Stretch Transition Research Articles

Effect of Solvent Quality on the Coil−Stretch Transition

Polymers undergo a sharp coil−stretch transition in extension dominated flows when the strain rate exceeds a critical strain rate. We investigate this transition in both Θ solvents and good solvents using Brownian dynamics simulations. The polymer is represented by a bead−spring chain model undergoing elongational flow and solvent-mediated effects such as fluctuating hydrodynamic interactions (HI) and excluded volume (EV) are included rigorously. A 1-D energy landscape theory with an activation energy for transition(1) is used to gain qualitative insights into the dynamics. A key factor in determining the influence of solvent quality is the use of a proper measure of solvent quality.(2, 3) Contrary to earlier findings, it is observed that with improvement in solvent quality, the critical strain rate at which the coil to stretch transition takes place decreases. Furthermore, the solvent quality has a profound effect on the scaling of the critical strain rate with molecular weight and on both the transient ...

Globule−Stretch Transitions of Collapsed Polymers in Elongational Flow Fields

Here we present our studies on the behavior of collapsed polymer chains in elongational flow fields. In particular, we present scaling and hydrodynamic simulation results on the conformation and dynamics of these macromolecules. In the noncollapsed state, we verify via our simulations that there is a smooth transition from a coil to a stretched conformation. The introduction of self-interactions or nonsolvent effects in a polymer, however, suppresses this transition up to a well-defined threshold flow rate e* at which the chain undergoes an immediate and irreversible transition to a stretched conformation. We characterize this behavior under both freely draining and hydrodynamic interacting assumptions and develop scaling arguments to describe the globule−stretch transition in a variety of regimes. The unraveling dynamics and topologies are characterized with relation to these mechanisms, and the elongational viscosity of dilute solutions of collapsed chains is also investigated.

Coil-stretch Transition of DNA Molecules in Slit-like Confinement.

We experimentally investigate the influence of slit-like confinement on the coil-stretch transition of single DNA molecules in a homogeneous planar elongational electric field. We observe a more gradual coil-stretch transition characterized by two distinct critical strain rates for DNA in confinement, different from the unconfined case where a single critical strain rate exists. We postulate that the change in the coil-stretch transition is due to a modified spring law in confinement. We develop a dumbbell model to extract an effective spring law by following the relaxation of an initially stretched DNA. We then use this spring law and kinetic theory modeling to predict the extension and fluctuations of DNA in planar elongational fields. The model predicts that a two-stage coil-stretch transition emerges in confinement, in accord with experimental observations.

Critical Strain for Shish-Kebab Formation

A combination of extensional rheological and in situ synchrotron radiation small-angle X-ray scattering (SR-SAXS) measurements was introduced to investigate critical strain ε* for shish formation and validate whether coil−stretch transition or stretched-network is responsible for shish-kebab formation in high density polyethylene melt. With strain rates ε̇ larger than a specific value, the critical strain ε* required to induce shish formation turns out to be a constant of about 1.57, which ensure full extension of chain segments with critical entanglement molecular weight locked between two adjacent entanglement points. The results clearly demonstrate that the formation of shish-kebab in polymer melt stems from stretched network instead of coil−stretch transition.

Structure and properties of the Zn+–D2 complex

The infrared spectrum of the (66)Zn(+)-D(2) complex is measured in the D-D stretch region (2815-2866 cm(-1)) by detecting Zn(+) photofragments. The spectrum is consistent with the Zn(+)-D(2) complex consisting of a slightly distorted D(2) molecule attached to a ground state Zn(+) ion in a T-shaped equilibrium configuration. From the rotational constants, the vibrationally averaged intermolecular bond length is deduced to be 2.32 A, contracting by 0.02 A upon excitation of the D-D stretch vibrational mode. The band center of the D-D stretch transition is shifted by -154.8 cm(-1) from the Q(0) (1) transition of the free D(2) molecule. Density functional theory calculations are performed to elucidate the molecular bonding in the complex. The current spectroscopic and calculated data for Zn(+)-D(2), together with the previously determined binding energy for Zn(+)-H(2) [1310 cm(-1); P. Weis, et al., J. Phys. Chem. A 101, 2809 (1997)], result in a comprehensive characterization of the Zn(+)-D(2) and Zn(+)-H(2) complexes.

