Exploring the Molecular Conformation Space by Soft Molecule–Surface Collision

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.

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NO(X 2Π) product state distributions in molecule–surface collision‐induced dissociation: Direct inelastic scattering of n,i‐C3F7NO from MgO(100) at Eincident≤7.0 eV

The Journal of Chemical Physics ◽

10.1063/1.459905 ◽

1991 ◽

Vol 94 (3) ◽

pp. 2330-2345 ◽

Cited By ~ 14

Author(s):

E. Kolodney ◽

P. S. Powers ◽

L. Hodgson ◽

H. Reisler ◽

C. Wittig

Keyword(s):

Inelastic Scattering ◽

Collision Induced Dissociation ◽

Product State ◽

Surface Collision ◽

Molecule Surface

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Relating Airport Surface Collision Potential to Taxiway Geometry and Traffic Flow

14th AIAA Aviation Technology, Integration, and Operations Conference ◽

10.2514/6.2014-2156 ◽

2014 ◽

Cited By ~ 3

Author(s):

Andrew T. Ford ◽

Timothy P. Waldron

Keyword(s):

Traffic Flow ◽

Surface Collision

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Faculty Opinions recommendation of Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1010558.176464 ◽

2002 ◽

Author(s):

H Jane Dyson

Keyword(s):

Amyloid Fibril ◽

Molecular Conformation ◽

Peptide Fragment

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Fundamental Studies of Molecule-Surface Encounters Relevant to Molecular Adsorption, Size and Chemically Selective Collection, and Trace Identification/C and L (CBT)

10.21236/ada545390 ◽

2011 ◽

Author(s):

Steven J. Sibener

Keyword(s):

Molecular Adsorption ◽

Chemically Selective ◽

Selective Collection ◽

Molecule Surface

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

Protein and Peptide Letters ◽

10.2174/0929866526666191014152207 ◽

2020 ◽

Vol 27 (4) ◽

pp. 321-328 ◽

Cited By ~ 2

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.

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Homologation: A Versatile Molecular Modification Strategy to Drug Discovery

Current Topics in Medicinal Chemistry ◽

10.2174/1568026619666190808145235 ◽

2019 ◽

Vol 19 (19) ◽

pp. 1734-1750 ◽

Cited By ~ 2

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. • Homologation: definition and types • Homologous series in nature • Comparative physico-chemical and conformational properties • Application in lead-identification and lead-optimization • Impact on pharmacodynamic property • Impact on pharmacokinetic property • Impact on protein structure • Concluding remarks • Acknowledgment • References

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