Theoretical and Practical Reasoning in Chemistry

Traditional philosophy of science regards theoretical reasoning, based on the example of Euclidian geometry, as the hallmark of a mature science. There is, however, a parallel tradition of practical reasoning based on specific cases that goes back to Aristotle. In this paper I argue that practical reasoning is an essential part of the practice of chemistry and should be understood and appreciated on its own merits rather than regarded as a symbol of the immaturity and inferiority of chemistry as a science. This revised version was published online in July 2006 with corrections to the Cover Date.     

Active site reactant center geometry in the Co(II)-product radical pair state of coenzyme B12-dependent ethanolamine deaminase determined by using orientation-selection electron spin-echo envelope modulation spectroscopy

The distances and orientations among reactant centers in the active site of coenzyme B12-dependent ethanolamine deaminase from Salmonella typhimurium have been characterized in the Co(II)-product radical pair state by using X-band electron paramagnetic resonance (EPR) and two-pulse electron spin-echo envelope modulation (ESEEM) spectroscopies in the disordered solid state. The unpaired electron spin in the product radical is localized on C2. Our approach is based on the orientation-selection created in the EPR spectrum of the biradical by the axial electron-electron dipolar interaction. Simulation of the EPR line shape yielded a best-fit Co(II)-C2 distance of 9.3 A. ESEEM spectroscopy performed at four magnetic field values addressed the hyperfine coupling of the unpaired electron spin on C2 with 2H in the C5' methyl group of 5'-deoxyadenosine and in the beta-2H position at C1 of the radical. Global ESEEM simulations (over the four magnetic fields) were weighted by the orientation dependence of the EPR line shape. A Nelder-Mead direct search fitting algorithm was used to optimize the simulations. The results lead to a partial model of the active site, in which C5' is located a perpendicular distance of 1.6 A from the Co(II)-C2 axis, at distances of 6.3 and 3.5 A from Co(II) and C2, respectively. The van der Waals contact of the C5'-methyl group and C2 indicates that C5' remains close to the radical species during the rearrangement step. The C2-Hs-C5' angle including the strongly coupled hydrogen, Hs, and the C5'-Hs orientation relative to the C1-C2 axis are consistent with a linear hydrogen atom transfer coordinate and an in-line acceptor p-orbital orientation. The trigonal plane of the C2 atom defines sub-spaces within the active site for C5' radical migration and hydrogen atom transfers (side of the plane facing Co(II)) and amine migration (side of the plane facing away from Co(II)).     

Multiply doped nanostructured silicate sol-gel thin films: spatial segregation of dopants, energy transfer, and distance measurements

Physical and chemical strategies that place designed molecules in spatially separated regions of surfactant-templated mesostructured silicate thin films are used to prepare films containing rhodamine 6G (R6G), lanthanide complexes, and both simultaneously. Fluorescence and photoexcitation spectra of R6G in amorphous and structured thin films show that it is located inside the surfactant micelles of structured thin films. A silylated ligand that binds lanthanides condenses to form part of the silica framework and causes the lanthanide to localize in the silica. Luminescence and photoexcitation spectra show that energy transfer from the metal complex to R6G occurs in the films. R6G quenches Tb emission in a concentration-dependent manner. Energy transfer efficiency is calculated using the Tb luminescence lifetime, and this quantity is used to calculate the distance between Tb and R6G with the aid of Forster theory.     

A new class of hybrid materials via salt inclusion: novel copper(II) arsenates Na(5)ACu(4)(AsO(4))(4)Cl(2) (A = Rb,Cs) composed of alternating covalent and ionic lattices

Two novel copper(II) arsenates Na5ACu4(AsO4)4Cl2 (A = Rb, Cs) were synthesized by conventional solid-state methods using reactive molten salt media. These compounds are isostructural and crystallize in an orthorhombic lattice (Fmmm, No. 69; Z = 8). The cell constants are a = 14.632(3) A, b = 18.872(2) A, c = 14.445(3) A, V = 3989(1) A3, for A = Rb; a = 14.638(3) A, b = 18.990(4) A, c = 14.418(3) A, V = 4008(1) A3, for A = Cs. Single-crystal structure studies reveal a new composite framework consisting of alternating covalent and ionic lattices. The covalent lattice contains highly oriented oligomeric mu-oxo [Cu4O12]16- tetrameric units with a cyclo-S8-like Cu4O4 magnetic core that resembles the building block of layered cuprates. The ionic slab consists of a novel framework of mixed alkali metal chloride lattice and rarely seen Na6O8 clusters. Similar to organic-inorganic hybrid materials, the title compounds present a new class of host-guest chemistry via salt inclusion reactions.     

Stabilization of a K+-(bis-Cage-Annulated 20-Crown-6) Complex by Bidentate Picrate

Bis-cage-annulated 18-crown-6 and 20-crown-6 macrocyclic ethers (i.e., 1 and 2, respectively) have been synthesized, and their alkali metal picrate extraction profiles have been determined. Host system 1 proved to be a significantly more avid alkali metal cation complexant than 2 and somewhat more avid than 18-crown-6. Both 1 and 18-crown-6 display modest selectivity toward K⁺ and Rb⁺. A stable host–guest complex was prepared by slow evaporation of a CH₂Cl₂–hexane solution of an equimolar mixture of 2 and potassium picrate. The X-ray crystal structure of this complex reveals that picrate anion functions as a bidentate ligand therein. The gas-phase interaction energy between the 2 K⁺ complex and picrate anion was calculated to be ca. –64.9 kcal mol^–1, thereby indicating that participation of picrate anion as an additional bidentate ligand results in significant stabilization of complex 10.     

