How does the coupling of secondary and tertiary interactions control the folding of helical macromolecules?

The authors study how the simultaneous presence of short-range secondary and long-range tertiary interactions controls the folding and collapse behavior of a helical macromolecule. The secondary interactions stabilize the helical conformation of the chain, while the tertiary interactions govern its overall three-dimensional shape. The authors have carried out Monte Carlo simulations to study the effect of chain length on the folding and collapse behavior of the chain. They have calculated state diagrams for four chain lengths and found that the physics is very rich with a plethora of stable conformational states. In addition to the helix-coil and coil-globule transitions, their model describes the coupling between them which takes place at low temperatures. Under these conditions, their model predicts a cascade of continuous, conformational transitions between states with an increase in the strength of the tertiary interactions. During each transition the chain shrinks, i.e., collapses, in a rapid and specific manner. In addition, the number of the transitions increases with increasing chain length. They have also found that the low-temperature regions of the state diagram between the transition lines cannot be associated with specific structures of the chain, but rather, with ensembles of various configurations of the chain with similar characteristics. Based on these results the authors propose a mechanism for the folding and collapse of helical macromolecules which is further supported by the analysis of configurational, configurational, and thermodynamic properties of the chain.     

CO2 deactivation of supported amines: does the nature of amine matter?

Adsorption of CO(2) was investigated on a series of primary, secondary, and tertiary monoamine-grafted pore-expanded mesoporous MCM-41 silicas, referred to as pMONO, sMONO, and tMONO, respectively. The pMONO adsorbent showed the highest CO(2) adsorption capacity, followed by sMONO, whereas tMONO exhibited hardly any CO(2) uptake. As for the stability in the presence of dry CO(2), we showed in a previous contribution [J. Am. Chem. Soc.2010, 132, 6312-6314] that amine-supported materials deactivate in the presence of dry CO(2) via the formation of urea linkages. Here, we showed that only primary amines suffered extensive loss in CO(2) uptake, whereas secondary and tertiary amines were stable even at temperature as high as 200 °C. The difference in the stability of primary vs secondary and tertiary amines was associated with the occurrence of isocyanate as intermediate species toward the formation of urea groups, since only primary amines can be precursors to isocyanate in the presence of CO(2). However, using a grafted propyldiethylenetriamine containing both primary and secondary amines, we demonstrated that while primary amines gave rise to isocyanate, the latter can react with either primary or secondary amines to generate di- and trisubstituted ureas, leading to deactivation of secondary amines as well.     

Perspective: Do macromolecules play a role in the mechanisms of nerve stimulation and nervous transmission?

Fibrillar macromolecular networks are ubiquitous in biological systems, from cellular cytoskeletons to tissues such as muscle and tendon. The presence of such networks in neuronal tissue is known, for example, in the cytoskeleton and extracellular matrix in and around neuronal and glial cells, but their function is believed to be principally mechanical/structural in nature. However, there has long been speculation regarding a broader role for neuronal fibrillar macromolecules, which are anionic polyelectrolytes, specifically regarding their participation in nervous stimulation and transmission. This Perspective reviews literature that spans more than a century, including very recent work, and attempts to build a case for considering a multifunctional role for such macromolecules that includes participation in not only nervous activity but also in diverse phenomena including electric communication within and between cells and mechanisms of anesthetic action. Perhaps the creation and utilization of “artificial axons” is within reach with design rules coming at least in part from fundamental considerations of macromolecular science. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 7–14     

Temperature dependence of homogeneous nucleation rates for water: near equivalence of the empirical fit of Wölk and Strey, and the scaled nucleation model

It is pointed out that the temperature fitting function of W?lk and Strey [J. Phys. Chem. 105, 11683 (2001)], recently shown to convert the Becker-D?ring [Ann. Phys. (Leipzig) 24, 719 (1935)] nucleation rate into an expression in agreement with much of the experimental water nucleation rate data, also converts the Becker-D?ring rate into a form nearly equivalent with the scaled nucleation rate model, J(scaled)=J(oc) exp[-16piOmega(3)(T(c)T-1)(3)3(ln S)(2)]. In the latter expression J(oc) is the inverse thermal wavelength cubed/sec, evaluated at T(c).     

