Death,taxes, and the genetic code?

The genetic code is an enduring feature of biology: only rare circumstances result in changes to translation of the code, at least in nature. Researchers are devising methods to engineer ribosome-synthesized polypeptides containing novel and potentially useful amino acids.     

Interplay of thermochemistry and Structural Chemistry,the journal (volume 28, 2017, issues 5–6), and the discipline

The contents of issues 5 and 6 of Structural Chemistry from the calendar year 2017 are summarized in the present review. A brief thermochemical commentary and recommendations for future research have been added to the summary of each paper.

     

Exploring the activities of vanadium,niobium, and tantalum PNP pincer complexes in the hydrogenation of phenyl-substituted CN,CN, CC,CC, and CO functional groups

The structures and stability of the designed PNP pincer amido M(NO)₂(PNP) and amino ^HM(NO)₂(PN^HP) complexes [M = V, Nb, and Ta, PNP = N(CH₂CH₂P(isopropyl)₂)₂, PN^HP = HN(CH₂CH₂P(isopropyl)₂)₂] and their hydrogenation mechanisms for phenyl-substituted unsaturated functional groups have been explored at the B3PW91 level of density functional theory. Under H₂ environment, these conjugated complexes can form equilibrium and fulfill the criteria of metal–ligand cooperated bifunctional hydrogenation catalysts. For the hydrogenation of Ph-CN, Ph-CHNH, Ph-CHNH-Ph, Ph-CHNCH₂Ph, Ph-CCH, Ph-CHCH₂, Ph-CHO, and Ph-COCH₃, the reaction prefers either a two-step or one-step mechanism for the hydridic MH and protonic NH transfer. These results clearly show that the V, Nb, and Ta complexes are promising catalysts for the hydrogenation reactions, and these provide experimental challenges.     

Effect of the Charge and the Nature of Both Cations and Anions on the Solubility of Zwitterionic Amino Acids,Measurements and Modeling

The effect of the charge and the nature of both the cations and the anions of some electrolytic salts: sodium fluoride (NaF), potassium fluoride (KF), sodium bromide (NaBr), potassium bromide (KBr), sodium iodide (NaI), potassium iodide (KI), sodium sulfate (Na₂SO₄), potassium sulfate (K₂SO₄), calcium chloride (CaCl₂), and barium chloride (BaCl₂), on the solubility of zwitterionic amino acids (glycine, DL-alanine, DL-valine, and DL-serine) in aqueous solutions at 298.15 K are studied and discussed. A salting-in effect is observed for all amino acids under investigation with all electrolytes used in the present study, except for DL-alanine and DL-valine in aqueous solutions containing sodium fluoride where a salting-out effect was observed. The orders of the effect of the nature and the charge of both the anions and the cations are: F^- < Cl^- < Br^- < I^- < NO₃^- < SO₄^2-\mathrm{F}^{-}<{}\mathrm{Cl}^{-}<{}\mathrm{Br}^{-}<{}\mathrm{I}^{-}<\mathrm{NO}_{3}^{-}<{}\mathrm{SO}_{4}^{2-} with both sodium and potassium cations; Na⁺<K⁺<Ca²⁺<Ba²⁺ with chloride anion.     

Energetics, structures, bonding, and kinetics of the HSCl–HClS system

The [H,S,Cl] potential-energy surface has been investigated at the self-consistent field (SCF), complete active space self-consistent field (CASSCF), second-order M?ller–Plesset, coupled-cluster single-double and perturbative triple excitation, [CCSD(T)]/6-31G(d,p), 6-31G(2df,2pd), and correlation-consistent polarized valence triple zeta (cc-pVTZ) levels of theory. CCSD(T)/ cc-pVTZ results predict a very stable HSCl species, an isomer HClS, 51.84 kcal/mol higher in energy, and a transition state 57.68 kcal/mol above HSCl. Independent of the level of theory, results with the smaller 6-31G(d,p) basis set turned out to be poor, especially for HClS. Vibrational analysis indicates that both species can be easily differentiated if isolated. Bonding differences between these molecules are illustrated by contour plots of valence orbitals. Viewed classically, bonding in HClS involves a dative bond. Transition-state rate constants, and equilibrium constants for the HSCl ↔ HClS isomerization have been estimated for various temperatures (200–1000 K). At 298.15 K, the forward rate is predicted to be 7.95 × 10⁻²⁹ s⁻¹, and the equilibrium constant to be 2.31 × 10⁻³⁸. Tunneling corrections vary from 1.57 at 298.15 K to 1.05 at 1000 K. Activation energies have been obtained by a two-points linear fit to the Arrhenius equation. Received: 7 May 1999 / Accepted: 22 July 1999 / Published online: 4 October 1999     

