steric repulsion
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2021 ◽  
Vol 8 ◽  
Author(s):  
Batuhan Kav ◽  
Bruno Demé ◽  
Christian Gege ◽  
Motomu Tanaka ◽  
Emanuel Schneck ◽  
...  

Glycolipids mediate stable membrane adhesion of potential biological relevance. In this article, we investigate the trans- and cis-interactions of glycolipids in molecular dynamics simulations and relate these interactions to the glycolipid-induced average separations of membranes obtained from neutron scattering experiments. We find that the cis-interactions between glycolipids in the same membrane leaflet tend to strengthen the trans-interactions between glycolipids in apposing leaflets. The trans-interactions of the glycolipids in our simulations require local membrane separations that are significantly smaller than the average membrane separations in the neutron scattering experiments, which indicates an important role of membrane shape fluctuations in glycolipid trans-binding. Simulations at the experimentally measured average membrane separations provide a molecular picture of the interplay between glycolipid attraction and steric repulsion of the fluctuating membranes probed in the experiments.


Author(s):  
Karolis Norvaisa ◽  
Sophie Maguire ◽  
Claire Donohoe ◽  
John E. O'Brien ◽  
Brendan Twamley ◽  
...  

2021 ◽  
Author(s):  
Jacob O. Rothbaum ◽  
Alessandro Motta ◽  
Yosi Kratish ◽  
Tobin Marks

C-H activation and functionalization of pyridinoid azines is a key transformation forthe synthesis of many natural products, pharmaceuticals, and materials. Reflecting the azinyl nitrogen lone-pair steric repulsion, tendency to irreversibly bind to metal ion catalysts, and the electron-deficient nature of pyridine, C-H functionalization at the important a-position remains challenging. Thus, the development of earth abundant catalysts for the a-selective mono-functionalization of azines is a crucial hurdle for modern chemical synthesis. Here, the selective organolanthanide catalyzed a-mono-borylation of a diverse series of pyridines is reported, affording a valuable precursor for cross-coupling reactions. Experimental and theoretical mechanistic evidence support the formation of a C-H activated η2-lanthanide-azine complex, followed by intermolecular a-mono-borylation via σ-bond metathesis. Notably, varying the lanthanide identity and substrate electronics promotes chemodivergence of the catalytic selectivity: smaller/more electrophilic lanthanide3+ ions and electron-rich substrates favor selective a-C-H functionalization, whereas larger/less electrophilic lanthanide3+ 1 ions and electron poor substrates favor selective B-N bond-forming 1,2-dearomatization. Such organolanthanide series catalytic chemodivergence is, to our knowledge, unprecedented.


Materials ◽  
2021 ◽  
Vol 14 (20) ◽  
pp. 6147
Author(s):  
Mirosław Jabłoński

This article discusses the properties of as many as 30 carbene–ZnX2 (X = H, Me, Et) complexes featuring a zinc bond C⋯Zn. The group of carbenes is represented by imidazol-2-ylidene and its nine derivatives (labeled as IR), in which both hydrogen atoms of N-H bonds have been substituted by R groups with various spatial hindrances, from the smallest Me, iPr, tBu through Ph, Tol, and Xyl to the bulkiest Mes, Dipp, and Ad. The main goal is to study the relationship between type and size of R and X and both the strength of C⋯Zn and the torsional angle of the ZnX2 plane with respect to the plane of the imidazol-2-ylidene ring. Despite the considerable diversity of R and X, the range of dC⋯Zn is quite narrow: 2.12–2.20 Å. On the contrary, D0 is characterized by a fairly wide range of 18.5–27.4 kcal/mol. For the smallest carbenes, the ZnX2 molecule is either in the plane of the carbene or is only slightly twisted with respect to it. The twist angle becomes larger and more varied with the bulkier R. However, the value of this angle is not easy to predict because it results not only from the presence of steric effects but also from the possible presence of various interatomic interactions, such as dihydrogen bonds, tetrel bonds, agostic bonds, and hydrogen bonds. It has been shown that at least some of these interactions may have a non-negligible influence on the structure of the IR–ZnX2 complex. This fact should be taken into account in addition to the commonly discussed R⋯X steric repulsion.


2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Sun Yan

The adsorptions of CO on Ni(110) surface at different coverages have been investigated by first-principle calculations. The results show that CO will be bonded at short bridge site preferentially. And CO preferentially absorbs upright at short bridge sites and top sites at 1/6 monolayer coverage. With increasing coverage to 0.5 ML, the enhanced steric repulsion leads to the slope of CO. For 1/6 and 1/2 monolayer coverage, CO is mainly bonded at short bridge site and atop site simultaneously at a certain ratio. When CO coverage is 1 monolayer, CO absorbs at short bridge site and forms p2mg configuration. As the coverage of CO is increased to finally form the p2mg structure, there is a continuous frequency shift up to the value 1962.27 cm-1. The vibration frequencies we calculated are consistent with relative experimental results. DOS of CO molecules and Ni atoms are discussed too.


