Relativistic effects in physics and chemistry of element 105. [Part] II.

Relativistic self-consistent charge Dirac-Slater discrete variational method calculations have been done for the series of molecules MBr_5, where M = Nb, Ta, Pa, and element 105, Ha. The electronic structure data show that the trends within the group 5 pentabromides resemble those for the corresponding pentaclorides with the latter being more ionic. Estimation of the volatility of group 5 bromides has been done on the basis of the molecular orbital calculations. According to the results of the theoretical interpretation HaBr_5 seems to be more volatile than NbBr_5 and TaBr_5.

Relativistic effects in physics and chemistry of element 105. [Part] III.

Electronic structures of MOCl_3 and MOBr_3 molecules, where M = V, Nb, Ta, Pa, and element 105, hahnium, have been calculated using the relativistic Dirac-Slater discrete variational method. The character of bonding has been analyzed using the Mulliken population analysis of the molecular orbitals. It was shown that hahnium oxytrihalides have similar properties to oxytrihalides of Nb and Ta and that hahnium has the highest tendency to form double bond with oxygen. Some peculiarities in the electronic structure of HaOCl_3 and HaOBr_3 result from relativistic effects. Volatilities of the oxytrihalides in comparison with the corresponding pentahalides were considered using results of the present calculations. Higher ionic character and lower covalency as well as the presence of dipole moments in MOX_3 (X = Cl, Br) molecules compared to analogous MX_5 ones are the factors contributing to their lower volatilities.

Relativistic calculations of atomic structure

A review of relativistic atomic structure calculations is given with a emphasis on the Multiconfigurational-Dirac-Fock method. Its problems and deficiencies are discussed together with the contributions which go beyond the Dirac-Fock procedure.

Relativistic atomic level calculations with nuclei carrying additional fractional charges

One-electron energy levels and wavelengths have been calculated for Na-like ions whose nuclei carry quarks with additional charges ±e/3, ±2e/3. The calculations are based on relativistic self-consistent field procedures. The deviations from experimental values exhibit regularities which allow an extrapolation for the wavelengths of 3s - 3p, 3s - 4p, 3p - 3d, and 3p - 4s transitions for the nuclear charge Z = 11± 1/3, ±2/3. A number of transitions are found in the region of visible light which could be used in an optical search for quark atoms.

Ionization potentials and radii of atoms and ions of element 104 (unnilquadium) and of hafnium (2+) derived from multiconfiguration Dirac-Fock calculations

Multiconfiguration relativistic Dirac-Fock (MCDF) values have been computed for the first four ionization potentials (IPs) of element 104 (unnilquadium) and of the other group 4 elements (Ti, Zr, and Hf). Factors were calculated that allowed correction of the systematic errors between the MCDF IPs and the experimental IPs. Single "experimental" IPs evaluated in eV (to ± 0.1 eV) for element 104 are: [104(0),6.5]; [104( 1 + ),14.8]; [104(2 + ),23.8]; [104(3 + ),31.9]. Multiple experimental IPs evaluated in eV for element 104 are: [(0-2+ ),21.2±0.2]; [(0-3+ ),45.1 ±0.2]; [(0-4+ ),76.8±0.3].Our MCDF results track 11 of the 12 experimental single IPs studied for group 4 atoms and ions. The exception is Hf( 2 + ). We submit our calculated IP of 22.4 ± 0.2 eV as much more accurate than the value of 23.3 eV derived from experiment.

Ionization potentials and radii of atoms and ions of element 105 (unnilpentium) and ions of tantalum derived from multiconfiguration Dirac-Fock calculations

Multiconfiguration relativistic Dirac-Fock (MCDF) values were calculated for the first five ionization potentials of element 105 (unnilpentium) and of the other group 5b elements (V, Nb, and Ta). Some of these ionization potentials in electron volts (eV) with uncertainties are: 105(0), 7.4±0.4; 105(1 +), 16.3 ±0.2; 105(2 +), 24.3 ± 0.2; 105(3 + ), 34.9 ± 0.5; and 105(4 + ), 44.9 ± 0.1. Ionization potentials for Ta(1+), Ta(2 +), and Ta(3 + ) were also calculated. Accurate experimental values for these ionization potentials are not available. Ionic radii are presented for the 2+, 3+, 4 +, and 5+ ions of element 105 and for the + 2 ions of vanadium and niobium. These radii for vanadium and niobium are not available elsewhere. The ionization potentials and ionic radii obtained are used to determine some standard electrode potentials for element 105. Born-Haber cycles and a form of the Born equation for the Gibbs free energy of hydration of ions were used to calculate the standard electrode potentials.

