Abstract

In this work, experimental and data analysis procedures were developed and applied for studying amino acid crystals by means of X-ray phase measurements. The results clearly demonstrated the sensitivity of invariant triplet phases to electronic charge distribution in d-alanine crystals, providing useful information for molecular dynamics studies of intermolecular forces. The feasibility of using phase measurements to investigate radiation damage mechanisms is also discussed on experimental and theoretical grounds.

Highlights

  • The hydrogen bond is the most important of all directional intermolecular interactions

  • Phase measurements rely on the fact that in a crystal undergoing dynamical diffraction the integrated intensity of one reflection, reflection G, when measured as a function of the excitation of another reflection, reflection H, gives rise to an intensity profile whose asymmetry depends on the triplet phase: É 1⁄4 H þ GÀH À G

  • The main achievement of this work is to have demonstrated in practice the full potential of phase measurements applied to current trends in crystallography

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Summary

Introduction

The hydrogen bond is the most important of all directional intermolecular interactions. In protein X-ray crystallography, the detection of H atoms is one of the major problems, since they display only weak contributions to diffraction data (Ogata et al, 2015) Nuclear methods such as neutron diffraction are sensitive to the proton position and combined with X-ray methods have been able to locate important H atoms to improve our understanding of macromolecular structure and function (Blakeley et al, 2015). The largely incomplete understanding of the physical and chemical mechanisms behind structural damage has recently motivated the development of computational tools for investigating damage creation mechanisms (Bernasconi & Brandao-Neto, 2016) In this sense, it is desirable to have an X-ray tool capable of experimentally probing small structural features such as electron charge in hydrogen bonds and radiation damage effects at atomic scales, or to validate high-resolution structures obtained from other experimental or purely computational methods

Physical phase measurements in X-ray crystallography
Model structures
Principles of phase measurements
Graphical indexing of Renninger scans
Experimental
Results and discussion
Model structure refinement
Radiation damage
Conclusions
Calculation codes for triplet phases and ionization cross sections
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