Molecular structures and conformations: Experiment and theory

Theoretical calculations in combination with experimental gas phase structure research can be performed in two ways. The first is to support and improve experimental analyses by including additional data from theoretical calculations. This is to the advantage of the experiment. The second way is a comparison of geometric structures and conformational properties obtained with different theoretical methods with the experimental result. This comparison indicates which theoretical method or methods are suitable for a specific compound. This approach is to the advantage of the theory. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 123–128, 1998     

Coordinate measurements and operators

Relativistic quantum-field theory provides the machinery for calculating wave functions or probability amplitudes depending upon space-time coordinates. The currently accepted theory, however, fails to provide position operators and a means of measuring particle coordinates that are consistent with Dirac's properties of physical observables. This is because it calls for a space position probability distribution at a specified time. This paper shows, however, that space-time event coordinate operators, together with a corresponding measurement procedure, can be found that are consistent with Dirac's requirements. This is done through a reinterpretation of the amplitudes computed by field theory and does not involve any change in that mathematical formalism. The measurement of the space-time coordinates of an event is accomplished by detecting the absorption of a photon by a particle from each of two light pulses designed to overlap at a given point at a given time. If a final emitted photon has an energy whose sum with the final particle energy approximately equals the sum of the mean energies of the pulses, then the absorption of the two pulse photons must certainly have taken place within a distance the order of a Compton wavelength of the small space-time region of overlapping pulses. This is clear from the fact that the high energy required to confine the pulses to very small volumes must throw a particle absorbing them far off the mass shell. Thus the absorption of the two photons throws the particle into a narrowly confined spatial wave function that must decay extremely rapidly—to within a Compton wavelength, a delta function in space-time. This delta function is the eigenfunction of space-time coordinate operators X^μ and is the scalar product of vectors in a Hilbert space spanned by spin–space-time kets large enough to contain the operators of the Poincaré group. These event operators transform properly under the action of Poincaré operators but do not commute with the mass. If the Compton wavelength is not negligible compared to the accuracy desired in the coordinate measurements, individual coordinate measurements are no longer possible. Nevertheless, a large number of repeated coordinate measurements can be carried out to produce a coordinate probability distribution. This distribution can be unfolded to find a true coordinate probability distribution if the charge form factor is known from basic theory. An analysis of laboratory particle detection techniques shows that they actually determine space coordinates and energy rather than spatial coordinates at a given time. When this fact is included, the Klein–Nishina formula can be derived using the electromagnetic four-vector potential as the photon probability amplitude wave. To clarify the meaning of the observables, a mass-momentum measurement is described.     

Noise filtering and deconvolution of XPS data by wavelets and Fourier transform

In experimental sciences, the recorded data are often modelled as the noisy convolution product of an instrumental response with the ‘true’ signal to find. Different models have been used for interpreting x‐ray photoelectron spectroscopy (XPS) spectra. This article suggests a method of estimate the ‘true’ XPS signal that relies upon the use of wavelets, which, because they exhibit simultaneous time and frequency localization, are well suited to signal analysis. First, a wavelet shrinkage algorithm is used to filter the noise. This is achieved by decomposing the noisy signal into an appropriate wavelet basis and then thresholding the wavelet coefficients that contain noise. This algorithm has a particular threshold related to frequency and time. Secondly, the broadening due to the instrumental response is eliminated through a deconvolution process similar to that developed in the previous paper in this series for the analysis of HREELS data. This step mainly rests on least‐squares and on the existing relation between the Fourier transform, the wavelet transform and the convolution product. Copyright © 2004 John Wiley & Sons, Ltd.     

Spatial and Temporal Control Over Multilayer Bio‐Polymer Film Assembly and Composition

Biosensing applications have taken advantage of lab‐on‐a‐chip technologies for sample handling and sensors integration for highly sensitive, specific detection with high throughput. These systems are based on 2.5D fabrication principles with sensing elements restricted to an array format in two dimensions. In this report, a sensing platform that recovers biosensing capabilites in three spatial dimensions is presented. This is achieved by leveraging chitosan, a stimulus responsive polyaminosaccharide that undergoes a sol–gel transition driven by a change of pH. This process can be repeated, resulting in a multilayered hydrogel stack where each layer carries a unique chemical identity. In addition, the functionality of chitosan can be modified prior to or during the assembly process. This is demonstrated by introducing both a carboxylic acid functionality and additional primary amines to the base chitosan polymer. The assembly process is shown to be compatible with microfluidic dimensions.     

Capillary electrochromatography of proteins and peptides

This review summarizes applications of CEC for the analysis of proteins and peptides. This "hybrid" technique is useful for the analysis of a broad spectrum of proteins and peptides and is a complementary approach to liquid chromatographic and capillary electrophoretic analysis. All modes of CEC are described--granular packed columns, monolithic stationary phases as well as open-tubular CEC. Attention is also paid to pressurized CEC and the chip-based platform.     

