Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides,m(3)Psi and Psi

The synthesis of 3-methylpseudouridine (m(3)Psi) phosphoramidite, 5'-O-[benzhydryloxybis(trimethylsilyloxy)silyl]-2'-O-[bis(2-acetoxyethoxy)methyl]-3-methylpseudouridine-3'-(methyl-N,N-diisopropyl)phosphoramidite, is reported. Selective pivaloyloxymethyl protection of the Psi N1 followed by methylation at N3 was used to generate the naturally occurring pseudouridine analogue. The m(3)Psi phosphoramidite was used in combination with pseudouridine (Psi) and standard base phosphoramidites to synthesize a 19-nucleotide RNA representing helix 69 of Escherichia coli 23S ribosomal RNA (rRNA) (residues 1906-1924), containing a single m(3)Psi at position 1915 and two Psi's at positions 1911 and 1917. Our synthesis of the fully modified helix 69 RNA demonstrates the ability to make milligram quantities of RNA that can be used for further high-resolution structure studies. Site-selective introduction of the methyl group at the N3 position of pseudouridine at position 1915 causes a slight increase in the thermodynamic stability of the RNA hairpin relative to pseudouridine; RNAs containing either uridine or 3-methyluridine at position 1915 have similar stability. One-dimensional imino proton NMR and circular dichroism spectra of the modified RNAs reveal that the methyl group does not cause any substantial changes in the RNA hairpin structure.     

2,8'-disubstituted-1,1'-binaphthyls: a new pattern in chiral ligands

The title binaphthyls 19 and 26, which are the positional isomers of 2-methoxy-2'-(diphenylphosphino)-1,1'-binaphthyl (MOP, 19) and 2-amino-2'-hydroxy-1,1'-binaphthyl (NOBIN, 26), have been synthesized by Suzuki coupling as the key step (10 + 15-->18), followed by functional group transformations, involving C-P and C-N bond formation (18-->19 and 18-->23). Racemic intermediate 22 was resolved by co-crystallization with N-benzylcinchonidinium chloride and the absolute configuration determined by X-ray crystallography. These novel binaphthyls are configurationally stable and, as such, potentially usable as chiral ligands in asymmetric reactions. Michael addition of the glycine-derived enolate 40 to methyl acrylate, carried out in the presence of (R)-(-)-27 as the chiral phase-transfer catalyst, afforded L-glutamic acid (S)-(+)-43 of 92% ee (after hydrolysis of the primary product).     

Preparation of some substituted imidazo[1,2-a]pyridine derivatives

2-Bromopyridine derivatives 2a-2c were prepared. Compounds 2b and 2c and ammonia yielded aminopyridines 3b and 3c which were converted to imidazo[1,2-a]pyridine derivatives 4b and 4c . Compound 4b was nitrated giving the analogue 5b of metronidazole 1 .     

Infrared and Raman spectra, conformational stability, ab initio calculations of structure, and vibrational assignment of 2-hexyne

The infrared spectra (3500–50 cm⁻¹) of the gas and solid and the Raman spectra (3500–50 cm⁻¹) of the liquid and solid have been recorded for 2-hexyne, CH₃–CC–CH₂CH₂CH₃. Variable temperature studies of the infrared spectrum (3500–400 cm⁻¹) of 2-hexyne dissolved in liquid krypton have also been recorded. Utilizing four anti/gauche conformer pairs, the anti(trans) conformer is found to be the lower energy form with an enthalpy difference of 74±8 cm⁻¹ (0.88±0.10 kJ/mol) determined from krypton solutions over the temperature range −105 to −150 °C. At room temperature it is estimated that there is 42% of the anti conformer present. Equilibrium geometries and energies of the two conformers have been determined by ab initio (HF and MP2) and hybrid DFT (B3LYP) methods using a number of basis sets. Only the HF and DFT methods predict the anti conformer as the more stable form as found experimentally. A vibrational assignment is proposed based on the force constants, relative intensities, depolarization ratios from the ab initio and DFT calculations and on rotational band contours obtained using the calculated equilibrium geometries. From calculated energies it is shown that the CH₃ group exhibits almost completely free rotation which is in agreement with the observation of sub-band structure for the degenerate methyl vibrations from which values of the Coriolis coupling constants, ζ, have been determined. The results are compared to similar properties of some corresponding molecules.     