Counterpoise-corrected geometries and harmonic frequencies of N-body clusters: application to (HF)n (n=3,4)

A study was conducted on the methods of basis set superposition error (BSSE)-free geometry optimization and frequency calculations in clusters larger than a dimer. In particular, three different counterpoise schemes were critically examined. It was shown that the counterpoise-corrected supermolecule energy can be easily obtained in all the cases by using the many-body partitioning of energy

Sampling uncertainties in surface radiation budget calculations in RADAGAST

In the Radiative Atmospheric Divergence Using ARM Mobile Facility GERB and AMMA Stations (RADAGAST) project we calculate the divergence of radiative flux across the atmosphere by comparing fluxes measured at each end of an atmospheric column above Niamey, in the African Sahel region. The combination of broadband flux measurements from geostationary orbit and the deployment for over 12 months of a comprehensive suite of active and passive instrumentation at the surface eliminates a number of sampling issues that could otherwise affect divergence calculations of this sort. However, one sampling issue that challenges the project is the fact that the surface flux data are essentially measurements made at a point, while the top-of-atmosphere values are taken over a solid angle that corresponds to an area at the surface of some 2500 km2. Variability of cloud cover and aerosol loading in the atmosphere mean that the downwelling fluxes, even when averaged over a day, will not be an exact match to the area-averaged value over that larger area, although we might expect that it is an unbiased estimate thereof. The heterogeneity of the surface, for example, fixed variations in albedo, further means that there is a likely systematic difference in the corresponding upwelling fluxes. In this paper we characterize and quantify this spatial sampling problem. We bound the root-mean-square error in the downwelling fluxes by exploiting a second set of surface flux measurements from a site that was run in parallel with the main deployment. The differences in the two sets of fluxes lead us to an upper bound to the sampling uncertainty, and their correlation leads to another which is probably optimistic as it requires certain other conditions to be met. For the upwelling fluxes we use data products from a number of satellite instruments to characterize the relevant heterogeneities and so estimate the systematic effects that arise from the flux measurements having to be taken at a single point. The sampling uncertainties vary with the season, being higher during the monsoon period. We find that the sampling errors for the daily average flux are small for the shortwave irradiance, generally less than 5 W m−2, under relatively clear skies, but these increase to about 10 W m−2 during the monsoon. For the upwelling fluxes, again taking daily averages, systematic errors are of order 10 W m−2 as a result of albedo variability. The uncertainty on the longwave component of the surface radiation budget is smaller than that on the shortwave component, in all conditions, but a bias of 4 W m−2 is calculated to exist in the surface leaving longwave flux.

The microwave spectrum of thietan-2,2,4,4-d4

The microwave spectrum for thietan-2,2,4,4-d4 is analysed in six of its lowest puckering states and up to J = 25. The close lying pairs of states of vp = 0/1, 2/3 and 4/5 are treated with a vibration-rotation hamiltonian which includes an off-diagonal coupling term in vp. Additional corrections to this coupling term in higher powers of the angular momentum operator are derived and their importance for improving the fit of calculated to observed data is tested. The variation of the centrifugal distortion constants with vp follows the model of Creswell and Mills (1974, J. molec. Spectrosc., 52, 392). A value is determined for the derivative with respect to the puckering coordinate of the ac-component of the inverse moment of inertia tensor.

The molecular structure of hexamethyldigermane determined by gas-phase electron diffraction with theoretical calculations for (CH3)3M-M(CH3)3 Where M = C, Si, and Ge

Gas-phase electron diffraction (GED) data together with results from ab initio molecular orbital calculations (HF and MP2/6-311+G(d,p)) have been used to determine the structure of hexamethyldigermane ((CH3)3Ge-Ge(CH3)3). The equilibrium symmetry is D3d, but the molecule has a very low-frequency, largeamplitude, torsional mode (φCGeGeC) that lowers the thermal average symmetry. The effect of this largeamplitude mode on the interatomic distances was described by a dynamic model which consisted of a set of pseudoconformers spaced at even intervals. The amount of each pseudoconformer was obtained from the ab initio calculations (HF/6-311+G(d,p)). The results for the principal distances (ra) and angles (∠h1) obtained from the combined GED/ab initio (with estimated 1σ uncertainties) are r(Ge-Ge) ) 2.417(2) Å, r(Ge-C) ) 1.956(1) Å, r(C-H) ) 1.097(5) Å, ∠GeGeC ) 110.5(2)°, and ∠GeCH ) 108.8(6)°. Theoretical calculations were performed for the related molecules ((CH3)3Si-Si(CH3)3 and (CH3)3C-C(CH3)3).

