scholarly journals Asymmetric Attosecond Photoionization in Molecular Shape Resonance

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiaochun Gong ◽  
Wenyu Jiang ◽  
Jihong Tong ◽  
Junjie Qiang ◽  
Peifen Lu ◽  
...  
Keyword(s):  
Molecular Shape ◽  
Shape Resonance

Application of complex coordinate SCF techniques to a molecular shape resonance: The 2Πg state of N2−

1980 ◽  
Vol 73 (12) ◽  
pp. 6347-6348 ◽  
Author(s):  
T. N. Rescigno ◽  
A. E. Orel ◽  
C. W. McCurdy
Keyword(s):  
Molecular Shape ◽  
Shape Resonance

scholarly journals Attosecond timing of electron emission from a molecular shape resonance

2020 ◽  
Vol 6 (31) ◽  
pp. eaba7762 ◽  
Author(s):  
S. Nandi ◽  
E. Plésiat ◽  
S. Zhong ◽  
A. Palacios ◽  
D. Busto ◽  
...  
Keyword(s):  
Potential Barrier ◽  
Molecular Spectroscopy ◽  
Molecular Shape ◽  
High Spectral Resolution ◽  
Shape Resonance ◽  
Nuclear Motion ◽  
Centrifugal Barrier ◽  
Ionization Time ◽  
Molecular Photoionization ◽  
Franck Condon

Shape resonances in physics and chemistry arise from the spatial confinement of a particle by a potential barrier. In molecular photoionization, these barriers prevent the electron from escaping instantaneously, so that nuclei may move and modify the potential, thereby affecting the ionization process. By using an attosecond two-color interferometric approach in combination with high spectral resolution, we have captured the changes induced by the nuclear motion on the centrifugal barrier that sustains the well-known shape resonance in valence-ionized N2. We show that despite the nuclear motion altering the bond length by only 2%, which leads to tiny changes in the potential barrier, the corresponding change in the ionization time can be as large as 200 attoseconds. This result poses limits to the concept of instantaneous electronic transitions in molecules, which is at the basis of the Franck-Condon principle of molecular spectroscopy.

scholarly journals Evolution of a Molecular Shape Resonance Along a Stretching Chemical Bond

2020 ◽  
Vol 125 (12) ◽  
Author(s):  
Felix Brausse ◽  
Florian Bach ◽  
Faruk Krečinić ◽  
Marc J. J. Vrakking ◽  
Arnaud Rouzée
Keyword(s):  
Chemical Bond ◽  
Molecular Shape ◽  
Shape Resonance

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Liquid Crystal Trimers Incorporating Saturated Isosteres of Benzene and Exhibiting Modulated Nematic Phases

2019 ◽  
Author(s):  
Adam Al-Janabi ◽  
Richard Mandle
Keyword(s):  
Liquid Crystal ◽  
Helical Structure ◽  
Molecular Shape ◽  
Saturated Hydrocarbons ◽  
Fluid System ◽  
Structural Requirement ◽  
Disubstituted Benzene ◽  
Bona Fide ◽  
Nematic Phases ◽  
Bend Angles

<p>The nematic twist-bend (N<sub>TB</sub>) liquid crystal phase possesses a local helical structure with a pitch length of a few nanometres and is the first example of spontaneous symmetry breaking in a fluid system. All known examples of the N­<sub>TB­</sub> phase occur in materials whose constituent mesogenic units are aromatic hydrocarbons. It is not clear if this is due to synthetic convenience or a <i>bona fide</i> structural requirement for a material to exhibit this phase of matter. In this work we demonstrate that materials consisting largely of saturated hydrocarbons could also give rise to this mesophase. Furthermore, replacement of 1,4-disubstituted benzene with <i>trans</i> 1,4-cyclohexane or even 1,4-cubane does not especially alter the transition temperatures of the resulting material nor does it appear to impact upon the heliconical tilt angle, suggesting the local structure of the phase is unperturbed. Calculating the probability distribution of bend angles reveals that the choice of isosteric group has little impact on the overall molecular shape, demonstrating the shape-driven nature of the N<sub>TB</sub> phase. </p>

