Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH

The stability of DNA is highly dependent on the properties of the surrounding solvent, such as ionic strength, pH, and the presence of denaturants and osmolytes. Addition of pyridine is known to unfold DNA by replacing π–π stacking interactions between bases, stabilizing conformations in which the nucleotides are solvent exposed. We show here experimental and theoretical evidences that pyridine can change its role and in fact stabilize the DNA under acidic conditions. NMR spectroscopy and MD simulations demonstrate that the reversal in the denaturing role of pyridine is specific, and is related to its character as pseudo groove binder. The present study sheds light on the nature of DNA stability and on the relationship between DNA and solvent, with clear biotechnological implications.     

Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH

The stability of DNA is highly dependent on the properties of the surrounding solvent, such as ionic strength, pH, and the presence of denaturants and osmolytes. Addition of pyridine is known to unfold DNA by replacing π–π stacking interactions between bases, stabilizing conformations in which the nucleotides are solvent exposed. We show here experimental and theoretical evidences that pyridine can change its role and in fact stabilize the DNA under acidic conditions. NMR spectroscopy and MD simulations demonstrate that the reversal in the denaturing role of pyridine is specific, and is related to its character as pseudo groove binder. The present study sheds light on the nature of DNA stability and on the relationship between DNA and solvent, with clear biotechnological implications.     

Can Weakly Coordinating Anions Stabilize Mercury in Its Oxidation State + IV?

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access the actual ChemInform Abstract, please click on HTML or PDF.     

Do Aviram-Ratner diodes rectify?

We present state-of-the-art first principles calculations for the IV characteristics of a donor-insulator-acceptor (DsigmaA) type molecular diode anchored with thiolate bonds to two gold electrodes. We find very poor diode characteristics of the device, and the origin of this is analyzed in terms of the bias-dependent electronic structure. At zero bias, the highest occupied molecular orbital (HOMO) is confined to the D part, and the lowest unoccupied molecular orbital (LUMO) is confined to the A part, while at 3.8 V the two states align, and this gives rise to an increasing current. The latter is a potential mechanism for rectification and may in some cases lead to favorable diode characteristics. We identify the origin of the vanishing rectification for the investigated molecule, and on the basis of this we suggest parameters which are important for successful chemical engineering of DsigmaA rectifiers.     

Tetrabenzononacene: “Butterfly Wings” Stabilize the Core

In combination with bulky substituents at the core, fourfold benzannulation at the cata-positions stabilizes a nonacene sufficiently to allow its isolation and characterization by ¹H NMR and X-ray analysis. The four benzo units blueshift the absorption spectrum in comparison to a solely linear nonacene, but significantly increase the stability in the solid state.     

Bonding Trends in Tetravalent Th–Pu Monosalen Complexes

The synthesis of three complex series of the form [AnCl₂(salen)(Pyx)₂] (H₂salen=N,N′-bis(salicylidene)ethylenediamine; Pyx=pyridine, 4-methylpyridine, 3,5-dimethylpyridine) with tetravalent early actinides (An=Th, U, Np, Pu) is reported with the goal to elucidate the affinity of these heavy elements for small neutral N-donor molecules. Structure determination by single-crystal XRD and characterization of bulk powders with infrared spectroscopy reveals isostructurality within each respective series and the same complex conformation in all reported structures. Although the trend of interatomic distances for An−Cl and An−N (imine nitrogen of salen or pyridyl nitrogen of Pyx) was found to reflect an ionic behavior, the trend of the An−O distances can only be described with additional covalent interactions for all elements heavier than thorium. All experimental results are supported by quantum chemical calculations, which confirm the mostly ionic character in the An−N and An−Cl bonds, as well as the highest degree of covalency of the An−O bonds. Structurally, the calculations indicate just minor electronic or steric effects of the additional Pyx substituents on the complex properties.     

