Electrification of volcanic plumes

Volcanic lightning, perhaps the most spectacular consequence of the electrification of volcanic plumes, has been implicated in the origin of life on Earth, and may also exist in other planetary atmospheres. Recent years have seen volcanic lightning detection used as part of a portfolio of developing techniques to monitor volcanic eruptions. Remote sensing measurement techniques have been used to monitor volcanic lightning, but surface observations of the atmospheric electric Potential Gradient (PG) and the charge carried on volcanic ash also show that many volcanic plumes, whilst not sufficiently electrified to produce lightning, have detectable electrification exceeding that of their surrounding environment. Electrification has only been observed associated with ash-rich explosive plumes, but there is little evidence that the composition of the ash is critical to its occurrence. Different conceptual theories for charge generation and separation in volcanic plumes have been developed to explain the disparate observations obtained, but the ash fragmentation mechanism appears to be a key parameter. It is unclear which mechanisms or combinations of electrification mechanisms dominate in different circumstances. Electrostatic forces play an important role in modulating the dry fallout of ash from a volcanic plume. Beyond the local electrification of plumes, the higher stratospheric particle concentrations following a large explosive eruption may affect the global atmospheric electrical circuit. It is possible that this might present another, if minor, way by which large volcanic eruptions affect global climate. The direct hazard of volcanic lightning to communities is generally low compared to other aspects of volcanic activity.

A model for stretch-bend interactions in molecular force fields

Interaction force constants between bond-stretching and angle-bending co-ordinates in polyatomic molecules have been attributed, by some authors, to changes of hybridization due to orbital-following of the bending co-ordinate, and consequent changes of bond length due to the change of hybridization. A method is described for using this model quantitatively to reduce the number of independent force constants in the potential function of a polyatomic molecule, by relating stretch-bend interaction constants to the corresponding diagonal stretching constants. It is proposed to call this model the Hybrid Orbital Force Field. The model is applied to the tetrahedral four co-ordinated carbon atom (as in methane) and to the trigonal planar three coordinated carbon atom (as in formaldehyde).

Vibration–rotation variational calculations: precise results on HCN up to 25 000 cm−1

Variation calculations of the vibration–rotation energy levels of many isotopomers of HCN are reported, for J=0, 1, and 2, extending up to approximately 8 quanta of each of the stretching vibrations and 14 quanta of the bending mode. The force field, which is represented as a polynomial expansion in Morse coordinates for the bond stretches and even powers of the angle bend, has been refined by least squares to fit simultaneously all observed data on the Σ and Π state vibrational energies, and the Σ state rotational constants, for both HCN and DCN. The observed vibrational energies are fitted to roughly ±0.5 cm−1, and the rotational constants to roughly ±0.0001 cm−1. The force field has been used to predict the vibration rotation spectra of many isotopomers of HCN up to 25 000 cm−1. The results are consistent with the axis‐switching assignments of some weak overtone bands reported recently by Jonas, Yang, and Wodtke, and they also fit and provide the assignment for recent observations by Romanini and Lehmann of very weak absorption bands above 20 000 cm−1.

The two-dimensional anharmonic oscillator I: vibration-rotation constants of fulminic acid, HCNO

The lowest-wavenumber vibration of HCNO and DCNO, ν5, is known to involve a largeamplitude low-frequency anharmonic bending of the CH bond against the CNO frame. In this paper the anomalous vibrational dependence of the observed rotational constants B(v5, l5), and of the observed l-doubling interactions, is interpreted according to a simple effective vibration-rotation Hamiltonian in which the appropriate vibrational operators are averaged in an anharmonic potential surface over the normal coordinates (Q5x, Q5y). All of the data on both isotopes are interpreted according to a single potential surface having a minimum energy at a slightly bent configuration of the HCN angle ( 170°) with a maximum at the linear configuration about 2 cm−1 higher. The other coefficients in the Hamiltonian are also interpreted in terms of the structure and the harmonic and anharmonic force fields; the substitution structure at the “hypothetical linear configuration” determined in this way gives a CH bond length of 1.060 Å, in contrast to the value 1.027 Å determined from the ground-state rotational constants. We also discuss the difficulties in rationalizing our effective Hamiltonian in terms of more fundamental theory, as well as the success and limitations of its use in practice.

The harmonic force field and rz structure of HNCO

The presently available microwave, millimeter wave, and far-infrared data of five isotopic species of isocyanic acid, namely, HNCO, H15NCO, HN13CO, HNC18O, and DNCO, have been used to obtain improved values of the ground-state rotational constants, the five quartic distortion constants, and some higher-order distortion constants in the Ir S reduced Hamiltonian of Watson. The appropriate planarity relation among the quartic centrifugal distortion constants has been imposed in the fitting procedure. The general harmonic force field of isocyanic acid has been determined using all existing data, and assuming a trans bent equilibrium geometry of the molecule with an NCO angle of 170°. Finally an rz structure has been obtained using the Az, Bz, and Cz rotational constants of five isotopic species. The bending of the NCO chain is found to be 8° in the trans configuration.

Vibration-rotation spectra of 13C containing acetylene: anharmonic resonances

High resolution vibration-rotation spectra of 13C2H2 were recorded in a number of regions from 2000 to 5200 cm−1 at Doppler or pressure limited resolution. In these spectral ranges cold and hot bands involving the bending-stretching combination levels have been analyzed up to high J values. Anharmonic quartic resonances for the combination levels ν1 + mν4 + nν5, ν2 + mν4 + (n + 2) ν5 and ν3 + (m − 1) ν4 + (n + 1) ν5 have been studied, and the l-type resonances within each polyad have been explicitly taken into account in the analysis of the data. The least-squares refinement provides deperturbed values for band origins and rotational constants, obtained by fitting rotation lines only up to J ≈ 20 with root mean square errors of ≈ 0.0003 cm−1. The band origins allowed us to determine a number of the anharmonicity constants xij0.

