Mechanophores in polymer mechanochemistry: Insights from single-molecule experiments and computer simulations

2021 ◽  
pp. 113-139
Author(s):  
Wenjin Li
2015 ◽  
Vol 7 (4) ◽  
pp. 323-327 ◽  
Author(s):  
Junpeng Wang ◽  
Tatiana B. Kouznetsova ◽  
Zhenbin Niu ◽  
Mitchell T. Ong ◽  
Hope M. Klukovich ◽  
...  

Synlett ◽  
2021 ◽  
Author(s):  
Robert T O'Neill ◽  
Roman Boulatov

The exciting field of polymer mechanochemistry has made great empirical progress in discovering reactions in which a stretching force accelerates scission of strained bonds using single molecule force spectroscopy and ultra-sonication experiments. Understanding why these reactions happen, i.e., the fundamental physical processes that govern coupling of macroscopic motion to chemical reactions, as well as discovering other patterns of mechanochemical reactivity require complementary techniques, which permit a much more detailed characterization of reaction mechanisms and the distribution of force in reacting molecules than are achievable in SMFS or ultrasonication. A molecular force probe allows the specific pattern of molecular strain that is responsible for localized reactions in stretched polymers to be reproduced accurately in non-polymeric substrates using molecular design rather than atomistically intractable collective motions of millions of atoms comprising macroscopic motion. In this review, we highlight the necessary features of a useful molecular force probe and describe their realization in stiff stilbene macrocycles. We describe how studying these macrocycles using classical tools of physical organic chemistry has allowed detailed characterizations of mechanochemical reactivity, explain some of the most unexpected insights enabled by these probes and speculate how they may guide the next stage of mechanochemistry.


2008 ◽  
Vol 9 (3-4) ◽  
pp. 317-325 ◽  
Author(s):  
D. Marenduzzo

There is now a considerable literature on computer simulations of DNA packaging inside bacteriophage capsids. While most studies have reached a semiquantitative or qualitative agreement with single molecule packaging and ejection studies, several quantitative answers are to date still lacking, needing either more accurate measurements or more realistic or difficult simulations. Here, I briefly review the outstanding questions in this field and report some new numerical results on DNA packaging inside the phi29 phage, modelled either as a capped sphero-cylinder or as a sphere with the same internal volume. These simulations include electrostatics and a realistic genome length, and contribute to seriously questioning the inverse spool model, which arises from a purely continuum mechanics view of the problem, and is still commonly adopted to describe the shape of the packaged genome.


Author(s):  
R. Gronsky

The phenomenon of clustering in Al-Ag alloys has been extensively studied since the early work of Guinierl, wherein the pre-precipitation state was characterized as an assembly of spherical, ordered, silver-rich G.P. zones. Subsequent x-ray and TEM investigations yielded results in general agreement with this model. However, serious discrepancies were later revealed by the detailed x-ray diffraction - based computer simulations of Gragg and Cohen, i.e., the silver-rich clusters were instead octahedral in shape and fully disordered, atleast below 170°C. The object of the present investigation is to examine directly the structural characteristics of G.P. zones in Al-Ag by high resolution transmission electron microscopy.


Author(s):  
R. Herrera ◽  
A. Gómez

Computer simulations of electron diffraction patterns and images are an essential step in the process of structure and/or defect elucidation. So far most programs are designed to deal specifically with crystals, requiring frequently the space group as imput parameter. In such programs the deviations from perfect periodicity are dealt with by means of “periodic continuation”.However, for many applications involving amorphous materials, quasiperiodic materials or simply crystals with defects (including finite shape effects) it is convenient to have an algorithm capable of handling non-periodicity. Our program “HeGo” is an implementation of the well known multislice equations in which no periodicity assumption is made whatsoever. The salient features of our implementation are: 1) We made Gaussian fits to the atomic scattering factors for electrons covering the whole periodic table and the ranges [0-2]Å−1 and [2-6]Å−1.


Author(s):  
George C. Ruben

Single molecule resolution in electron beam sensitive, uncoated, noncrystalline materials has been impossible except in thin Pt-C replicas ≤ 150Å) which are resistant to the electron beam destruction. Previously the granularity of metal film replicas limited their resolution to ≥ 20Å. This paper demonstrates that Pt-C film granularity and resolution are a function of the method of replication and other controllable factors. Low angle 20° rotary , 45° unidirectional and vertical 9.7±1 Å Pt-C films deposited on mica under the same conditions were compared in Fig. 1. Vertical replication had a 5A granularity (Fig. 1c), the highest resolution (table), and coated the whole surface. 45° replication had a 9Å granulartiy (Fig. 1b), a slightly poorer resolution (table) and did not coat the whole surface. 20° rotary replication was unsuitable for high resolution imaging with 20-25Å granularity (Fig. 1a) and resolution 2-3 times poorer (table). Resolution is defined here as the greatest distance for which the metal coat on two opposing faces just grow together, that is, two times the apparent film thickness on a single vertical surface.


Author(s):  
George C. Ruben ◽  
William Krakow

Tobacco primary cell wall and normal bacterial Acetobacter xylinum cellulose formation produced a 36.8±3Å triple-stranded left-hand helical microfibril in freeze-dried Pt-C replicas and in negatively stained preparations for TEM. As three submicrofibril strands exit the wall of Axylinum , they twist together to form a left-hand helical microfibril. This process is driven by the left-hand helical structure of the submicrofibril and by cellulose synthesis. That is, as the submicrofibril is elongating at the wall, it is also being left-hand twisted and twisted together with two other submicrofibrils. The submicrofibril appears to have the dimensions of a nine (l-4)-ß-D-glucan parallel chain crystalline unit whose long, 23Å, and short, 19Å, diagonals form major and minor left-handed axial surface ridges every 36Å.The computer generated optical diffraction of this model and its corresponding image have been compared. The submicrofibril model was used to construct a microfibril model. This model and corresponding microfibril images have also been optically diffracted and comparedIn this paper we compare two less complex microfibril models. The first model (Fig. 1a) is constructed with cylindrical submicrofibrils. The second model (Fig. 2a) is also constructed with three submicrofibrils but with a single 23 Å diagonal, projecting from a rounded cross section and left-hand helically twisted, with a 36Å repeat, similar to the original model (45°±10° crossover angle). The submicrofibrils cross the microfibril axis at roughly a 45°±10° angle, the same crossover angle observed in microflbril TEM images. These models were constructed so that the maximum diameter of the submicrofibrils was 23Å and the overall microfibril diameters were similar to Pt-C coated image diameters of ∼50Å and not the actual diameter of 36.5Å. The methods for computing optical diffraction patterns have been published before.


Author(s):  
Vladimir Yu. Kolosov ◽  
Anders R. Thölén

In this paper we give a short overview of two TEM applications utilizing the extinction bend contour technique (BC) giving the advantages and disadvantages; especially we consider two areas in which the BC technique remains unique. Special attention is given to an approach including computer simulations of TEM micrographs.BC patterns are often observed in TEM studies but are rarely exploited in a serious way. However, this type of diffraction contrast was one of the first to be used for analysis of imperfections in crystalline foils, but since then only some groups have utilized the BC technique. The most extensive studies were performed by Steeds, Eades and colleagues. They were the first to demonstrate the unique possibilities of the BC method and named it real space crystallography, which developed later into the somewhat similar but more powerful convergent beam method. Maybe, due to the difficulties in analysis, BCs have seldom been used in TEM, and then mainly to visualize different imperfections and transformations.


2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.


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