Do Nonbonded H--H Interactions in Phenanthrene Stabilize It Relative to Anthracene? A Possible Resolution to this Question and Its Implications for Ligands such as 2,2'-Bipyridyl

The problem of whether interactions between the hydrogen atoms at the 1,10-positions in the "cleft" of the "bent" phenanthrene stabilize the latter molecule thermodynamically relative to "linear" anthracene, or whether the higher stability of phenanthrene is due to a more energetically favorable π-system, is considered. DFT calculations at the X3LYP/cc-pVTZ(-f)++ level of the ground state energies (E) of anthracene, phenanthrene, and the set of five benzoquinolines are reported. In the gas phase, "bent" phenanthrene was computed to be thermodynamically more stable than "linear" anthracene by -28.5 kJ mol(-1). This fact was attributed predominantly to the phenomenon of higher aromatic stabilization of the π-system of phenanthrene relative to anthracene, and not to the stabilizing influence of the nonbonding H--H interactions in its cleft. In fact, these interactions in phenanthrene were shown to be destabilizing. Similar calculations for five benzoquinolines (bzq) indicate that ΔE values vary as: 6,7-bzq (linear) ≤ 2,3-bzq (linear) < 5,6-bzq (bent) ≤ 3,4-bzq (bent) < 7,8-bzq (bent, no H--H nonbonding interactions in cleft), supporting the idea that it is a more stable π-system that favors 7,8-bzq over 2,3-bzq and 6,7-bzq, and that the H--H interactions in the clefts of 3,4-bzq and 5,6-bzq are destabilizing. Intramolecular hydrogen bonding in the cleft of 7,8-bzq plays a secondary role in its stabilization relative 6,7-bzq. The question of whether H--H nonbonded interactions between H atoms at the 3 and 3' positions of 2,2'-bipyridyl (bpy) coordinated to metal ions are stabilizing or destabilizing is then considered. The energy of bpy is scanned as a function of N-C-C-N torsion angle (χ) in the gas-phase, and it is found that the trans form is 32.8 kJ mol(-1) more stable than the cis conformer. A relaxed coordinate scan of energy of bpy in aqueous solution as a function of χ is modeled using the PBF approach, and it is found that the trans conformer is still more stable than the cis, but now only by 5.34 kJ mol(-1). The effect that the latter energy has on the thermodynamic stability of complexes of metal ions with bpy in aqueous solution is discussed.     

Do you believe in wavefunctions?

The Computational Perspective

Do you believe in wavefunctions?     

Do benzodiazepines mimic reverse-turn structures?

The role of benzodiazepine derivatives (BZD) as a privileged scaffold that mimics beta-turn structures (Ripka et al. (1993) Tetrahedron 49:3593-3608) in peptide/protein recognition was reexamined in detail. Stable BZD ring conformers were determined with MM3, and experimental reverse-turn structures were extracted from the basis set of protein crystal structures previously defined by Ripka et al. Ideal beta-turns were also modeled and similarly compared with BZD conformers. Huge numbers of conformers were generated by systematically scanning the torsional degrees of freedom for BZDs, as well as those of ideal beta-turns for comparison. Using these structures, conformers of BZDs were fit to experimental structures as suggested by Ripka et al., or modeled classical beta-turn conformers, and the root-mean-square deviation (RMSD) values were calculated for each pairwise comparison. Pairs of conformers with the smallest RMSD values for overlap of the four alpha-beta side-chain orientations were selected. All overlaps of BZD conformers with experimental beta-turns yielded one or more comparisons where the least RMSD was significantly small, 0.48-0.86 angstroms, as previously suggested. Utilizing a different methodology, the overall conclusion that benzodiazepines could serve as reverse-turn mimetics of Ripka et al. is justified. The least RMSD values for the overlap of BZDs and modeled classical beta-turns were also less than 1 angstrom. When comparing BZDs with experimental or classical beta-turns, the set of experimental beta-turns selected by Ripka et al. fit the BZD scaffolds better than modeled classical beta-turns; however, all the experimental beta-turns did not fit a particular BZD scaffold better. A single BZD ring conformation, and/or chiral orientation, can mimic some, but not all, of the experimental beta-turn structures. BZD has two central ring conformations and one chiral center that explains why the four variations of the BZD scaffold can mimic all types of beta-turn structure examined. It was found, moreover, that the BZD scaffold also mimics each of the nine clusters of experimental orientations of side chains of reverse turns in the Protein Data Bank, when the new classification scheme for the four side-chain directions (the relative orientations of alpha-beta vectors of residues i through i+3) was considered (Tran et al. (2005) J Comput-Aided Mol Des 19:551-566).     

Do enzymes sleep and work?

Single-enzyme studies suggest that dynamic disorder is a general characteristic of enzyme catalysis.     

Do Xylylenes Isomerize in Pyrolysis?

