Vicinal deuterium perturbations on hydrogen NMR chemical shifts in cyclohexanes

The substitution of a deuterium for a hydrogen is known to perturb the NMR chemical shift of a neighboring hydrogen atom. The magnitude of such a perturbation may depend on the specifics of bonding and stereochemical relationships within a molecule. For deuterium-labeled cyclohexanes held in a chair conformation at -80 degrees C or lower, all four possible perturbations of H by D as H-C-C-H is changed to D-C-C-H have been determined experimentally, and the variations seen, ranging from 6.9 to 10.4 ppb, have been calculated from theory and computational methods. The predominant physical origins of the NMR chemical shift perturbations in deuterium-labeled cyclohexanes have been identified and quantified. The trends defined by the Delta delta perturbation values obtained through spectroscopic experiments and by theory agree satisfactorily. They do not match the variations typically observed in vicinal J(H-H) coupling constants as a function of dihedral angles.     

Independent Components Analysis of the Overlapping Voltammetric Signals

This paper introduces the Independent Components Analysis (ICA) to voltammetry and extends possibility of the qualitative and quantitative analysis of binary mixtures of similar oxidation/reduction potentials. It was demonstrated that even in the case of distance between peaks potentials equal to 10 mV, determinations may be realized according to typical validation criteria. The methodology was presented using the simulated data and capabilities and limitations of the method were described. Further, the usefulness of ICA was presented for voltammograms registered during simultaneous determination of copper and antimony, and thallium and indium. The results of high practical importance for chemical analysis were achieved and documented. In the quantitative analysis a property was extensively used, that ICA is an unsupervised method.     

Neon‐Bearing Ammonium Metal Formates: Formation and Behaviour under Pressure

The incorporation of noble gas atoms, in particular neon, into the pores of network structures is very challenging due to the weak interactions they experience with the network solid. Using high‐pressure single‐crystal X‐ray diffraction, we demonstrate that neon atoms enter into the extended network of ammonium metal formates, thus forming compounds Ne_x[NH₄][M(HCOO)₃]. This phenomenon modifies the compressional and structural behaviours of the ammonium metal formates under pressure. The neon atoms can be clearly localised within the centre of [M(HCOO)₃]₅ cages and the total saturation of this site is achieved after ～1.5 GPa. We find that by using argon as the pressure‐transmitting medium, the inclusion inside [NH₄][M(HCOO)₃] is inhibited due to the larger size of the argon. This study illustrates the size selectivity of [NH₄][M(HCOO)₃] compounds between neon and argon insertion under pressure, and the effect of inclusion on the high‐pressure behaviour of neon‐bearing ammonium metal formates.     

Many Valued Topologies and Lower Semicontinuity

On the basis of join-continuous semigroups , this paper demonstrates among other things that on every complete ortholattice there exists an L-valued topology such that order convergence is L-topological (this is not always the case with respect to ordinary topologies). Further, the concept of lower semicontinuous lattice-valued maps permits an extension of the omega-functor to the general setting of L-valued topological spaces where the importance of lies in the replacement of ordinary topologies by L-valued topologies. It is shown that has a right adjoint functor iff the underlying lattice is continuous.     

Bond dissociation energies and radical stabilization energies: an assessment of contemporary theoretical procedures

Various contemporary theoretical procedures have been tested for their accuracy in predicting the bond dissociation energies (BDEs) and the radical stabilization energies (RSEs) for a test set of 22 monosubstituted methyl radicals. The procedures considered include the high-level W1, W1', CBS-QB3, ROCBS-QB3, G3(MP2)-RAD, and G3X(MP2)-RAD methods, unrestricted and restricted versions of the double-hybrid density functional theory (DFT) procedures B2-PLYP and MPW2-PLYP, and unrestricted and restricted versions of the hybrid DFT procedures BMK and MPWB1K, as well as the unrestricted DFT procedures UM05 and UM05-2X. The high-level composite procedures show very good agreement with experiment and are used to evaluate the performance of the comparatively less expensive DFT procedures. RMPWB1K and both RBMK and UBMK give very promising results for absolute BDEs, while additionally restricted and unrestricted X2-PLYP methods and UM05-2X give excellent RSE values. UM05, UB2-PLYP, UMPW2-PLYP, UM05-2X, and UMPWB1K are among the less well performing methods for BDEs, while UMPWB1K and UM05 perform less well for RSEs. The high-level theoretical results are used to recommend alternative experimental BDEs for propyne, acetaldehyde, and acetic acid.     

