A Raman spectroscopic and ab initio investigation of aqueous boron speciation under alkaline hydrothermal conditions: evidence for the structure and thermodynamic stability of the diborate ion.

Raman spectra of aqueous sodium borate solutions, with and without excess NaOH, NaCl, and LiCl, have been obtained from perpendicular and parallel polarization measurements acquired using a custom-built sapphire flow cell over the temperature range 25 to 300 °C at 20 MPa. The solvent-corrected reduced isotropic spectra include a large well-defined band at 865 cm-1 which overlaps with the boric acid B(OH)3 band at 879 cm-1, and becomes increasingly intense at elevated temperatures. This band does not correspond to the spectrum of any other previously reported aqueous polyborate ions, all of which have symmetric stretching bands at frequencies below that of borate, [B(OH)4]-, at 745 cm-1. Based on the classic high-temperature potentiometric titration study by R. E. Mesmer, C. F. Baes and F. H. Sweeton, Acidity measurements at elevated temperatures. VI. Boric acid equilibriums, Inorg. Chem., 1972, 11, 537-543, the new band was postulated to arise from a diborate ion, [B2(OH)7]- or [B2O(OH)5]-. Ab initio density functional theory (DFT), together with chemical modelling studies, suggest that it is most likely [B2(OH)7]-. Thermodynamic formation quotients derived from the peak areas showed variations with ionic strength as well as charge-balance discrepancies, which suggest one or more unidentified minor equilibrium species may also be present. The most likely candidate is the divalent diborate species [B2O2(OH)4]2- which is also predicted to have a band near 865 cm-1 and is postulated to be present as a sodium ion pair. These are the first quantitative Raman spectra ever reported for borate-rich solutions under such conditions and provide the first spectroscopic evidence of a diborate species at PWR reactor coolant temperatures.

Bio-physical and computational studies on serum albumin / target protein binding of a potential anti-cancer agent.

The successful evolution of an effective drug depends on its pharmacokinetics, efficiency and safety and these in turn depend on the drug-target/drug-carrier protein binding. This work, deals with the interaction of a pyridine derivative, 2-hydroxy-5-(4-methoxyphenyl)-6-phenylpyridine 3-carbonitrile (HDN) with serum albumins at physiological conditions utilizing the steady state and time-resolved fluorescence techniques by probing the emission behavior of Trp in BSA and HSA. In-silico studies revealed a combined static and dynamic quenching mechanism for the interactions. The binding studies suggests a spontaneous binding between HDN and the albumins with a moderate binding affinity (Kb ∼ 10-5 M-1) with a single class of binding site. The FRET mediated emission from HDN indicates preferential binding of HDN in subdomain IIA of the albumins with Trp residue in close proximity. Circular dichroism results indicate HDN induced conformational changes for BSA and HSA, but the α-helical secondary structure was well preserved even up to a concentration of 10 µM HDN. Moderate binding affinity of HDN with BSA and HSA and the unaltered secondary structure of proteins on binding propose the potential application of HDN as an efficient drug. The application of docking method on the affinity of HDN towards the proposed target/receptor is discussed.

Second Dissociation Constant of Carbonic Acid in H2O and D2O from 150 to 325 °C at p = 21 MPa Using Raman Spectroscopy and a Sapphire-Windowed Flow Cell.

Solvent-corrected reduced isotropic spectra of carbonate and bicarbonate in light and heavy water have been measured from 150 to 325 °C at 21 MPa using a confocal Raman microscope and a custom-built titanium flow cell with sapphire windows. The positions of the symmetric vibrational modes of CO32- and HCO3-/DCO3- were compared to density functional theory (DFT) calculations with a polarizable continuum model in light and heavy water. The experimental Raman peak positions shifted linearly toward lower wavenumbers with increasing temperatures. Raman scattering coefficients, measured relative to a perchlorate internal standard, were used to determine equilibrium molalities of the carbonate and bicarbonate species. These yielded quantitative thermodynamic equilibrium quotients for the reaction CO32- + H2O ⇌ HCO3- + OH- and its deuterium counterpart. Ionization constants for HCO3- and DCO3-, K2a,H,m and K2a,D,m, calculated in their standard states using the Meissner-Tester activity coefficient model, were combined with critically evaluated literature data to derive expressions for their dependence on temperature and pressure, expressed as solvent molar volume, over the range 25 to 325 °C from psat to 21 MPa. These are the first experimental values to be reported for this reaction in light water above 250 °C and in heavy water above 25 °C. The value of the deuterium isotope effect on the chemical equilibrium constant, ΔpK2a,m = pK2a,D,m - pK2a,H,m, decreased from ΔpK2a,m = 0.67 ± 0.07 at 25 °C to ΔpK2a,m = 0.17 ± 0.13 at 325 °C and psat.