We report infrared spectra of xylylene isomers in the gas phase, using free electron laser (FEL) radiation. All xylylenes were generated by flash pyrolysis. The IR spectra were obtained by monitoring the ion dip signal, using a IR/UV double resonance scheme. A gas phase IR spectrum of para-xylylene  was recorded, whereas ortho- and meta-xylylene were found to partially rearrange to benzocyclobutene and styrene. Computations of the UV oscillator strength  for all molecules were carried out and provde an explanation for the observation of the isomerization products.     

Do all-metal antiaromatic clusters exist?

As shown by detailed nucleus-independent chemical shift (NICS) analyses of the contributions of each molecular orbital, the very recently reported gas-phase all-metal Al4Li3- anion and its relatives (Kuznetsov, A.E.; Birch, K.A.; Boldyrev, A.I.; Li, X.; Zhai, A.I.; Wang, L.S. Science 2003, 300, 622) are aromatic rather than antiaromatic. The paratropic (antiaromatic) four-pi-electron contribution is overcome by the predominating diatropic effects of sigma aromaticity. However, true antiaromatic all-metal clusters, such as Sn62- (Schiemenz, B.; Huttner, G. Angew. Chem., Int. Ed. Engl. 1993, 32, 297), do exist.     

Surface-Regulated Rhodium–Antimony Nanorods for Nitrogen Fixation

Surface regulation is an effective strategy to improve the performance of catalysts, but it has been rarely demonstrated for nitrogen reduction reaction (NRR) to date. Now, surface-rough Rh₂Sb nanorod (RNR) and surface-smooth Rh₂Sb NR (SNR) were selectively created, and their performance for NRR was investigated. The high-index-facet bounded Rh₂Sb RNRs/C exhibit a high NH₃ yield rate of 228.85±12.96 μg h⁻¹ mg⁻¹_Rh at −0.45 V versus reversible hydrogen electrode (RHE), outperforming the Rh₂Sb SNRs/C (63.07±4.45 μg h⁻¹ mg⁻¹_Rh) and Rh nanoparticles/C (22.82±1.49 μg h⁻¹ mg⁻¹_Rh), owing to the enhanced adsorption and activation of N₂ on high-index facets. Rh₂Sb RNRs/C also show durable stability with negligible activity decay after 10 h of successive electrolysis. The present work demonstrates that surface regulation plays an important role in promoting NRR activity and provides a new strategy for creating efficient NRR electrocatalysts.     

Thermodynamic and Electrochemical Investigations of Potassium–Antimony Alloys

Russian Journal of Applied Chemistry - In September 1975, the head of Russian electrochemists, Academician A.N. Frumkin (1895–1976), in his report at the XI Mendeleev Congress on General and...     

Do Sulfonamides Interact with Aromatic Rings?

Aromatic rings form energetically favorable interactions with many polar groups in chemical and biological systems. Recent molecular studies have shown that sulfonamides can chelate metal ions and form hydrogen bonds, however, it is presently not established whether the polar sulfonamide functionality also interacts with aromatic rings. Here, synthetic, spectroscopic, structural, and quantum chemical analyses on 2,6-diarylbenzenesulfonamides are reported, in which two flanking aromatic rings are positioned close to the central sulfonamide moiety. Fine-tuning the aromatic character by substituents on the flanking rings leads to linear trends in acidity and proton affinity of sulfonamides. This physical-organic chemistry study demonstrates that aromatic rings have a capacity to stabilize sulfonamides via through-space NH–π interactions. These results have implications in rational drug design targeting electron-rich aromatic rings in proteins.     

When and How Do Diaminocarbenes Dimerize?

No example of a simple uncatalyzed dimerization of a diaminocarbene has been clearly established, so it is timely to ask what factors control the thermodynamics of this reaction, and what mechanisms are responsible for the observed dimerizations? In agreement with qualitative experimental observations, the dimerizations of simple five‐ and six‐membered‐ring diaminocarbenes are calculated to be 100 kJ mol^?1 less favorable than those of acyclic counterparts. This large difference is semiquantitatively accounted for by bond and torsional angle changes around the carbene centers. Carbenes such as (Et₂N)₂C are kinetically stable in THF at 25 °C in agreement with calculated energy barriers, but they rapidly dimerize in the presence of the corresponding formamidinium ion. This proton‐catalyzed process is probably the most common mechanism for dimer formation, and involves formation of C‐protonated dimers, which can be observed in suitable cases. The possibility of alkali‐metal‐promoted dimerization is raised, and circumstantial evidence for this is presented.