Wolfram W. Rudolph

Raman spectroscopic investigation of speciation in MgSO4(aq)

Careful measurements have been made of the Raman spectra of aqueous solutions of Mg(ClO4)2, MgCl2, (NH4)2SO4 and MgSO4 down to 50 cm−1 and, in some cases, to extremely low concentrations (≥0.06 mmol kg−1) and high temperatures (≤200 °C). In MgSO4(aq), the well known asymmetry in the ν1-SO42− mode at ∼980 cm−1 that develops with increasing concentration has been assigned to a mode at 993 cm−1 associated with the formation of an MgOSO3 contact ion pair (CIP). Confirmation of this assignment is provided by the simultaneous and quantitative appearance of stretching modes for the Mg–OSO3 bond of the ligated SO42− at 245 cm−1 and for the (H2O)5MgOSO3 unit at 328 cm−1. The CIP becomes the dominant species at higher temperatures. Alternative explanations of the broadening of the ν1-SO42− mode are shown to be inconsistent with this and other Raman spectral evidence such as the similarity of the ν1-SO42− mode for MgSO4 in H2O and D2O. After subtraction of the CIP component at 993 cm−1, the ν1-SO42− band in MgSO4(aq) showed systematic differences from that in (NH4)2SO4(aq). This is consistent with a previously undetected ν1-SO42− mode at 982.2 cm−1 that can be assigned to the presence of solvent-shared ion pairs (SIPs). In solutions with high Mg2+/SO42− concentration ratios, a further ν1-SO42− mode was observed at 1005 cm−1, which has been tentatively assigned to a Mg2SO42+(aq) triple ion. All of these observations are shown to be in excellent agreement with recent dielectric relaxation spectroscopy measurements. In addition, the correct relationship between the Mg2+/SO42− association constant determined by Raman spectroscopic measurements and those obtained by other techniques is derived. It is shown that thermodynamic data measured by Raman spectroscopy for systems involving other (Raman-undetected) ion-pair types in addition to CIPs, cannot and should not be compared directly with those obtained by traditional techniques.

Protein-Primed and De Novo Initiation of RNA Synthesis by Norovirus 3Dpol

ABSTRACT Noroviruses (Caliciviridae) are RNA viruses with a single-stranded, positive-oriented polyadenylated genome. To date, little is known about the replication strategy of norovirus, a so-far noncultivable virus. We have examined the initiation of replication of the norovirus genome in vitro, using the active norovirus RNA-dependent RNA polymerase (3Dpol), homopolymeric templates, and synthetic subgenomic or antisubgenomic RNA. Initiation of RNA synthesis on homopolymeric templates as well as replication of subgenomic polyadenylated RNA was strictly primer dependent. In this context and as observed for other enteric RNA viruses, i.e., poliovirus, a protein-primed initiation of RNA synthesis after elongation of the VPg by norovirus 3Dpol was postulated. To address this question, norovirus VPg was expressed in Escherichia coli and purified. Incubation of VPg with norovirus 3Dpol generated VPg-poly(U), which primed the replication of subgenomic polyadenylated RNA. In contrast, replication of antisubgenomic RNA was not primer dependent, nor did it depend on a leader sequence, as evidenced by deletion analysis of the 3′ termini of subgenomic and antisubgenomic RNA. On nonpolyadenylated RNA, i.e., antisubgenomic RNA, norovirus 3Dpol initiated RNA synthesis de novo and terminated RNA synthesis by a poly(C) stretch. Interestingly, on poly(C) RNA templates, norovirus 3Dpol initiated RNA synthesis de novo in the presence of high concentrations of GTP. We propose a novel model for initiation of replication of the norovirus genome by 3Dpol, with a VPg-protein-primed initiation of replication of polyadenylated genomic RNA and a de novo initiation of replication of antigenomic RNA.

