The Charge Density Distribution in a Model Compound of the Catalytic Triad in Serine Proteases

Overgaard, Jacob; Schiøtt, Birgit; Larsen, Finn; Iversen, Bo B.

doi:10.1002/1521-3765(20010903)7:17<3756::aid-chem3756>3.0.co;2-q

Cited by 72 publications

(62 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, it is shown that strong hydrogen bonding can indeed lead to the formation of relatively rigid linkers in a framework structure, resembling other CPs with NTE behavior. Furthermore, the study used source function calculations to show that this N‐H‐N hydrogen bond followed all the established hydrogen bond classifications developed for oxygen containing hydrogen bonds, especially the fact that the contribution from hydrogen and acceptor atom to the hydrogen bond BCP increases significantly with the covalency of the hydrogen bond (Figure ) . This purely density based descriptor even seems to be sensitive to the nature of the hydrogen vibration potential with significantly larger contributions from the hydrogen atom for LBHB than for asymmetric single‐well hydrogen bonds.…”

Section: Materials Classesmentioning

confidence: 94%

Electron Density Studies in Materials Research

Tolborg

Iversen

2019

Chemistry A European J

Self Cite

View full text Add to dashboard Cite

Rational material design requires a deep understanding about the relationship between the structure and properties of materials, which are both intimately related to their chemical bonding. Through the experimentally observable electron density, chemical bonding can be understood from experimental and theoretical points of view on an equal footing, and advances in accurate X‐ray diffraction measurements and computational techniques over the past decades have provided access to electron density distributions in increasingly complex functional materials. In this Review, selected electron density studies from the literature on a wide range of materials classes are presented, including studies of thermoelectric materials, high pressure electrides, coordination polymers and non‐linear optical materials. These studies demonstrate how detailed analysis of chemical bonding based on the electron density provides important understanding of materials beyond arguments based on structure and simple chemical concepts. In cases such as understanding the conducting properties of Zintl semiconductors or the effect of mutual electrical polarization in host–guest systems, it is clearly imperative to go beyond structure and examine the chemical bonding in detail. In the Review, the complementarity between theory and experiment is underlined, which allows for mutual validation of new chemical bonding concepts, and indeed experiment and theory may challenge each other based on the different strengths and weaknesses of each method.

show abstract

Section: Materials Classesmentioning

confidence: 94%

Electron Density Studies in Materials Research

Tolborg

Iversen

2019

Chemistry A European J

Self Cite

View full text Add to dashboard Cite

show abstract

“…Comparing the ADPs of the 33 heavy atoms in 1 by using the program UIJXN leads to a mean deviation ${\left\langle {\Delta U} \right\rangle }$ of 0.00058 Å 2 ,67 which, for such a large system, is an excellent correspondence compared with other X/N studies 68. The hydrogen nuclear positions and ADPs, which are important in accurate ED modeling of hydrogen‐bonded systems such as 1 ,69 were therefore expected to be of excellent quality. Increasing the complexity of the multipole model of the host structure, for example, by removing the center of symmetry, removing constraints (electronic, positional, and thermal), or adding additional radial expansion–contraction parameters did not result in a significant improvement of the residual density or the agreement factors.…”

Section: Methodsmentioning

confidence: 99%

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

Clausen

Jørgensen

Cenedese

et al. 2014

Chemistry A European J

Self Cite

View full text Add to dashboard Cite

X-ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host-guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X-ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light-atom-only crystal. Atomic displacement parameters obtained independently from the X-ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Å(2) indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host-guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host-guest interaction (e.g., in protein-drug complexes), at least for polar molecules.

show abstract

“…The source function was recently developed by Gatti and Bader [8] and successfully supported other investigations [30,31].…”

Section: Geometry Of the Rahb And Topological Parametersmentioning

confidence: 99%

Electron-density studies on hydrogen bonding in chromone derivatives. Part II: comparative study

2011

View full text Add to dashboard Cite

The experimental electron density of a chromone derivative was determined from a multipole refinement of 100 K X-ray synchrotron data and complemented by theoretical calculations with experimental and optimized geometry. Atomic and topological properties were obtained using the Quantum Theory of Atoms in Molecules approach. The examination of topological parameters unambiguously showed p-delocalization within the H-bonded ring. The application of source function analysis confirmed the intramolecular N-HÁÁÁO hydrogen bond to be a resonance-assisted hydrogen bond. The topological study confirmed the covalent nature of N-HÁÁÁO interaction and the electrostatic nature of weak C-HÁÁÁO interactions.

show abstract

The Charge Density Distribution in a Model Compound of the Catalytic Triad in Serine Proteases

Cited by 72 publications

References 75 publications

Electron Density Studies in Materials Research

Electron Density Studies in Materials Research

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

Electron-density studies on hydrogen bonding in chromone derivatives. Part II: comparative study

Contact Info

Product

Resources

About