Review and patents and literature

The use of the insect cell/baculovirus expression system for producing recombinant proteins of bacterial, plant, insect, and mammalian origin has become widespread. The popularity of this eukaryotic expression system is due to many factors, including (1) potentially high protein expression levels, (2) ease and speed of genetic engineering, (3) ability to accommodate large DNA inserts, (4) protein processing similar to higher eukaryotic cells (e.g., mammalian cells), and (5) ease of insect cell growth (e.g., suspension growth). The following review of the literature discusses two engineering aspects of recombinant protein synthesis by insect cell cultures: bioreactor scale-up and insect cell line selection. Following this review patent abstracts and additional literature pertaining to expression of recombinant proteins in insect cell culture are listed.     

Hard and soft acids and bases: structure and process

Under investigation is the structure and process that gives rise to hard-soft behavior in simple anionic atomic bases. That for simple atomic bases the chemical hardness is expected to be the only extrinsic component of acid-base strength, has been substantiated in the current study. A thermochemically based operational scale of chemical hardness was used to identify the structure within anionic atomic bases that is responsible for chemical hardness. The base's responding electrons have been identified as the structure, and the relaxation that occurs during charge transfer has been identified as the process giving rise to hard-soft behavior. This is in contrast the commonly accepted explanations that attribute hard-soft behavior to varying degrees of electrostatic and covalent contributions to the acid-base interaction. The ability of the atomic ion's responding electrons to cause hard-soft behavior has been assessed by examining the correlation of the estimated relaxation energies of the responding electrons with the operational chemical hardness. It has been demonstrated that the responding electrons are able to give rise to hard-soft behavior in simple anionic bases.     

Ground- and excited-state aromaticity and antiaromaticity in benzene and cyclobutadiene

The aromaticity and antiaromaticity of the ground state (S 0), lowest triplet state (T 1), and first singlet excited state (S 1) of benzene, and the ground states (S 0), lowest triplet states (T 1), and the first and second singlet excited states (S 1 and S 2) of square and rectangular cyclobutadiene are assessed using various magnetic criteria including nucleus-independent chemical shifts (NICS), proton shieldings, and magnetic susceptibilities calculated using complete-active-space self-consistent field (CASSCF) wave functions constructed from gauge-including atomic orbitals (GIAOs). These magnetic criteria strongly suggest that, in contrast to the well-known aromaticity of the S 0 state of benzene, the T 1 and S 1 states of this molecule are antiaromatic. In square cyclobutadiene, which is shown to be considerably more antiaromatic than rectangular cyclobutadiene, the magnetic properties of the T 1 and S 1 states allow these to be classified as aromatic. According to the computed magnetic criteria, the T 1 state of rectangular cyclobutadiene is still aromatic, but the S 1 state is antiaromatic, just as the S 2 state of square cyclobutadiene; the S 2 state of rectangular cyclobutadiene is nonaromatic. The results demonstrate that the well-known "triplet aromaticity" of cyclic conjugated hydrocarbons represents a particular case of a broader concept of excited-state aromaticity and antiaromaticity. It is shown that while electronic excitation may lead to increased nuclear shieldings in certain low-lying electronic states, in general its main effect can be expected to be nuclear deshielding, which can be substantial for heavier nuclei.     

Concentrations and distributions of trace and minor elements in Chinese and Canadian coals and ashes

A total of 35 trace and minor elements including some of environmental significance were determined in each of a selection of 15 Chinese and 6 Canadian thermal coals and their ashes by using the SLOWPOKE-2 nuclear reactor facility of the University of Toronto. The concentrations and distributions of these constituents among the coals and their combustion products (viz. ash and volatile matter) are presented together with an interpretation of their significance in relation to the large scale combustion of these coals as thermal fuels in industrialized countries such as China and Canada. The detailed results showed wide variations in trace impurity concentrations (up to a factor of 100 and more) among the coals studied with few large differences between those of Chinese and Canadian origin except that the rare earths, Sc, Th, U, I, and Se were much higher in the former, other halogens, As and Na were lower. Values for elemental enrichment factors (EF) relative to normal crustal abundances indicated that only As(EF=13), Br(5.7), I(16), S(230), Sb(11) and Se(320) were appreciably enriched in coal. During static ashing at 750°C most of the halogens, S and Se were volatilized whereas most other inorganic constituents were highly retained and concentrated in the ash by factors of 6 to 11.     

