Anisotropic formation mechanism and nanomechanics for the self-assembly process of cross-β peptides

Nanostructures self-assembled by cross-β peptides with ordered structures and advantageous mechanical properties have many potential applications in biomaterials and nanotechnologies. Quantifying the intra-and inter-molecular driving forces for peptide self-assembly at the atomistic level is essential for understanding the formation mechanism and nanomechanics of various morphologies of self-assembled peptides. We investigate the thermodynamics of the intra-and inter-sheet structure formations in the self-assembly process of cross-β peptide KIIIIK by means of steered molecular dynamics simulation combined with umbrella sampling. It is found that the mechanical properties of the intra-and inter-sheet structures are highly anisotropic with their intermolecular bond stiffness at the temperature of 300 K being 5.58 N/m and0.32 N/m, respectively. This mechanical anisotropy comes from the fact that the intra-sheet structure is stabilized by enthalpy but the inter-sheet structure is stabilized by entropy. Moreover, the formation process of KIIIIK intra-sheet structure is cooperatively driven by the van der Waals(VDW) interaction between the hydrophobic side chains and the electrostatic interaction between the hydrophilic backbones, but that of the inter-sheet structure is primarily driven by the VDW interaction between the hydrophobic side chains. Although only peptide KIIIIK is studied, the qualitative conclusions on the formation mechanism should also apply to other cross-β peptides.     

The heterogeneous distribution of the liquid phase in partially filled porous glasses and its effect on self-diffusion

The spatial distribution of the liquid phase in a typical, partially filled, porous glass (VitraPor #5) has been examined with the aid of magnetic resonance microscopy and field gradient nuclear magnetic resonance diffusometry techniques. The correlation length of the material turned out to be long enough to permit the visualization of the microscopic heterogeneity of the material by magnetic resonance imaging. Contrasts are dominated by transverse relaxation depending on local filling degree, which in turn depends on local microstructure. The bimodal heterogeneity of the latter was also visualized by scanning electron microscopy. The effect of heterogeneity on an effective diffusion coefficient has been examined for polar (water) and nonpolar (cyclohexane) molecules.     

Hierarchical processes in β-sheet peptide self-assembly from the microscopic to the mesoscopic level

Under appropriate physicochemical conditions, short peptide fragments and their synthetic mimics have been shown to form elongated cross-β nanostructures through self-assembly. The self-assembly process and the resultant peptide nanostructures are not only related to neurodegenerative diseases but also provide inspiration for the development of novel bionanomaterials. Both experimental and theoretical studies on peptide self-assembly have shown that the self-assembly process spans multiple time and length scales and is hierarchical. β-sheet self-assembly consists of three sub-processes from the microscopic to the mesoscopic level: β-sheet locking, lateral stacking, and morphological transformation. Detailed atomistic simulation studies have provided insight into the early stages of peptide nanostructure formation and the interplay between different non-covalent interactions at the microscopic level. This review gives a brief introduction of the hierarchical peptide self-assembly process and focuses on the roles of various non-covalent interactions in the sub-processes based on recent simulation, experimental, and theoretical studies.     

The mutual relationship between H-bonding and π-stacking interactions: the estimation of individual binding energies in the phenylalanine:G ··· C ternary complex

The mutual relationship between stacked interaction and the individual hydrogen bonds in the phenylalanine:guanine?···?cytosine (Ph:G-C) and phenylalanine:cytosine?···?guanine (Ph:C-G) complexes have been studied at the MPWB1K/6-311++G** and M05-2X/cc-pVDZ levels of theory. The interplay of π-stacking and H-bonding results in the weakening of both interactions. The effect of π-stacking on the geometries and individual hydrogen bond (HB) energies of guanine–cytosine (G-C) base pair have been investigated using electron densities calculated by the atoms in molecules (AIM) method at the hydrogen bond critical points (BCP). The results of AIM analysis are in good agreement with the calculated individual hydrogen bond energies. The π-stacking interactions strengths the HB1 and weakens HB2 and HB3 in the Ph:G-C complexes, while the opposite is true in the Ph:C-G complex. With the increase in the distance between phenylalanine ring and the groups involved in H-bond interactions the change in the H-bond energy increases and the changes in the individual H-bond and π-stacking energies decrease in the ternary complexes.     