Triborate Formation Constants and Polyborate Speciation under Hydrothermal Conditions by Raman Spectroscopy using a Titanium/Sapphire Flow Cell.

Solvent-corrected reduced isotropic Raman spectra of aqueous boric acid + sodium borate solutions have been obtained from perpendicular and parallel polarization measurements in a novel custom-made titanium flow cell with sapphire windows over the temperature range 25 to 300 °C at 20 MPa using the perchlorate anion, ClO4-, as an internal standard. The reduced isotropic spectra of solutions yielded the first reported quantitative speciation results for polyborate ions in equilibrium with boric acid and borate in high-temperature aqueous solutions above 200 °C. The spectra obtained from solutions at low sodium/boron ratios, 0 < mNaST/ mBST < 0.254, displayed well-defined bands at 880, 747, 615, and 532 cm-1, corresponding to the species B(OH)3 > [B(OH)4]- > [B3O3(OH)4]- ≫ [B5O6(OH)4]-, respectively. The triborate ion, [B3O3(OH)4]-, was found to be the major polyborate species in these boric acid-rich solutions in the range 25 to 300 °C. Thermodynamic formation constants for the triborate species, [B3O3(OH)4]-, calculated from the peak areas, are in agreement with the literature values reported by Mesmer et al at 50, 100, and 200 °C to within the combined experimental uncertainties. At 300 °C, the value for the formation constant, log K31, m b= 2.259 ± 0.060, is larger than the value extrapolated from the results of Mesmer et al. by a factor of ∼3.

Initial Excited-State Structural Dynamics of dT and dA Oligonucleotide Homopentamers Using Resonance Raman Spectroscopy.

Photochemical damage of DNA is initiated by absorption of ultraviolet light, and the photoproducts are formed as a result of excited-state structural and electronic dynamics. We have used UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of homopentamers of adenosine monophosphate (3'-dApdApdApdApdAp-5') and thymidine monophosphate (3'-dTpdTpdTpdTpdTp-5') and compare them to those of the monomeric nucleobases. The resonance Raman spectra of the homopentamers are similar to those of the corresponding monomers. Initial excited-state slopes, homogeneous and inhomogeneous broadening, and other excited-state parameters were extracted by self-consistent simulation of the resonance Raman excitation profiles and absorption spectra with a time-dependent formalism and are also similar to the initial excited-state slopes and broadening in the nucleotide monomers. The lack of differences between the initial excited-state structural dynamics of the nucleotides within the pentamer and the isolated nucleobases is consistent with a model in which the formation of photochemical products in oligonucleotides and DNA is dependent on the formation of the transition-state structure within these polymers, dictated by their large-scale dynamics. These results are discussed in light of the known photochemistry of DNA and the nucleobases.

Initial excited-state dynamics of an N-alkylated indanylidene-pyrroline (NAIP) rhodopsin analog.

N-Alkylated indanylidene-pyrroline-based molecular switches mimic different aspects of the light-induced retinal chromophore isomerization in rhodopsin: the vertebrate dim-light visual pigment. In particular, they display a similar ultrashort excited-state lifetime, subpicosecond photoproduct appearance time, and photoproduct vibrational coherence. To better understand the early light-induced dynamics of such systems, we measured and modeled the resonance Raman spectra of the Z-isomer of the N-methyl-4-(5'-methoxy-2',2'-dimethyl-indan-1'-ylidene)-5-methyl-2,3-dihydro-2H-pyrrolium (NAIP) switch in methanol solution. It is shown that the data, complemented with a <70 fs excited-state trajectory computation, demonstrate initial excited-state structural dynamics dominated by double-bond expansion and single-bond contraction stretches. This mode subsequently couples with the five-membered ring inversion and double-bond torsion. These results are discussed in the context of the mechanism of the excited-state photoisomerization of NAIP switches in solution and the 11-cis retinal in rhodopsin.

Initial excited-state structural dynamics of 5,6-dimethyluracil from resonance Raman spectroscopy.

In order to understand the effect of methyl substitution patterns on the initial excited-state structural dynamics of uracil derivatives, we measured the resonance Raman spectra of 5,6-dimethyluracil (5,6-DMU). The results show that the resonance Raman spectrum is a combination of that of 5-methyl- and 6-methyluracil. The resonance Raman excitation profiles (RREPs) and absorption spectrum are simulated with a self-consistent, time-dependent formalism to yield the excited-state slopes and broadening parameters. The initial excited-state structural dynamics occur primarily along the C5═C6 stretching mode, as expected, but with lesser excited-state slopes along each mode compared to 5-methyluracil and 6-methyluracil. This study along with previous experiments with different uracil derivatives show that the presence and positions of the methyl groups seems to determine the partitioning of initial excited-state structural dynamics.