Cumulative indices for Spectrochima Acta, Part A and Spectrochimica Acta, Part B

This article is an electronic publication in Spectrochimica Acta Electronica (SAE), a section of Spectrochimica Acta, Part B (SAB). The hardcopy text is accompanied by an electronic archive, stored on the SAE homepage at http://www.elsevier.nl/locate/sabe. The archive contains data, index and program files. The main article discusses the bibliographical purpose of the program and data files. A collective index for Spectrochimica Acta for volumes since it was split into Parts A and B, and continuing through 1991 for SAA and 1997 for SAB, is presented in DBF format, along with rudimentary data entry and access software.     

The Dinitramide Anion, N(NO(2))(2)(-)

The infrared and Raman spectra of the NH(4)(+), K(+), and Cs(+) salts of N(NO(2))(2)(-) in the solid state and in solution have been measured and are assigned with the help of ab initio calculations at the HF/6-31G and MP2/6-31+G levels of theory. In agreement with the variations observed in the crystal structures, the vibrational spectra of the N(NO(2))(2)(-) anion are also strongly influenced by the counterions and the physical state. Whereas the ab initio calculations for the free N(NO(2))(2)(-) ion indicate a minimum energy structure of C(2) symmetry, Raman polarization measurements on solutions of the N(NO(2))(2)(-) anion suggest point group C(1) (i.e., no symmetry). This is attributed to the very small (<3 kcal/mol) N-NO(2) rotational barrier in N(NO(2))(2)(-) which allows for easy deformation.     

MECHANISM OF OXYGEN DETOXIFICATION IN NEONATAL RAT LUNG TISSUE

Abstract— Pulmonary macrophages obtained from neonatal rats contain approximately four times the activity of cyanide resistant superoxide dismutase and catalase compared with the cells from adult animals. The activity is highest immediately after birth and diminishes with age until the minimum level is reached at approximately 3 weeks of age. Superimposed upon this change in basal activity is the capability of neonatal cells to synthesize additional cyanide resistant superoxide dismutase and catalase when either the animals or isolated pulmonary macrophages are exposed to 95–100% oxygen. The inductive effect begins at 2–3 days after birth, peaks at 10 days, and disappears at approximately 15 days after birth. In contrast to adult rats, neonatal rats are extremely resistant to the toxic effects of oxygen. If, however, the oxygen mediated increase in both enzymes is prevented or the maximum effective pulmonary macrophage number is diminished in test animals, these animals become vulnerable to toxic effects of oxygen exposure, observed by gross and histologic examination of lung tissue, in a manner similar to adult animals. These data indicate that both cyanide-resistant superoxide dismutase and catalase may be part of the endogenous defense mechanisms which provide neonatal rats with an exceptional resistance to oxygen toxicity.     

Chemoproteomic profiling of kinases in live cells using electrophilic sulfonyl triazole probes

Sulfonyl-triazoles are a new class of electrophiles that mediate covalent reaction with tyrosine residues on proteins through sulfur-triazole exchange (SuTEx) chemistry. Recent studies demonstrate the broad utility and tunability of SuTEx chemistry for chemical proteomics and protein ligand discovery. Here, we present a strategy for mapping protein interaction networks of structurally complex binding elements using functionalized SuTEx probes. We show that the triazole leaving group (LG) can serve as a releasable linker for embedding hydrophobic fragments to direct molecular recognition while permitting efficient proteome-wide identification of binding sites in live cells. We synthesized a series of SuTEx probes functionalized with a lipid kinase fragment binder for discovery of ligandable tyrosines residing in catalytic and regulatory domains of protein and metabolic kinases in live cells. We performed competition studies with kinase inhibitors and substrates to demonstrate that probe binding is occurring in an activity-dependent manner. Our functional studies led to discovery of probe-modified sites within the C2 domain that were important for downregulation of protein kinase C-alpha in response to phorbol ester activation. Our proof of concept studies highlight the triazole LG of SuTEx probes as a traceless linker for locating protein binding sites targeted by complex recognition elements in live cells.

Sulfonyl-triazole probes modified with a kinase recognition element are developed for live cell activity-based profiling to identify tyrosine sites located in catalytic and regulatory domains that are important for kinase function.     

Bronsted acid-promoted olefin aziridination and formal anti-aminohydroxylation

A straightforward synthesis of aziridines is reported from an electron-rich azide (alkyl or aryl azide), electron-deficient olefin, and triflic acid in cold acetonitrile. The only coproduct of the reaction is dinitrogen (N2). Active ester substrates bearing a nucleophilic carbonyl engage the putative protonated aziridine intermediate to produce the product of olefin aminohydroxylation in which the nitrogen is benzyl protected and the oxygen is acylated. The possibility that a triazoline need not be an intermediate in aziridine production is advanced.