Microscopic characterization of peptide nanostructures

Peptide-based nanomaterials have been utilized for various applications from regenerative medicine to electronics since they provide several advantages including easy synthesis methods, numerous routes for functionalization and biomimicry of secondary structures of proteins which leads to design of self-assembling peptide molecules to form nanostructures. Microscopic characterization at nanoscale is critical to understand processes directing peptide molecules to self-assemble and identify structure-function relationship of the nanostructures. Here, fundamental studies in microscopic characterization of peptide nanostructures are discussed to provide insights in widely used microscopy tools. In this review, we will encompass characterization studies of peptide nanostructures with modern microscopes, such as TEM, SEM, AFM, and advanced optical microscopy techniques. We will also mention specimen preparation methods and describe interpretation of the images.     

Aggregation of trichogin analogs in weakly polar solvents: PELDOR and ESR studies

The technique of pulsed electron-electron double-resonance is used to study the self-aggregation of spin labeled trichogin GA IV analogs in weakly polar solvents. The dipole-dipole spinspin relaxation of spin labels has been experimentally studied in glassy solutions of spin-labeled peptides frozen to 77 K in the mixtures of chloroform-toluene, chloroform-decalin, tetrachloromethanetoluene, dichloroethan-toluene depending on the label position in peptide and the structure of terminal groups. It is shown that the studied trichogin analogs in weakly polar solvents form aggregates whose structure depends on solvent properties and peptide structure. It is also demonstrated that the distances between spin labels which can be measured in aggregates amount to the values of 2.3, 2.6 and 3.3 nm. The lower estimate is given for the average number of peptide molecules in aggregates to within 3.1–4.3 depending on peptide structure and solvent composition.     

Cold atoms and molecules in self-assembled dipolar lattices

We study the realization of lattice models, where cold atoms and molecules move as extra particles in a dipolar crystal of trapped polar molecules. The crystal is a self-assembled floating mesoscopic lattice structure with quantum dynamics given by phonons. We show that within an experimentally accessible parameter regime extended Hubbard models with tunable long-range phonon-mediated interactions describe the effective dynamics of dressed particles.     

分子极性对类胡萝卜素共振拉曼光谱的影响

测量了非极性分子β胡萝卜素和极性分子角黄素, 在非极性溶剂CS₂和极性溶 剂1,2二氯乙烷中243–293 K的温度范围内的共振拉曼光谱. 结果表明, 溶质和溶剂的极性对拉曼光谱影响很大. 非极性分子β胡萝卜素在非极性溶剂CS₂中的拉曼散射截面最大, 线宽最窄, 而极性分子角黄素在极性溶剂1,2二氯乙烷中的拉曼散射截面最小, 线宽最大. 用溶剂效应及线性多烯分子的“相干弱阻尼电子-晶格振动”, “有效共轭长度”模型给予了解释.     

The Solvent Effect on Spin Exchange in Long-Chain Nitroxide Biradicals

Intramolecular electron spin exchange, as a function of temperature and the solvent viscosity, polarity and relaxation properties of the solvent molecules, has been studied by X-band electron paramagnetic resonance (EPR) spectroscopy in two long-chain flexible nitroxide biradicals existing in fluid solutions in three spectroscopically different spatial conformations. Certain thermodynamic parameters of the conformational rearrangements were calculated from the EPR spectra. Spin exchange in two biradicals dissolved in five different alcohols was compared with that in a nonpolar solvent (toluene), polar protic (water) and aprotic (acetonitrile), and with thermodynamic characteristics of the solvents. Distinct correlations were found between macroscopic (solvent viscosity, polarity) and microscopic (solvent longitudinal relaxation time) characteristics of solvents, and thermodynamic parameters of the intramolecular conformational transitions. Authors' address: Van Anh Tran, Institute of Physical and Theoretical Chemistry, Graz University of Technology, Technikerstrasse 4, 8010 Graz, Austria     