The electrochemistry of particles, droplets, and vesicles �C the present situation and future tasks

Presently, a plethora of techniques is available to study the electrochemical properties of solid inorganic and organic micro- and nano-particles immobilized on electrode surfaces, provided that they possess a faradaic electroactivity. Similarily, immobilized droplets of liquids and solutions, which are immiscible with the electrolyte solution, give access to the three-phase electrochemistry of redox centers in the droplets, allowing determinations of free energies of ion transfer between the immiscible liquid phases. Possible and necessary future activities in the field of immobilized particles and droplets will be discussed here. The electrochemistry of suspended micro- and nano-particles possessing faradaic electroactivity is much more complex and needs special attention in future research. Finally, the electrochemistry of liposomes and biological vesicles, which do not possess faradaic activity, but the ability to produce capacitive signals upon attachment to electrodes, will be discussed focusing on possible future developments.     

Bimetallic system for the synthesis of diorganyl selenides and sulfides, chiral β-seleno amines, and seleno- and thioesters

The bimetallic reagent Sn(II)/Cu(II) in [bmim]BF₄ was efficiently used for the cleavage of diaryl diselenides and disulfides and reacts with a variety of organic substrates, such as organic halides, acid chlorides, and β-amino mesylates affording the diorganyl selenides and sulfides within very short reaction times, under mild conditions and with excellent yields, using BMIM-BF₄ as a reusable solvent.     

d–d Dative Bonding Between Iron and the Alkaline-Earth Metals Calcium,Strontium, and Barium

Double deprotonation of the diamine 1,1′-(tBuCH₂NH)-ferrocene ( 1 -H₂) by alkaline-earth (Ae) or Eu^II metal reagents gave the complexes 1 -Ae (Ae=Mg, Ca, Sr, Ba) and 1 -Eu. 1 -Mg crystallized as a monomer while the heavier complexes crystallized as dimers. The Fe⋅⋅⋅Mg distance in 1 -Mg is too long for a bonding interaction, but short Fe⋅⋅⋅Ae distances in 1 -Ca, 1 -Sr, and 1 -Ba clearly support intramolecular Fe⋅⋅⋅Ae bonding. Further evidence for interactions is provided by a tilting of the Cp rings and the related ¹H NMR chemical-shift difference between the Cp α and β protons. While electrochemical studies are complicated by complex decomposition, UV/Vis spectral features of the complexes support Fe→Ae dative bonding. A comprehensive bonding analysis of all 1 -Ae complexes shows that the heavier species 1 -Ca, 1 -Sr, and 1 -Ba possess genuine Fe→Ae bonds which involve vacant d-orbitals of the alkaline-earth atoms and partially filled d-orbitals on Fe. In 1 -Mg, a weak Fe→Mg donation into vacant p-orbitals of the Mg atom is observed.     

Understanding the Impacts of AFEX™ Pretreatment and Densification on the Fast Pyrolysis of Corn Stover,Prairie Cord Grass,and Switchgrass

