scholarly journals Vibration Effect on the Extracted Molecular Structure from Laser-Induced Electron Diffraction

10.29007/xj9p ◽  
2020 ◽  
Author(s):  
Thi Hien Nguyen ◽  
Ngoc Loan Phan Thi
Keyword(s):  
Molecular Structure ◽  
Electron Diffraction ◽  
Cross Section ◽  
Scattering Theory ◽  
Structural Information ◽  
Molecular Structures ◽  
Molecular Vibration ◽  
Initial Structure ◽  
Vibration Effect ◽  
Advanced Model

It is well-known that the laser-induced electron diffraction (LIED) contains molecular structural information that can be extracted with a spatial resolution of angström and time resolution of a few femtoseconds [1, 2]. The retrieval is based on the quantitative rescattering method (QRS) allowing the LIED signal to be split into two components [3], one of which is a laser-free differential cross-section (DCS) containing molecular structure. The method based on fitting the experimental DCS extracted from the LIED spectra to the theoretical DCS calculated with assumed initial structure parameters then allows one to reveal the real molecular structures. The theoretical DCS of molecules is treated within the independent atoms model (IAM) [1, 4] or the more advanced model based on the multiple scattering theory (MS) [2, 5].In this report, we talk about how to consider the molecular vibration effect to the MS model and examine this effect of molecular vibrations on the DCS by comparing the oscillation component with the component of the MS second-order describing the interference of the scattering waves. We perform an application of the developed theory for some diatomic molecules.

The infrared spectrum and molecular structure of sulphur trioxide

1970 ◽  
Vol 314 (1518) ◽  
pp. 329-339 ◽  
Keyword(s):  
Molecular Structure ◽  
Fine Structure ◽  
Electron Diffraction ◽  
Infrared Spectrum ◽  
Molecular Vibration ◽  
Electron Diffraction Data ◽  
Vibration Frequencies ◽  
Coriolis Coupling ◽  
Coupling Coefficients ◽  
Sulphur Trioxide

The rotational fine structure of several parallel and perpendicular type bands of sulphur trioxide, an oblate symmetric top, has been partially resolved and analysed. A more convincing assignment of the molecular vibration frequencies has been made than that based upon earlier measurements of the infrared and Ram an spectra. Rotational constants and Coriolis coupling coefficients have been derived, and a more accurate value of the S ═ O bond length has been obtained (1.41 ± 0.01 Å) than that previously assumed on the basis of electron diffraction data. Some vibrational-rotational interactions which affect the appearance of certain bands have been explained.

scholarly journals Leveraging molecular structure and bioactivity with chemical language models for drug design

2021 ◽  
Author(s):  
Michael Moret ◽  
Francesca Grisoni ◽  
Cyrill Brunner ◽  
Gisbert Schneider
Keyword(s):  
Molecular Structure ◽  
De Novo ◽  
Molecular Design ◽  
Structural Information ◽  
Molecular Structures ◽  
Language Models ◽  
Structure Generation ◽  
Compound Screening ◽  
Phosphoinositide 3 Kinase ◽  
Chemical Language

Generative chemical language models (CLMs) can be used for de novo molecular structure generation. These CLMs learn from the structural information of known molecules to generate new ones. In this paper, we show that “hybrid” CLMs can additionally leverage the bioactivity information available for the training compounds. To computationally design ligands of phosphoinositide 3-kinase gamma (PI3Kγ), we created a large collection of virtual molecules with a generative CLM. This primary virtual compound library was further refined using a CLM-based classifier for bioactivity prediction. This second hybrid CLM was pretrained with patented molecular structures and fine-tuned with known PI3Kγ binders and non-binders by transfer learning. Several of the computer-generated molecular designs were commercially available, which allowed for fast prescreening and preliminary experimental validation. A new PI3Kγ ligand with sub-micromolar activity was identified. The results positively advocate hybrid CLMs for virtual compound screening and activity-focused molecular design in low-data situations.