Unifying interfacial self-assembly and surface freezing

X-ray investigations reveal that the monolayers formed at the bulk alkanol-sapphire interface are densely packed with the surface-normal molecules hydrogen bound to the sapphire. About 30-35 °C above the bulk, these monolayers both melt reversibly and partially desorb. This system exhibits balanced intermolecular and molecule-substrate interactions which are intermediate between self-assembled and surface-frozen monolayers, each dominated by one interaction. The phase behavior is rationalized within a thermodynamic model comprising interfacial interactions, elasticity, and entropic effects. Separating the substrate from the melt leaves the monolayer structurally intact.     

The Use of Molecular Probes for the Characterization of Nanoporous Adsorbents

Molecular probes can be employed in three different ways for the characterization of nanoporous adsorbents. The simplest approach is to use a range of globular nonpolar molecules of different diameter in order to assess the effective size of the pore entrances in a molecular sieve. For this purpose, conventional gas adsorption (static or dynamic measurements) or gas chromatographic techniques can be used. The aim of the second approach is to characterize the nanopore structure with the aid of nitrogen adsorption at 77 K together with isotherm and adsorption energy measurements with a variety of adsorptives of different molecular size, shape and polarity. The third approach is to make use of polar probe molecules (notably water and alcohols) to investigate the surface chemistry and stability of the adsorbent.     

分子动力学模拟研究方解石表面润湿性反转机理

利用分子动力学模拟技术从分子尺度探究方解石表面润湿性反转机理.首先,研究方解石表面润湿性反转过程;而后,从原油分子-方解石表面与原油分子-原油分子/水分子相互作用两个方面系统揭示方解石表面润湿性反转机理.结果:(1)水分子能够驱离方解石表面弱吸附的非极性分子造成润湿性的改变,但不能驱离强吸附的极性分子使润湿性反转难以实现;(2)原油分子极性越强与方解石表面相互作用越强,极性分子与方解石表面之间主要为静电力,非极性分子与方解石表面之间主要为范德华力;(3)原油分子极性越相近分子之间的相互作用越强,分子极性相差越大分子之间的相互作用越弱.非极性分子之间主要是范德华力,极性分子之间主要是静电力;(4)原油分子在方解石表面和水分子的共同作用下形成乙酸-吡啶-水-甲苯-己烷的稳定吸附序列.本研究为靶向提高采收率技术的设计与应用提供理论基础.     

Structure correlations of water molecules in a concentrated aqueous solution of ethanol

Monte Carlo calculation results for water–ethanol mixtures calculated in the isothermal and isobaric ensemble at T=300 K are presented. The analysis of the radial distribution functions for hydrogen bonding between ethanol molecule and water molecules was done. The concentrations of ethanol 0.75 show characteristics features of hydrogen-bonded liquids. The influence of the polar solvent molecule on water local structure and the hydrogen bond nets ware analyzed. Radial distribution functions for water–water interactions calculated in pure water and water–ethanol system are compared.     

Anion bridges drive salting out of a simple amphiphile from aqueous solution

Neutron diffraction with isotope substitution has been used to determine the structural changes that occur on the addition of a simple salting-out agent to a dilute aqueous alcohol solution. The striking results obtained demonstrate a relatively simple process occurs in which interamphiphile anionic salt bridges are formed between the polar groups of the alcohol molecules. These ion bridges drive an increase in the exposure of the alcohol molecule nonpolar surface to the solvent water and hence point the way to their eventual salting out by the hydrophobic effect.     

Study of the complexation and solvation of polar molecules in binary solvents by differential spectroscopy

A method of application of differential absorption spectroscopy for determining the absorption spectra of primary 1: 1 solvated complexes between polar molecules of an organic dye and the active component of a binary solvent whose neutral component is a nonpolar liquid is proposed. The method was tested on diluted solutions of 4-dimethylaminochalcone (4-DMC) (which is one of the most efficient spectral-luminescent probes used in present-day medical and biological investigations) in mixtures of n-hexane with acetone at extremely small concentrations of the polar component. It is shown that the experimentally found absolute shift of the long-wavelength absorption band of 4-DMC is in satisfactory quantitative agreement with the analogous value obtained independently on the basis of the theory describing the joint effect of nonlinear (complexation) and linear (solvation) dipole-dipole interactions on the spectral band positions.     