Corannulenes with Electron-Withdrawing Substituents: Synthetic Approaches and Resulting Structural and Electronic Properties

Corannulene is a multifaceted polyaromatic compound. It has many interesting properties; for example, it has a bowl-shaped molecular structure that, in addition, undergoes a dynamic inversion process. It has attracted much attention within the last decades. This is not only due to its structural properties but also its electronic properties and its various potential applications to materials chemistry. Here, synthetic approaches towards corannulene derivatives with electron-withdrawing substituents are summarized. This includes both selective and unselective methods. Further, the electrochemical properties, that is, the reduction potentials, are analyzed and compared. As a main conclusion, one can state that the electron affinity depends roughly linearly on the number of substituents. Finally, the structural behavior of the substituted buckybowls in the solid state is highlighted. This also allows a general statement about the influence of the electronic and steric nature of substituents on the molecular structures and the solid-state packing of the corannulene derivatives.     

Pyrolysis of agricultural residues from rape and sunflowers: Production and characterization of bio-fuels and biochar soil management

This research explores the opportunities of combining energy production with a biochar soil management using a pyrolysis process. Real-world issues justify this approach: the need to provide sustainable production systems that minimize on- and off-site pollution and soil degradation; and the demand for solutions to global warming. The proposed technology is a pyrolysis process that yields gas, bio-oil and biochar. The composition and heating value of the gas makes it suitable for use as a fuel. The bio-oil obtained may be evaluated as an environmentally friendly green biofuel candidate. The biochar product is carbon-rich and a potential solid biofuel. Other ways it might be used as a C and N source in soil amendment. This is a key to securing environmental benefits: the production of a biochar which can be applied to soil.     

Fast and Cysteine-Specific Modification of Peptides,Proteins and Bacteriophage Using Chlorooximes

This work reports a novel chlorooxime mediated modification of native peptides and proteins under physiologic conditions. This method features fast reaction kinetics (apparent k₂=306±4 M⁻¹s⁻¹ for GSH) and exquisite selectivity for cysteine residues. This cysteine conjugation reaction can be carried out with just single-digit micromolar concentrations of the labeling reagent. The conjugates show high stability towards acid, base, and external thiol nucleophiles. A nitrile oxide species generated in situ is likely involved as the key intermediate. Furthermore, a bis-chlorooxime reagent is synthesized to enable facile Cys-Cys stapling in native peptides and proteins. This highly efficient cysteine conjugation and stapling was further implemented on bacteriophage to construct chemically modified phage libraries.     

Practical and General Alcohol Deoxygenation Protocol

Herein, we describe a practical protocol for the removal of alcohol functional groups through reductive cleavage of their benzoate ester analogs. This transformation requires a strong single electron transfer (SET) reductant and a means to accelerate slow fragmentation following substrate reduction. To accomplish this, we developed a photocatalytic system that generates a potent reductant from formate salts alongside Brønsted or Lewis acids that promote fragmentation of the reduced intermediate. This deoxygenation procedure is effective across structurally and electronically diverse alcohols and enables a variety of difficult net transformations. This protocol requires no precautions to exclude air or moisture and remains efficient on multigram scale. Finally, the system can be adapted to a one-pot benzoylation-deoxygenation sequence to enable direct alcohol deletion. Mechanistic studies validate that the role of acidic additives is to promote the key C(sp³)−O bond fragmentation step.     

Non-racemic (scalemic) planar-chiral five-membered metallacycles: routes, means, and pitfalls in their synthesis and characterization

This critical review provides a systematic classification of the synthetic routes to planar-chiral five-membered metallacycles into several routes, namely C-H bond activation, oxidative addition, transmetallation and optical resolution. As a characteristic of these bulk compounds is that they are synthesized as binary mixtures of enantiomers in proportions varying from the racemate to enantiopure, a review of absolute-configuration determination of the title planar-chiral scalemates is presented. This review is of interest to organic and organometallic synthetic chemists involved in asymmetric synthesis (97 references).     

Directed Evolution and Biocatalysis

This review describes the current state of biocatalysis in the chemical industry. Although we recognize the advantages of chemical approaches, we suggest that the use of biological catalysis is about to expand dramatically because of the recent developments in the artificial evolution of genes that code for enzymes. For the first time it is possible to consider the rapid development of an enzyme that is designed for a specific chemical reaction. This technology offers the opportunity to adapt the enzyme to the needs of the process. We describe herein the development of enzyme evolution technology and particularly DNA shuffling. We also consider several classes of enzymes, their current applications, and the limitations that should be addressed. In a review of this length it is impossible to describe all the enzymes with potential for industrial exploitation; there are other classes, which given appropriate activity, selectivity, and robustness, could become useful tools for the industrial chemist. This is an exciting era for biocatalysis and we expect great progress in the future.     