Die Molekülstruktur des Vanadium-(N-chlorimid)-trichlorids, Cl3V=NCl, und des Vanadiumoxidtrichlorids, Cl3V = O, in der Gasphase / The Gas Phase Molecular Structure of Vanadium(N-Chlorimide)Trichloride, Cl3V=NCl, and Vanadium Oxide Trichloride, Cl3V=O

1975 ◽  
Vol 30 (3) ◽  
pp. 296-303 ◽  
Author(s):  
H. Oberhammer ◽  
J. Strähle
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Electron Diffraction ◽  
Force Field ◽  
Vanadium Oxide ◽  
Gas Phase ◽  
Infrared Spectra ◽  
Bond Distance ◽  
Molecular Structures ◽  
Gas Phase Electron Diffraction

The molecular structures of Cl3V = NCl and Cl3V = O were determined by gas-phase electron diffraction. For both molecules the rα0-structure was converted to restructure. In the case of Cl3V=O the necessary corrections were taken from the literature while for Cl3V=NCl an approximate force field was evaluated from the infrared spectra of the solid compound for calculating these corrections. The following rα0 parameters were derived for Cl3V = NCl: V = N = 1,651 (6), N-Cl = 1,597 (8), V - Cl = 2,138 (2), ⦓ ClVCl = 113,4° (0,3) and ⦓ VNCl = 169,7° (4,2). The most interesting result of this investigation is the structure of the V = N -Cl group which is almost linear and has a very short N -CI bond distance. Concerning the VNCl group the gas-phase results agree very well with the crystal structure. For vanadyl chloride the following rα0-values were obtained: V = 0 = 1,571 (4), V - Cl = 2,137 (1) and ⦓ ClVCl = 111,0° (0,1°). The error limits given in thousandth parts of an Angstrom or degrees are the threefold standard deviations of the least squares analysis.

Structural studies of small amorphous volumes by electron diffraction

1990 ◽  
Vol 48 (4) ◽  
pp. 122-123
Author(s):  
Pierre Moine
Keyword(s):  
Electron Diffraction ◽  
Born Approximation ◽  
Structural Information ◽  
Fundamental Relation ◽  
X Rays ◽  
Structural Studies ◽  
Diffraction Experiment ◽  
Transmission Electron ◽  
Amorphous Structures ◽  
Diffraction Patterns

Qualitatively, amorphous structures can be easily revealed and differentiated from crystalline phases by their Transmission Electron Microscopy (TEM) images and their diffraction patterns (fig.1 and 2) but, for quantitative structural information, electron diffraction pattern intensity analyses are necessary. The parameters describing the structure of an amorphous specimen have been introduced in the context of scattering experiments which have been, so far, the most used techniques to obtain structural information in the form of statistical averages. When only small amorphous volumes (< 1/μm in size or thickness) are available, the much higher scattering of electrons (compared to neutrons or x rays) makes, despite its drawbacks, electron diffraction extremely valuable and often the only feasible technique.In a diffraction experiment, the intensity IN (Q) of a radiation, elastically scattered by N atoms of a sample, is measured and related to the atomic structure, using the fundamental relation (Born approximation) : IN(Q) = |FT[U(r)]|.

Dynamical Scattering in Electron Diffraction of wet Protein Crystals

1980 ◽  
Vol 38 ◽  
pp. 42-43
Author(s):  
B. B. Chang ◽  
D. F. Parsons
Keyword(s):  
Electron Diffraction ◽  
Scattering Theory ◽  
Protein Crystals ◽  
Electron Diffraction Data ◽  
Specimen Thickness ◽  
Major Question ◽  
X Ray ◽  
Scattering Effects ◽  
Diffraction Patterns ◽  
Acceleration Voltage

The significance of dynamical scattering effects remains the major question in the structural analysis by electron diffraction of protein crystals preserved in the hydrated state. In the few cases (single layers of purple membrane and 400-600 Å thick catalase crystals examined at 100 kV acceleration voltage) where electron-diffraction patterns were used quantitatively, dynamical scattering effects were considered unimportant on the basis of a comparison with x-ray intensities. The kinematical treatment is usually justified by the thinness of the crystal. A theoretical investigation by Ho et al. using Cowley-Moodie multislice formulation of dynamical scattering theory and cytochrome b5as the test object2 suggests that kinematical analysis of electron diffraction data with 100-keV electrons would not likely be valid for specimen thickness of 300 Å or more. We have chosen to work with electron diffraction patterns obtained from actual wet protein crystals (rat hemoglobin crystals of thickness range 1000 to 2500 Å) at 200 and 1000 kV and to analyze these for dynamical effects.

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