A. N. Semenov

Self-assembling β-Sheet Tape Forming Peptides

Biological proteins have intrinsically the ability to self-assemble, and this has been implicated in pathological situations called amyloid diseases. Conversely understanding protein self-assembly and how to control it can open up the route to new nanodevices and nanostructured materials for a wide range of applications in medicine, chemical industry and nanotechnology. Biological peptides and proteins have complex chemical structure and conformation. This makes it difficult to decipher the fundamental principles that drive their self-assembling behaviours. Here we review our work on the self-assembly of simple de novo peptides in solution. These peptides are designed so that: (i) the chemical complexity of the primary structure and (ii) the conformational complexity are both kept to a minimum. Each peptide adopts an extended β-strand conformation in solution and these β-strands self-assemble in one dimension to form elongated tapes as well as higher order aggregates with pure antiparallel β-sheet structure, without the presence of any other conformations such as turns, loops, α-helices or random coils. Experimental data of the self-assembling properties are fitted with an appropriate theoretical model to build a quantitative relationship between peptide primary structure and self-assembly. These simple systems provide us with the opportunity to reveal the generic properties of the pure β-sheet structures and expose the underlying physicochemical principles that drive the self-assembling behaviour of this biological motif.

Microphase separation in block copolymer/homopolymer blends: Theory and experiment

The process of microphase separation in diblock copolymer/homopolymer blends is studied both theoretically and experimentally for an asymmetric diblock copolymer and for homopolymer concentration less than 25%. The degree of polymerization of the added homopolymer (Nh) covered all possible cases; N≈Nh, N>Nh, and N<Nh. SAXS and rheology are employed and provide the order–disorder transition temperature through the discontinuous changes of the structure factor and the storage modulus. The minority phase can solubilize only a small amount of added homopolymer; addition of a higher amount results in the formation of nonequilibrium structures. Theoretical calculations performed in the strong segregation limit provide the period and the critical value of χN for the stability of the disordered phase. The theory predicts that (χN)c always increases with the addition of the majority phase. When the minority phase is added, (χN)c can increase (N≫Nh and N⩾Nh) or decrease (N≪Nh). The experimental results are in good ...

Viscoelastic response of hyperstar polymers in the linear regime

We compare the linear viscoelastic spectra of star polymer melts, with varying functionality (4-128) and chemistry (isoprenes, butadienes), with a recent parameter-free theory of arm relaxation [S. T. Milner and T. C. B. McLeish, Macromolecules 30, 2159 (1997)]. The theory, which considers this activated process within the framework of dynamic dilution and with appropriate account of the entanglement length scaling and the higher Rouse modes, is universal as it works remarkably well for a very wide range of star functionalities and arm molecular weights. However, for hyperstars consisting of 64 or 128 arms, the viscoelastic response is characterized by the presence of a slow relaxation process in addition to the faster arm relaxation. This additional process is due to the soft ordering of these systems because of their nonuniform monomer density distribution, and exhibits a very strong functionality and molecular weight dependence. It is accounted for by a mean field approach which considers the structura...

Dynamics of polyisoprene in star block copolymers confined in microstructures: A dielectric spectroscopy study

Dielectric spectroscopy has been employed to study selectively the local and global dynamics of polyisoprene (PI) in three microphase separated star diblock copolymers (SI)4, where PI and polystyrene (PS) form the core and corona, respectively. The thermally induced order-to-disorder transition (ODT) has been identified by rheology and small-angle x-ray scattering (SAXS). All dielectric measurements were made at temperatures well below the ODT and the polystyrene glass transition temperatures, where the four PI chain ends are tethered by the glassy polystyrene domains. The ordered state morphology, studied by SAXS, revealed the formation of PS spheres (fPS=0.25, where fPS is the polystyrene volume fraction), polyisoprene cylinders (fPS=0.68), and a lamellar structure (fPS=0.41) in the three copolymers. In contrast to the local segmental motions, the chain orientational dynamics associated with the amplitude and the characteristic relaxation time are strongly influenced by the spatial confinement. The main...

Ro-vibrational quenching of CO (v = 1) by He impact in a broad range of temperatures: A benchmark study using mixed quantum/classical inelastic scattering theory.

The mixed quantum/classical approach is applied to the problem of ro-vibrational energy transfer in the inelastic collisions of CO(v = 1) with He atom, in order to predict the quenching rate coefficient in a broad range of temperatures 5 < T < 2500 K. Scattering calculations are done in two different ways: direct calculations of quenching cross sections and, alternatively, calculations of the excitation cross sections plus microscopic reversibility. In addition, a symmetrized average-velocity method of Billing is tried. Combination of these methods allows reproducing experiment in a broad range of temperatures. Excellent agreement with experiment is obtained at 400 < T < 2500 K (within 10%), good agreement in the range 100 < T < 400 K (within 25%), and semi-quantitative agreement at 40 < T < 100 K(within a factor of 2). This study provides a stringent test of the mixed quantum/classical theory, because the vibrational quantum in CO molecule is rather large and the quencher is very light (He atom). For heavier quenchers and closer to dissociation limit of the molecule, the mixed quantum/classical theory is expected to work even better.