Structure and dynamics of metallomacrocycles: recognition of zinc xylyl-bicyclam by an HIV coreceptor

As platforms for the design of metal-based therapeutic and diagnostic agents, macrocycles are rigid enough to provide strong metal binding sites and orient functional groups stereoselectively, yet flexible enough to accommodate structural changes required for induced-fit recognition of biological targets. We consider the recognition of the Zn(II) complex of the bis-tetraazamacrocycle xylyl-bicyclam, a potent anti-HIV agent, by the coreceptor CXCR4, a G-protein-coupled receptor used by HIV for membrane fusion and cell entry. NMR studies show that the macrocycles of Zn(II)(2)-xylyl-bicyclam perchlorate exist in aqueous solution as two major configurations, trans-I (nitrogen chirality R,S,R,S), and trans-III (S,S,R,R). Acetate addition induced a major structural change. X-ray crystallography shows that the acetate complex contains the unusual cis-V cyclam configuration (R,R,R,R and folded) with bidentate coordination of acetate to Zn(II) plus second-coordination-sphere double H-bond formation between diagonal NH protons on the opposite cyclam face and acetate carboxylate oxygens. Detailed 1D and 2D NMR studies show that the major configuration of Zn(II)(2)-xylyl-bicyclam acetate in aqueous solution is cis-V/trans-I. Molecular modeling shows that an analogous cis-V site can be formed when Zn(II)(2)-xylyl-bicyclam binds to CXCR4, involving the carboxylate groups of Asp262 (Zn(II) coordination) and Glu288 (double H-bonding). The second cyclam can adopt the trans-I (or trans-III) configuration with Zn(II) binding to Asp171. These interactions are consistent with the known structure-activity relationships for bicyclam anti-HIV activity and receptor mutation. Consideration of the anti-HIV activity of xylyl-bicyclam complexes of other metal ions suggests that affinity for carboxylates, configurational flexibility, and kinetic factors may all play roles in receptor recognition. For example, Pd(II) cyclam complexes interact only weakly with axial ligands and are inflexible and inactive, whereas Co(III) cyclams bind carboxylates strongly, are configurationally flexible, and yet have low activity. Our findings should aid the design of new generations of active macrocycles including highly specific chemokine receptor antagonists.     

Two-particle dynamics on an electrode in ac electric fields

The relative motion between pairs of negatively charged latex particles 9.7 microm in diameter and deposited on an electrode was measured by optical microscopy and image analysis. At an rms field of approximately 30 V cm(-1), the two particles moved toward each other at frequencies below 500 Hz, but they separated at 1000 Hz. In the cases of aggregation, there are several interesting characteristics. First, when the center-to-center separation of a pair was initially 6 particle radii or more apart, a transient 'incubation' period of tens of seconds was observed before the particles began to move toward each other. Second, the two particles never came into contact, rather at long times the pair maintained a stationary gap between them equal to approximately one-half the particle radius. This stationary gap between particles was also observed for the aggregation of clusters of three or more particles. Finally, the rate of approach for a pair of particles decreased as the frequency increased. Larger fields are required to move particles together in ac compared to dc fields; at 30 Hz the ac field must be 130 times greater than the dc field to achieve the same rate of approach. Taking advantage of the qualitative and quantitative differences of the cooperative motion of particles in dc vs. ac fields, one should be able to re-position particles by alternating between these two modes. We demonstrated that the same pair of particles can be brought together at low frequency (100 or 200 Hz) and then separated at high frequency (1000 Hz).     

Novel approach to the zaragozic acids. Enantioselective total synthesis of 6,7-dideoxysqualestatin H5

The total synthesis of 6,7-dideoxysqualestatin H5 (3) has been completed by a concise approach that features the stereoselective intramolecular vinylogous aldol reaction of the furoic ester 25a to give 30 or its trimethylsilyl ether derivative 34, which possess the requisite absolute stereochemistry at C(3)-C(5) of 3. Compound 34 was reduced to the saturated bislactone 39, and the C(1) side chain subunit 47 was introduced leading to a mixture of the hemiacetals 48 and the corresponding ketone 49. When this mixture was stirred with methanolic acid, transketalization occurred to give a mixture of 50 and the spirocyclic methyl acetals 51a,b. Oxidation of the primary alcohol group in 50 followed by saponification of the two remaining ester groups gave 3. The longest linear sequence in the synthesis commences with commercially available erythronolactone (26) and requires 17 chemical steps with only 10 isolated intermediates.     

An informative subtlety of itemperature-jump or coulostatic responses for surface-attached species

Theoretical relationships are developed to describe the open-circuit responses associated with the indirect laser-induced temperature-jump (ILIT) method, a method for measuring fast electron-transfer rate constants of surface-attached redox species. The analysis is also applicable to data obtained using the coulostatic charge-injection method. The unique relationship between k_m, the relaxation rate constant for the ILIT (or coulostatic) response, and E_i, the potential at which the system is initially poised, exhibits a surprising sensitivity to the values of k₀, E_i^0′ (the standard rate constant and formal potential for the redox couple), α (the transfer coefficient in the Butler–Volmer equation) and γ (a dimensionless parameter which is directly proportional to the total surface concentration of the redox moiety). ILIT data for several examples of surface-attached ferrocene moieties confirm the theoretically predicted k_m vs E_i behavior. Values of E_i^0′ and γ extracted from the ILIT data agree well with the values obtained from cyclic voltammetric data thereby confirming that the ILIT and cyclic voltammogram (CV) experiments are sampling the same ferrocene population.