Ferrocene and ferrocenium modified clays and their styrene and EVA composites

In this work, ferrocene- and ferrocenium-containing salts were employed to modify montmorillonite. X-ray measurements show an increase in the interlayer spacing upon clay modification, which means that the larger and more organophilic cations were inserted into the gallery space of montmorillonite. Attempts to prepare nanocomposites of polystyrene and ethylene vinyl acetate copolymers lead to immiscible systems; the morphology of these systems was elucidated with TEM, XRD and cone calorimetry. The thermal stability of the composites is greater than that of the virgin polymer.     

Supercomputing and supercomputers for science and engineering in general and for chemistry and biosciences in particular

We start by pointing out relationships between production of information, global simulation, and supercomputing, thus placing our research activities in today's society context. Then we detail the evolution in hardware and software for 1CAP, our experimental supercomputer, which we claim to be especially well suited for supercomputing in science and engineering. A preliminary discussion of 1CAP/3090 (our latest experimental effort) is included. Many examples from different disciplines are provided to verify our assertions. We “prove” our point by presenting an example of global supercomputing. Starting with 3 nuclei and 10 electrons, building up to a single water molecule, then to a few hundred, we learn, for example, about Raman, infrared, and neutron scattering; we then move up to a few hundred thousand molecules to analyze particle flow and obstructions; finally we experiment, but only preliminarily, with a few million particles to learn more on nonequilibrium dynamics as in the Rayleigh-Benard systems. In this way, quantum mechanics is overlapped with statistical mechanics and expanded into microdynamics. The entire paper is finally reanalyzed from a different perspective, presenting rather systematically, even if most briefly, our ideas on “modern” computational chemistry, where quantum mechanics is as much needed as fluid dynamics and graphics. In this section the main computational techniques are analyzed in terms of computer programs and their associated flow diagrams to solve the basic equations using parallel supercomputers.     

Preparation and photolysis of poly-p-ethylacrylophenone and poly-p-chloroacrylophenone and their copolymers with styrene and methyl methacrylate

Poly-p-ethylacrylophenone (PPEtAP) and poly-p-chloroacrylophenone (PPClAP) and their copolymers with styrene (PEtAP/S) and (PClAP/S) and with methyl methacrylate (PEtAP/MMA) and (PClAP/MMA) were prepared. Quantum yields of main-chain scissions at 366 nm at room temperature in benzene solution are of the same order as those of the unsubstituted polyacrylophenone and its copolymers. Substitution with chlorine and ethyl group in the para position compared to the unsubstituted polyacrylophenone and its copolymers leads to an increase of the lifetime for the n–π^* excited triplet state, as is evident from the measured quenching constants of photolysis. The low-temperature emission spectra of the copolymers are similar to the spectra of the model compounds in a polymer film. For the homopolymer, however, the character of the emission spectrum changes considerably.     

Resurrection and Reactivation of Acetylcholinesterase and Butyrylcholinesterase

Organophosphorus (OP) nerve agents and pesticides present significant threats to civilian and military populations. OP compounds include the nefarious G and V chemical nerve agents, but more commonly, civilians are exposed to less toxic OP pesticides, resulting in the same negative toxicological effects and thousands of deaths on an annual basis. After decades of research, no new therapeutics have been realized since the mid-1900s. Upon phosphylation of the catalytic serine residue, a process known as inhibition, there is an accumulation of acetylcholine (ACh) in the brain synapses and neuromuscular junctions, leading to a cholinergic crisis and eventually death. Oxime nucleophiles can reactivate select OP-inhibited acetylcholinesterase (AChE). Yet, the fields of reactivation of AChE and butyrylcholinesterase encounter additional challenges as broad-spectrum reactivation of either enzyme is difficult. Additional problems include the ability to cross the blood brain barrier (BBB) and to provide therapy in the central nervous system. Yet another complication arises in a competitive reaction, known as aging, whereby OP-inhibited AChE is converted to an inactive form, which until very recently, had been impossible to reverse to an active, functional form. Evaluations of uncharged oximes and other neutral nucleophiles have been made. Non-oxime reactivators, such as aromatic general bases and Mannich bases, have been developed. The issue of aging, which generates an anionic phosphylated serine residue, has been historically recalcitrant to recovery by any therapeutic approach—that is, until earlier this year. Mannich bases not only serve as reactivators of OP-inhibited AChE, but this class of compounds can also recover activity from the aged form of AChE, a process referred to as resurrection. This review covers the modern efforts to address all of these issues and notes the complexities of therapeutic development along these different lines of research.     