Chiral plasmonics and enhanced chiral light-matter interactions

Chirality, which describes the broken mirror symmetry in geometric structures, exists macroscopically in our daily life as well as microscopically down to molecular levels. Correspondingly, chiral molecules interact differently with circularly polarized light exhibiting opposite handedness(left-handed and right-handed). However, the interaction between chiral molecules and chiral light is very weak. In contrast, artificial chiral plasmonic structures can generate "super-chiral" plasmonic near-field, leading to enhanced chiral light-matter(or chiroptical) interactions. The "super-chiral" near-field presents different amplitude and phase under opposite handedness incidence, which can be utilized to engineer linear and nonlinear chiroptical interactions. Specifically,in the interaction between quantum emitters and chiral plasmonic structures, the chiral hot spots can favour the emission with a specific handedness. This article reviews the state-of-the-art research on the design, fabrication and chiroptical response of different chiral plasmonic nanostructures or metasurfaces. This review also discusses enhanced chiral light-matter interactions that are essential for applications like chirality sensing, chiral selective light emitting and harvesting. In the final part, the review ends with a perspective on future directions of chiral plasmonics.     

Dipole orientational order at liquid/vapor surfaces

We present ellipsometric observations of the orientational order alpha(2) of highly polar molecules at the noncritical liquid/vapor surface of critical polar+nonpolar mixtures. The dipoles, which are repelled from the interface via interactions with their image dipoles, are preferentially oriented with their axes parallel to the surface and possess an orientational order which is well described by alpha(2) approximately -t(2beta)D+(z/xi), where t=[T-T(c)]/T(c) is the reduced temperature, beta=0.328 is a critical exponent, and D+ is a universal function of the dimensionless depth z/xi with surface correlation length xi.     

Controllable growth of low-dimensional nanostructures on well-defined surfaces

The controllable growth of nanostructures with desired geometric order and well-defined shapes has stimulated great interest due to its applicability in the development of microelectronic devices. Self-assembly is an efficient and versatile way to guide the atoms or molecules into low-dimensional nanostructures as a consequence of balancing complex interplay between adsorbate-adsorbate and adsorbate-substrate interfacial interactions. The tailoring of low-dimensional nanostruc- tures by control of inter-adsorbate and adsorbate-substrate interfacial interactions is reviewed. Such inherent interactions greatly influence not only the size and shape of the growing nanostructures, but also their chemical identity. The degree of interaction between adsorbates can be controlled via preparation procedures, opening up the study of the influence of this phenomenon with respect to reactivity and catalytic behavior. The formation of well-defined molecular layers can be controlled not only by repulsive molecule-molecule interaction but also by symmetry matching or charge transfer be- tween adsorbed molecules and the substrate. It has become obvious that inter-adsorbate and adsorbate-substrate interfacial interactions can be tuned to fabricate diverse surface nanostructures from semiconductor, metallic, and molecular materials.     

Vibrational relaxation study in carbonyl containing molecule: role of hydrodynamic and dispersion forces

The isotropic Raman component of the C = O stretching mode of ethyl acetate (EA) was analyzed using various polar and nonpolar solvents. It was found that the bandshape approaches towards Lorentzian at high dilution using the curve‐fitting method. The isotropic Raman band was also analyzed by estimating the correlation coefficient with reference to the Lorentzian lineshape using a simple method of linear‐curve fitting. The effects of dispersion and hydrodynamic forces on bandwidth were studied in details. The vibrational relaxation rate was studied using certain parameters and it was found that the microscopic based parameter can explain the complexities occurring in solute–solvent interactions. Copyright © 2007 John Wiley & Sons, Ltd.