Raman and Infrared Spectroscopic Investigations on Aqueous Alkali Metal Phosphate Solutions and Density Functional Theory Calculations of Phosphate–Water Clusters

Phosphate (PO43−) solutions in water and heavy water have been studied by Raman and infrared spectroscopy over a broad concentration range (0.0091–5.280 mol/L) including a hydrate melt at 23 °C. In the low wavenumber range, spectra in R-format have been constructed and the R normalization procedure has been briefly discussed. The vibrational modes of the tetrahedral PO43−(aq) (Td symmetry) have been assigned and compared to the calculated values derived from the density functional theory (DFT) method for the unhydrated PO43− (Td) and phosphate–water clusters: PO43− · H2O (C2v), PO43− · 2H2O (D2d), PO43− · 4H2O (D2d), PO43− · 6H2O (Td), and PO43− · 12H2O (T), a cluster with a complete first hydration sphere of water molecules. A cluster with a second hydration sphere of 12 water molecules and 6 in the first sphere, PO43− · 18H2O (T), has also been calculated. Agreement between measured and calculated vibrational modes is best in the case of the PO43− · 12H2O cluster and the PO43− · 18H2O cluster but far less so in the case of the unhydrated PO43− or phosphate–water cluster with a lower number of water molecules than 12. The asymmetric, broad band shape of ν1(a1) PO43− in aqueous solutions has been measured as a function of concentration and the asymmetric and broad band shape was explained. However, the same mode in heavy water has only half the full width at half-height compared to the mode in normal water. The PO43− is strongly hydrated in aqueous solutions. This has been verified by Raman spectroscopy comparing ν2(H2O), the deformation mode of water, and the stretching modes, the ν1OH and ν3OH of water, in K3PO4 solutions as a function of concentration and comparison with the same modes in pure water. A mode at ∼240 cm−1 (isotropic R spectrum) has been detected and assigned to the restricted translational mode of the strong hydrogen bonds formed between phosphate and water, P–O ··· HOH. In very concentrated K3PO4 solutions (C0 ≥ 3.70 mol/L) and in the hydrate melt, formation of contact ion pairs (CIPs) could be detected. The phosphate in the CIPs shows a symmetry lowering of the Td symmetry to C3v. In the less concentrated solutions, PO43−(aq) solvent separated ion pairs and doubly solvent separated ion pairs exist, while in very dilute solutions fully hydrated ions are present (C0 ≤ 0.005 mol/L). Quantitative Raman measurements have been carried out to follow the hydrolysis of PO43−(aq) over a very broad concentration range. From the hydrolysis data, the pK3 value for H3PO4 has been determined to be 12.45 at 23 °C.

Vibrational Spectroscopic Studies and Density Functional Theory Calculations of Speciation in the CO2—Water System

Raman spectra of CO2 dissolved in water and heavy water were measured at 22 °C, and the Fermi doublet of CO2, normally at 1285.45 and 1388.15 cm−1 in the gaseous state, revealed differences in normal water and heavy water, although no symmetry lowering of the hydrated CO2 could be detected. Raman spectra of crystalline KHCO3 and KDCO3 were measured at 22 °C and compared with the infrared data from the literature. In these solids, (H(D)CO3)22– dimers exist and the spectra reveal strong intramolecular coupling. The vibrational data of the dimer (C2h symmetry) were compared with the values from density functional theory (DFT) calculations and the agreement is fair. Careful measurements were made of the Raman spectra of aqueous KHCO3, and KDCO3 solutions in D2O down to 50 cm−1 and, in some cases, down to very low concentrations (≥0.0026 mol/kg). In order to complement the spectroscopic assignments, infrared solution spectra were also measured. The vibrational spectra of HCO3−(aq) and DCO3−(D2O) were assigned, and the measured data compared well with data derived from DFT calculations. The symmetry for HCO3−(aq) is C1, while the gas-phase structure of HCO3− possesses Cs symmetry. No dimers could be found in aqueous solutions, but at the highest KHCO3 concentration (3.270 mol/kg) intermolecular coupling between HCO3−(aq) anions could be detected. KHCO3 solutions do not dissolve congruently, and with increasing concentrations of the salt increasing amounts of carbonate could be detected. Raman and infrared spectra of aqueous Na2 –, K2 –, and Cs2CO3 solutions in water and heavy water were measured down to 50 cm−1 and in some cases down to extremely low concentrations (≥0.002 mol/kg) and up to the saturation state. For carbonate in aqueous solution a symmetry breaking of the D3h symmetry could be detected similar to the situation in aqueous nitrate solutions. Strong hydration of carbonate in aqueous solution could be detected by Raman spectroscopy. The hydrogen bonds between carbonate in heavy water are stronger than the ones in normal water. In sodium and potassium carbonate solutions no contact ion pairs could be detected even up to the saturated solutions. However, solvent separated ion pairs were inferred in concentrated solutions in accordance with recent dielectric relaxation spectroscopy (DRS) measurements. Quantitative Raman measurements of the hydrolysis of carbonate in aqueous K2CO3 solutions were carried out and the hydrolysis degree a was determined as a function of concentration at 22 °C. The second dissociation constant, pK2, of the carbonic acid was determined to be equal to 10.38 at 22 °C.

