Paradigms and paradoxes: decoding the “genetic code”

We propose to keep the term “genetic code” to describe the nucleotide sequence in DNA and RNA and use the term “genetic cipher” to describe the key for decoding the genetic codes of DNA and RNA into the amino acid sequences of proteins.

     

Paradigms and paradoxes: why is the electron affinity of the azide radical, N3, so large?

The consensus value for the electron affinity of azide radical is 261 kJ mol⁻¹, anomalously higher than many species that are also made of highly electronegative elements. N₃ ⁻ has two equivalent resonance structures analogous to NO₂ ⁻ that has a lower electron affinity. Electronegativity trends rationalize why the electron affinity of N₃ is higher than that of P₃; however, those of N and N₂ are lower than those of P and P₂. We suggest the reason for the observed high electron affinity of azide radical is Coulombic stabilization in the ionic triplet resonance structure, ⁻N=N⁺=N⁻.     

Paradigms and paradoxes: Hess’ law and the thermodynamic validity of Jolly’s method for estimating bond dissociation energies

This study evaluates Jolly’s method to estimate the difference in homolytic bond dissociation energy between two isoelectronic molecules by the use of atomic and ionic electronegativities. The use of intermediate species as an energetic “stepping stone” between the two diatomic species in question is discussed, particularly within the context of Hess’ law. We also show a sample calculation for a pair of diatomic species that is fully consistent with data from atomic physics.     

What are the Implications of Nonequilibrium in the O+OH and O+HO2 Reactions?

Vibrationally excited O2, OH, and HO2 species have been suggested (J. Phys. Chem. A 2004, 108, 758) to provide clues for explaining the "ozone deficit problem" and "HOx dilemma" in the middle atmosphere under conditions of local thermodynamic disequilibrium (LTD), but the question arises of how much LTD will affect the title ozone sink reactions. Besides providing novel kinetic results, it is shown that LTD tends to disfavor ozone depletion relative to traditional atmospheric modeling under Boltzmann equilibration, which is partly due to competition between the various reactive channels. The calculations also suggest that the title LTD processes can be important sources of highly vibrationally excited O2 in the middle atmosphere. Moreover, LTD is shown to offer an explanation for the fact that some down revision of the O + HO2 rate constant, or the ratio of the O + HO2 to O + OH rate constants, is required to improve agreement between the predictions of traditional modeling and observation. This, in turn, provides significant evidence supporting LTD at such altitudes.     

Fracture of polymer interfaces: what are the relevant length scales?

While it is tempting to relate directly the molecular structure of an interface (between glassy or between semi‐cristalline polymers) with its fracture toughness, these two parameters are simply the two end‐points of a complex network which needs to be understood in order to control the mechanical strength of the interface. The important mechanisms occur at three different length scales: the molecular scale (stress‐transfer across the interface), the microscopic scale (plastic deformation at the crack tip) and the macroscopic scale (loading geometry and elastic constants of the polymers). The couplings existing between these length scales in glassy polymer interfaces are reviewed in this paper in light of the latest experimental studies.     

Proton-bound homodimers: how are the binding energies related to proton affinities?

High-level quantum chemical calculations [G3(MP2)-RAD//MP2/6-31+G(d,p)] have been employed to investigate the relationship between the binding energy (BE) of a substrate (X) and its protonated form [H-X]+ with the proton affinity (PA) of the substrate (X) in several series of protonated homodimers ([X...H-X]+). We find that for each series of closely related substrates, the binding energy (BE) is correlated with the proton affinity (PA) in an approximately quadratic manner. Thus, for a given series, the BE initially increases in magnitude with increasing PA, reaches a point of maximum binding, and then becomes smaller as the PA increases further. This behavior can be attributed to the competing effects of the exothermic partial protonation of the substrate and the endothermic partial deprotonation of the protonated substrate. As the PA increases, protonation of X contributes to increased binding but the penalty for partial deprotonation of [H-X]+ also increases. Once the PA becomes sufficiently high, the penalty for the partial deprotonation of [H-X]+ dominates, leading to maximum binding occurring at intermediate PA.     

Should negative electron affinities be used for evaluating the chemical hardness?

Despite recent advances in computing negative electron affinities using density-functional theory, it is an open issue as to whether it is appropriate to use negative electron affinities, instead of zero electron affinity, to compute the chemical hardness of atoms and molecules with metastable anions. We seek to answer this question using the accepted empirical rules linking the chemical hardness to the atomic size and the polarizability; we also propose a new correlation with the C6 London dispersion coefficient. For chemical reactivity in the gas phase, it seems to make no difference whether negative, or zero, electron affinities are used for systems with metastable anions. For reactions in solution the evidence that is presently available is insufficient to establish a preference. In addressing this issue, we noted that electron affinity data from which atomic chemical hardness values are computed are out of date; an update to Pearson's classic 1988 table [Inorg. Chem., 1988, 27, 734-740] is thus provided.     

