Time‐resolved dynamic light scattering as a method to monitor compaction during protein folding

The mechanisms and the dynamics of protein folding are subject of a still increasing number of theoretical and experimental studies. While spectroscopic methods are already used for many years to measure the folding rates and to monitor the formation of secondary and tertiary structure, kinetic measurements of the compactness are only beginning to emerge. Time‐resolved dynamic light scattering (DLS) is a useful tool to follow the compaction during protein folding by measuring the hydrodynamic Stokes radius R_S. Additionally, changes in the state of association can be detected by simultaneous measurements of the scattering intensity. The usefulness of different techniques for time‐resolved DLS measurements and the general limits for kinetic DLS experiments are discussed first. Then we describe the adaptation of a stopped‐flow system (SFM‐3) to a DLS apparatus, the particular data acquisition schemes, and the experimentally attainable limits. The feasibility of stopped‐flow DLS is demonstrated by the results of folding investigations with ribonuclease A, phosphoglycerate kinase, and bovine α‐lactalbumin. Refolding was initiated by denaturant dilution jumps, which were repeated up to 100 times in order to obtain a reasonable signal‐to‐noise ratio. Kinetic DLS experiments can be performed fairly with a time resolution of one second. The time resolution of 100ms is probably the attainable limit. The capabilities of time‐resolved DLS and time‐resolved small‐angle X‐ray scattering are compared.     

Absolute rate constants for some hydrogen atom abstraction reactions by a primary fluoroalkyl radical in water

A combination of laser flash photolysis and competitive kinetic methods have been used to measure the absolute bimolecular rate constants for hydrogen atom abstraction in water from a variety of organic substrates including alcohols, ethers, and carboxylic acids by the perfluoroalkyl radical, *CF(2)CF(2)OCF(2)CF(2)SO(3)(-) Na(+). Comparison, where possible, of these rate constants with those previously measured for analogous reactions in the non-polar organic solvent, 1,3-bis(trifluoromethyl)benzene (J. Am. Chem. Soc, 1999, 121, 7335) show that the alcohols react 2-5 times more rapidly in the water solvent and that the ethers react at the same rate in both solvents. A transition state for hydrogen abstraction that is more reminiscent of an "intimate ion pair" than a "solvent separated ion pair" is invoked to explain these modest solvent effects.     

Kinetics for the hydrogen‐abstraction of CH4 with NO2

The detailed mechanism of the NO₂+CH₄ reaction has been computationally investigated at the M06‐2X/MG3S, B3LYP/6‐311G(2d,d,p), and MP2/6‐311+G(2df,p) levels. The direct dynamics calculations were preformed using canonical transition state theory with tunneling correction and scaled generalized normal‐mode frequencies including anharmonic torsion. The calculated results indicate that the NO₂+CH₄ reaction proceeds by three distinct channels simultaneously, leading to the formation of trans‐HONO (1a), cis‐HONO (1b), and HNO₂ (1c), and each channel involves the formation of intermediate having lower energy than the final product. The anti‐Hammond behavior observed in channel 1a is well analyzed. Proper treatment of anharmonic torsions about the C···H···O (or N) axis in the transition structures greatly improves the accuracy of kinetics predictions. The activation energy for each channel increases substantially with temperature, but is not strictly a linear function of temperature. Therefore, the thermal rate constants are fitted to the four‐parameter expression recommended for this case over the wide temperature range 400–4000 K. © 2012 Wiley Periodicals, Inc.     