Nucleation: What Happens at the Initial Stage?

Crystallizing growth : The initial structure of crystal nuclei is supersaturation‐dependent. At low degrees of supersaturation, liquid‐like nuclei are formed initially, which undergo a continuous structure transition from liquid‐like to crystal‐like as the size N increases. This gradual structure evolution substantially lowers the nucleation barrier ΔG* and facilitates the nucleation relative to the formation of crystal‐like clusters from the beginning.

     

Theory of electrochemical nucleation and growth—revisited?

Journal of Solid State Electrochemistry -     

How does organic matter constrain the nature, size and availability of Fe nanoparticles for biological reduction?

Few studies have so far examined the kinetics and extent of the formation of Fe-colloids in the presence of natural organic ligands. The present study used an experimental approach to investigate the rate and amount of colloidal Fe formed in presence of humic substances, by gradually oxidizing Fe(II) at pH 6.5 with or without humic substances (HS) (in this case, humic acid--HA and fulvic acid--FA). Without HS, micronic aggregates (0.1-1 μm diameter) of nano-lepidocrocite is obtained, whereas, in a humic-rich medium (HA and FA suspensions at 60 and 55 ppm of DOC respectively), nanometer-sized Fe particles are formed trapped in an organic matrix. A proportion of iron is not found to contribute to the formation of nanoparticles since iron is complexed to HS as Fe(II) or Fe(III). Humic substances tend to (i) decrease the Fe oxidation and hydrolysis, and (ii) promote nanometer-sized Fe oxide formation by both inhibiting the development of hydroxide nuclei and reducing the aggregation of Fe nanoparticles. Bioreduction experiments demonstrate that bacteria (Shewanella putrefaciens CIP 80.40 T) are able to use Fe nanoparticles associated with organic matter about eight times faster than in the case of nano-lepidocrocite. This increase in bioreduction rate appears to be related to the presence of humic acids that (i) indirectly control the size, shape and density of oxyhydroxides and (ii) directly enhance biological reduction of nanoparticles by electron shuttling and Fe complexation. These results suggest that, in wetlands but also elsewhere where mixed organic matter-Fe colloids occur, Fe nanoparticles closely associated with organic matter represent a bioavailable Fe source much more accessible for microfauna than do crystallized Fe oxyhydroxides.     

Protein crystal nucleation: is the pair interaction potential the primary determinant of kinetics?

Fundamental understanding of protein crystal nucleation facilitates crystallization of biological macromolecules for structure determination and control of crystal size distribution. In the studies presented here, nucleation kinetics of hen egg-white lysozyme crystals were measured at solution conditions that exhibited equal solubility by adjusting pH, temperature, or sodium chloride concentration. It was observed that solution conditions that lead to equal solubility resulted in equal nucleation rates and hence kinetic parameters. Since the solubility of globular proteins correlates with the osmotic second virial coefficient, B(22), an integral measure of the protein pair interaction potential, this observation indicates that the protein pair interaction plays a key role in determining nucleation kinetic parameters.     

Examining the performance of DFT methods in uranium chemistry: does core size matter for a pseudopotential?