Why are the Ca2+ and K+ binding energies of formaldehyde and ammonia reversed with respect to their proton affinities?

The binding energies (BEs) of alkali metal monocations and alkaline-earth metal dications to a series of small oxygen and nitrogen bases have been evaluated by means of CCSD(T) calculations on B3-LYP optimized structures. These calculations were carried out both using all-electron basis sets, and additionally using an effective-core potential (ECP) to describe the inner electrons of the metal. A theoretical model aiming at analyzing the effects on the binding energy trends of electrostatic, polarization, and covalent contributions, as well as geometry distortion, was employed. From this analysis, we conclude that although the neutral-ion interaction energy for alkali and alkaline-earth metal cations is dominated by electrostatic contributions, in many cases the correct basicity trends are only attained once polarization effects are also included in the model. This is indeed the case when Ca2+ and K+ are bound to ammonia and formaldehyde. Geometry distortions triggered by polarization are also necessary, in some cases, to obtain the correct basicity trends. In addition, in particular for alkaline-earth dications, the energy associated with covalent interactions sometimes dictates the basicity trend. Our observations imply that simple models based on ion-dipole interactions, that are frequently used in the literature to explain affinity trends in ion-molecule reactions, are generally not likely to be reliable.     

The theory of electron transfer reactions: what may be missing?

Molecular dynamics simulations are presented for condensed-phase electron transfer (ET) systems where the electronic polarizability of both the solvent and the solute is incorporated. The solute polarizability is allowed to change with electronic transition. The results display notable deviation from the standard free energy parabolas of traditional ET theories. A new three-parameter ET model is applied, and the theory is shown to accurately model the free energy surfaces. This paper presents conclusive evidence that the traditional theory for the free energy barrier of ET reactions requires modification.     

Paradigms and paradoxes: the ionization potential of atomic astatine (Z =85), polonium (Z = 84), and some other elements—what does this value tell us about the energetics of atomic and diatomic halogens

Structural Chemistry - The newly measured ionization potential of atomic astatine is discussed and compared with that of the recently determined value for polonium and for the other atomic...     

An independently addressable microbiosensor array: what are the limits of sensing element density?

A microdisc sensor array, prepared by thin film technology, has been used as a model for miniaturized multi-functional biosensors. It consists of a series of wells, 20 microns in diameter, possessing a 1000 A Pt layer at the bottom that serves as the indicating electrode. The depth of the wells ranged from 2.3-24 microns, depending on the photoresist employed and the spinning speed used to coat the electrode interconnect grid. Ten such wells were arranged in a circular array within an area of radius 130 microns. The center to center distance between any two of the discs ranged from 30 to 155 microns. Each disc is connected by a conductive film line to corresponding pads on the side of the sensor chip. A cylinder placed on top of the chip array formed the electrochemical cell into which a common reference and counter electrode were placed. The reference electrode was operated at ground potential. Prior to the evaluation of enzyme sensors, an assessment of "chemical cross-talk", the perturbation of sensor response resulting from the overlap of proximal diffusion layers, was made using Fe(CN)6(4-). The preliminary conclusion is that the sensing elements probably must be separated by about 100 microns in order to avoid interference from adjacent sensors. A technique was developed for the precision delivery of enzyme and cross-linking agent to the 2.3 microns cavity, having a capacity of 4 pL. This procedure makes possible the preparation of sensor arrays capable of detecting different analytes by employing different enzymes. The sensors gave reasonably rapid (2-4 s) response with linearity (up to about 10 mM. However, the sensors in the center of the array clearly showed the effects of depletion of substrates by the surrounding sensors.     

What are the enthalpy of formation and the stabilization energy of acrolein?

Acrolein (propenal) is a ubiquitous compound in the global environment with diverse deleterious ramifications for human health. Despite its importance, its measured enthalpy of formation is still contentious. Using high level quantum chemical calculations, we recommend a consensus value of ?65 ± 3 kJ mol^?1 for the gas phase species. Comparison is made with the other “acrylo” species, acrylonitrile and acrylic acid, and to other conjugated species such as butadiene and crotonaldehyde.     

Carbohydrate-pi interactions: what are they worth?