A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies

In this work we present the experimental and theoretical vibrational absorption (VA) and the theoretical vibrational circular dichroism (VCD) spectra for aframodial. In addition, we present the theoretical VA and VCD spectra for the diasteriomers of aframodial. Aframodial has four chiral centers and hence has 2⁴ = 16 diasteriomers, which occur in eight pairs of enantiomers. In addition to the four chiral centers, there is an additional chirality due to the helicity of the entire molecule, which we show by presenting 12 configurations of the 5S,8S,9R,10S enantiomer of aframodial. The VCD spectra for the diasteriomers and the 12 configurations of one enantiomer are shown to be very sensitive not only to the local stereochemistry at each chiral center, but in addition, to the helicity of the entire molecule. Here one must be careful in analyzing the signs of the VCD bands due to the ‘non-chiral’ chromophores in the molecule, since one has two contributions; one due to the inherent chirality at the four chiral centers, and one due to the chirality of the side chain groups in specific conformers, that is, its helicity. Theoretical simulations for various levels of theory are compared to the experimental VA recorded to date. The VCD spectra simulations are presented, but no experimental VCD and Raman spectra have been reported to date, though some preliminary VCD measurements have been made in Stephens’ lab in Los Angeles. The flexible side chain is proposed to be responsible for the small size of the VCD spectra of this molecule, even though the chiral part of the molecule is very rigid and has four chiral centers. In addition to VCD and Raman measurements, Raman optical activity (ROA) measurements would be very enlightening, as in many cases bands which are weak in both the VA and VCD, may be large in the Raman and/or ROA spectra. The feasibility of using vibrational spectroscopy to monitor biological structure, function and activity is a worthy goal, but this work shows that a careful theoretical analysis is also required, if one is to fully utilize and understand the experimental results. The reliability, reproduceability and uniqueness of the vibrational spectroscopic experiments and the information which can be gained from them is discussed, as well as the details of the computation of VA, VCD and Raman (and ROA) spectroscopy for molecules of the complexity of aframodial, which have multiple chiral centers and flexible side chains. Festschrift in Honor of Philip J. Stephens’ 65th Birthday.     

Electronic structures and reactivities of methyl-substituted thienothiazoles and thieno- and furopyridines

The electronic structures of a number of methyl-substituted heterocyclces containing a thiophene or furan ring condensed with a thiazole or pyridine ring and of their quaternary salts and methylene bases were calculated by the Pariser-Parr-Pople method. The features of the electronic structures of the investigated molecules were ascertained. It is shown that methyl-substituted thienothiazoles and thieno- and furopyridines and their quaternary salts are appreciably inferior to the corresponding benzothiazoles and quinoline derivatives used for the synthesis of polymethine dyes with respect to the reactivity of the methyl group.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1202–1206, September, 1976.     

Photocatalytic and Electrochemical Borylation and Silylation Reactions

Due to their high versatility borylated and silylated compounds are inevitable synthons for organic chemists. To escape the classical hydroboration/hydrosilylation paradigm, chemists turned their attention to more modern and green methods such as photoredox chemistry and electrosynthesis. This account focuses on novel methods for the generation of boryl and silyl radicals to forge C−B and C−Si bonds from our group.     

Electron Transfer and Collision Induced Dissociation of Non-Derivatized and Derivatized Desmosine and Isodesmosine