Lignocellulosic feedstocks corn stover, prairie cord grass, and switchgrass were subjected to ammonia fiber expansion (AFEX?) pretreatment and densified using extrusion pelleting and ComPAKco densification technique. The effects of AFEX? pretreatment and densification were studied on the fast pyrolysis product yields. Feedstocks were milled in a hammer mill using three different screen sizes (2, 4, and 8 mm) and were subjected to AFEX? pretreatment. The untreated and AFEX?-pretreated feedstocks were moisture adjusted at three levels (5, 10, and 15 % wb) and were extruded using a lab-scale single screw extruder. The barrel temperature of the extruder was maintained at 75, 100, and 125 °C. Durability of the extruded pellets made from AFEX?-pretreated corn stover, prairie cord grass, and switchgrass varied from 94.5 to 99.2, 94.3 to 98.7, and 90.1 to 97.5 %, respectively. Results of the thermogravimetric analysis showed the decrease in the decomposition temperature of the all the feedstocks after AFEX? pretreatment indicating the increase in thermal stability. Loose and densified feedstocks were subjected to fast pyrolysis in a lab-scale reactor, and the yields (bio-oil and bio-char) were measured. Bio-char obtained from the AFEX?-pretreated feedstocks exhibited increased bulk and particle density compared to the untreated feedstocks. The properties of the bio-oil were statistically similar for the untreated, AFEX?-pretreated, and AFEX?-pretreated densified feedstocks. Based on the bio-char and bio-oil yields, the AFEX?-pretreated feedstocks and the densified AFEX?-pretreated feedstocks (pellets and PAKs) exhibited similar behavior. Hence, it can be concluded that densifying the AFEX?-pretreated feedstocks could be a viable option in the biomass-processing depots to reduce the transportation costs and the logistical impediments without affecting the product yields.     

Cross-validation and evaluation of the performance of methods for the elemental analysis of forensic glass by μ-XRF, ICP-MS, and LA-ICP-MS

Elemental analysis of glass was conducted by 16 forensic science laboratories, providing a direct comparison between three analytical methods [micro-x-ray fluorescence spectroscopy (μ-XRF), solution analysis using inductively coupled plasma mass spectrometry (ICP-MS), and laser ablation inductively coupled plasma mass spectrometry]. Interlaboratory studies using glass standard reference materials and other glass samples were designed to (a) evaluate the analytical performance between different laboratories using the same method, (b) evaluate the analytical performance of the different methods, (c) evaluate the capabilities of the methods to correctly associate glass that originated from the same source and to correctly discriminate glass samples that do not share the same source, and (d) standardize the methods of analysis and interpretation of results. Reference materials NIST 612, NIST 1831, FGS 1, and FGS 2 were employed to cross-validate these sensitive techniques and to optimize and standardize the analytical protocols. The resulting figures of merit for the ICP-MS methods include repeatability better than 5 % RSD, reproducibility between laboratories better than 10 % RSD, bias better than 10 %, and limits of detection between 0.03 and 9 μg g^?1 for the majority of the elements monitored. The figures of merit for the μ-XRF methods include repeatability better than 11 % RSD, reproducibility between laboratories after normalization of the data better than 16 % RSD, and limits of detection between 5.8 and 7,400 μg g^?1. The results from this study also compare the analytical performance of different forensic science laboratories conducting elemental analysis of glass evidence fragments using the three analytical methods.

Effect of a rigid,non-polar solute on the dielectric anisotropy,the splay and bend elastic constants,and on the rotational viscosity coefficient of 4-4′-n-heptylcyanobiphenyl

The effect of mixing a rigid, non-polar, non-mesogenic solute, biphenyl (C₆H₅-C₆H₅), in the nematic solvent 7CB (4,4′-n-heptylcyanobiphenyl) is investigated. The solute is found to reduce the nematic order and a two-phase region appears. We report measurements of the transition temperatures, dielectric anisotropy, and splay and bend elastic constants, as well as the rotational viscosity coefficient by the method of electric field-induced Fréedericksz transition for biphenyl concentrations up to 8.0%.     

Humphry Davy: Analogy,Priority, and the “true philosopher”

This essay explores how Davy fashioned himself as, what he called in his poetry, a “true philosopher.” He defined the “true philosopher” as someone who eschewed monetary gain for his scientific work, preferring instead to give knowledge freely for the public good, and as someone working at a higher level than the mere experimentalist. Specifically, Davy presented himself as using the method of analogy to reach his discoveries and emphasised that he understood the “principle” behind his findings. He portrayed himself as one who perceived analogies because he had a wider perspective on the world than many others in his society. The poem in which he describes the “true philosopher” offers us Davy’s private view of this character; the essay then demonstrates how Davy attempted to depict his own character in this way during critical moments in his career.     