Elastic stresses in random flow of a dilute polymer solution and the turbulent drag reduction problem

Abstract In this short review I argue that the progress in our understanding the mechanism of turbulent drag reduction is conditioned by obtaining experimental data on dynamics and statistics of polymer stretching and elastic stresses in inertial turbulence at high Reynolds numbers that is a technically challenging task. The suggested way out of the currently unresolved technical problem is to collect the same data in elastic turbulence, which is a smooth random flow similar to that found in inertial turbulence below the dissipation scale. Since the polymer stretching and elastic stresses in inertial turbulence are influenced only by small scales, it is appropriate to use information on the polymer stretching and elastic stresses obtained in elastic turbulence. The experimental data on the statistics of the polymer stretching, the coil–stretch transition, and elastic stresses together with spatial distribution and values of the rms of the velocity gradients were collected in elastic turbulence for the last several years. This information serves a basis for a new hypothesis of turbulent drag reduction. To cite this article: V. Steinberg, C. R. Physique 10 (2009).

Spectroscopic Study of the Benchmark Mn+−H2 Complex

We have recorded the rotationally resolved infrared spectrum of the weakly bound Mn+-H2 complex in the H-H stretch region (4022-4078 cm(-1)) by monitoring Mn+ photodissociation products. The band center of Mn+-H2, the H-H stretch transition, is shifted by -111.8 cm(-1) from the transition of the free H2 molecule. The spectroscopic data suggest that the Mn+-H2 complex consists of a slightly perturbed H2 molecule attached to the Mn+ ion in a T-shaped configuration with a vibrationally averaged intermolecular separation of 2.73 A. Together with the measured Mn+...H2 binding energy of 7.9 kJ/mol (Weis, P.; et al. J. Phys. Chem. A 1997, 101, 2809.), the spectroscopic parameters establish Mn+-H2 as the most thoroughly characterized transition-metal cation-dihydrogen complex and a benchmark for calibrating quantum chemical calculations on noncovalent systems involving open d-shell configurations. Such systems are of possible importance for hydrogen storage applications.

Carbon-deuterium vibrational probes of peptide conformation: Alanine dipeptide and glycine dipeptide

The utility of alpha-carbon deuterium-labeled bonds (C(alpha)-D) as infrared reporters of local peptide conformation was investigated for two model dipeptide compounds: C(alpha)-D labeled alanine dipeptide (Adp-d(1)) and C(alpha)-D(2) labeled glycine dipeptide (Gdp-d(2)). These model compounds adopt structures that are analogous to the motifs found in larger peptides and proteins. For both Adp-d(1) and Gdp-d(2), we systematically mapped the entire conformational landscape in the gas phase by optimizing the geometry of the molecule with the values of phi and psi, the two dihedral angles that are typically used to characterize the backbone structure of peptides and proteins, held fixed on a uniform grid with 7.5 degrees spacing. Since the conformations were not generally stationary states in the gas phase, we then calculated anharmonic C(alpha)-D and C(alpha)-D(2) stretch transition frequencies for each structure. For Adp-d(1) the C(alpha)-D stretch frequency exhibited a maximum variability of 39.4 cm(-1) between the six stable structures identified in the gas phase. The C(alpha)-D(2) frequencies of Gdp-d(2) show an even more substantial difference between its three stable conformations: there is a 40.7 cm(-1) maximum difference in the symmetric C(alpha)-D(2) stretch frequencies and an 81.3 cm(-1) maximum difference in the asymmetric C(alpha)-D(2) stretch frequencies. Moreover, the splitting between the symmetric and asymmetric C(alpha)-D(2) stretch frequencies of Gdp-d(2) is remarkably sensitive to its conformation.

Attachment of Molecular Hydrogen to an Isolated Boron Cation: An Infrared and ab initio Study

Structural properties of the B(+)-H2 electrostatic complex are investigated through its rotationally resolved infrared spectrum in the H-H stretch region (3905-3975 cm(-1)). The spectrum, which was obtained by monitoring B(+) photofragments while the IR wavelength was scanned, is consistent with the complex having a T-shaped structure and a vibrationally averaged intermolecular separation of 2.26 A, which decreases by 0.04 A when the H2 subunit is vibrationally excited. The H-H stretch transition of B(+)-H2 is red-shifted by 220.6 +/- 1.5 cm(-1) from that of the free H2 molecule, much more than for other dihydrogen complexes with comparable binding energies. Properties of B(+)-H2 and the related Li(+)-H2, Na(+)-H2, and Al(+)-H2 complexes are explored through ab initio calculations at the MP2/aug-cc-pVTZ level. The unusually large red-shift for B(+)-H2 is explained as due to electron donation from the H2 sigma(g) bonding orbital to the unoccupied 2p(z) orbital on the B(+) ion.

