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.     

Liquid chromatographic assay of phenothiazine, thioxanthene and butyrophenone neuroleptics and antihistamines in blood and plasma with conventional and radial compression columns and UV and electrochemical detection

An assay strategy for determining a wide range of phenothiazine, thioxanthene and butyrophenone neuroleptics and antihistamines both alone and in combination in blood and plasma is described. The general method employs liquid chromatography with both conventional and radial compression nitrile bonded columns. Detection is by ultraviolet absorption spectrophotometry or by amperometry depending on the concentrations to be measured. Ultraviolet absorption is suitable down to 10 ng/ml. Below this level amperometry is preferable. The various compounds are used as internal standards for each other. The lower limit of detection is approximately 0.1 ng ml-1 with 10-ml sample. The with-run coefficient of variation is a maximum of 7.3%.     

Cellulose and chitin esters,and the reactivity of cellulose and chitin

Summary On comparison of the reactivities of chitin and cellulose in their conversion into ethers and esters it is found that chitin is considerably less reactive than cellulose, which is to be attributed to a difference in the internal active surfaces.Paper read at a General Meeting of the Division of Chemical Sciences, Academy of Sciences, USSR, Moscow, March 10, 1961     

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.     

Sizes of atoms and ions and covalency of bonding in molecules and crystals

A new system of atomic radii for the elements up to barium inclusive is constructed. Values of the radii are chosen so as the dependence between the dissociation energy of diatomic homonuclear molecules and a depth of atom overlapping is monotonous, and the scatter of data is minimal. The depth of overlapping is calculated as a difference between the sum of atomic radii and an experimental interatomic distance. Conclusions are made that: the radii of free atoms and ions are determined by the value of the electron density equal to 0.01 au; they considerably change in molecules and crystals only as a result of the charge transfer from cation to anion; covalent bonding is well described by the overlapping of free atoms (ions), confined by the surface of the given radius, and its energy depends upon the depth of overlapping of valence electron densities of atoms. A method of overlapping atoms is proposed for the approximate estimation of ionic sizes and charges in bound systems.     

Direct and sensitized photoprocesses of bis-benzimidazole dyes and the effects of surfactants and DNA

The photoprocesses of two bis-benzimidazole dyes, Hoechst 33258 (1) and an analog, where the phenolic group in p-position is replaced by an ethoxy group, Hoechst 33342 (2), were studied. For 1 and 2 in aqueous solution the quantum yield of fluorescence is strongly pH dependent; it decreases from a maximum value of phi f = 0.4 at pH 5 to phi f = 0.02 at pH 8. The effects of absorption and fluorescence, induced by sodium dodecyl sulfate surfactants below and above the critical micelle concentration and by double-stranded DNA, are interpreted by assuming that in bulk aqueous solution the dyes are essentially present as monomers. The strong enhancement of phi f, when the dye is bound to double-stranded DNA or solubilized in micelles, is suggested to be due to different environments at the benzimidazole rings. A quinoid intermediate with absorption maximum at 380 nm is formed for 1 at neutral pH using lambda exc = 248 or 308 nm. N-centered radicals of 1 or 2 in aqueous solution were observed by laser flash photolysis after electron ejection using wavelengths of 193 or 248 nm (mono and biphotonic, respectively). The precursor radical cation escaped observation but is transformed into the above radicals by deprotonation. Electron transfer from 1 in aqueous solution to triplet acetone takes place, and subsequent deprotonation is proposed to yield N-centered radicals. In addition, energy transfer from acetone to 1 is suggested, leading to T-T absorption with the maximum at 700 nm. The photoprocesses are discussed and the results compared with those known from pulse radiolysis.     

Net,excess and absolute adsorption and adsorption of helium

The definitions of absolute, excess and net adsorption in microporous materials are used to identify the correct limits at zero and infinite pressure. Absolute adsorption is shown to be the fundamental thermodynamic property and methods to determine the solid density that includes the micropore volume are discussed. A simple means to define when it is necessary to distinguish between the three definitions at low pressure is presented. To highlight the practical implications of the analysis the case of adsorption of helium is considered in detail and a combination of experiments and molecular simulations is used to clarify how to interpret adsorption measurements for weakly adsorbed components.     

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.     

Walk counts, labyrinthicity, and complexity of acyclic and cyclic graphs and molecules

It is demonstrated how the complexity of a (molecular) graph can be quantified in terms of the walk counts, extremely easily obtained graph invariants that depend on size, branching, cyclicity, and edge and vertex weights (unsaturation, heteroatoms). The influence of symmetry is easily accounted for. The term labyrinthicity is proposed for what is measured by walk counts alone, neglecting symmetry. The total walk count and recently advanced measures of labyrinthicity or complexity are compared with respect to the ordering of structures and to the computational effort required to obtain numerical values.     

