A cyclopentane conformational restraint for a peptide nucleic acid: design,asymmetric synthesis,and improved binding affinity to DNA and RNA

[structure: see text] A strategy to restrict the highly flexible backbone conformation of a peptide nucleic acid (PNA) by incorporation of a cyclopentane ring is proposed. An asymmetric synthesis of cyclopentane-modified PNA is reported, and its binding properties were determined. The cyclopentane ring leads to a significant improvement in the binding properties of the resulting PNA to DNA and RNA.     

Characterisation of oligosaccharides from a glycoprotein variant of human serum albumin (albumin Casebrook) using high-performance anion-exchange chromatography and nuclear magnetic resonance spectroscopy.

The characterisation of oligosaccharides present on albumin Casebrook, a glycoprotein variant of human serum albumin, which contains an N-linked oligosaccharide at an attachment site formed by a point mutation of 494 Asp-->Asn, is described. The monosaccharide compositional analysis of purified glycopeptides suggested the presence of complex biantennary carbohydrate structures. The oligosaccharides which were released by N-glycosidase-F appeared to be a single molecular species according to their retention on high-performance anion-exchange chromatography. The structure of the oligosaccharide was suggested by sequential exoglycosidase digestions and confirmed by proton nuclear magnetic resonance spectroscopy. It was concluded that the oligosaccharides were essentially homogeneous and consisted of an alpha(2-6)-desialylated complex biantennary glycan.     

Ring opening of pyridines: the pseudo‐cis and pseudo‐trans isomers of tetra‐n‐butylammonium 4‐nitro‐5‐oxo‐2‐pentenenitrilate

The reaction of 2‐chloro‐5‐nitropyridine with two equivalents of base produces the title carbanion as an intermediate in a ring‐opening/ring‐closing reaction. The crystal structures of the tetra‐n‐butylammonium salts of the intermediates, C₁₆H₃₆N⁺·C₅H₃N₂O₃⁻, revealed that pseudo‐cis and pseudo‐trans isomers are possible. One crystal structure displayed a mixture of the two isomers with approximately 90% pseudo‐cis geometry and confirms the structure predicted by the S_N(ANRORC) mechanism. The pseudo‐cis intermediate undergoes a slow isomerization over a period of months to the pseudo‐trans isomer, which does not have the appropriate geometry for the subsequent ring‐closing reaction. The structure of the pure pseudo‐trans isomer is also reported. In both isomers, the negative charge is highly delocalized, but relatively small differences in C—C bond distances indicate a system of conjugated double bonds with the nitro group bearing the negative charge. The packing of the two unit cells is very similar and largely determined by the interactions between the planar carbanion and the bulky tetrahedral cation.     

Chiral bisphosphinite metalloligands derived from a P-chiral secondary phosphine oxide

Interaction of PdCl(2)(MeCN)(2) with 2 equiv of (S(P))-(t)BuPhP(O)H (1H) followed by treatment with Et(3)N gave [Pd((1)(2)H)](2)(micro-Cl)(2) (2). Reaction of 2 with Na[S(2)CNEt(2)] or K[N(PPh(2)S)(2)] afforded Pd[(1)(2)H](S(2)CNEt(2)) (3) or Pd[(1)(2)H)[N(PPh(2)S)(2)] (4), respectively. Treatment of 3 with V(O)(acac)(2) (acac = acetylacetonate) and CuSO(4) in the presence of Et(3)N afforded bimetallic complexes V(O)[Pd(1)(2)(S(2)CNEt(2))](2) (5) or Cu[Pd(1)(2)(S(2)CNEt(2))](2) (6), respectively. X-ray crystallography established the S(P) configuration for the phosphinous acid ligands in 3 and 6, indicating that 1H binds to Pd(II) with retention of configuration at phosphorus. The geometry around Cu in 6 is approximately square planar with the average Cu-O distance of 1.915(3) A. Treatment of 2 with HBF(4) gave the BF(2)-capped compound [Pd((1)(2)BF(2))](2)(micro-Cl)(2) (7). The solid-state structure of 7 containing a PdP(2)O(2)B metallacycle has been determined. Chloride abstraction of 7 with AgBF(4) in acetone/water afforded the aqua compound [Pd((1)(2)BF(2))(H(2)O)(2)][BF(4)] (8) that reacted with [NH(4)](2)[WS(4)] to give [Pd((1)(2)BF(2))(2)](2)[micro-WS(4)] (9). The average Pd-S and W-S distances in 9 are 2.385(3) and 2.189(3) A, respectively. Treatment of [(eta(6)-p-cymene)RuCl(2)](2) with 1H afforded the phosphinous acid adduct (eta(6)-p-cymene)RuCl(2)(1H) (10). Reduction of [CpRuCl(2)](x)() (Cp = eta(5)-C(5)Me(5)) with Zn followed by treatment with 1H resulted in the formation of the Zn(II) phosphinate complex [(CpRu(eta(6)-C(6)H(5)))(t)BuPO(2))](2)(ZnCl(2))(2) (11) that contains a Zn(2)O(4)P(2) eight-membered ring.     

Introducing ONETEP: linear-scaling density functional simulations on parallel computers

We present ONETEP (order-N electronic total energy package), a density functional program for parallel computers whose computational cost scales linearly with the number of atoms and the number of processors. ONETEP is based on our reformulation of the plane wave pseudopotential method which exploits the electronic localization that is inherent in systems with a nonvanishing band gap. We summarize the theoretical developments that enable the direct optimization of strictly localized quantities expressed in terms of a delocalized plane wave basis. These same localized quantities lead us to a physical way of dividing the computational effort among many processors to allow calculations to be performed efficiently on parallel supercomputers. We show with examples that ONETEP achieves excellent speedups with increasing numbers of processors and confirm that the time taken by ONETEP as a function of increasing number of atoms for a given number of processors is indeed linear. What distinguishes our approach is that the localization is achieved in a controlled and mathematically consistent manner so that ONETEP obtains the same accuracy as conventional cubic-scaling plane wave approaches and offers fast and stable convergence. We expect that calculations with ONETEP have the potential to provide quantitative theoretical predictions for problems involving thousands of atoms such as those often encountered in nanoscience and biophysics.     