IR and Raman spectra of liquid water: Theory and interpretation

IR and Raman (parallel- and perpendicular-polarized) spectra in the OH stretch region for liquid water were measured some years ago, but their interpretation is still controversial. In part, this is because theoretical calculation of such spectra for a neat liquid presents a formidable challenge due to the coupling between vibrational chromophores and the effects of motional narrowing. Recently we proposed an electronic structure/molecular dynamics method for calculating spectra of dilute HOD in liquid D(2)O, which relied on ab initio calculations on clusters to provide a map from nuclear coordinates of the molecules in the liquid to OH stretch frequencies, transition dipoles, and polarizabilities. Here we extend this approach to the calculation of couplings between chromophores. From the trajectories of the fluctuating local-mode frequencies, transition moments, and couplings, we use our recently developed time-averaging approximation to calculate the line shapes. Our results are in good agreement with experiment for the IR and Raman line shapes, and capture the significant differences among them. Our analysis shows that while the coupling between chromophores is relatively modest, it nevertheless produces delocalization of the vibrational eigenstates over up to 12 chromophores, which has a profound effect on the spectroscopy. In particular, our results demonstrate that the peak in the parallel-polarized Raman spectrum at about 3250 wavenumbers is collective in nature.

Dynamics of DNA molecules in a cross-slot microchannel

The conformation and dynamics of double-stranded DNA molecules in cross-slots with equal arm length are examined with the use of fluorescent labeled λ-DNA at 1.2 ⩽ De ⩽ 4.1. The stretching and diffusing of individual DNA molecules in the flow was visualized/recorded with confocal laser scanning microscopy (CLSM). The onset of coil–stretch transition of DNA molecules in the elongational flow was determined at the microscale. Time-dependent velocity distribution with a mean velocity of 50 µm s−1 for DNA molecules was observed by using FluoSpheres, carboylate-modified microspheres over a time period of 1.12 s. The effect of channel geometry (corner and outlet regions) and the solution viscosity (1.9 cP and 9.5 cP) on the conformation and diffusion are also studied and discussed. We report the maximum and the distribution of the fractional extension of DNA molecules, and show that the maximum fractional extension may be up to 0.64 at De = 4.1, and at a strain of 1.8 there is a corresponding stretching force of about 200 pN.

Asymmetric Distribution of Lipids in a Phase Segregated Phospholipid Bilayer Observed by Sum-Frequency Vibrational Spectroscopy

The intrinsic symmetry constraints on sum-frequency vibrational spectroscopy (SFVS) have been exploited to measure the asymmetric distribution of lipid domains in the proximal and distal layers of a planar supported lipid bilayer (PSLB) in the gel−liquid-crystalline (l.c.) coexistence region of the phase diagram for several lipid systems. Four saturated phospholipids, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-diheptadecanoyl-sn-glycero-3-phosphocholine (DHPC), and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), and two equal-molar binary mixtures of DSPC with DMPC, and DSPC with a unsaturated lipid DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) were investigated. The destructive interference of the symmetric stretch (vs) transition moments from the lipid fatty acid methyl groups (CH3) was used to monitor changes in the symmetry of the bilayer structure. A maximum in the CH3 vs intensity is observed at the phase transition temperature (Tm) due to the break in the local symmetry of lipid bilayers caused by the dislocation of the gel and l.c. phase domains. The SFVS results were correlated to phase segregation in the membranes as measured by fluorescence microscopy. The SFVS measured Tm for DMPC, DPPC, DHPC, and DSPC were 23.4 ± 0.9 °C, 41.0 ± 0.4 °C, 52.4 ± 0.7 °C, and 57.5 ± 0.5 °C, respectively. These values correlate well with the literature values of 23.6 ± 1.5 °C, 41.3 ± 1.8 °C, 49 ± 3 °C, and 54.5 ± 1.5 °C for DMPC obtained by differential scanning calorimetry (DSC). In addition to providing a direct spectroscopic probe of the Tm of PSLBs, these studies also provide evidence for the delocalization of the gel and l.c. domain structures between the two layers of lipid bilayers.