RKR potentials and radial wave equation

A RKR-Kaiser potential is obtained for the X¹Σ⁺CO state. This potential is tested through radial wave equation integration. In the application to the A ⁶LiH state there is not self-consistence. To improve it we present a mixed potential that is consistent. This is a Huffaker-RKR-van der Waals potential. This procedure is applicated to X′Σ⁺⁶LiH, A¹Σ⁺⁶LiH and A′Σ⁺⁶LiD states.     

Aqueous metal-free hydrothiolation of enamides and enecarbamates

An efficient and metal-free, anti-Markovnikov selective, hydrothioaltion reaction of enamides and enecarbamates in an aqueous medium is presented. This protocol is operationally simple, mild, and atom-economical. This process provides access to thioethers from available thiols and a variety of enamides and enecarbamates.     

Graft and block copolymers with polysiloxane and vinyl polymer segments

A convenient new process to make silicone/organic block and graft copolymers has been recently demonstrated. This dual copolymerization process combines conventional condensation polymerization of the siloxane segments with free radical polymerization of the organic vinyl polymer segments. The copolymerization process is relatively simple and economical compared with other copolymerization techniques as it uses commonly available starting materials and available process equipment. Silicone segments containing alkene side chains or end-groups are prepared in the usual way by polycondensation using an acid or base catalyst. The double bonds of the alkene groups are oxidized to carbonyls which are then used to initiate vinyl monomer polymerization and link the siloxane with the vinyl segments. This initiation step is based on a redox system of copper^(II) salts which generates free radicals on the alpha carbons next to the carbonyl groups. This copolymerization process is relatively fast and proceeds at high yields.     

Selective Curcuminoid Separation and Detection via Nickel Complexation and Adsorptive Stripping Voltammetry

Curcumin is a widely studied biologically active redox molecule. Although sensitive, electrochemical methods are commonly hindered by their lack of specificity. This article demonstrates how curcumin may be readily separated from other structurally and electrochemically similar redox moieties. This separation is achieved through exploitation of the molecules diketone functionality providing a route for its selective chelation to nickel(II). Recovery of the curcumin from the nickel complex is achieved simply and quantitatively through acidification of the precipitate. Adsorptive stripping voltammetry at a carbon screen‐printed electrode (SPE) is utilised both as a method for evidencing the effectiveness of the separation technique but further as a procedure for the analytical quantification of the curcumin concentration.     

The "resin-capture-release" hybrid technique: a merger between solid- and solution-phase synthesis

A polymer-assisted organic synthesis that combines the concept of solid-phase synthesis with the idea of polymer-supported scavenging reagents has recently appeared on the chemistry scene. This technique has frequently been termed the "resin-capture-release" methodology and is initiated by the immobilization of a small molecule on a polymeric support. This intermediate is subjected to a second transformation by adding a new reaction partner in solution. This reactant plays two roles: a) the chemical alteration of the polymer-bound intermediate and b) the simultaneous release of this reaction product from the resin back into solution. This new concept is presented and future prospects are discussed.     

One-pot and two-pot methods for chalcone derived pyrimidines synthesis and applications

Chalcone-derived pyrimidine is a well-known heterocyclic compound that is commonly present in ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) bio-isosteres. Pyrimidine derivatives are effective in both the electronic industry and drug industries. This review highlights the synthesis of pyrimidines, namely mono-pyrimidine, bis-pyrimidine, fused pyrimidine, symmetric, and asymmetric pyrimidine via one-pot and two-pot methods. The one-pot method is the direct reaction of amino derivatives with aldehydes and acetophenones, whereas the two-pot method is frequently reported for the synthesis of chalcone before the cyclization to a pyrimidine. This review is important in organic synthesis, particularly in the heterocyclic field, regarding pyrimidines and their significance in therapeutic and electronic industries.     

Fragmentation reactions of singly and doubly protonated thiourea- and sugar-substituted cyclams and their transition-metal complexes

Cyclam macrocycles tetrasubstituted with amino-, thiourea-, and sugar-terminated side chains are ionized by electrospray ionization mass spectrometry (ESI-MS) as singly or doubly protonated species or as transition-metal complexes. Their fragmentation behavior is examined in a Fourier-transform ion-cyclotron-resonance (FT-ICR) mass spectrometer by collision-induced dissociation (CID) experiments. Typically, fragmentation occurs within the side chains through a number of different 1,2-elimination reactions irrespective of the absence or presence of a transition metal ion such as Co(2+), Ni(2+), or Zn(2+). A remarkable exception is Cu(2+), which induces ring cleavage reactions. This is traced back to an electron transfer from the cyclam nitrogen atoms to the Cu(2+) ion. The electron transfer creates a cation-radical within the macrocycle, which induces typical fragmentation reactions such as alpha-cleavages that lead to fragmentation within the macrocycle. This interpretation is in line with fragmentation experiments on unsubstituted cyclam and its complexes.