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.     

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.

Progress and prospects in on-line-process gas and liquid chromatography

The present status of both process gas (PGC) and liquid (PLC) chromatographs is examined with regard to the main criteria that any process analyser should fulfil: reliability, credibility, fast response and low maintenance. Despite considerable improvements in the construction of these instruments, owing to the materials used, progress in technology and microelectronics and the advent of microprocessors, their reliability is still a matter of great concern.The deferred standard concept may offer a solution for these problems. Progress is also made by the introduction of fused-silica capillary columns in PGC, which allow a better resolution and a greater speed of analysis. However, this technology requires a redesign of PGCs.Further, particularly for PLC, a new approach based on the concept of instability instead of stability of the main parameters is proposed. This approach leads to a simpler, more reliable and less expensive PLC. The consequence is some radical changes in the design and functions of both the analytical and control units of the chromatograph. The analytical unit is plugged into the chemical reactor and is not temperature controlled. The control unit, incorporating a microcomputer and dedicated software, is able to characterize the peaks despite their fluctuating retention times, to readjust the time functions of the analytical sequence and to validate the detector response in the case of fluctuations of temperature or mobile phase flow-rate. This approach is useful for the implementation of temperature programming and, according to the validation function of the deferred standard, to allow the use of selective but unstable detectors in PGC.Simpler in hardware, PGCs and PLCs could become “intelligent apparatus” capable of new qualitative and quantitative tasks at a more competitive cost.     

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.     

Capsaicin and Gut Microbiota in Health and Disease

Capsaicin is a widespread spice known for its analgesic qualities. Although a comprehensive body of evidence suggests pleiotropic benefits of capsaicin, including anti-inflammatory, antioxidant, anti-proliferative, metabolic, or cardioprotective effects, it is frequently avoided due to reported digestive side-effects. As the gut bacterial profile is strongly linked to diet and capsaicin displays modulatory effects on gut microbiota, a new hypothesis has recently emerged about its possible applicability against widespread pathologies, such as metabolic and inflammatory diseases. The present review explores the capsaicin–microbiota crosstalk and capsaicin effect on dysbiosis, and illustrates the intimate mechanisms that underlie its action in preventing the onset or development of pathologies like obesity, diabetes, or inflammatory bowel diseases. A possible antimicrobial property of capsaicin, mediated by the beneficial alteration of microbiota, is also discussed. However, as data are coming mostly from experimental models, caution is needed in translating these findings to humans.     

Electronic and Magnetic Properties of Linear and Dimerized Titanium Nanochains Under Compressive and Tensile Strain

The magnetic and electronic properties of both linear and dimerized nanochains of titanium at different atomic distances are calculated within density functional theory with the generalized gradient approximation. Titanium which is a nonmagnetic in its bulk form is shown to become magnetic in its nanochain structure. Also, a close relationship is found between magnetic state and geometry of chain structure and the dependence of electronic properties on the atomic structures of chains is revealed. It is found that, for dimerized nanochains from equilibrium constant, compressive strain leads to a reduction in magnetism. Moreover, characteristics of the systems near the Fermi level are investigated and the charge densities of both nanostructures are studied in the ferromagnetic order. The results show that metallic bonding is mainly responsible for the linear structure; however, for the dimerized structure, the bonding is more directional, i.e. has a more covalent character. With increasing tension along the axis of the nanostructures, a change in the types of bonding is found.     

Determination of lanthanides and yttrium in rocks and minerals by atomic-absorption and flame-emission spectrometry

The sensitivity of atomic-absorption and flame-emission determination of lanthanides and yttrium is improved by a factor of 2-5 when an absolute ethanol solution of the perchlorate of the metal (instead of an aqueous solution) is aspirated into a nitrous oxide-acetylene flame. Based on this, a method has been developed for accurate determination of small amounts of certain rare earths and yttrium. Lanthanum (1%) is used as a spectroscopic buffer to eliminate interferences and to enhance the sensitivities in certain determinations. Where the use of lanthanum is not practicable because of interferences (such as in the determination of praseodymium and samarium by flame emission), sodium (2000 ppm) is used as the spectroscopic buffer. Studies with synthetic solutions indicate that yttrium and most lanthanides can be directly determined in minerals without any chemical separation. With rock samples it is necessary to preconcentrate the traces of the rare earths by fluoride or oxalate precipitation with calcium as the carrier, followed by removal of calcium by hydroxide precipitation using mg amounts of iron as the carrier. The method developed has been applied to the determination of certain lanthanides and yttrium in a variety of rocks, including the Canadian reference rocks, syenites SY-1, SY-2 and SY-3, and some minerals such as britholite, cenosite, chevkinite, allanite, apatite and sphene.     