Time‐resolved method for the measurement of volume changes during polymerization

A new laser scanning dilatometer, based on a simplified capillary‐type dilatometer using a laser scan micrometer for the detection of changes of the sample dimension, is described. The method can be applied to time‐resolved measurements of volume changes for transparent and nontransparent samples. The time resolution of the setup is below 1 s, the absolute error in determining the volume change is below 0.0004 cm³, and the accuracy of the measured shrinkage is better than 0.2 vol. %. The operation temperature ranges from room temperature to 160 °C. The setup has been applied to the investigation of the volume shrinkage during the curing of epoxy resins [diglycidyl ether of bisphenol A (DGEBA)] without and with fillers. Furthermore, the effect of a phase transformation on the volume has been demonstrated by the melting of a crystalline phase (succinic anhydride) dispersed in a DGEBA matrix due to the heat of reaction. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2314–2325, 2005     

Variational transition state theory as a tool to determine kinetic selectivity in reactions involving a valley-ridge inflection point

Variational transition state theory has been used to calculate the kinetic isotope effects affecting product ratios in the reaction between (1)O(2) and d(6)-tetramethylethylene. The minimum energy path on the potential energy surface for this process reaches a valley-ridge inflection point and then bifurcates leading to the two final products. Using canonical variational transition state theory, two distinct dynamical bottlenecks were located corresponding to the H- and the D-abstraction, respectively. The calculated KIE at 263 K turns out to be 1.126. Analogously, a H/T KIE of 1.17 at the same temperature has been found for the reaction of (1)O(2) with the tritiated derivative of tetramethylethylene.     

Time‐resolved crystallization study of absorbable polymers by synchrotron small‐angle X‐ray scattering

Changes in the lamellar morphology that occurred during the quiescent isothermal crystallization of absorbable poly(p‐dioxanone) (PDS) and PDS/poly(glycolide) block copolymer were studied by synchrotron small‐angle X‐ray scattering. Important morphological parameters such as the lamellar long period, the thicknesses of the crystal and amorphous phases, and the scattering invariant were estimated as a function of time, and trends observed over a wide range of experimental conditions are discussed. Thicker but more perfect lamellae were detected at higher crystallization temperatures. The breadth of the normalized semilog Lorentz‐corrected intensity peak systematically decreased with increasing temperature. In addition, the values of the crystallization half‐time and the Avrami exponent (n = 2.5), determined from the real‐time changes in the lamellar development, showed superb agreement with the bulk crystallinity data generated from other experimental techniques, such as calorimetry and dielectric relaxation spectroscopy. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 39: 153–167, 2001     

Morphology of polyanhydride copolymers: Time‐resolved small‐angle X‐ray scattering studies of crystallization

Synchrotron small‐angle X‐ray scattering (SAXS) was used to study the isothermal crystallization kinetics of a family of polyanhydride copolymers consisting of 1,6‐bis(p‐carboxyphenoxy)hexane and sebacic acid monomers. In situ SAXS experiments permitted the direct observation of the crystallization kinetics. The structural parameters (the long period, lamellar thickness, and degree of crystallinity) were obtained from Lorentz‐corrected intensity profiles, one‐dimensional correlation functions, and interface distribution functions to form a comprehensive picture of the crystal morphology. The combination of these three analyses provided information not only on the lamellar dimensions but also on the polydispersity (nonuniformity) of these dimensions. Where possible, the crystallization kinetics were interpreted with a modified version of the Avrami equation. The results can be used to perform the rational design of controlled‐drug‐release formulations because crystallinity affects drug‐release kinetics. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 463–477, 2005     

Time‐dependent density functional theory study on the absorption spectrum of Coumarin 102 and its hydrogen‐bonded complexes

The effect of both solvent polarity and hydrogen bonding (HB) on the electronic transition energy of Coumarin 102 (C102) has been examined using the time‐dependent density functional theory (TDDFT). Solvent effect on both geometry and electronic transition energy is evaluated using the polarizable continuum model (PCM). A linear relation of the absorption maximum of C102 with the solvent polarity function Δf is found using the TDDFT‐PCM method for all solvents except dimethyl sulfoxide. The solvent polarity and the type B HB between the carbonyl oxygen and solvent hydrogen atom make the absorption wavelength redshift, whereas the type A HB between the amino nitrogen atom and solvent hydrogen atom has an opposite effect on the absorption wavelength. The calculated absorption wavelengths of C102 with two type B HB between the carbonyl oxygen and solvent hydrogen atom are in excellent agreement with experimental measurements. The solvatochromism of C102 is analyzed in terms of the Kamlet–Taft equation and the parameters s and a are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Temperature resolved X-ray diffraction as a tool of thermal analysis