Protein-carbohydrate interactions play an important role in many biologically important processes. The recognition is mediated by a number of noncovalent interactions, including an interaction between the alpha-face of the carbohydrate and the aromatic side chain of the protein. To elucidate this interaction, it has been studied in the context of a beta-hairpin in aqueous solution, in which the interaction can be investigated in the absence of other cooperative noncovalent interactions. In this beta-hairpin system, both the aromatic side chain and the carbohydrate were varied in an effort to gain greater insight into the driving force and magnitude of the carbohydrate-pi interaction. The magnitude of the interaction was found to vary from -0.5 to -0.8 kcal/mol, depending on the nature of the aromatic ring and the carbohydrate. Replacement of the aromatic ring with an aliphatic group resulted in a decrease in interaction energy to -0.1 kcal/mol, providing evidence for the contribution of CH-pi interactions to the driving force. These findings demonstrate the significance of carbohydrate-pi interactions within biological systems and also their utility as a molecular recognition element in designed systems.     

The third edition of ISO Guide 34: what were the drivers for the revision and what is new?

After the International Laboratory Accreditation Cooperation (ILAC) had taken in 2004, the resolution to conduct accreditation of producers of reference materials according to ISO Guide 34 ‘General requirements for the competence of reference material producers’ in combination with ISO/IEC 17025 ‘General requirements for the competence of testing and calibration laboratories’, ISO/REMCO, the ISO Committee on Reference Materials, decided in 2005 to revise ISO Guide 34 to align it closer with ISO/IEC 17025 and to clarify certain issues for accreditors and producers seeking accreditation without adding new requirements. Moreover, the publication in 2007 of ISO/IEC Guide 99 ‘International vocabulary of metrology—Basic and general concepts and associated terms (VIM)’ triggered additional adaptations of the guide.     

Calculated vibrational structure of the first band of the photoelectron spectrum of HO 2 − and the electron affinity of HO2

The vibrational structure of the first band of the photoelectron (PE) spectrum of HO ₂ ^? and DO ₂ ^? has been calculated on the basis of (slightly modified) ab initio potentials. The best agreement with the experimental spectrum of HO ₂ ^? is obtained for a vibrational temperature of ca. 600 K. “Peak D”, which has been under debate in earlier work, is composed of two transitions, with the “hot” transition 3 ₁ ¹ being more intense than the adiabatic transition. Since thev ₂ bending mode of DO₂ has significant OO stretching character, the vibrational structure of the PE spectrum of DO ₂ ^? is more complex than that of HO ₂ ^? . Large-scale RCCSD(T) calculations of the equilibrium electron affinity of HO₂ yield 1.058 eV which agrees with the experimental value of 1.044 ± 0.020 eV.     

The electronic structure of Bi2−xGdxRu2O7 and RuO2: A study by electron spectroscopy

The bismuth gadolinium pyrochlore ruthenates Bi_2−xGd_xRu₂O₇ have been studied in relation to RuO₂ by the techniques of X-ray and ultraviolet photoelectron spectroscopy (XPS and UPS) and high-resolution electron-energy-loss spectroscopy (HREELS). The composition-dependent metal-to-semiconductor transition in the pyrochlore system is mirrored by the progressive decrease with composition parameter in (i) the density of electronic states at the Fermi energy in UPS, (ii) the plasmon frequency in HREELS, and (iii) the probability of screening a Ru : 3d core hole in XPS. These changes are too gradual in themselves to pinpoint the transition, but are generally consistent with transport and X-ray diffraction data that indicate a metal-to-nonmetal transition at x = 1.55 mediated by an interplay between disorder and correlation-induced electron localization. Comparison of the results for the pyrochlores with those from RuO₂ suggest that the fine structure in the Ru : 3d spectrum of the latter material, previously believed to arise from differing oxidation states at the surface, should in fact be attributed to final-state screening effects in a stoichiometric material. Our conclusion is confirmed by the signals associated with Ru : 4d electrons in XPS, UPS, and HREELS: each of these three techniques appears to probe a conduction-electron concentration essentially equal to its bulk value. In particular, UPS confirms details of the band structure of RuO₂ not obvious from previous photoemission experiments.     

SCC-DFTB: what is the proper degree of self-consistency?

The approximate SCC-DFTB method (Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, Th.; Suhai, S.; Seifert, G. Phys. Rev. B 1998, 58, 7260) is derived from DFT by a second-order expansion of the total energy expression. In this article, basic approximations and assumptions underlying the DFTB method are discussed in detail, and further extensions to include third-order terms are proposed. Further, the SCC-DFTB and semiempirical NDDO formalisms are compared to elucidate similarities and differences.