Inkjet printing of polymer solutions and the role of chain entanglement

The influence of polymer concentration, going from the dilute through the overlap into the concentrated regime, during drop on demand inkjet printing is investigated for a range of cellulose ester (CE) polymers from visual examination of ligament stretching as a function of applied wave form. The physical behaviour of the polymer fluids in drop formation is indicative of the dominance of viscoelastic effects within the timescale of the process, in preventing ligament break-up at the pinch point compared with a water–glycerol–isopropanol blend Newtonian fluid of similar viscosity. This has previously been described in terms of the polymer chain undergoing a coil–stretch transition at the strain rates experienced in the inkjet process. When formulated at the coil overlap concentration all polymers showed qualitatively similar behaviour with respect to time and length of ligament at rupture irrespective of polymer molecular weight. Beyond the overlap concentration the ligament rupture time continues to increase with increasing elasticity of the solution but the ligament rupture length decreases rapidly. In this regime chain entanglement becomes important, dramatically increasing the elastic nature of the ligament. Additionally it is proposed that in the case of weakly associating polymers such as cellulose esters, the effective relaxation time is further increased due to the possibility that on chain extension intramolecular H-bonds are broken and may reform as intermolecular associations whilst the polymer chains are extended. These intermolecular associations act as physical crosslinks, thereby creating a transient network structure. This network structure is capable of having a finite large viscosity. Once the strain is removed the network will decay as the chains return to the more thermodynamically stable coil state.

Hydrodynamic properties of DNA and DNA–lipid complex in an elongational flow field

The aim of this study was to determine the difference between hydrodynamic properties of DNA–cetyltrimethylammonium (CTA) complex and those of DNA, which may be related to the difference in fibre-forming ability of DNA–CTA from that of DNA. Responses of DNA and DNA–CTA complex to an elongational flow field were investigated. In both solution systems, results suggesting a coil–stretch transition were obtained. From a critical strain rate value, the radius of gyration of DNA–CTA molecules in ethanol–glycerol solution was revealed to be 0.3–0.5 times of that of DNA in aqueous NaCl solution. Shear viscosity of DNA–CTA solution was much smaller than that of DNA solution, also suggesting a smaller size of DNA–CTA in ethanol–glycerol solution than that of DNA in aqueous NaCl solution. The plateau birefringence value of the DNA–CTA system, a parameter that indicates the local molecular conformation and the molecular arrangement, was only about 1/10 of that of the DNA system. There is an empirically determined molecular model of DNA–CTA complex in which a DNA molecule is sheathed by a cylindrical crust made of CTA chains. This structure reduces the DNA molecular density in a pure elongational flow field region but cannot explain the observed reduction of birefringence intensity. The small plateau birefringence value of DNA–CTA compared with that of DNA was attributed to the reduced molecular polarizability by the particular conformation of DNA molecules and CTA chains in the DNA–CTA system such as that expected by the conformational models.

Dynamics of Wormlike Micelles in Elongational Flows

Wormlike micelles provide an opportunity to study the behavior of semiflexible macromolecules in elongational flows. We constructed a microfluidic cross-flow device coupled with fluorescence microscopy to image individual wormlike micelles and measure their dynamics in planar elongational flow. These polymer micelles prove stable in elongational flow and exhibit a sharp transition between regimes where Brownian motion dominates the micellar dynamics and where the micelles stretch with the flow. The coil−stretch transition and micellar relaxation time were identified by examining a distribution of micelle lengths at various flow rates. The relationship between micellar relaxation time and length is consistent with hydrodynamic theory. At higher Weissenberg number, micelle stretching is nearly as rapid as the rate of stretching of the surrounding fluid, yet also results more frequently in sharply folded conformations. In contrast to DNA in extensional flow, these relatively more stiff macromolecules exhibit...

Origin of the Attraction in Aliphatic C−H/π Interactions: Infrared Spectroscopic and Theoretical Characterization of Gas-Phase Clusters of Aromatics with Methane

An attractive intermolecular interaction between an aliphatic C-H bond and a pi-electron system (C-H/pi interaction) was characterized on the basis of infrared spectroscopy and high level ab initio calculations. Infrared spectroscopy was applied to several isolated methane clusters with benzene, toluene, p-xylene, mesitylene, and naphthalene in the gas phase, and the spectral changes of the C-H stretch bands in the methane moiety upon the cluster formation were observed. In the theoretical approach, interaction energies of the clusters were evaluated by high-level ab initio calculations. The forbidden symmetric C-H stretch transition weakly appeared in the IR spectra of the clusters, and it confirmed the small deformation of the methane moiety from the T(d)() symmetry, which was predicted by the ab initio calculations. On the other hand, the degenerated asymmetric C-H stretch band showed complicated splitting, which is qualitatively interpreted by a hindered rotor model. Low-frequency shifts upon the cluster formation were seen in the symmetric C-H stretch frequency, though the magnitude of the shifts was extremely small and no clear correlation with the interaction energy was found. On the other hand, the size of the calculated interaction energy well correlates with the polarizability of aromatics. The S(1)-S(0) electronic transition of the aromatic moiety was also observed, and it showed low-frequency shifts upon cluster formation. These results support the dominance of the dispersion interaction over the electrostatic and charge-transfer terms in the aliphatic C-H/pi interaction.