We have investigated the performance of DFT in U(VI) chemistry. A large, representative selection of functionals has been tested, in combination with two ECPs developed in Stuttgart that have different-sized cores (60 and 78 electrons for U). In addition, several tests were undertaken with another 14 electron pseudopotential, which was developed in Los Alamos. The experimental database contained vibrational wavenumbers, thermochemical data, and (19)F chemical shifts for molecules of the type UF(6-n)Cl(n). For the prediction of vibrational wavenumbers, the large-core RECP (14 electrons) gives results that are at least as good as those obtained with the small-core RECP (32 electrons). GGA functionals are as successful as hybrid GGA for vibrational spectroscopy; typical errors are only a few percent with the Stuttgart pseudopotentials. For thermochemistry, hybrid versions of DFT are more successful than GGA, LDA, or meta-GGA. Marginally better results are obtained with a 32 electron ECP than with 14; since the experimental uncertainties are at least 25 kJ/mol for each reaction, the best functionals give results that are essentially indistinguishable from experiment. However, large-basis CCSD(T) results match experiment better than any DFT that we examined. Our findings for NMR spectroscopy are rather disappointing; no combination of pseudopotential, functional, and basis yields even a qualitatively correct prediction of trends in the (19)F chemical shifts of UF(6-n)Cl(n) species. Results yielded by the large-core RECP are, in general, slightly less bad than those obtained with the small core. We conclude that DFT cannot be recommended for predictions of NMR spectra in this series of compounds, though this conclusion should not be generalized. Our most important result concerns the good performance of the large-core Stuttgart pseudopotential. Given its computational efficiency, we recommend that it be used with DFT methods for the prediction of molecular geometries, vibrational frequencies, and thermochemistry of a given oxidation state. The hybrid GGA functionals MPW1PW91 and PBE0 give the best results overall.     

Liquid chromatography of polyethylene glycol mono- and diesters: functional macromolecules or block copolymers?

The chromatographic behavior of polyoxyethylene-based polymers with adsorbing hydrophobic end-fragments was studied under two types of interaction conditions for the ethylene oxide (EO) component of such heteropolymers (which are either critical or of the size-exclusion type). In a theoretical part we assume a wide-pore situation, where the molecules are smaller than pores, and consider models of two-component diblock and triblock copolymers having quite strongly adsorbing blocks. A new step is made to extend a theory from difunctional macromolecules with point-type end-groups to triblock copolymers. It is shown that A-B-A triblocks with adsorbing A-blocks and with a "critical" B-block behave in chromatography like difunctionals with effective end-group interactions. Another important finding is the existence of a second critical region, which was observed on most of the studied columns. This region can be used to separate di- and triblocks from each other. Additionally, the individual oligomers of triblocks can be separated to the baseline. Complete separations of both diblocks and triblocks in one single chromatogram can be achieved by using a step gradient between two types of studied condtions.     

Nucleation of the β-modification of isotactic polypropylene

The effects of the organic pigments C.I.P. RED 177 and C.I.P. Yellow 83 as nucleating agents on the crystallization of polypropylene were studied by DSC. The anthraquinone pigment exerted a significant effect, resulting in structural modifications with lower melting point, and particularly the -modification. The DSC curves exhibit four transition regions, with the following temperature intervals: I. 415–417 K, II. 423–425 K, III. 430–432 K and IV. 438–439 K. For evaluation of the -nucleation effect of pigments, the ratio (H ₁+H ₂)/(H ₃+H ₄) was suggested.     

Electrochemical nucleation and growth of three-dimensional clusters: the case of multi-step ions discharge–I

Journal of Solid State Electrochemistry - Electrochemical nucleation and growth of three-dimensional spherical clusters on a foreign substrate are considered in case of multi- and single-step ions...     

Insight from molecular modelling: does the polymer side chain length matter for transport properties of perfluorosulfonic acid membranes?

We present a detailed analysis of the nanostructure of the short side chain (SSC) perfluorosulfonic acid membrane and its effect on H(2)O clustering, H(3)O(+) and H(2)O diffusion, and mean residence times of H(2)O near SO(3)(-) groups based on molecular dynamics simulations. We studied a range of hydration levels (λ) at temperatures of 300 and 360 K, and compare the results to our findings in the benchmark Nafion? membrane. The water cluster diameter is nearly the same in the two membranes, while the extent of SO(3)(-) clustering is more in the SSC membrane. The calculated cluster diameter of about 2.4 nm is in excellent agreement with the recently proposed cylindrical water channel model of these membranes. The diffusion coefficients of H(2)O and H(3)O(+) are similar in SSC and Nafion membranes. Raising the temperature of the SSC membrane from 300 to 360 K provides a much bigger increase in proton vehicular diffusion coefficient (by a factor of about 4) than changing the side chain length. H(3)O(+) ions are found to exchange more frequently with SO(3)(-) partners at the higher temperature. Our key findings are that (a) the hydrophobic-hydrophilic separation in the two membranes is surprisingly similar; (b) at all hydration levels studied, the long side chain of Nafion is bent and is effectively equivalent to a short side chain in terms of extension into the water domain; (c) vehicular proton transport occurs mainly between SO(3)(-) groups; and (d) changing the size of the simulation cell does not change the results significantly. The simulations are validated in good agreement with the corresponding experimental values for the simulated membrane density and diffusion coefficients of H(2)O.     

