol for the Λ-R,R(en:λ) structure of a β(mer-N) isomer, the Λ-S,R(δ,δ) structure of an α isomer, and a Λ-R,S(λ,λ) structure of a β(fac-N) isomer, respectively.From the results, configurations and conformations of the enantiomers of the resolved β(mer-N) and its isomers were deduced. An unfound isomer, β(fac-N) isomer, is thought to be very unstable; it would exist as less than 2% of the amount of β(mer- N) isomer, even if it were present in the reaction mixture.     

The new anticancer drug [(2R )-aminomethylpyrrolidine](1,1-cyclobutanedicarboxylato)platinum(II) and its toxic S enantiomer do interact differently with nucleic acids

 The interaction of the two chiral isomers of the new anticancer agent [Pt(ampyr)(cbdca)] (ampyr=aminomethylpyrrolidine, cbdca=cyclobutanedicarboxylate) with 5′-GMP and with short G-containing oligonucleotides has been studied using ¹H and ³¹P NMR, UV-vis spectroscopy and molecular modelling. Each isomer loses the cbdca ligand upon binding to the DNA fragments. Two geometrical isomers of the DNA adducts are formed owing to the presence of the unsymmetric ampyr ligand. These isomers prove to be GG-N7,N7 chelates for d(GpG), d(pGpG) and d(CpGpG). A slight preference for the formation of one geometrical isomer is found in the case of DNA fragments having a phosphate moiety and/or a C base at the 5′-site of the GG sequence. H-bonding interactions from the NH₂ moiety towards the 5′-phosphate group and/or the O atom of the C base clearly favour the formation of one geometrical isomer. The presence of these H-bonds, together with the bulky pyrrolidine ring, has resulted in the unique observation (by ¹H NMR) of NH protons of coordinated amines that do not rapidly exchange in a 99.95% D₂O solution. Temperature-dependence studies show an extremely slow stack ⇄ destack conformational change for the CGG adducts of the S isomer, which could be related to these stable H-bonds of the amine protons towards the oligonucleotide. For the R isomer this stack ⇄ destack conformational change is faster, probably owing to more steric hindrance of the pyrrolidine ring as deduced from the NOESY data, and as also suggested by molecular modelling. The observation of extremely slow rotation around the Pt-N7 bond for [Pt(R-ampyr)(GMP-N7)₂] provides further evidence for increased steric hindrance of the R isomer compared to the S isomer. The rate of binding of the drug to G bases proved to be second order for both isomers; in fact the (toxic) S isomer is about two times more reactive than the (non-toxic) R isomer, as seen from k ₂ values of 0.17±0.01 M^–1s^–1 for [Pt(S-ampyr)(cbdca)] and 0.09±0.01 M^–1s^–1 for [Pt(R-ampyr)(cbdca)]. No solvent-assisted pathway is involved in these reactions, since the complexes prove to be stable in solution for weeks and therefore only a direct attack of the G base on the Pt must be involved. Because hardly any intermediate species can be detected during the reaction, coordination of the second G base must occur much faster than the binding of the first G base. Since direct attack of the nucleobases takes place, steric interactions become extremely important and therefore are likely to determine the reactivity, activity and even the toxicity of such Pt complexes. Received: 12 January 1999 / Accepted: 17 June 1999     

Synthesis and hydrogenolysis of the methylene,ethylidene, isopropylidene,and diastereoisomeric 1-phenylethylidene acetals of β-l-arabino- and α-l-rhamnopyranoside derivatives

Both diastereoisomers of 1-phenylethylidene acetals (acetophenone acetals) of methyl and benzyl β-l-arabinopyranoside and α-l-rhamnopyranoside were prepared. Acetal-exchange reactions gave only the endo-phenyl isomers; their 2-O- and 4-O-acetyl derivatives were isomerised into the exo-phenyl compounds. ¹H-N.m.r. data were used to determine the absolute configuration at the acetal carbon atom in these compounds. The protons of the methyl group of the exo-phenyl isomers resonate at lower field than those of the endo-phenyl isomers. Hydrogenolysis of various methylene, ethylidene, and isopropylidene derivatives gave axial ethers. The endo-phenyl isomers of the acetophenone derivatives also gave axial 1-phenylethyl ethers in two diastereoisomeric forms. The exo-phenyl isomers of the arabinosides were stable towards the reagent (LiAlH₄AlCl₃), whereas the corresponding rhamnopyranosides gave the 2-(1-phenylethyl) ethers, but cleavage required prolonged reaction time and higher temperature.     