Aluminium(III) hydration in aqueous solution. A Raman spectroscopic investigation and an ab initio molecular orbital study of aluminium(III) water clusters

Raman spectra of aqueous Al(III) chloride, nitrate, and perchlorate solutions were measured over a broad concentration (0.21–3.14 mol L−1) and temperature (25–125°C) range. The weak, polarized band at 525 cm−1 and two depolarized modes at 438 and 332 cm−1 have been assigned to ν1(a1g), ν2(eg) and ν5(f2g) of the hexaaquaaluminium(III) ion, respectively. The IR-active mode at 598 cm−1 has been assigned to ν3(f1u). The vibrational analysis of the species [Al(OH2)63+] was done on the basis of Oh symmetry (OH2 as point mass). The polarized mode ν1(a1g) AlO6 has been followed over the full temperature range and band parameters (band maximum, full width at half height and band intensity) have been examined. The position of the ν1(a1g) AlO6 mode shifts only about 3 cm−1 to lower frequencies and broadens about 20 cm−1 for a 100°C temperature increase. The Raman spectroscopic data suggest that the hexaaquaaluminium(III) ion is thermodynamically stable in chloride, nitrate and perchlorate solutions over the temperature and concentration range measured. No inner-sphere complexes in these solutions could be detected spectroscopically. Aluminium sulfate solutions show a different picture and thermodynamically stable aluminium sulfato complexes could be detected. The sulfato complexes are entropically driven, so that their formation is favoured at higher temperatures. Ab initio geometry optimizations and frequency calculations of [Al(OH2)63+] were carried out at the Hartree–Fock and second-order Moller–Plesset levels of theory, using various basis sets up to 6-31 + G*. The global minimum structure of the hexaaqua Al(III) species corresponds to symmetry Th. The unscaled vibrational frequencies of the [Al(OH2)63+] were reported. The unscaled vibrational frequencies of the AlO6 unit are lower than the experimental frequencies (ca. 15%), but scaling the frequencies reproduces the measured frequencies. The theoretical binding enthalpy for [Al(OH2)63+] was calculated and accounts for ca. 64% of the experimental single ion hydration enthalpy for Al(III). Ab initio geometry optimizations and frequency calculations are also reported for the [Al(OH2)183+] (Al[6 + 12]) cluster with 6 water molecules in the first sphere and 12 water molecules in the second sphere. The global minimum corresponds to T symmetry. Calculated frequencies of the aluminium [6 + 12] cluster correspond with the observed frequencies in solution. The ν1 AlO6 (unscaled, HF/6-31G*) mode occurs at 542 cm−1, in fair agreement with the experimental value. The theoretical binding enthalpy for [Al(OH2)183+] was calculated and is a slightly underestimate of the experimental single ion hydration enthalpy for Al(III). The water molecules of the first sphere form strong H-bonds with water molecules in the second hydration shell because of the strong polarizing effect of the Al(III) ion.

Zinc(II) hydration in aqueous solution. A Raman spectroscopic investigation and an ab-initio molecular orbital study