Vibrational Renner-Teller effects in the infrared spectrum of carbonsuboxide

The infrared spectrum of carbon suboxide has been recorded with a resolution of 0•01cm-1 from 400 to 700 cm-1. The region from 530 to 570 cm-1 shows intense absorption due to the v6(Πu) band system, of which the fundamental band only has been assigned and analysed, giving v6=540•221 cm-1. The region 590 to 660 cm-1 shows weaker absorption due to the v5(Πg) band system appearing in combination with odd quanta of the v7(Πu) fundamental at 18 cm-1. The v5 + v7 band and several hot bands have been assigned and analysed, and the effective v7 bending potential in the v5 state has been deduced. This potential shows a splitting as the large amplitude bending coordinate q7 is displaced due to interaction between v5 and v7 analogous to the Renner-Teller effect in electronic spectroscopy. This splitting is about 4 cm-1 for the classical turning points in q7 and the mean q7 bending potential is closely similar to that in the ground state.

The infrared spectrum, equilibrium structure and harmonic and anharmonic force field of thioborine, HBS

Infrared spectra of the two stretching fundamentals of both HBS and DBS have been observed, using a continuous flow system through a multiple reflection long path cell at a pressure around 1 Torr and a Nicolet Fourier Transform spectrometer with a resolution of about 0•1 cm-1. The v3 BS stretching fundamental of DBS, near 1140 cm-1, is observed in strong Fermi resonance with the overtone of the bend 2v2. The bending fundamental v2 has not been observed and must be a very weak band. The analysis of the results in conjunction with earlier work gives the equilibrium structure (re(BH) = 1•1698(12) , re(BS) = 1•5978(3) ) and the harmonic and anharmonic force field.

Quartic anharmonic resonances in acetylene molecules

Formulas are derived for the quartic anharmonic resonance coefficients observed to be important between C–H stretching and the combination of one quantum of C≡C stretching and two quanta of H–C≡C bending in a number of acetylene molecules. Examples of this resonance are ν3 with ν2+ν4+ν5 in 12C2H2, ν1 with ν2+2ν5 in 13C2H2, and ν1 with ν2+2ν4 in monofluoroacetylene and monochloroacetylene. The coefficients characterizing the resonances in these examples, which we denote K3,245, K1,255, and K1,244, arise from cubic and quartic terms in the anharmonic force field, in the normal coordinate representation, through second order and first order perturbation treatments respectively, where the second order resonances are calculated by a Van Vleck resonance formalism. The experimentally determined values of these coefficients are compared with values calculated from model anharmonic force fields.

The calculation of force constants and normal co-ordinates--VII Normal co-ordinates in the E species of allene

Force constant and normal co-ordinate calculations are reported for the E species vibrations of the allene molecule. Data on the fundamental vibration frequencies of allene-h4, allene-d4 and allene-1.1-d2 and on the five experimentally determined Coriolis zeta constants of C3H4 and C3D4, were used in a force constant refinement procedure. Allowing for product and sum rules this gives 21 independent data which were used to refine to the most general harmonic force field (10 parameters) with one constraint (in the absence of any constraints the refinement was not satisfactory). The results have been used to calculate the complete ζz Coriolis interaction matrix for the allene-1.1-d2 molecule, and hence to calculate the expected rotational structure of the perpendicular bending vibrations of this molecule; the good agreement obtained with the observed spectra is a check on our results.

Analysis of the SDS−Lysozyme binding isotherm

A scheme to describe SDS−lysozyme complex formation has been proposed on the basis of isothermal titration calorimetry (ITC) and FTIR spectroscopy data. ITC isotherms are convoluted and reveal a marked effect of both SDS and lysozyme concentration on the stoichiometry of the SDS−lysozyme complex. The binding isotherms have been described with the aid of FTIR spectroscopy in terms of changes in the lysozyme structure and the nature of the SDS binding. At low SDS concentrations, ITC isotherms feature an exothermic region that corresponds to specific electrostatic binding of SDS to positively charged amino acid residues on the lysozyme surface. This leads to charge neutralization of the complex and precipitation. The number of SDS molecules that bind specifically to lysozyme is approximately 8, as determined from our ITC isotherms, and is independent of lysozyme solution concentration. At high SDS concentrations, hydrophobic cooperative association dominates the binding process. Saturated binding stoichiometries as a molar ratio of SDS per molecule of lysozyme range from 220:1 to 80:1, depending on the lysozyme solution concentration. A limiting value of 78:1 has been calculated for lysozyme solution concentrations above 0.25 mM.

Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein

Conserved among all coronaviruses are four structural proteins: the matrix (M), small envelope (E), and spike (S) proteins that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in the lumen. The N-terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding, while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C terminus of the N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17 A (monoclinic) and at 1.85 A (cubic), respectively, resolved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the beta-sheet core. The functionally important positively charged beta-hairpin protrudes out of the core, is oriented similarly to that in the IBV N-NTD, and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggests a common mode of RNA recognition, but they probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs suggests that they use different modes of both RNA recognition and oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Molecular structures of 3-hydroxybenzoic acid and 4-hydroxybenzoic acid, obtained by gas-phase electron diffraction and theoretical calculations

The structures of 3-hydroxybenzoic acid and 4-hydroxybenzoic acid have been determined by gas-phase electron diffraction using results from quantum chemical calculations to inform the choice of restraints applied to some of the structural parameters. The results from the study presented here demonstrate that resonance hybrids are not as helpful in rationalizing the structures of 2-, 3-, and 4-hydroxybenzoic acids as are models based upon electrostatic effects.