Exploration of structure, potential energy surface, and stability of planar C3B3

The geometrical structures, potential energy surface, stability, and bonding character of low-energy isomers of planar C₃B₃ were systematically explored and investigated at the B3LYP/6-311+G(d)// CCSD(T)/6-311+G(d) level for the first time. A large number of planar structures for low-energy isomers of C₃B₃ are located and reported. In particular, isomers 1 (C_s,²A’) and 2 (C_s,²A’), with a belt-like structure corresponding to the lowest-energy structures of planar C₃B₃, are revealed. Based on molecular orbital (MO) and natural bond orbital (NBO) analyses, delocalized σ MOs, multi-centered σ MOs, and delocalized π MOs play an important role in stabilizing the structures of low-energy isomers of C₃B₃. It is interesting to note from isomerization analysis that the interconversion of isomers 2 and 7 can be realized through two isomerization channels. The results demonstrate that isomers 1, 2, 3, 4, 7, 9, 12, 17, 19, and 20 of C₃B₃ are stable both thermodynamically and kinetically at the B3LYP/ 6-311+G(d)//CCSD(T)/ 6-311+G(d) level, and that they are observable in the laboratory, which is helpful for future experimental studies of C₃B₃.     

Reactivity difference between protolytic forms of some macrocyclic chromium(III) complexes in ligand substitution and electron transfer processes

The review provides insight into the mechanism of ligand substitution and electron transfer (from chromium(III) to iron(III)) by comparison of the reactivity of some tetraazamacrocyclic chromium(III) complexes in the conjugate acid-base forms. Use of two geometrical isomers made possible to estimate the influence of geometry and protolytic reactions in trans and cis position towards the leaving group on the rate enhancement. Studies on the reaction rates in different media demonstrated the role played by outer sphere interactions in a monodentate ligand substitution.     

Sequence analysis of twin ATP binding cassette proteins involved in translational control, antibiotic resistance, and ribonuclease L inhibition

The urea-induced unfolding of 'N' isomer (occurring at pH 7.0) and 'B' isomer (occurring at pH 9.0) of human serum albumin was studied by fluorescence and circular dichroism spectroscopic measurements. Urea-induced destabilization in different domains of both the isomers was monitored by using domain specific ligands, hemin (domain-I), chloroform, bilirubin (domain-II), and diazepam (domain-III). Urea-induced denaturation of N and B isomers of HSA showed a two-step, three-state transition with accumulation of intermediates around 4.8-5.2M and 3.0-3.4M urea concentrations, respectively. During first transition (0-4.8M urea for N isomer and 0-3.0M urea for B isomer) a continuous decrease in diazepam binding suggested major conformational changes in domain-III prior to intermediate formation. On the other hand, binding of hemin, a ligand for domain-IB and chloroform, whose binding site is located in domain-IIA remains unchanged up to 5.0M urea for N isomer and 3.0M urea for B isomer. Similarly, fluorescence intensity of Trp-214 that resides in domain-IIA remained unchanged up to the above-said urea concentrations and decreased thereafter. Absence of any decrease in hemin binding, chloroform binding, and Trp-214 fluorescence suggested the non-involvement of domain-IB and domain-IIA in intermediate formation. A significant increase in bilirubin binding prior to intermediate formation showed favorable conformational rearrangement in bilirubin binding cavity formed by loop 4 of domain-IB and loop 3 of domain-IIA. Further, a nearly complete abolishment of bilirubin binding to both isomers around 7.0M and 6.0M urea concentrations, respectively, indicated complete separation of domain-I from domain-II from each other. From these observations it can be concluded that N to B transition of human serum albumin shifted the intermediate formation towards lower urea concentration (3.0-3.4M urea for B isomer as against 4.8-5.2M urea for N isomer). Further both the intermediates were found to possess similar alpha-helical (approximately 39%) content and ligand binding properties.     

Escherichia coli thioredoxin folds into two compact forms of different stability to urea denaturation