Polymers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2031
Author(s):  
Panayotis Benetatos ◽  
Mohammadhosein Razbin

Semiflexible nunchucks are block copolymers consisting of two long blocks with high bending rigidity jointed by a short block of lower bending stiffness. Recently, the DNA nanotube nunchuck was introduced as a simple nanoinstrument that mechanically magnifies the bending angle of short double-stranded (ds) DNA and allows its measurement in a straightforward way [Fygenson et al., Nano Lett. 2020, 20, 2, 1388–1395]. It comprises two long DNA nanotubes linked by a dsDNA segment, which acts as a hinge. The semiflexible nunchuck geometry also appears in dsDNA with a hinge defect (e.g., a quenched denaturation bubble or a nick), and in end-linked stiff filaments. In this article, we theoretically investigate various aspects of the conformations and the tensile elasticity of semiflexible nunchucks. We analytically calculate the distribution of bending fluctuations of a wormlike chain (WLC) consisting of three blocks with different bending stiffness. For a system of two weakly bending WLCs end-jointed by a rigid kink, with one end grafted, we calculate the distribution of positional fluctuations of the free end. For a system of two weakly bending WLCs end-jointed by a hinge modeled as harmonic bending spring, with one end grafted, we calculate the positional fluctuations of the free end. We show that, under certain conditions, there is a pronounced bimodality in the transverse fluctuations of the free end. For a semiflexible nunchuck under tension, under certain conditions, there is bimodality in the extension as a function of the hinge position. We also show how steric repulsion affects the bending fluctuations of a rigid-rod nunchuck.


2021 ◽  
Author(s):  
Tu Tran

The stabilizing behaviour of soluble soy polysaccharide (SSPS) on acidified dispersions of soy protein isolate (SPI) and SPI-stabilized emulsions was studied. SPI and SSPS suspensions were characterized via light scattering, surface charge measurement, turbidity, sedimentation analysis, and light microscopy. At acidic pH (pH 6-3), it was found the addition of at least 0.25 wt% SSPS was required to stabilize 0.75 wt% SPI suspensions against aggregation and phase separation, likely via steric repulsion. The mechanism of SPI-SSPS interaction was shown to be electrostatic in nature by testing the effects of increased ionic strength of the suspensions. The stabilizing effect of SSPS on SPI was then applied to 5% oil-in-water emulsions. The presence of SSPS stabilized the emulsions against droplet size increases and phase separation over time. Overall, the results demonstrated that it was possible for SSPS to stabilize SPI suspensions and that SPI-SSPS interactions may be used as a tool to stabilize O/W emulsions.


2021 ◽  
Author(s):  
Tu Tran

The stabilizing behaviour of soluble soy polysaccharide (SSPS) on acidified dispersions of soy protein isolate (SPI) and SPI-stabilized emulsions was studied. SPI and SSPS suspensions were characterized via light scattering, surface charge measurement, turbidity, sedimentation analysis, and light microscopy. At acidic pH (pH 6-3), it was found the addition of at least 0.25 wt% SSPS was required to stabilize 0.75 wt% SPI suspensions against aggregation and phase separation, likely via steric repulsion. The mechanism of SPI-SSPS interaction was shown to be electrostatic in nature by testing the effects of increased ionic strength of the suspensions. The stabilizing effect of SSPS on SPI was then applied to 5% oil-in-water emulsions. The presence of SSPS stabilized the emulsions against droplet size increases and phase separation over time. Overall, the results demonstrated that it was possible for SSPS to stabilize SPI suspensions and that SPI-SSPS interactions may be used as a tool to stabilize O/W emulsions.


2021 ◽  
Author(s):  
Silvia Acosta Guitierrez ◽  
Joseph Buckley ◽  
Giuseppe Battaglia

Long and complex chains of sugars, called glycans, often coat both the cell and protein surface. Glycans both modulate specific interactions and protect cells. On the cell surface, these sugars form a cushion known as the glycocalyx. Here, we show that Heparan Sulfate (HS) chains - part of the glycocalyx - and other glycans - expressed on the surface of both host and virus proteins - have a critical role in modulating both attractive and repulsive potentials during viral infection. We analyse the SARS-CoV-2 virus, modelling its spike proteins binding to HS chains and two key entry receptors, ACE2 and TMPRSS2. We include the volume exclusion effect imposed on the HS chains impose during virus insertion into glycocalyx and the steric repulsion caused by changes in the conformation of the ACE2 glycans involved in binding to the spike. We then combine all these interactions, showing that the interplay of all these components is critical to the behaviour of the virus. We show that the virus tropism depends on the combinatorial expression of both HS chains and receptors. Finally, we demonstrate that when both HS chains and entry receptors express at high density, steric effects dominate the interaction, preventing infection.


Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 897
Author(s):  
Ryusei Hoshikawa ◽  
Kosuke Yoshida ◽  
Ryoji Mitsuhashi ◽  
Masahiro Mikuriya ◽  
Takashi Okuno ◽  
...  

Oxido bridges commonly form between iron(III) ions, but their bond angles and symmetry vary with the circumstances. A large number of oxido-bridged dinuclear iron(III) complexes have been structurally characterized. Some of them belong to the C2 point group, possessing bent Fe–O–Fe bonds, while some others belong to the Ci symmetry, possessing the linear Fe–O–Fe bonds. The question in this study is what determines the structures and symmetry of oxido-bridged dinuclear iron(III) complexes. In order to gain further insights, three oxido-bridged dinuclear iron(III) complexes were newly prepared with 2,2′-bipyridine (bpy) and 1,10-phenanthroline (phen) ligands: [Fe2OCl2(bpy)4][PF6]2 (1), [Fe2O(NO3)2(bpy)4][PF6]2·0.6MeCN·0.2(2-PrOH) (2), and [Fe2OCl2(phen)4][PF6]2·MeCN·0.5H2O (3). The crystal structures of 1, 2, and 3 were determined by the single-crystal X-ray diffraction method, and all of them were found to have the bent Fe–O–Fe bonds. Judging from the crystal structure, some intramolecular interligand hydrogen bonds were found to play an important role in fixing the structures. Additional density functional theory (DFT) calculations were conducted, also for a related oxido-bridged dinuclear iron(III) complex with a linear Fe–O–Fe bond. We conclude that the Fe–O–Fe bridge tends to bend like a water molecule, but is often stretched by interligand steric repulsion, and that the structures are mainly controlled by the intramolecular interligand interactions.


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