Electron transfer dissociation (ETD) has attracted increasing interest due to its complementarity to collision-induced dissociation (CID). ETD allows the direct localization of labile post-translational modifications, which is of main interest in proteomics where differences and similarities between ETD and CID have been widely studied. However, due to the fact that ETD requires precursor ions to carry at least two charges, little is known about differences in ETD and CID of small molecules such as metabolites. In this work, ETD and CID of desmosine (DES) and isodesmosine (IDS), two isomers that due to the presence of a pyridinium group can carry two charges after protonation, are studied and compared. In addition, the influence of DES/IDS derivatization with propionic anhydride and polyethyleneglycol (PEG) reagents on ETD and CID was studied, since this is a common strategy to increase sensitivity and to facilitate the analysis by reversed-phase chromatography. Clear differences between ETD and CID of non-derivatized and derivatized-DES/IDS were observed. While CID is mainly attributable to charge-directed fragmentation, ETD is initiated by the generation of a hydrogen atom at the initial protonation site and its subsequent transfer to the pyridinium ring of DES/IDS. These differences are reflected in the generation of complex CID spectra dominated by the loss of small, noninformative molecules (NH₃, CO, H₂O), while ETD spectra are simpler and dominated by characteristic side-chain losses. This constitutes a potential advantage of ETD in comparison to CID when employed for the targeted analysis of DES/IDS in biological samples.

Synthesis and properties of benzophenone-spiropyran and naphthalene-spiropyran conjugates

We have designed and synthesized four compounds integrating luminescent and photochromic components in their molecular skeletons. Two of them combine a nitrospiropyran photochrome with either one or two naphthalene fluorophores and can be prepared in three synthetic steps. The other two consist of a nitrospiropyran photochrome and a benzophenone phosphore connected by either ether or ester linkages and can be prepared in six or five, respectively, synthetic steps. The luminescent components of these assemblies are expected to transfer energy intramolecularly to the photochromic species upon excitation and encourage their photoisomerization. Consistently, the phosphorescence of the benzophenone units and the fluorescence of the naphthalene components are effectively quenched when these species are connected covalently to a nitrospiropyran. Nonetheless, the photoisomerization of the photochrome becomes significantly less efficient after the covalent attachment to the luminescent partner. The fraction of incident radiations absorbed by either the benzophenone or the naphthalene fragment does not promote the isomerization of the photochromic appendage. Instead, irreversible transformations occur upon irradiation of the luminophore-photochrome assemblies. Thus, the covalent attachment of a benzophenone or a naphthalene to a nitrospiropyran is not a viable strategy to improve the photocoloration efficiency of the photochromic component. Even although the very same luminophores are known to sensitize intermolecularly the isomerization of nitrospiropyrans, the transition to covalent luminophore-photochrome assemblies tends to promote degradation, rather than sensitization, upon irradiation.     

Melting and freezing characteristics and structural properties of supported and unsupported gold nanoclusters

Molecular dynamics simulations in conjunction with MEAM potential models have been used to study the melting and freezing behavior and structural properties of both supported and unsupported Au nanoclusters within a size range of 2 to 5 nm. In contrast to results from previous simulations regarding the melting of free Au nanoclusters, we observed a structural transformation from the initial FCC configuration to an icosahedral structure at elevated temperatures followed by a transition to a quasimolten state in the vicinity of the melting point. During the freezing of Au liquid clusters, the quasimolten state reappeared in the vicinity of the freezing point, playing the role of a transitional region between the liquid and solid phases. In essence, the melting and freezing processes involved the same structural changes which may suggest that the formation of icosahedral structures at high temperatures is intrinsic to the thermodynamics of the clusters, rather than reflecting a kinetic phenomenon. When Au nanoclusters were deposited on a silica surface, they transformed into icosahedral structures at high temperatures, slightly deformed due to stress arising from the Au-silica interface. Unlike free Au nanoclusters, an icosahedral solid-liquid coexistence state was found in the vicinity of the melting point, where the cluster consisted of coexisting solid and liquid fractions but retained an icosahedral shape at all times. These results demonstrated that the structural stability in the structures of small Au nanoclusters can be enhanced through interaction with the substrate. Supported Au nanoclusters demonstrated a structural transformation from decahedral to icosahedral motifs during Au island growth, in contrast to the predictions of the minimum-energy growth sequence: icosahedral structures appear first at very small cluster sizes, followed by decahedral structures, and finally FCC structures recovered at very large cluster sizes. The simulations also showed that island shapes are strongly influenced by the substrate, more specifically, the structural characteristic of a Au island is not only a function of size, but also depends on the contact area with the surface, which is controlled by the wetting of the cluster to the substrate.     