Thermodynamic, structural, and nanomechanical properties of a fluorous biphasic material

The dynamics of the amphiphilic semifluorinated F(CF2)12(CH2)12H (F12H12) alkane that undergoes two condensed phase transitions have been investigated by Brillouin light spectroscopy, shear rheometry, small- (SAXS) and wide-angle (WAXS) X-ray scattering, and thermodynamic PVT measurements. The solid (I)-solid (II) transition (Ts) is marked by a stronger temperature dependence of the sound velocity in phase II and by a 2 orders of magnitude drop of the shear modulus. Between the Ts and the melting transition (Tm), the presence of two phonons implies a coexistence of solid (II) and amorphous (liquid) regions in the submicrometer range at thermal equilibrium as revealed by the SAXS pattern of a single reflection superimposed on a very broad amorphous halo. This intriguing finding of a transient, very slow (over 10 h) solid/liquid coexistence within phase II is rationalized by a two-stage mechanism for melting of the smectic phase (II) of F12H12. A refinement of the known packing motifs for the two solid-state structures is proposed.

Mixed quantum/classical theory of rotationally and vibrationally inelastic scattering in space-fixed and body-fixed reference frames

We formulated the mixed quantum/classical theory for rotationally and vibrationally inelastic scattering process in the diatomic molecule + atom system. Two versions of theory are presented, first in the space-fixed and second in the body-fixed reference frame. First version is easy to derive and the resultant equations of motion are transparent, but the state-to-state transition matrix is complex-valued and dense. Such calculations may be computationally demanding for heavier molecules and/or higher temperatures, when the number of accessible channels becomes large. In contrast, the second version of theory requires some tedious derivations and the final equations of motion are rather complicated (not particularly intuitive). However, the state-to-state transitions are driven by real-valued sparse matrixes of much smaller size. Thus, this formulation is the method of choice from the computational point of view, while the space-fixed formulation can serve as a test of the body-fixed equations of motion, and the code. Rigorous numerical tests were carried out for a model system to ensure that all equations, matrixes, and computer codes in both formulations are correct.

Equivalence of the Ehrenfest theorem and the fluid-rotor model for mixed quantum/classical theory of collisional energy transfer

The theory of two seemingly different quantum∕classical approaches to collisional energy transfer and ro-vibrational energy flow is reviewed: a heuristic fluid-rotor method, introduced earlier to treat recombination reactions [M. Ivanov and D. Babikov, J. Chem. Phys. 134, 144107 (2011)], and a more rigorous method based on the Ehrenfest theorem. It is shown analytically that for the case of a diatomic molecule + quencher these two methods are entirely equivalent. Notably, they both make use of the average moment of inertia computed as inverse of average of inverse of the distributed moment of inertia. Despite this equivalence, each of the two formulations has its own advantages, and is interesting on its own. Numerical results presented here illustrate energy and momentum conservation in the mixed quantum∕classical approach and open opportunities for computationally affordable treatment of collisional energy transfer.

Accurate Calculations of Rotationally Inelastic Scattering Cross Sections Using Mixed Quantum/Classical Theory

For computational treatment of rotationally inelastic scattering of molecules, we propose to use the mixed quantum/classical theory, MQCT. The old idea of treating translational motion classically, while quantum mechanics is used for rotational degrees of freedom, is developed to the new level and is applied to Na + N2 collisions in a broad range of energies. Comparison with full-quantum calculations shows that MQCT accurately reproduces all, even minor, features of energy dependence of cross sections, except scattering resonances at very low energies. The remarkable success of MQCT opens up wide opportunities for computational predictions of inelastic scattering cross sections at higher temperatures and/or for polyatomic molecules and heavier quenchers, which is computationally close to impossible within the full-quantum framework.

COMPOSITION FLUCTUATION-INDUCED DEPOLARIZED RAYLEIGH-SCATTERING FROM DIBLOCK COPOLYMER MELTS

Dynamic light scattering in the depolarized geometry has been used to investigate the pretransitional behavior of diblock copolymer melts near the order–disorder transition (ODT). Besides the segmental orientational dynamics, an additional slow relaxation process contributes to the dynamic depolarized intensity. This new relaxation mode exhibits an almost exponential shape, a wave vector (q) independent relaxation rate, and a strongly temperature dependent amplitude that compares with the temperature dependence of the maximum of the static structure factor at q*, measured with small‐angle x‐ray scattering. An account for the characteristics of this new relaxation process is based on the coupling between orientation and order parameter fluctuations. The depolarized intensity is due to orientation and/or extension of the copolymer chains in the pretransitional state above the ODT, with the relevant length scale of the slow orientation fluctuations being close to 2π/q*.