Time and temperature resolved X-ray diffraction was used for thermal analysis. Series of diffraction patterns were measured, while the samples are heated/cooled stepwise or isothermally with freely selectable temperature programs.The method was applied for the investigation of the phase transitions of ammonium nitrate and HMX (1,3,5,7-tetranitro-1,3,5,7-tetraaza-cyclooctane), when the identification of phases was required. Its capability in the field of kinetics is demonstrated with the isothermal investigation of the solid state reaction of ammonium nitrate with copper oxide and the non-isothermal investigation of the high temperature corrosion of nickel, which was performed by means of a difference procedure. For obtaining structural details peak fitting and Rietveld refinement were applied for the investigation of ammonium nitrate and HMX.We are indebted to Mr. K. O. Hartmann, Mr. H. Fietzek and Mr. H. G. Farr for their assistance during the measurements and for the maintenance of the measuring systems.     

Theoretical calculations of energetics, structures, and rate constants for the H + CH3OH hydrogen abstraction reactions

Barrier heights, structures, reaction energies, and rate constants are calculated with the DFT, MP2, and CCSD(T) methods for the first two channels of the H + CH₃OH reactions. The best estimate results based on CCSD(T) calculations give reaction enthalpies () for the first (−8.4 kcal/mol) and second (0.8 kcal/mol) reactive channels, which are comparable to the experimental values, −8.8 ± 0.9 and −0.3 ± 0.9 kcal/mol, respectively. Rate constants and activation energies calculated with the IVTST-0 method using CCSD(T)/cc-pVTZ geometries and frequencies are also in excellent agreement with experiment data.     

Barrier heights of hydrogen‐transfer reactions with diffusion quantum monte carlo method

Hydrogen‐transfer reactions are an important class of reactions in many chemical and biological processes. Barrier heights of H‐transfer reactions are underestimated significantly by popular exchange–correlation functional with density functional theory (DFT), while coupled‐cluster (CC) method is quite expensive and can be applied only to rather small systems. Quantum Monte‐Carlo method can usually provide reliable results for large systems. Performance of fixed‐node diffusion quantum Monte‐Carlo method (FN‐DMC) on barrier heights of the 19 H‐transfer reactions in the HTBH38/08 database is investigated in this study with the trial wavefunctions of the single‐Slater–Jastrow form and orbitals from DFT using local density approximation. Our results show that barrier heights of these reactions can be calculated rather accurately using FN‐DMC and the mean absolute error is 1.0 kcal/mol in all‐electron calculations. Introduction of pseudopotentials (PP) in FN‐DMC calculations improves efficiency pronouncedly. According to our results, error of the employed PPs is smaller than that of the present CCSD(T) and FN‐DMC calculations. FN‐DMC using PPs can thus be applied to investigate H‐transfer reactions involving larger molecules reliably. In addition, bond dissociation energies of the involved molecules using FN‐DMC are in excellent agreement with reference values and they are even better than results of the employed CCSD(T) calculations using the aug‐cc‐pVQZ basis set. © 2017 Wiley Periodicals, Inc.     

Understanding supported reactions in spherical compartments: a general algorithm to model and determine rate constants, diffusion coefficients, and spatial product distributions

A general algorithm allowing the numerical modeling of the time and space dependence of product formation in spherical reaction volumes is described. The algorithm is described by the complete set of mass balance equations. On the basis of these equations, the effects of the diffusion coefficient, reaction rate, bead size, reagent excess, and packing density of the resin beads on the overall reaction rates are determined for second-order reactions. Experimental data of reaction progress are employed to calculate reaction rates and diffusion coefficients in polymer-supported reactions. In addition, the conditions for shell-like product formation are determined, and various strategies for the radial patterning of resin beads are compared. The effect of diffusion on polymer-supported enzyme-catalyzed reactions of the Michaelis-Menten type is treated, as well. Finally, the effects of typical nonideal solid-phase phenomena, namely, the inhomogeneity of rate constants and the concentration dependence of diffusion coefficients, on overall rates are discussed.     