The urea-induced denaturation of Escherichia coli thioredoxin and thioredoxin variants has been examined by electrophoresis on urea gradient slab gels by the method of Creighton [Creighton, T. (1986) Methods Enzymol. 131, 156-172]. Thioredoxin has only two cysteine residues, and these form a redox-active disulfide at the active site. Oxidized thioredoxin-S2 and reduced thioredoxin-(SH)2 each show two folded isomers with a large difference in stability to urea denaturation. The difference in stability is greater for the isomers of oxidized than for the isomers of reduced thioredoxin. At 2 degrees C, the urea concentrations at the denaturation midpoint are approximately 8 and 4.3 M for the oxidized isomers and 4.8 and 3.7 M for the reduced isomers. The difference between the gel patterns of samples applied in native versus denaturing buffer, and at 2 and 25 degrees C, is characteristic for the involvement of a cis-proline-trans-proline isomerization. The data very strongly suggest that the two folded forms of different stabilities correspond to the cis and trans isomers of the highly conserved Pro 76 peptide bond, which is cis in the crystal structure of oxidized thioredoxin. Urea gel experiments with the mutant thioredoxin P76A, with alanine substituted for proline at position 76, corroborate this interpretation. The electrophoretic banding pattern diagnostic for an involvement of proline isomerization in urea denaturation is not observed for oxidized P76A. In broad estimates of delta G degree for the native-denatured transition, the difference in delta G degree (no urea) between the putative cis and trans isomers of the Ile 75-Pro 76 peptide bond is approximately 3 kcal/mol for oxidized thioredoxin and approximately 1.5 kcal/mol for reduced thioredoxin. Since cis oxidized thioredoxin is much more stable than trans, folded oxidized thioredoxin is essentially all cis. In folded reduced thioredoxin, cis and trans interconvert slowly, on the minute time scale at 2 and 25 degrees C. In the absence of urea, the folded reduced thioredoxin is less than a few percent trans. Three additional mutants with additions or substitutions at the active site also show electrophoresis banding patterns consistent with a difference in stability between cis and trans isomers.     

Fractionation of trinucleotides from partial micrococcal nuclease digests of calf thymus DNA

The enzymic digest is first fractionated according to chain length by column chromatography on DEAE-Sephadex in 7 M urea at neutral pH. The trimer fraction is further resolved according to Gp content on DEAE-Sephadex in 50% MeOH and NH₄-formate buffers at pH 5.2. The three subgroups of trinucleotides containing 0, 1, and 2 Gp residues, respectively, are then separated according to Ap, Cp, and Tp content on DEAE-cellulose in 7 M urea and 0.1 M formic acid. Among the 23 trimers so obtained, sequence isomers such as TpGpAp and ApGpTp are resolved by partition chromatography on cellulose columns with 30% NH₄-sulfate at neutral pH.     

Geometrical isomers of bis(benzimidazol-2-ylethyl)sulfide)cobalt(II) diperchlorates: synthesis, structure, spectra and redox behavior of pink-[Co(bbes)2](ClO4)2 and blue-[Co(bbes)2](ClO4)2

1:1 and 1:2 cobalt complexes of bis(benzimidazol-2-ylmethyl)amine (bbma) bis(benzimidazol-2-ylmethyl)sulfide (bbms), bis(benzimidazol-2-ylethyl)sulfide (bbes) and diethylenetriamine (dien) were prepared and their spectral and redox behavior studied. Two geometrical isomers pink-[Co(bbes)₂]²⁺ and blue-[Co(bbes)₂]²⁺ were obtained when the complexes were prepared by using with bbes and they were separated manually and recrystallized. The octahedral structure of pink-[Co(bbes)₂]²⁺ was resolved by X-ray analysis. The electronic spectra show the presence of two geometrical isomers for Co(bbes)₂²⁺ in the solid state; for example, the spectral bands of pink-[Co(bbes)₂]²⁺ differs markedly with those of blue-[Co(bbes)₂]²⁺. This is consistent with the results obtained from magnetic measurements (5.10 BM for pink-Co(bbes)₂²⁺ and 4.72 BM for blue-[Co(bbes)₂]²⁺). Further, the behavior of the ligands (bbma, bbms, bbes) at different pH conditions was determined on the basis of ¹³C NMR studies. The redox potentials [Co(II)/Co(I)] of the complexes follow the trend [Co(bbma)₂]²⁺ < [Co(bbms)₂]²⁺ ≈ [Co(bbes)₂]²⁺ which demonstrates the stabilization of the Co(II) ion is more by both weak σ-donor and weak π-acceptor ligands rather than by σ-donor ligand.     

Ab initio calculation of the geometries, stabilities, and electronic properties for the bimetallic Be2Au(n) (n = 1-9) clusters: comparison with pure gold clusters

Ab initio methods based on density functional theory at BP86 level were applied to the study of the geometrical structures, relative stabilities, and electronic properties of small bimetallic Be₂Au _n (n = 1–9) clusters. The optimized geometries reveal that the most stable isomers have 3D structures at n = 3, 5, 7, 8, and 9. Here, the relative stabilities were investigated in terms of the averaged atomic binding energies, fragmentation energies and second-order difference of energies. The results show that the planar Be₂Au₄ structure is the most stable structure for Be₂Au _n clusters. The HOMO−LUMO gap, vertical ionization potential, vertical electron affinity and chemical hardness exhibit a pronounced even–odd alternating phenomenon. In addition, charge transfer and natural electron configuration were analyzed and compared.     