Sarin and Soman: Structure and Properties

The most stable conformers of sarin (isopropyl methylphosphonoflouridate) and soman (pinacolyl methylphosphonofluoridate) are determined in high-level-correlated calculations with extended Gaussian basis sets. The two molecules are found to have three low-energy conformers each. For both molecules two of the lowest energy conformers have almost the same energies with a very small barrier separating the corresponding minima. The third conformer of sarin is found to lie about 1 kcal/mol above the lowest energy form. For soman the corresponding value is equal to about 4 kcal/mol. The significance of these data for the mechanism of the toxic action of sarin and soman is discussed. According to our investigations sarin and soman are highly similar electronically and differences in their features arise mostly from the size and spatial arrangement of the alkoxy substituent at phosphorus. Also the influence of solvents on the conformations and solvation energies of sarin and soman is investigated.     

Phosphonodifluoromethyl and phosphonothiodifluoromethyl radicals. Generation and addition onto alkenes and alkynes

[reaction: see text] Selanylated difluoromethylphosphonates and difluoromethylphosphonothioates are good precursors to phosphonodifluoromethyl and phosphonothiodifluoromethyl radicals, respectively. When generated in the presence of alkenes and a hydrogen donor, the corresponding alpha,alpha-difluorinated alkylphosphonates or alkylphosphonothioates are produced in fair to good yields. The use of alkynes results in the formation of alpha,alpha-difluorinated allyl derivatives in useful yields. The presence of the sulfur atom in phosphonothiodifluoromethyl radicals usually translates into higher isolated yields.     

Second- and third-order triples and quadruples corrections to coupled-cluster singles and doubles in the ground and excited states

Second- and third-order perturbation corrections to equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) incorporating excited configurations in the space of triples [EOM-CCSD(2)T and (3)T] or in the space of triples and quadruples [EOM-CCSD(2)TQ] have been implemented. Their ground-state counterparts--third-order corrections to coupled-cluster singles and doubles (CCSD) in the space of triples [CCSD(3)T] or in the space of triples and quadruples [CCSD(3)TQ]--have also been implemented and assessed. It has been shown that a straightforward application of the Rayleigh-Schrodinger perturbation theory leads to perturbation corrections to total energies of excited states that lack the correct size dependence. Approximations have been introduced to the perturbation corrections to arrive at EOM-CCSD(2)T, (3)T, and (2)TQ that provide size-intensive excitation energies at a noniterative O(n(7)), O(n(8)), and O(n(9)) cost (n is the number of orbitals) and CCSD(3)T and (3)TQ size-extensive total energies at a noniterative O(n(8)) and O(n(10)) cost. All the implementations are parallel executable, applicable to open and closed shells, and take into account spin and real Abelian point-group symmetries. For excited states, they form a systematically more accurate series, CCSD1 eV) and the ground-state wave function has single-determinant character. In other cases, however, the corrections tend to overestimate the triples and quadruples effects, the origin of which is discussed. For ground states, the third-order corrections lead to a rather small improvement over the highly effective second-order corrections [CCSD(2)T and (2)TQ], which is a manifestation of the staircase convergence of perturbation series.     

Nucleophilicities and Nucleofugalities of Thio- and Selenoethers

Rate constants for the reactions of dialkyl chalcogenides with laser flash photolytically generated benzhydrylium ions have been measured photometrically to integrate them into the comprehensive benzhydrylium-based nucleophilicity scale. Combining these rate constants with the previously reported equilibrium constants for the same reactions provided the corresponding Marcus intrinsic barriers and made it possible to quantify the leaving group abilities (nucleofugalities) of dialkyl sulfides and dimethyl selenide. Due to the low intrinsic barriers, dialkyl chalcogenides are fairly strong nucleophiles (comparable to pyridine and N-methylimidazole) as well as good nucleofuges; this makes them useful group-transfer reagents.     

Formation and control of Turing patterns and phase fronts in photonics and chemistry

We review the main mechanisms for the formation of regular spatial structures (Turing patterns) and phase fronts in photonics and chemistry driven by either diffraction or diffusion. We first demonstrate that the so-called ‘off-resonance’ mechanism leading to regular patterns in photonics is a Turing instability. We then show that negative feedback techniques for the control of photonic patterns based on Fourier transforms can be extended and applied to chemical experiments. The dynamics of phase fronts leading to locked lines and spots are also presented to outline analogies and differences in the study of complex systems in these two scientific disciplines.