Rate constants for hydrogen abstraction reactions of the sulfate radical,SO4−. Alcohols

Rate constants have been determined for the reactions of SO₄^? with a series of alcohols, including hydrated formaldehyde. The SO₄^? radical was produced by the laser-flash photolysis of persulfate, S₂O₈^2?. Rate constants for the reactions of SO₄^? with alcohols range from 1.0 × 10⁷ for methanol to 3.4 × 10⁸ M^?1 s^?1 for 1-octanol. Rate constants for the reactions of SO₄^? with deuterated methanol and ethanol are lower by about a factor of 2.5. For methanol, ethanol, and 2-propanol, the temperature dependence of the rate constant was determined over the range 10–45°C.     

Use of capillary electrophoresis as a versatile tool to measure interaction constants between a KDR‐binding PEGylated lipopeptide and pegylated phospholipid micelles

In the frame of our molecular imaging activities, a PEGylated lipopeptide has been developed as a specific ligand for the human vascular endothelial growth factor receptor 2, which is considered as one of the important molecular marker of angiogenesis. In this study, the potential of affinity capillary electrophoresis (ACE) is evaluated to measure the interactions of an active PEGylated lipopeptide, its hydrolysis product and its precursor consisting of a peptide structure with different micelles including Brij‐35, Tween‐20, and pegylated phospholipids. Given the amphiphilic structure of the PEGylated lipopeptide, a MEKC method allowing the simultaneous separation of the compounds of interest was set up, using low percentages of acetonitrile. Analytes were resolved using a BGE consisting of 100 mM borate buffer pH 9.0, 1 mM Brij, and 25% acetonitrile. Optimized conditions were then used to perform ACE experiments. The affinity constants of the analytes with the micelles were calculated on the basis of their mobility decrease when surfactant concentration increased in the electrolyte. The use of different linearization models to estimate affinity constants was discussed and comparison of different surfactants was reported. PEGylated lipopeptide interacted more strongly with pegylated phospholipid micelles than with Brij‐35 or Tween‐20. Moreover, it is likely that the chemical structure of the compounds, and particularly the lipidic part of the molecules, significantly affects the interaction with micelles. In conclusion, the ACE method can be readily applied to investigate interactions of our targeting lipopeptides with various micelles currently used for the preparation of pharmaceutical vehicles.     

Isothermal titration calorimetry as a new tool to investigate chiral interactions at crystal surfaces

In this communication we describe for the first time the use of isothermal titration calorimetry (ITC) to measure the energetics of adsorption of enantiomers from aqueous onto chiral crystal surfaces. Our results demonstrate that ITC can be used to measure chiral interactions at crystal surfaces.     

Ion–molecule reactions by chemical ionization: Determination of rate constants

Tungsten hexacarbonyl was studied by chemical ionization mass spectrometry using carbon monoxide as reagent gas. The variation of the relative abundances of ions as a function of reactant gas pressure was used for evaluating the relative rate constants for consecutive reactions. The results are in agreement with the rate constant ratios obtained from ion trap mass spectrometric data.     