Raman spectra of aqueous Zn(II) perchlorate solutions were measured over a broad concentration (0.50–3.54 mol L-1) and temperature (25–120°C) range. The weak polarized band at 390 cm-1 and two depolarized modes at 270 and 214 cm-1 have been assigned to ν1(a1g), ν2(eg) and ν5(f2g) of the hexaaquazinc(II) ion, respectively. The infrared active mode at 365 cm-1 has been assigned to ν3(f1u). The vibrational analysis of the species [Zn(OH2)62+] was done on the basis of Oh symmetry (OH2 as point mass). The polarized mode ν1(a1g) ZnO6 has been followed over the full temperature range and band parameters (band maximum, full width of half height and band intensity) have been examined. The position of the ν1(a1g) ZnO6 mode shifts only about 4 cm-1 to lower frequencies and broadens about 32 cm-1 for a 95°C temperature increase. The Raman spectroscopic data suggest that the hexaaquazinc(II) ion is thermodynamically stable in perchlorate solution over the temperature and concentration range measured. Abinitio geometry optimizations and frequency calculations of [Zn(OH2)62+] were carried out at the Hartree–Fock and second order Moller–Plesset levels of theory, using various basis sets up to 6-31+G*. The global minimum structure of the hexaaqua Zn(II) species corresponds with symmetry Th. The unscaled vibrational frequencies of the [Zn(OH2)62+] were reported. The unscaled vibrational frequencies of the ZnO6 unit are lower than the experimental frequencies (ca. 15%), but scaling the frequencies reproduces the measured frequencies. The theoretical binding enthalpy for [Zn(OH2)62+] was calculated and accounts for ca. 64% of the experimental single ion hydration enthalpy for Zn(II). Abinitio geometry optimizations and frequency calculations are also reported for a [Zn(OH2)182+] (Zn[6+12]) cluster with 6 water molecules in the first sphere and 12 water molecules in the second sphere. The global minimum corresponds with T symmetry. Calculated frequencies of the zinc [6+12] cluster correspond well with the observed frequencies in solution. The ν1 ZnO6 (unscaled) mode occurs at 389 cm-1 in good agreement with the experimental value. The theoretical binding enthalpy for [Zn(OH2)182+] was calculated and is very close to the experimental single ion hydration enthalpy for Zn(II). The water molecules of the first sphere form strong H-bonds with water molecules in the second hydration shell because of the strong polarizing effect of the Zn(II) ion. The importance of the second hydration sphere is discussed.

Feline Foamy Virus Genome and Replication Strategy

ABSTRACT Crucial aspects of the foamy virus (FV) replication strategy have so far only been investigated for the prototypic FV (PFV) isolate, which is supposed to be derived from nonhuman primates. To study whether the unusual features of this replication pathway also apply to more-distantly related FVs, we constructed feline FV (FFV) infectious molecular clones and vectors. It is shown by quantitative RNA and DNA PCR analysis that FFV virions contain more RNA than DNA. Full-length linear DNA was found in extracellular FFV by Southern blot analysis. Similar to PFV, azidothymidine inhibition experiments and the transfection of nucleic acids extracted from extracellular FFV indicated that DNA is the functional relevant FFV genome. Unlike PFV, no evidence was found indicating that FFV recycles its DNA into the nucleus.

Indium(III) hydration in aqueous solutions of perchlorate, nitrate and sulfate. Raman and infrared spectroscopic studies and ab-initio molecular orbital calculations of indium(III)–water clusters

Raman and infrared spectra of aqueous In3+-perchlorate, -nitrate and -sulfate solutions were measured as a function of concentration and temperature. Raman spectra of In3+ perchlorate solutions reveal a strongly polarized mode of medium to strong intensity at 487 cm−1 and two broad, depolarized modes at 420 cm−1 and 306 cm−1 of much lesser intensity. These modes have been assigned to ν1(a1g), ν2(eg) and ν5(f2g) of the hexaaquaindium(III) ion, [In(OH2)63+] (Oh symmetry), respectively. The infrared active mode at 472 cm−1 has been assigned to ν3(f1u). The Raman spectra suggest that [In(OH2)63+] is stable in acidified perchlorate solutions, with no inner-sphere complex formation or hydroxo species formed over the concentration range measured. In concentrated In(NO3)3 solutions, In3+ can exist in form of both an inner-sphere complex, [In(OH2)5ONO2]2+ and an outer-sphere complex [In(OH2)63+·NO3−]. Upon dilution the inner-sphere complex dissociates and the amount of the outer-sphere complex increases. In dilute solutions the cation, [In(OH2)63+], exists together with free nitrate. In indium sulfate solutions, a stable In3+ sulfato complex could be detected using Raman spectroscopy and 115-In NMR. Sulfato complex formation is favoured with increase in temperature and thus is entropically driven. At temperatures above 100 °C a basic In3+ sulfate, In(OH)SO4 is precipitated and characterised by wet chemical analysis and X-ray diffraction. Ab initio geometry optimizations and frequency calculations of [In(OH2)n3+] clusters (n = 1–6) were carried out at the Hartree–Fock and second order Moller–Plesset levels of theory, using various basis sets up to 6-31+G*. The global minimum structure of the aqua In3+ species was reported. The unscaled vibrational frequencies of the [In(OH2)63+] cluster do not correspond well with experimental values because of the missing second hydration sphere. The theoretical binding enthalpy for [In(OH2)63+] accounts for ca. 60% of the experimental single ion hydration enthalpy for In3+. Calculations are reported for the [In(OH2)183+] cluster (In[6 + 12]) with two full hydration spheres (T symmetry), for which the calculated ν1(InO6) mode occurs at 483 cm−1 (HF/6-31G*), which is in good agreement with the experimental value at 487 cm−1, as are the other frequencies. The theoretical binding enthalpy for [In(OH2)183+] was calculated and underestimates by about 15% the experimental single ion hydration enthalpy of In3+.