DNA interaction and phosphotransfer of the C-4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli

The DcuS-DcuR system of Escherichia coli is a two-component sensor-regulator that controls gene expression in response to external C-4-dicarboxylates and citrate. The DcuS protein is particularly interesting since it contains two PAS domains, namely a periplasmic C-4-dicarboxylate-sensing PAS domain (PASp) and a cytosolic PAS domain (PASc) of uncertain function. For a study of the role of the PASc domain, three different fragments of DcuS were overproduced and examined: they were PASc-kinase, PASc, and kinase. The two kinase-domain-containing fragments were autophosphorylated by [gamma-P-32]ATP. The rate was not affected by fumarate or succinate, supporting the role of the PASp domain in C-4-dicarboxylate sensing. Both of the phosphorylated DcuS constructs were able to rapidly pass their phosphoryl groups to DcuR, and after phosphorylation, DcuR dephosphorylated rapidly. No prosthetic group or significant quantity of metal was found associated with either of the PASc-containing proteins. The DNA-binding specificity of DcuR was studied by use of the pure protein. It was found to be converted from a monomer to a dimer upon acetylphosphate treatment, and native polyacrylamide gel electrophoresis suggested that it can oligomerize. DcuR specifically bound to the promoters of the three known DcuSR-regulated genes (dctA, dcuB, and frdA), with apparent K(D)s of 6 to 32 muM for untreated DcuR and less than or equal to1 to 2 muM for the acetylphosphate-treated form. The binding sites were located by DNase I footprinting, allowing a putative DcuR-binding motif [tandemly repeated (T/A)(A/T)(T/C)(A/T)AA sequences] to be identified. The DcuR-binding sites of the dcuB, dctA, and frdA genes were located 27, 94, and 86 bp, respectively, upstream of the corresponding +1 sites, and a new promoter was identified for dcuB that responds to DcuR.

Molecular structure of 2,5-dihydropyrrole (C4NH7), obtained by gas-phase electron diffraction and theoretical calculations

The structure of 2,5-dihydropyrrole (C4NH7) has been determined by gas-phase electron diffraction (GED), augmented by the results from ab initio calculations employing third-order Moller-Plesset (MP3) level of theory and the 6-311+G(d,p) basis set. Several theoretical calculations were performed. From theoretical calculations using MP3/6-311+G(d,p) evidence was obtained for the presence of an axial (63%) (N-H bond axial to the CNC plane) and an equatorial conformer (37%) (N-H bond equatorial to the CNC plane). The five-membered ring was found to be puckered with the CNC plane inclined at 21.8 (38)° to the plane of the four carbon atoms.

Molecular structures of benzoic acid and 2-hydroxybenzoic acid, obtained by gas-phase electron diffraction and theoretical calculations

The structures of benzoic acid (C6H5COOH) and 2-hydroxybenzoic acid (C6H4OHCOOH) have been determined in the gas phase by electron diffraction using results from quantum chemical calculations to inform restraints used on the structural parameters. Theoretical methods (HF and MP2/6-311+G(d, p)) predict two conformers for benzoic acid, one which is 25.0 kJ mol(-1) (MP2) lower in energy than the other. In the low-energy form, the carboxyl group is coplanar with the phenyl ring and the O-H group eclipses the C=O bond. Theoretical calculations (HF and MP2/6-311+ G(d, p)) carried out for 2-hydroxybenzoic acid gave evidence for seven stable conformers but one low-energy form (11.7 kJ mol-1 lower in energy (MP2)) which again has the carboxyl group coplanar with the phenyl ring, the O-H of the carboxyl group eclipsing the C=O bond and the C=O of the carboxyl group oriented toward the O-H group of the phenyl ring. The effects of internal hydrogen bonding in 2-hydroxybenzoic acid can be clearly observed by comparison of pertinent structural parameters between the two compounds. These differences for 2-hydroxybenzoic acid include a shorter exocyclic C-C bond, a lengthening of the ring C-C bond between the substituents, and a shortening of the carboxylic single C-O bond.

Metal complexes of a tetraazacyclophane: solution and molecular modelling studies

An alternative synthetic approach to yield the compound 2,3,5,6,8,9,11,14-octahydrobenzo[1][ 1,4,7,10]tetraazacyclotetradecine (bz[14]N-4) is presented. The protonation constants of bz[14]N-4 and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+, Pb2+ were determined in H2O at 25degreesC with ionic strength 0.10 mol dm(-3) in KNO3 and they were compared with structurally related macrocycles cyclam (1,4,8,11-tetraazacyclotetradecane) and cyclen (1,4,7,10-tetraazacyclododecane). These studies indicate that only 1 : 1 ( M : L) species are formed in solution, and the ligand exhibits a high affinity for larger ions such as Cd2+ and Pb2+. The X-ray study of [bz[14]N4H3](3+) shows that an inclusion compound with a chloride counter-anion is formed through NH...Cl hydrogen bonds. Spectroscopic data in solution ( electronic and NMR spectra) showed that the macrocycle adopts a planar arrangement upon metal complexation. Molecular mechanics calculations reveal that in spite of the presence of the benzene ring in the macrocyclic framework this ligand can encapsulate metal ions with different stereo-electronic sizes in square planar arrangements. Our results indicate that the presence of the benzene ring in the backbone of the bz[14]N-4 confers a coordination behaviour intermediate between that of cyclam and cyclen.