PubChem and ChEMBL Beyond Lipinski

2019 ◽  
Author(s):  
Jean-Louis Reymond ◽  
Mahendra Awale ◽  
Daniel Probst ◽  
Alice Capecchi
Keyword(s):  
Nearest Neighbor ◽  
Molecular Shape ◽  
Biological Properties ◽  
Web Based ◽  
Large Molecules ◽  
Interactive Tools ◽  
Small Molecule Drugs ◽  
Pubchem Database ◽  
Nearest Neighbor Searches ◽  
Insight Into

<p>Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.</p>

Membrane Alterations Induced by Amphiphiles

1989 ◽  
Vol 16 (3) ◽  
pp. 274-280
Author(s):  
Boris Isomaa ◽  
Henry Hägerstrand ◽  
Gun I.L. Paatero
Keyword(s):  
Ion Transport ◽  
Lipid Bilayer ◽  
Erythrocyte Membrane ◽  
Cell Shape ◽  
Osmotic Fragility ◽  
Molecular Shape ◽  
Specific Interactions ◽  
Amphiphilic Compounds ◽  
Rapid Formation ◽  
Polar Parts

Amphiphilic compounds with distinct apolar and polar parts are readily intercalated into the erythrocyte membrane. When intercalated into the membrane, amphiphiles are probably orientated so that the polar head is at the polar-apolar interface of the lipid bilayer and the hydrophobic part within the apolar core of the bilayer. However, by virtue of their difference in molecular shape from the bulk lipids of the lipid bilayer, it is possible that the intercalated amphiphiles are partly segregated from bulk lipids and accumulate at protein-lipid interfaces in the bilayer, where the packing of the bilayer lipids may be less ordered. Our studies show that amphiphiles, when intercalated into the erythrocyte membrane, trigger alterations in several membrane-connected functions. Some of the alterations induced (decreased osmotic fragility, increased passive potassium fluxes) seem to be due to non-specific interactions of the amphiphiles with the membrane, whereas other functions (ion transport mediated by membrane proteins, regulation of cell shape) seem to be sensitive to particular features of the amphiphiles. Our studies indicate that the intercalation of amphiphiles into the erythrocyte membrane must involve rearrangements within the lipid bilayer. We have suggested that, when intercalated into the lipid bilayer, amphiphiles trigger a rapid formation of non-bilayer phases, which protect the bilayer against a collapse and bring about a trans-bilayer redistribution of intercalated amphiphiles as well as of bilayer lipids. At high sublytic concentrations, this process may also involve a release of microvesicles from the membrane.

scholarly journals Molecular Shape Descriptors. 2. Quantitative Structure-Activity Relationships Based Upon Three-Dimensional Molecular Shape Descriptor

1985 ◽  
Vol 40 (11) ◽  
pp. 1114-1120
Author(s):  
loan Motoc ◽  
Garland R. Marshall
Keyword(s):  
Enzyme Inhibitor ◽  
Three Dimensional ◽  
Shape Descriptor ◽  
Molecular Shape ◽  
Quantitative Structure Activity Relationship ◽  
Quantitative Structure ◽  
E Coli ◽  
Interactional Pattern ◽  
Structure Activity ◽  
Quantitative Structure Activity Relationships

A methodology to incorporate the three-dimensional molecular shape descriptor (3 D-MSD) into a quantitative structure-activity relationship is discussed in detail. The 3 D-MSD is calculated and correlated with Kiapp values for a set of 2,4-diamino-5-benzylpyrimidines which inhibit E. coli DHFR. The correlation (n = 22, r = 0.95, s = 0.214, F = 55.10) indicates that the polarization interaction dominates the enzyme-inhibitor interactional pattern.

ChemInform Abstract: SOLUTION PROPERTIES OF PHYCOCYANIN PART 2, STUDIES OF THE MOLECULAR SHAPE AND SIZE BY USING THE SHELL MODEL

1975 ◽  
Vol 6 (27) ◽  
pp. no-no
Author(s):  
AKIRA KOTERA ◽  
TAKAHIDE SAITO ◽  
NAOMICHI ISO ◽  
HARUO MIZUNO ◽  
NOBUO TAKI
Keyword(s):  
Shell Model ◽  
Molecular Shape ◽  
Solution Properties ◽  
Shape And Size
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