Five-coordinate Fe(III)NO and Fe(II)CO porphyrinates: where are the electrons and why does it matter?

Recent years have seen dramatic growth in our understanding of the biological roles of nitric oxide (NO). Yet, the fundamental underpinnings of its reactivities with transition metal centers in proteins and enzymes, the stabilities of their structures, and the relationships between structure and reactivity remains, to a significant extent, elusive. This is especially true for the so-called ferric heme nitrosyls ([FeNO](6) in the Enemark-Feltham scheme). The Fe-CO and C-O bond strengths in the isoelectronic ferrous carbonyl complexes are widely recognized to be inversely correlated and sensitive to structural, environmental, and electronic factors. On the other hand, the Fe-NO and N-O bonds in [FeNO](6) heme complexes exhibit seemingly inconsistent behavior in response to varying structure and environment. This report contains resonance Raman and density functional theory results that suggest a new model for FeNO bonding in five-coordinate [FeNO](6) complexes. On the basis of resonance Raman and FTIR data, a direct correlation between the nu(Fe)(-)(NO) and nu(N)(-)(O) frequencies of [Fe(OEP)NO](ClO(4)) and [Fe(OEP)NO](ClO(4)).CHCl(3) (two crystal forms of the same complex) has been established. Density functional theory calculations show that the relationship between Fe-NO and N-O bond strengths is responsive to FeNO electron density in three molecular orbitals. The highest energy orbital of the three is sigma-antibonding with respect to the entire FeNO unit. The other two comprise a lower-energy, degenerate, or nearly degenerate pair that is pi-bonding with respect to Fe-NO and pi-antibonding with respect to N-O. The relative sensitivities of the electron density distributions in these orbitals are shown to be consistent with all published indicators of Fe-N-O bond strengths and angles, including the examples reported here.     

Structure and reaction pathway of TMP-Zincate: amido base or alkyl base?

The novel directed ortho metalation (DoM) reagents for functionalized aromatic rings, TMP-Zn-ates (R2Zn(TMP)Li (R = Me, 1; tBu, 2)), have been reported to be synthetically useful for the chemo- and regioselective construction of multi-functionalized aromatic compounds. Here, we present the first comprehensive structural and mechanistic investigation by means of X-ray, NMR, and DFT studies on the DoM reaction employing our original TMP-Zn-ate base. The structures of TMP-Zn-ates in solution and in the solid state were determined. The DFT study strongly suggested that the deprotonation involving the TMP ligand on the TMP-Zn-ate is kinetically more favorable than that involving the alkyl ligand, and this view was supported by monitoring of the 13C NMR spectrum of the reaction mixture.     

Critical chromatography of macromolecules as a tool for reading the amino acid sequence of biomacromolecules: Reality or science fiction?

The capabilities of critical chromatography to study the amino acid sequences in biopolymer, peptide, and protein macromolecules are discussed. The rearrangement of two or more amino acid residues and the occurrence and location of modified residues in a chain are considered. The mechanism of an inversion in the order of peptide elution under changes in the gradient of the solvent composition is discussed.     

How does mechanism of biosorption determine the differences between the initial and equilibrium adsorption states?

The analysis of various models assumed to represent the influence of pH on heavy metals biosorption equilibrium is presented. It shows that all of them lead to the same mathematical expressions (e.g. the Langmuir or the Flory adsorption isotherm equations) when the pH effects are neglected. Even if considering the pH effects, some of them (competitive adsorption and ion-exchange models, for instance) still lead to analogical expressions for sorption isotherm equations. The accepted mechanism of biosorption may, however, influence strongly the differences between the initial and equilibrium states of biosorption system.