Structural and functional insights into the inhibition of human voltage-gated sodium channels by μ-conotoxin KIIIA disulfide isomers

μ-Conotoxins are components of cone snail venom, well-known for their analgesic activity through potent inhibition of voltage-gated sodium channel (Na_V) subtypes, including Na_V1.7. These small, disulfide-rich peptides are typically stabilized by three disulfide bonds arranged in a ‘native’ CysI-CysIV, CysII-CysV, CysIII-CysVI pattern of disulfide connectivity. However, μ-conotoxin KIIIA, the smallest and most studied μ-conotoxin with inhibitory activity at Na_V1.7, forms two distinct disulfide bond isomers during thermodynamic oxidative folding, including Isomer 1 (CysI-CysV, CysII-CysIV, CysIII-CysVI) and Isomer 2 (CysI-CysVI, CysII-CysIV, CysIII-CysV), but not the native μ-conotoxin arrangement. To date, there has been no study on the structure and activity of KIIIA comprising the native μ-conotoxin disulfide bond arrangement. Here, we evaluated the synthesis, potency, sodium channel subtype selectivity, and 3D structure of the three isomers of KIIIA. Using a regioselective disulfide bond-forming strategy, we synthetically produced the three μ-conotoxin KIIIA isomers displaying distinct bioactivity and Na_V subtype selectivity across human Na_V channel subtypes 1.2, 1.4, and 1.7. We show that Isomer 1 inhibits Na_V subtypes with a rank order of potency of Na_V1.4 > 1.2 > 1.7 and Isomer 2 in the order of Na_V1.4≈1.2 > 1.7, while the native isomer inhibited Na_V1.4 > 1.7≈1.2. The three KIIIA isomers were further evaluated by NMR solution structure analysis and molecular docking with hNa_V1.2. Our study highlights the importance of investigating alternate disulfide isomers, as disulfide connectivity affects not only the overall structure of the peptides but also the potency and subtype selectivity of μ-conotoxins targeting therapeutically relevant Na_V subtypes.     

Reorienting the Fab Domains of Trastuzumab Results in Potent HER2 Activators

The structure of the Fab region of antibodies is critical to their function. By introducing single cysteine substitutions into various positions of the heavy and light chains of the Fab region of trastuzumab, a potent antagonist of HER2, and using thiol chemistry to link the different Fabs together, we produced a variety of monospecific F(ab′)₂-like molecules with activities spanning from activation to inhibition of breast tumor cell growth. These isomers (or bis-Fabs) of trastuzumab, with varying relative spatial arrangements between the Fv-regions, were able to either promote or inhibit cell-signaling activities through the PI3K/AKT and MAPK pathways. A quantitative phosphorylation mapping of HER2 indicated that the agonistic isomers produced a distinct phosphorylation pattern associated with activation. This study suggests that antibody geometric isomers, found both in nature and during synthetic antibody development, can have profoundly different biological activities independent of their affinities for their target molecules.     

Base composition of intact nucleic acid oligomers

The base composition of intact, purified, oligonucleotides has been determined by comparing the absorption spectrum of each oligomer with calculated curves. The spectral curve of each oligomer was measured in 7M urea at three pH values and digitized at 1-mμ intervals. The calculated curves consisted of the sums of the absorption spectra of mononucleotides in 7M urea at the same pH's. A computer was used to make the comparisons and establish the best fit. Results are presented for nine of the ten possible dimer composition isomers; trimers from pancreatic and T₁ ribonuclease hydrolyzates of TMV-RNA; poly-A, poly-C, and poly-U; and intact tobacco mosaic virus-RNA.     

Role of ureogenesis in tackling problems of ammonia toxicity during exposure to higher ambient ammonia in the air-breathing walking catfish<Emphasis Type="Italic">clarias batrachus</Emphasis>

In the present study, the possible role of ureogenesis to avoid the accumulation of toxic ammonia to a lethal level under hyper-ammonia stress was tested in the air-breathing walking catfishClarias batrachus by exposing the fish at 25 mM NH₄Cl for 7 days. Excretion of ammonia by the NH₄Cl-exposed fish was totally suppressed, which was accompanied by significant accumulation of ammonia in different body tissues. The walking catfish, which is otherwise predominantly ammoniotelic, turned totally towards ureotelism from ammoniotelism with a 5-to 6-fold increase of urea-N excretion during exposure to higher ambient ammonia. Stimulation of ureogenesis was accompanied with significant increase of some of the key urea cycle enzymes such as carbamyl phosphate synthetase (urea cycle-related), argininosuccinate synthetase and argininosuccinate lyase both in hepatic and non-hepatic tissues. Due to this unique physiological strategy of turning towards ureotelism from ammoniotelism via the induced urea cycle, this air-breathing catfish is able to survive in very high ambient ammonia, which they face in certain seasons of the year in the natural habitat.