Time‐resolved wide‐angle X‐ray scattering measurements during the isothermal crystallization and ferroelectric phase‐transition processes of a vinylidene fluoride/trifluoroethylene copolymer

The time‐resolved measurement of wide‐angle X‐ray scattering was performed with a synchrotron radiation source during the processes of the isothermal crystallization and ferroelectric phase transition of a vinylidene fluoride/trifluoroethylene copolymer with 73 mol % vinylidene fluoride. When the sample was cooled rapidly from the melt to the temperature region of the paraelectric high‐temperature phase, the peak position of the 200/110 reflection shifted toward the higher angle side and the half‐width became narrower. This indicated an increase in the crystallite size with a more compact chain‐packing mode. Even when the temperature jump was made from the melt into the region of the ferroelectric or low‐temperature phase, the crystallization of the high‐temperature phase was first observed before the appearance of the low‐temperature phase. This was consistent with a prediction based on the so‐called Ostwald state rule: the thermodynamically unstable but kinetically preferable high‐temperature phase can appear first even when the thermodynamically more stable low‐temperature phase should be created. The time‐dependent intensity changes were analyzed with the Avrami kinetic equation. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4175–4181, 2004     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Weakly oriented liquid-crystal NMR solvents as a general tool to determine relative configurations

A new NMR method to determine the relative configuration of asymmetric centres is presented. It proceeds through the use of a weakly ordered solvent and the measurement of orientational order parameters. The method is illustrated by using dihydropyridone derivatives for which the orientations and the relative configurations of the asymmetric carbon atoms are determined unambiguously.     

Sulfur as hydrogen‐bond acceptor in cocrystals of 2‐thio‐modified thymine

Doubly and triply hydrogen‐bonded supramolecular synthons are of particular interest for the rational design of crystal and cocrystal structures in crystal engineering since they show a high robustness due to their high stability and good reliability. The compound 5‐methyl‐2‐thiouracil (2‐thiothymine) contains an ADA hydrogen‐bonding site (A = acceptor and D = donor) if the S atom is considered as an acceptor. We report herein the results of cocrystallization experiments with the coformers 2,4‐diaminopyrimidine, 2,4‐diamino‐6‐phenyl‐1,3,5‐triazine, 6‐amino‐3H‐isocytosine and melamine, which contain complementary DAD hydrogen‐bonding sites and, therefore, should be capable of forming a mixed ADA–DAD N—H…S/N—H…N/N—H…O synthon (denoted synthon 3s_{N·S;N·N;N·O}), consisting of three different hydrogen bonds with 5‐methyl‐2‐thiouracil. The experiments yielded one cocrystal and five solvated cocrystals, namely 5‐methyl‐2‐thiouracil–2,4‐diaminopyrimidine (1/2), C₅H₆N₂OS·2C₄H₆N₄, (I), 5‐methyl‐2‐thiouracil–2,4‐diaminopyrimidine–N,N‐dimethylformamide (2/2/1), 2C₅H₆N₂OS·2C₄H₆N₄·C₃H₇NO, (II), 5‐methyl‐2‐thiouracil–2,4‐diamino‐6‐phenyl‐1,3,5‐triazine–N,N‐dimethylformamide (2/2/1), 2C₅H₆N₂OS·2C₉H₉N₅·C₃H₇NO, (III), 5‐methyl‐2‐thiouracil–6‐amino‐3H‐isocytosine–N,N‐dimethylformamide (2/2/1), (IV), 2C₅H₆N₂OS·2C₄H₆N₄O·C₃H₇NO, (IV), 5‐methyl‐2‐thiouracil–6‐amino‐3H‐isocytosine–N,N‐dimethylacetamide (2/2/1), 2C₅H₆N₂OS·2C₄H₆N₄O·C₄H₉NO, (V), and 5‐methyl‐2‐thiouracil–melamine (3/2), 3C₅H₆N₂OS·2C₃H₆N₆, (VI). Synthon 3s_{N·S;N·N;N·O} was formed in three structures in which two‐dimensional hydrogen‐bonded networks are observed, while doubly hydrogen‐bonded interactions were formed instead in the remaining three cocrystals whereby three‐dimensional networks are preferred. As desired, the S atoms are involved in hydrogen‐bonding interactions in all six structures, thus illustrating the ability of sulfur to act as a hydrogen‐bond acceptor and, therefore, its value for application in crystal engineering.