Sulfur X-ray absorption and vibrational spectroscopic study of sulfur dioxide, sulfite, and sulfonate solutions and of the substituted sulfonate ions X3CSO3- (X = H, Cl, F)

Sulfur K-edge X-ray absorption near-edge structure (XANES) spectra have been recorded and the S(1s) electron excitations evaluated by means of density functional theory-transition potential (DFT-TP) calculations to provide insight into the coordination, bonding, and electronic structure. The XANES spectra for the various species in sulfur dioxide and aqueous sodium sulfite solutions show considerable differences at different pH values in the environmentally important sulfite(IV) system. In strongly acidic (pH < approximately 1) aqueous sulfite solution the XANES spectra confirm that the hydrated sulfur dioxide molecule, SO2(aq), dominates. The theoretical spectra are consistent with an OSO angle of approximately 119 degrees in gas phase and acetonitrile solution, while in aqueous solution hydrogen bonding reduces the angle to approximately 116 degrees . The hydration affects the XANES spectra also for the sulfite ion, SO32-. At intermediate pH ( approximately 4) the two coordination isomers, the sulfonate (HSO3-) and hydrogen sulfite (SO3H-) ions with the hydrogen atom coordinated to sulfur and oxygen, respectively, could be distinguished with the ratio HSO3-:SO3H- about 0.28:0.72 at 298 K. The relative amount of HSO3- increased with increasing temperature in the investigated range from 275 to 343 K. XANES spectra of sulfonate, methanesulfonate, trichloromethanesulfonate, and trifluoromethanesulfonate compounds, all with closely similar S-O bond distances in tetrahedral configuration around the sulfur atom, were interpreted by DFT-TP computations. The energy of their main electronic transition from the sulfur K-shell is about 2478 eV. The additional absorption features are similar when a hydrogen atom or an electron-donating methyl group is bonded to the -SO3 group. Significant changes occur for the electronegative trichloromethyl (Cl3C-) and trifluoromethyl (F3C-) groups, which strongly affect the distribution especially of the pi electrons around the sulfur atom. The S-D bond distance 1.38(2) A was obtained for the deuterated sulfonate (DSO3-) ion by Rietveld analysis of neutron powder diffraction data of CsDSO3. Raman and infrared absorption spectra of the CsHSO3, CsDSO3, H3CSO3Na, and Cl3CSO3Na.H2O compounds and Raman spectra of the sulfite solutions have been interpreted by normal coordinate calculations. The C-S stretching force constant for the trichloromethanesulfonate ion obtains an anomalously low value due to steric repulsion between the Cl3C- and -SO3 groups. The S-O stretching force constants were correlated with corresponding S-O bond distances for several oxosulfur species.     

Denaturation of hen egg white lysozyme in electromagnetic fields: a molecular dynamics study

Nonequilibrium molecular dynamics simulations of hen egg white lysozyme have been performed in the canonical ensemble at 298 K in the presence of external electromagnetic fields of varying intensity in the microwave to far-infrared frequency range. Significant nonthermal field effects were noted, such as marked changes in the protein's secondary structure which led to accelerated incipient local denaturation relative to zero-field conditions. This occurred primarily as a consequence of alignment of the protein's total dipole moment with the external field, although the enhanced molecular mobility and dipolar alignment of water molecules is influential on sidechain motion in solvent-exposed regions. The applied field intensity was found to be highly influential on the extent of denaturation in the frequency range studied, and 0.25-0.5 V Arms-1 fields were found to induce initial denaturation to a comparable extent to thermal denaturation in the 400 to 500 K range. In subsequent zero-field simulations following exposure to the e/m field, the extent of perturbation from the native fold and the degree of residual dipolar alignment were found to be influential on incipient folding.     

