scholarly journals Exploring the Molecular Conformation Space by Soft Molecule–Surface Collision

2020 ◽  
Vol 142 (51) ◽  
pp. 21420-21427
Author(s):  
Kelvin Anggara ◽  
Yuntao Zhu ◽  
Martina Delbianco ◽  
Stephan Rauschenbach ◽  
Sabine Abb ◽  
...  
Keyword(s):  
Molecular Conformation ◽  
Surface Collision ◽  
Molecule Surface ◽  
Conformation Space

Molecule—surface collision-induced dissociation of internally excited NO2 on MgO(100)

1994 ◽  
Vol 221 (5-6) ◽  
pp. 447-452 ◽  
Author(s):  
H. Ferkel ◽  
J.T. Singleton ◽  
H. Reisler ◽  
C. Wittig
Keyword(s):  
Collision Induced Dissociation ◽  
Surface Collision ◽  
Molecule Surface

scholarly journals Stopping molecular rotation using coherent ultra-low-energy magnetic manipulations.

2022 ◽  
Author(s):  
Helen Chadwick ◽  
Mark Somers ◽  
Aisling Stewart ◽  
Yosef Alkoby ◽  
Thomas Carter ◽  
...  
Keyword(s):  
Rotational Level ◽  
Theoretical Models ◽  
Surface Interactions ◽  
Rotational Energy ◽  
Molecular Rotation ◽  
Level Spacing ◽  
Control Scheme ◽  
Surface Collision ◽  
Cold Molecule ◽  
Molecule Surface

Abstract Rotational motion lies at the heart of intermolecular, molecule-surface chemistry and cold molecule science, motivating the development of methods to excite and de-excite rotations. Existing schemes involve perturbing the molecules with photons or electrons which supply or remove energy comparable to the rotational level spacing. Here, we study the possibility of de-exciting the molecular rotation of a D2 molecule, from a J=2 to the non-rotating J=0 state, without using an energy-matched perturbation. We show that a magnetic field which splits the rotational projection states by only pico eV, can change the probability that a molecule-surface collision will stop a molecule from rotating and lose rotational energy which is 9 orders larger than that of the magnetic manipulation. Calculations confirm the origin of the control scheme, but also underestimate rotational flips (Δm_J≠0), highlighting the importance of the results as a sensitive benchmark for further developing theoretical models of molecule-surface interactions.

An Effective Cumulative Torsion Angles Model for Prediction of Protein Folding Rates

2020 ◽  
Vol 27 (4) ◽  
pp. 321-328 ◽  
Author(s):  
Yanru Li ◽  
Ying Zhang ◽  
Jun Lv
Keyword(s):  
Protein Folding ◽  
Size Structure ◽  
Conformational Space ◽  
Coefficient Of Determination ◽  
Folding Rate ◽  
Torsion Angles ◽  
Folding Rates ◽  
Protein Folding Rate ◽  
Optimal Set ◽  
Conformation Space

Background: Protein folding rate is mainly determined by the size of the conformational space to search, which in turn is dictated by factors such as size, structure and amino-acid sequence in a protein. It is important to integrate these factors effectively to form a more precisely description of conformation space. But there is no general paradigm to answer this question except some intuitions and empirical rules. Therefore, at the present stage, predictions of the folding rate can be improved through finding new factors, and some insights are given to the above question. Objective: Its purpose is to propose a new parameter that can describe the size of the conformational space to improve the prediction accuracy of protein folding rate. Method: Based on the optimal set of amino acids in a protein, an effective cumulative backbone torsion angles (CBTAeff) was proposed to describe the size of the conformational space. Linear regression model was used to predict protein folding rate with CBTAeff as a parameter. The degree of correlation was described by the coefficient of determination and the mean absolute error MAE between the predicted folding rates and experimental observations. Results: It achieved a high correlation (with the coefficient of determination of 0.70 and MAE of 1.88) between the logarithm of folding rates and the (CBTAeff)0.5 with experimental over 112 twoand multi-state folding proteins. Conclusion: The remarkable performance of our simplistic model demonstrates that CBTA based on optimal set was the major determinants of the conformation space of natural proteins.

Homologation: A Versatile Molecular Modification Strategy to Drug Discovery

2019 ◽  
Vol 19 (19) ◽  
pp. 1734-1750 ◽  
Author(s):  
Lídia M. Lima ◽  
Marina A. Alves ◽  
Daniel N. do Amaral
Keyword(s):  
Protein Structure ◽  
Homologous Series ◽  
Molecular Conformation ◽  
Chemical Properties ◽  
Lead Optimization ◽  
Pharmacokinetic Property ◽  
Molecular Modification ◽  
Physico Chemical ◽  
Pharmacokinetic Properties ◽  
Lead Identification

Homologation is a concept introduced by Gerhard in 1853 to describe a homologous series in organic chemistry. Since then, the concept has been adapted and used in medicinal chemistry as one of the most important strategies for molecular modification. The homologation types, their influence on physico-chemical properties and molecular conformation are presented and discussed. Its application in lead-identification and lead optimization steps, as well as its impact on pharmacodynamics/pharmacokinetic properties and on protein structure is highlighted from selected examples. <p> • Homologation: definition and types <p> • Homologous series in nature <p> • Comparative physico-chemical and conformational properties <p> • Application in lead-identification and lead-optimization <p> • Impact on pharmacodynamic property <p> • Impact on pharmacokinetic property <p> • Impact on protein structure <p> • Concluding remarks <p> • Acknowledgment <p> • References

Temperature Dependence of Molecular Conformation, Dynamics, and Chemical Shift Anisotropy of α,α-Trehalose in D2O by NMR Relaxation

1997 ◽  
Vol 119 (6) ◽  
pp. 1336-1345 ◽  
Author(s):  
Gyula Batta ◽  
Katalin E. Kövér ◽  
Jacquelyn Gervay ◽  
Miklós Hornyák ◽  
Gareth M. Roberts
Keyword(s):  
Chemical Shift ◽  
Temperature Dependence ◽  
Molecular Conformation ◽  
Chemical Shift Anisotropy ◽  
Nmr Relaxation

Vibrational spectra and molecular conformation of ciliatine

1993 ◽  
Vol 298 ◽  
pp. 1-11 ◽  
Author(s):  
Keiichi Ohno ◽  
Yoshitaka Mandai ◽  
Hiroatsu Matsuura
Keyword(s):  
Vibrational Spectra ◽  
Molecular Conformation
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