Syntheses, structure, and selected physical properties of CsLnMnSe3 (Ln = Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb, Y) and AYbZnQ3 (A = Rb, Cs; Q = S, Se, Te)

CsLnMnSe(3) (Ln = Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb, Y) and AYbZnQ(3) (A = Rb, Cs; Q = S, Se, Te) have been synthesized from solid-state reactions at temperatures in excess 1173 K. These isostructural materials crystallize in the layered KZrCuS(3) structure type in the orthorhombic space group Cmcm. The structure is composed of LnQ(6) octahedra and MQ(4) tetrahedra that share edges to form [LnMQ(3)] layers. These layers stack perpendicular to [010] and are separated by layers of face- and edge-sharing AQ(8) bicapped trigonal prisms. There are no Q-Q bonds in the structure of the ALnMQ(3) compounds so the formal oxidation states of A/Ln/M/Q are 1+/3+/2+/2-. The CsLnMnSe(3) materials, with the exception of CsYbMnSe(3), are Curie-Weiss paramagnets between 5 and 300 K. The magnetic susceptibility data for CsYbZnS(3), RbYbZnSe(3), and CsYbMSe(3) (M = Mn, Zn) show a weak cusp at approximately 10 K and pronounced differences between field-cooled and zero-field-cooled data. However, CsYbZnSe(3) is not an antiferromagnet because a neutron diffraction study indicates that CsYbZnSe(3) shows neither long-range magnetic ordering nor a phase change between 4 and 295 K. Nor is the compound a spin glass because the transition at 10 K does not depend on ac frequency. The optical band gaps of the (010) and (001) crystal faces for CsYbMnSe(3) are 1.60 and 1.59 eV, respectively; the optical band of the (010) crystal faces for CsYbZnS(3) and RbYbZnSe(3) are 2.61 and 2.07 eV, respectively.     

The fragmentation of organic molecules under electron-IMPACT—II. The mass spectra of tetronic acid and some of its derivatives

The mass spectra of tetronic acid and of a number of its derivatives are recorded and discussed. Where necessary, the composition of the fragment ions has been checked by high resolution mass measurements. Fragmentation of the molecular ion is explained in terms of the rupture of a bond attached to C-4, and the predominant routes for many of the compounds can be explained on the basis of two schemes, the first involving preliminary ketonisation of the molecular ion, followed by elimination of carbon monoxide, the second involving rupture of the C-4? R³ bond prior to elimination of carbon monoxide. Special structural features, however, provide alternative routes.     

Energy landscapes for adsorption of a protein-like HP chain as a function of native-state stability

Dynamic Monte Carlo (DMC) simulations of the adsorption of simple protein-like chains are used to more clearly define the molecular basis for the dependence of adsorption thermodynamics on the stability of the unique lowest-energy "native state" conformation of the chain. Arai and Norde were among the first to show that proteins of low native-state stability strongly denature upon adsorption to weakly attractive sorbent surfaces, while relatively modest changes in conformation are observed in stable proteins under identical adsorption conditions. When the protein has a low native-state stability, favorable adsorption entropies are typically observed in such systems, leading to the general belief that the chain gains conformational entropy during adsorption through a net reduction in intramolecular interactions specific to the native-state structure. Analysis of energy landscapes generated from our DMC simulation results show that a net loss in specific intramolecular interactions can lead to a positive delta(ads)S under certain adsorption conditions. However, the influence of chain conformation on delta(ads)S is found to correlate more directly with the manner in which the unique states of the system are distributed among the energy levels available to the adsorbed chain. Delta(ads)S is found to tend toward a maximum for adsorption processes described by thermally averaged energy landscapes in which the energy levels carrying the highest Boltzmann weights have a high degree of conformational degeneracy. This condition is met when the average interaction energy between the chain and the sorbent equals that between two hydrophobic segments of the chain.     

Cyclopolymerization of amine-linked diacrylate monomers

New diacrylate monomers for cyclopolymerization were synthesized from the reaction of ethyl α-chloromethylacrylate (ECMA) and t-butyl α-bromomethyl acrylate (TBBr) with aniline, adamantyl amine, t-butyl amine, cyanamide, and 4-tetradecyl aniline in yields of ca. 50–70%. Bulk and solution polymerizations with azobisisobutyronitrile (AIBN) at 60–85°C gave soluble cyclopolymers with M_n and M_w ranging from 10,000–30,000 and 12,000–40,000, respectively. The ECMA–cyanamide derivative only gave crosslinked polymers. ¹H and ¹³C solution NMR indicated high cyclization efficiency (>93%). A prototype NLO polymer was synthesized from the reaction of the TBBr–aniline cyclopolymer with tetracyanoethylene. The p-hydroxyaniline derivative of ECMA was synthesized and used for further derivatizations; for example, the benzoate ester was made and polymerized (M_n = 21,260 and M_w = 40,317). The ester groups of the TBBrndash;aniline polymer were hydrolyzed completely to give a polymer with both acid and base moieties. DSC thermograms showed glass transitions of 132°C for the ECMA–aniline derivative, 192°C for the ECMA–adamantyl derivative, 53°C for the TBBr–tetradecylaniline derivative, and 120° for the ECMA–p-benzoylaniline derivative. The ECMA–t-butyl amine polymer showed no obvious T_g. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 2111–2121, 1997