Oxidation of quinazoline and quinoxaline by xanthine oxidase and aldehyde oxidase

Quinazoline is oxidized by xanthine oxidase initially (and rapidly) to 4-hydroxyquinazoline which subsequently is oxidized more slowly to 2,4-dihydroxyquinazoline. Both oxidative reactions are inhibited strongly by allopurinol. Quinazoline is oxidized by aldehyde oxidase to 4-hydroxyquinazoline but within a short time (3–5 minutes) the reaction ceases; the proposal that cessation of reaction is due to product inhibition is rendered untenable by our observation that 4-hydroxyquinazoline is rapidly oxidized by aldehyde oxidase to 2,4-dihydroxyquinazoline. Preincubation of aldehyde oxidase with quinazoline results in complete inhibition of the ability of the enzyme to oxidize 4-hydroxyquinazoline and the standard substrate N-methylnicotinamide. It appears therefore that quinazoline is able to react with aldehyde oxidase and inactivate it. Quinoxaline and 2-hydroxyquinoxaline are not oxidized by xanthine oxidase but are converted by aldehyde oxidase to 2,3-dihydroxyquinoxaline; all oxidations mediated by aldehyde oxidase are inhibited completely by menadione.     

Waveband and dose dependency of sunlight-induced immunomodulation and cellular changes

Both the UVB and UVA wavebands within sunlight are immunosuppressive. This article reviews the relationship between wavebands and dose in UV-induced immunosuppression mainly concentrating on responses in humans. It also contrasts the effects of UVB and UVA on cellular changes involved in immunosuppression. Over physiological sunlight doses to which humans can be exposed during routine daily living or recreational pursuits, both UVA and UVB suppress immunity. While there is a linear dose relationship with UVB commencing at doses less than half of what is required to cause sunburn, UVA has a bell-shaped dose response over the range to which humans can be realistically exposed. At doses too low for either waveband to be suppressive, interactions between UVA and UVB augment each other, enabling immunosuppression to occur. At doses beyond where UVA is immunosuppressive, it still contributes to sunlight-induced immunosuppression via this interaction with UVB. While there is little research comparing the mechanisms by which UVB, UVA and their interactions can cause immunosuppression, it is likely that different chromophores and early molecular events are involved. There is evidence that both wavebands disrupt antigen presentation and effect T cell responses. Different individuals are likely to have different immunomodulatory responses to sunlight.     

Structural stability and phase transition in OsC and RuC

The structural stability and phase transition of osmium and ruthenium carbides (OsC and RuC) were investigated by first principles. Nine structures were considered for each carbide. Zinc blende structure has the lowest energy among the considered structures at ambient conditions for both carbides. For OsC at elevated pressures, the most stable phase is zinc blende structure from 0 to 10 GPa, FeSi from 10 to 32 GPa. In these two structures, Os atom is fourfold coordinated. From 32 to 40 GPa, tungsten carbide (WC) and NiAs are energetically competitive with Os atom sixfold coordinated. NiAs becomes energetically the most stable structure above 40 GPa. For RuC, zinc blende structure is the most stable from 0 to 20 GPa. From 20 to 100 GPa, WC structure is the most stable.     

Tutorial and comprehensive computational study of acceptance and transmission of sinusoidal and digital ion guides

A quadrupoles acceptance is a measure of its ability to catch ions with certain trajectories. One way to calculate acceptance is the method of ellipses. The method arose partly from a simplification that trajectories could be calculated for an electrode axis independently of others. It has been used to calculate the acceptance and transmission of sine‐driven quadrupole mass filters for over 50 years. Although the method is straightforward, it is generally described with little detail or presented as a confusing string of equations. As such, it may not be decipherable by all practitioners. For this reason, the first half of this paper presents a practical explanation of the method of ellipses and the concepts that make it work. Only equations necessary to describe the method are introduced. The tutorial also prepares the reader for the second half, which presents an alternative approach for calculating acceptance based on an array of initial trajectories. The alternative approach is used to compare the acceptance of simplified sinusoidal and digital ion guides. The method of ellipses was applied to validate results of the new approach for calculation of acceptance.