Dinuclear ruthenium(ii) complexes with flexible bridges as non-duplex DNA binding agents

The stereoisomers of a series of dinuclear ruthenium(ii) complexes [{Ru(phen)(2)}(2)(micro-BL)](4+) (phen = 1,10-phenanthroline) with flexible bridging ligands (BL) bb2 {1,2-bis[4(4'-methyl-2,2'-bipyridyl)]ethane}, bb5 {1,5-bis[4(4'-methyl-2,2'-bipyridyl)]pentane}, bb7 {1,7-bis[4(4'-methyl-2,2'-bipyridyl)]heptane}, and bb10 {1,10-bis[4(4'-methyl-2,2'-bipyridyl)]decane} have been synthesised. Their binding to a control dodecanucleotide, d(CCGGAATTCCGG)(2), and a tridecanucleotide, d(CCGAGAATTCCGG)(2), which contains a single adenine bulge have been studied using fluorescence displacement assays involving intercalating and groove-binding dyes, equilibrium dialysis and binding affinity chromatography. The fluorescence intercalator displacement (FID) assay indicated that LambdaLambda-[{Ru(phen)(2)}(2)(micro-bb7)](4+) had the greatest binding affinity with all the oligonucleotides, whereas an analogous fluorescence technique using a minor-groove binding dye, equilibrium dialysis and affinity binding chromatography showed that DeltaDelta-[{Ru(phen)(2)}(2)(micro-bb7)](4+) had the strongest binding. An (1)H NMR study of the binding of the DeltaDelta-enantiomer of [{Ru(phen)(2)}(2)(micro-bb7)](4+) to d(CCGAGAATTCCGG)(2) confirmed the selectivity of the metal complex for the bulge site and provided the basis for an energy-minimised binding model of the dinuclear ruthenium complex with the single adenine bulge containing trinucleotide. The binding model demonstrated the ability of the flexibly-linked complex to follow the curvature of the DNA minor groove.     

3′‐Deoxyribopyranose (4′→2′)‐Oligonucleotide Duplexes (=p‐DNA Duplexes) as Substitutes of RNA Hairpin Structures

By automated synthesis, we prepared hybrid oligonucleotides consisting of covalently linked RNA and p‐DNA sequences (p‐DNA=3′‐deoxyribopyranose (4′→2′)‐oligonucleotides) (see Table 1). The pairing properties of corresponding hybrid duplexes, formed from fully complementary single strands were investigated. An uninterrupted π‐π‐stacking at the p‐DNA/RNA interface and cooperative pairing between the two systems was achieved by connecting them via a 4′‐p‐DNA‐2′→5′‐RNA‐3′ and 5′‐RNA‐2′→4′‐p‐DNA‐2′ phosphodiester linkage, respectively (see Fig. 4). The RNA 2′‐phosphoramidites 9 – 12 , required for the formation of the RNA‐2′→4′‐p‐DNA phosphodiester linkage were synthesized from the corresponding, 3′‐O‐tom‐protected ribonucleosides (tom=[(triisopropylsilyl)oxy]methyl; Scheme 1). Analogues of the flavin mononucleotide (=FMN) binding aptamer 22 and the hammerhead ribozyme 25 were prepared. Each of these analogues consisted of two p‐DNA/RNA hybrid single strands with complementary p‐DNA sequences, designed to substitute stem/loop and stem motifs within the parent compounds. By comparative binding and cleavage studies, it was found that mixing of the two complementary p‐DNA/RNA hybrid sequences resulted in the formation of the fully functional analogues 23 ⋅ 24 and 27 ⋅ 28 of the FMN‐binding aptamer and of the hammerhead ribozyme, respectively.     

Fast and Reliable Automated Synthesis of RNA and Partially 2′-O- Protected Precursors (`Caged RNA') Based on Two Novel,Orthogonal 2′-O-Protecting Groups,Preliminary Communication

Two sets of RNA phosphoramidites, carrying the (fluoride-labile) 2′-O-[(triisopropylsilyl)oxy]methyl (=tom) group and the (photolabile) [(R)-1-(2-nitrophenyl)ethoxy]methyl (=(R)-npeom) group, were prepared (see 1 – 4 and 5 – 8 , resp.). The two protecting groups were completely orthogonal to each other. Three ribozyme-substrate constructs, protected each by a (R)-npeom group, were synthesized; on photolysis, efficient cleavage of this remaining protecting group occurred (Scheme 3). It could be demonstrated that the presence of one (R)-npeom group within a RNA strand has only a minor influence on the pairing properties of corresponding duplexes.