High-resolution infrared studies in slit supersonic discharges: CH2 stretch excitation of jet-cooled CH2Cl radical

First high-resolution infrared spectra are presented for jet-cooled CH2 35Cl and CH2 37Cl radicals in the symmetric (nu1) CH2 stretching mode. A detailed spectral assignment yields refined lower and upper state rotational constants, as well as fine structure spin-rotation parameters from least-squares fits to the sub-Doppler line shapes for individual transitions. The rotational constants are consistent with a nearly planar structure, but do not exclude substantial large amplitude bending motion over a small barrier to planarity accessible with zero-point excitation. High level coupled cluster (singles/doubles/triples) calculations, extrapolated to the complete basis set limit, predict a slightly nonplanar equilibrium structure (theta approximately 11 degrees), with a vibrationally adiabatic treatment of the bend coordinate yielding a v = 1<--0 anharmonic frequency (393 cm(-1)) in excellent agreement with matrix studies (nu(bend) approximately 400 cm(-1)). The antisymmetric CH2 stretch vibration is not observed despite high sensitivity detection (signal to noise ratio >20:1) in the symmetric stretch band. This is consistent with density functional theory intensity calculations indicating a >35-fold smaller antisymmetric stretch transition moment for CH2Cl, and yet contrasts dramatically with high-resolution infrared studies of CH2F radical, for which both symmetric and antisymmetric CH2 stretches are observed in a nearly 2:1 intensity ratio. A simple physical model is presented based on a competition between bond-dipole and "charge-sloshing" contributions to the transition moment, which nicely explains the trends in CH2X symmetric versus asymmetric stretch intensities as a function of electron withdrawing group (X = D,Br,Cl,F).

Nonlinear elastic polymers in random flow

Polymer stretching in random smooth flows is investigated within the framework of the FENE dumbbell model. The advecting flow is Gaussian and short-correlated in time. The stationary probability density function of polymer extension is derived exactly. The characteristic time needed for the system to attain the stationary regime is computed as a function of the Weissenberg number and the maximum length of polymers. The transient relaxation to the stationary regime is predicted to be exceptionally slow in the proximity of the coil–stretch transition.

Coil−Stretch Transition of High Molar Mass Polymers in Packed-Column Hydrodynamic Chromatography

The elution behavior of high molar mass polystyrene (PS) in packed-column hydrodynamic chromatography (HDC) was studied at different eluent flow rates by using a multiangle laser light scattering (MALLS) detector. A chromatography mode transition from HDC to slalom chromatography (SC) was observed for high molar mass PS samples with abnormal elution behaviors. The critical polymer size Rg,c of the HDC to SC transition was determined by the plateau value of the Rg−Ve curve for the earliest eluting polymer fraction. The dependence of Rg,c on flow rate was explained by coil−stretch transitions of the polymer molecules in elongational flow through the packed column. The transition of chromatography mode may provide a new method to study the coil−stretch transition of polymers in elongational flow through packed beds. For high molar mass polymer samples, HDC must be performed at flow rates sufficiently low that the elongational rate in the column is less than the critical strain rate for coil−stretch transitions to occur for all species in the sample.

Direct observation of long-strand DNA conformational changing in microchannel flow and microfluidic hybridization assay

Conformational control of macromolecules is useful for efficient chemical and biochemical reactions. This article reports a direct observation method for macromolecules, such as long-strand DNA, in microchannel flow as well as a simple method for stretching DNA strands by microfluidics. Stretching and orientation of DNA molecules by control of flow within a microchannel was observed by optical microscopy. This DNA stretching is explained by coil–stretch transition of polymer molecules. This technique is useful for creating chemical reactions with macromolecules. It offers high selectivity and efficiency that are impossible to achieve in bulk solution. We also demonstrate that our microfluidic stretching method can accomplish efficient hybridization of long-strand DNA. This method will be useful for direct hybridization assay of long-strand DNA.