Raman- and infrared-spectroscopic investigations of dilute aqueous phosphoric acid solutions

Phosphoric acid in water and heavy water has been studied by Raman and infrared spectroscopy over a broad concentration range (0.00873-1.560 mol kg(-1)) at 23 °C. The vibrational modes of the PO(4) skeleton (C(3v) symmetry) of H(3)PO(4)(aq) and D(3)PO(4)(D(2)O) have been assigned. In addition to the P-O stretching modes a deformation mode has been detected, δPO-H(D) at 1250 and 935 cm(-1), respectively. In addition to the modes of the phosphoric acid and heavy phosphoric acid a mode of the dissociation product H(2)PO(4)(-) and D(2)PO(4)(-) has been detected at 1077 cm(-1) and 1084 cm(-1) respectively. H(3)PO(4) and D(3)PO(4) is hydrated in aqueous solution which could be verified by Raman spectroscopy following the νP[double bond, length as m-dash]O and ν(s)P(OH)(3) mode as a function of temperature. These modes show a pronounced temperature dependence inasmuch as νP[double bond, length as m-dash]O shifts to higher wavenumbers with temperature increase and ν(s)P(OH)(3) to lower wavenumbers. In the range between 300-600 cm(-1) the deformation modes have been observed. In very dilute H(3)PO(4) solutions however, the dissociation product is the dominant species. The dissociation degree, α for H(3)PO(4)(aq) and D(3)PO(4)(D(2)O) as a function of dilution has been measured at 23 °C. In these dilute H(3)PO(4)(aq) and D(3)PO(4)(D(2)O) solutions no spectroscopic features for a dimeric species of the formula H(6)P(2)O(8) and D(6)P(2)O(8) could be detected. Quantitative Raman measurements have been carried out to follow the dissociation of H(3)PO(4) and D(3)PO(4) over a very broad concentration range and also as a function of temperature. From the dissociation data, the pK(1) value for H(3)PO(4) has been determined to 2.14(1) and for D(3)PO(4) to 2.42(1) at 23 °C. In the temperature interval from 24.5 to 99.7 °C the pK(1) values for H(3)PO(4)(aq) have been determined and thermodynamic data have been derived.

Synthetic alunites of the potassium-oxonium solid solution series and some other members of the group: synthesis, thermal and X-ray characterization

Stoichiometric end-member alunites of the general formula (A)Al3(SO4)2(OH)6, with A = Na+, K+, Rb+, H3O+, and NH4+ have been synthesized under hydrothermal conditions together with samples of the potassium-oxonium solid solution series over the entire compositional range. A basic gallium sulfate of the alunite type was also synthesized and compared with the oxonium alunite structure. These alunites were characterized by chemical methods, thermal analysis (TA), and powder X-ray diffraction (XRD). The stages of thermal decomposition of these alunites show a common decomposition mechanism for all end-members (two main endothermic decomposition stages). Potassium and rubidium alunite show an additional exothermic step directly in front of the large second endothermic step. The thermogravimetric results confirmed the analytical results on the end-member alunites and reinforce these as synthetic stoichiometric alunites. Alunite, the pure potassium end-member, shows the highest decomposition temperature (490°C) while Na-alunite (480°C) and rubidium alunite (420°C) are less stable followed by ammonium alunite (350°C) and oxonium alunite (200°C). The thermal stability for the members of the solid solution series (H3O)1-XKXAl3(SO4)2(OH) 6 has also been deduced from the thermal analysis. Alunites with different monovalent cations in A site ( i. e. Na+, K+, Rb+, H3O+ and NH4+) are described and the unit-cell parameters for the rhombohedral space group R 3 m (# 166) with hexagonal cell dimensions a and c were determined. The c parameter increases with increasing effective ionic radius of cation in the A site, whereas the a parameter changes to a much lesser degree. The effects of substitution on the unit-cell parameters are rationalized in terms of the structural arrangements of alunite structure. The unit-cell parameters of the basic gallium sulfate have been determined and compared with the unit-cell parameters of oxonium alunite.