Cation-π effects in the complexation of Na+ and K+ with Phe, Tyr, and Trp in the gas phase

Na⁺ and K⁺ gas-phase affinities of the three aromatic amino acids Phe, Tyr, and Trp were measured by the kinetic method. Na⁺ binds these amino acids much more strongly than K⁺, and for both metal ions the binding strength was found to follow the order Phe ≤ Tyr < Trp. Quantum chemical calculations by density functional theory (DFT) gave the same qualitative ordering, but suggested a somewhat larger Phe/Trp increment. These results are in acceptable agreement with predictions based on the binding of Na⁺ and K⁺ to the side chain model molecules benzene, phenol, and indole, and are also in reasonable agreement with the predictions from purely electrostatic calculations of the side-chain binding effects. The binding energies were compared with those to the aliphatic amino acids glycine and alanine. Binding to the aromatic amino acids was found to be stronger both experimentally and computationally, but the DFT calculations indicate substantially larger increments relative to alanine than shown by the experiments. Possible reasons for this difference are discussed. The metal ion binding energies show the same trends as the proton affinities.     

Exploration of the π-electronic structure of singlet, triplet, and quintet states of fulvenes and fulvalenes using the electron localization function

The singlet ground states and lowest triplet states of penta- and heptafulvene, their benzannulated derivatives, as well as the lowest quintet states of pentaheptafulvalenes, either the parent compound or compounds in which the two rings are intercepted by either an alkynyl or a phenyl segment, were investigated at the (U)OLYP/6-311G(d,p) density functional theory level. The influence of (anti)aromaticity was analyzed by the structure-based aromaticity index HOMA, the harmonic oscillator model of aromaticity. The extent of (anti)aromatic character was also evaluated in terms of the π-electron (de)localization as measured by the π component of the electron localization function (ELF(π)). The natural atomic orbital (NAO) occupancies were calculated in order to evaluate the degree of π-electron shift caused by the opposing electron-counting rules for aromaticity in the electronic ground state (S(0); Hückel's rule) and the first ππ* excited triplet state (T(1); Baird's rule). Pentaheptafulvalene (5) shows a shift of 0.5 π electrons from the 5-ring to the 7-ring when going from the S(0) state to the lowest quintet state (Qu(1)). The pentaheptafulvalene 5 and [5.6.7]quinarene 7 were also investigated in their 90° twisted conformations. From our study it is apparent that excitation localization in fulvalenes, but not in fulvenes, to a substantial degree is determined by aromaticity localization to triplet biradical 4n π-electron cycles. Isolated benzene rings in these compounds tend to remain as closed-shell 6π-electron cycles.     

Surface Tension,Activity of Counterion,and Conductivity of the Quaternary System Dodecyldimethylamine Oxide,TX‐100, HCl,and Water

We have investigated the mixing behavior of the mixtures of dodecyldimethylamine oxide (DDAO) and Triton X‐100 (TX‐100) at different ratios of the two surfactants and at different values of pH. From the equilibrium surface tension measurements, the critical micelle concentration (CMC) and surface tensions at CMC data were obtained as functions of the composition. For the binary mixtures of dodecyldimethylamine oxide and TX‐100 at different ratios in the natural values of pH, the behaviors of the mixtures deviate positively from ideal during micellization. The minimum of CMC of the mixtures of dodecyldimethylamine oxide and Triton X‐100 was observed in the range 4.0?) increased with the decrease of pH. At pH=4.99, the activities of the counterion decreased with the increase of the concentration of TX‐100 at a constant concentration of DDAO. At pH=1.96, the activities of the counterion increased with the increase of the concentration of TX‐100. However, the conductivities of the solution decreased with the increase of the concentration of TX‐100 at both pH=4.99 and pH=1.96. The experimental results show that the effect of TX‐100 on the activities of the counterion at pH=4.99 is different from that at pH=1.96.     

Kinetic,isotherm, and mechanism investigations of the removal of nitrate and nitrite from water by the synthesized hydrotalcite Mg–Al

Research on Chemical Intermediates - The objective of this work is to test the effectiveness of hydrotalcite as an adsorbent for the retention of nitrate and nitrite ions and to study the influence...     

Combination of the Claisen-Schmidt reaction,the Michael addition,and the Hantzsch reaction in the synthesis of 2,6′-bis-aryl-3,4′-bipyridines

Russian Chemical Bulletin - Pyridine-3-carbaldehyde reacted with 1-(aryl)ethan-1-ones to give 1,5-diaryl-3-(pyridin-3-yl)pentane-1,5-diones, which were further converted to...