Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pK(a) prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pK(a) values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pK(a)'s with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pK(a) values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pK(a) predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy.
NMR spectra were collected for poly(N‐isopropylacrylamide) (PNIPAAm) hydrogel using high‐resolution magic angle spinning (HRMAS) after gel pieces were hydrated in the presence of D2O, NaF, NaCl, and NaI aqueous solutions. Changes in the peak height intensity of the spectra provide quantitative insight into the phase transition process. The thermodynamic values of the phase transition were calculated using a van't Hoff analysis of the NMR data. Unlike the trend observed for decreases in the (LCST), changes in the enthalpy and entropy did not clearly display a linear dependence with respect to salt concentration. Rather, it was observed that increases in salt concentration did not affect the enthalpy and entropy to the extent as the initial change observed between no salt and 100 mM solutions. Finally, the effect of salts on the hysteresis of the rehydrating process was observed. Hysteresis occurs due to the need for hydrophobic interactions to break down before water is able to infiltrate the polymer matrix. NaF stabilizes hydrophobic interactions while NaI destabilize hydrophobic interactions, causing them to break down at higher temperatures. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Different water environments in poly(N-isopropyl acrylamide) (PNIPAAm) hydrogels are identified and characterized using 1 H high resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR). Local water environments corresponding to a "free" highly mobile species, along with waters showing restricted dynamics are resolved in these swollen hydro-gels. For photo-initiated polymerized PNIPAAm gels, an additional entrapped water species is observed. Spin-spin R 2 relaxation experiments support the argument of reduced mobility in the restricted and entrapped water species. By com-bining pulse field gradient techniques with HRMAS NMR it is possible to directly measure the self-diffusion rate for these different water environments. The behavior of the heterogeneous water environments through the lower critical solution temperature transition is described.
The front-end of the nuclear fuel cycle encompasses several chemical and physical processes used to acquire and prepare uranium for use in a nuclear reactor. These same processes can also be used for weapons or nefarious purposes, necessitating the need for technical means to help detect, investigate, and prevent the nefarious use of nuclear material and nuclear fuel cycle technology. Over the past decade, a significant research effort has investigated uranium compounds associated with the front-end of the nuclear fuel cycle, including uranium ore concentrates (UOCs), UF 4 , UF 6 , and UO 2 F 2 . These efforts have furthered uranium chemistry with an aim to expand and improve the field of nuclear forensics. Focus has been given to the morphology of various uranium compounds, trace elemental and chemical impurities in process samples of uranium compounds, the degradation of uranium compounds, particularly under environmental conditions, and the development of improved or new techniques for analysis of uranium compounds. Overall, this research effort has identified relevant chemical and physical characteristics of uranium compounds that can be used to help discern the origin, process history, and postproduction history for a sample of uranium material. This effort has also identified analytical techniques that could be brought to bear for nuclear forensics purposes. Continued research into these uranium compounds should yield additional relevant chemical and physical characteristics and analytical approaches to further advance front-end nuclear fuel cycle forensics capabilities.
Polymers formed from N -isopropylacrylamide (NIPAM) are highly water soluble and undergo a temperature-induced phase transition to an insoluble state. The phase behavior is determined by competing hydrophilic and hydrophobic forces. In this report, additional insight regarding the effect soluble metals have on the phase transition process is provided by showing that cation solvation aids with stabilization of hydrophobic forces. This reduces barriers to rehydration and decreases thermodynamic entropy and enthalpy, obtained with variable-temperature 1 H nuclear magnetic resonance spectroscopy of NIPAM hydrogels in D 2 O, NaCl, MgCl 2 , and CaCl 2 . For the series of cations studied, it is observed that the order of increasing effect to facilitate the phase transition is Ca 2+ < Mg 2+ < Na + . NaCl and MgCl 2 exhibited similar effects on the thermodynamics of the collapsing process. However, signifi cant differences in the phase transition thermodynamics are observed between MgCl 2 and CaCl 2 salt solutions. The infl uence on Stage 1 enthalpy and entropy values for CaCl 2 solutions is approximately half that of the MgCl 2 solutions. This difference is likely related to their charge density of Ca 2+ , which is approximately half that of Mg 2+ . make them attractive for use in various separations processes. These applications often occur in the presence of alkali and alkali earth metal cations, and a more complete understanding of hydrogel chemistry is provided by examining the role of metals in the phase transition LCST. [13][14][15][16][17][18][19][20][21] Tanaka et al. concluded that the degree of ionization of the polymer is an important aspect of the phase transition of ionic gels. [ 22 ] An additional stimulus to affect hydrogel phase transitions is the ionic strength of the solution in which it is immersed. Ohmine et al. investigated the effects of varying salt concentrations of NaCl, CaCl 2 , BaCl 2 , and MnCl 2 on the phase transition of partially hydrolyzed polyacrylamide gels. [ 23 ] With increasing concentrations of NaCl in water, the gels undergo a continuous transition to a dehydrated state. For NaCl, the phase transition began at 10 −3 mol L -1 concentrations, whereas the phase transition was initiated by much lower concentrations, 10 −5 -10 −6 mol L -1 , of the divalent salts investigated. The difference between the effectiveness of NaCl and MgCl 2, at inducing the phase transition, was attributed to the fact that only half as many divalent ions are needed to
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