Atomic displacement parameters for Ni(ND3)4(NO2)2 from 9 K X-ray and 13 K time-of-flight neutron diffraction data

Iversen, Bo B.; Larsen, Finn; Figgis, B. N.; Reynolds, P. A.; Schultz, A. J.

doi:10.1107/s010876819600794x

Cited by 56 publications

(55 citation statements)

References 21 publications

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“…The accuracy of the model can be tested by comparing thermal parameters for the heavy atoms derived separately from the X-ray and neutron data. [12] In the present case we obtain hDU XÀN i 0.0009 2 and hU X /U N i 1.05. This demonstrates that the systematic errors are minimal, …”

Section: Methodssupporting

confidence: 52%

Strong N−H⋅⋅⋅O Hydrogen Bonding in a Model Compound of the Catalytic Triad in Serine Proteases

Overgaard

Schiøtt

Larsen

et al. 1999

Angew. Chem. Int. Ed.

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Low-barrier hydrogen bond (LBHB) involvement in enzyme catalysis is examined by analysis of experimental nuclear and electron densities of a model compound for the catalytic triad in serine proteases (shown schematically), which is based on a cocrystal of betaine, imidazole, and picric acid. The three short, strong N-H⋅⋅⋅O hydrogen bonds in the structure have varying degrees of covalent bonding contributions suggesting a gradual transition to the LBHB situation.

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Section: Methodssupporting

confidence: 52%

Strong N−H⋅⋅⋅O Hydrogen Bonding in a Model Compound of the Catalytic Triad in Serine Proteases

Overgaard

Schiøtt

Larsen

et al. 1999

Angew. Chem. Int. Ed.

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“…Iversen et al have shown that even in the most accurate single crystal diffraction studies there are often systematic differences between the ADPs determined separately from x-ray and neutron diffraction data. 42 Only if extreme care is taken in the experimental reduction of systematic errors and in the data analysis ͑e.g., use of flexible aspherical electron density models͒ can identical parameters be obtained. It is generally assumed that powder data are less accurate than single crystal data, and for thermal parameters, especially, single crystal neutron data rank the highest.…”

Section: Synchrotron Powder Diffraction Datamentioning

confidence: 99%

Crystal structures, atomic vibration, and disorder of the type-I thermoelectric clathratesBa8Ga16Si30,<

et al. 2005

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Temperature dependent synchrotron powder diffraction and single crystal neutron diffraction data are used for probing the vibrational states and disorder in type I an empirical disorder term is included, the temperature dependence of the atomic displacement factors ͑ADPs͒ of the framework and guest atoms can be described by a Debye and Einstein model, respectively. None of the guest atoms in the large cages are located in the center and the vibrational frequencies ͑ E ͒ are of the order 80 K or larger for all structures, in good agreement with theoretical predictions. Even though the Sr ADPs are larger than the Ba ADPs in all the clathrates, the data show that E of Sr in Sr 8 Ga 16 Ge 30 is larger than for the Ba atoms. This is due to stronger guest-host chemical bonding in Sr 8 Ga 16 Ge 30 . Since E of Sr has been reported to be much smaller in the literature we have also measured the specific heat of Sr 8 Ga 16 Ge 30 with Ba 8 Ga 16 Ge 30 as a reference. It is found that localized excitations with a characteristic energy of approximately 35 K exist in both compounds, however, the total number of states is too low to be associated with either tunneling states or localized vibration of each of the guest atoms.

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“…An indication of the data quality was obtained from the comparison of ADPs obtained independently from X-ray and neutron refinements. [51] The ADPs can absorb uncorrected systematic errors and a good agreement between the ADPs from a neutron experiment and a multipolar modeling of X-ray data therefore implies that systematic errors have been minimized. The non-hydrogen ADPs from the X-ray experiment were on average only 1 % larger than the corresponding ADPs from neutron data (hU ii (X)/U ii (N)i 1.011 (16)) .…”

Section: Tubementioning

confidence: 99%

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

et al. 2001

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Combined low temperature (28(1) K) X-ray and neutron diffraction measurements were carried out on the co-crystallised complex of betaine, imidazole, and picric acid (1). The experimental charge density was determined and compared with ab initio theoretical calculations at the B3LYP/6-311G(d,p) level of theory. The complex serves as a model for the active site in, for example, the serine protease class of enzymes, the so-called catalytic triad. The crystal contains three short strong N-H...O hydrogen bonds (HBs) with dN...O < 2.7 A. The three HBs have energies above 13 kcalmol(-1), although the hydrogen atoms are firmly localized in the "nitrogen wells". This suggests that low-barrier hydrogen bonding in catalytic enzyme reactions may be a sufficient, but not a necessary, condition for obtaining transition-state stabilization. Structural analysis (e.g., covalent N-H bond lengthening) indicates that the hydrogen bond between H3A and 08 of imidazole and betaine respectively (HB2) is slightly stronger than the bond between H1A and O1A of imidazole and picric acid (HB1), although HB1 is shorter than HB2: (dN...O(HB1)= 2.614(1) A, dN...O(HB2) = 2.684(1) A, dH...O(HB1) = 1.630(1) A, dH...O(HB2)= 1.635(1) A, dN-H(HB1) = 1.046(1) A, dN-H(HB2) = 1.057(1) A). Furthermore, the charge density analysis reveals that HB2 has a larger covalent character than HB1, with considerable polarization of the density towards the acceptor atom. The Gatti and Bader source function (S) is introduced to the analysis of strong HBs. The source function is found to be a sensitive measure for the nature of a hydrogen bond, and comparison with low-barrier and single-well hydrogen bonding systems (e.g., benzoylacetone and nitromalonamide) shows that the low-barrier hydrogen bond (LBHB) state is characterized by an enormously increased hydrogen atom source contribution to the bond critical point in the HB. In this context, HB2 can be characterized as intermediate between localized HBs and delocalized LBHBs.

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Atomic displacement parameters for Ni(ND₃)₄(NO₂)₂ from 9 K X-ray and 13 K time-of-flight neutron diffraction data

Cited by 56 publications

References 21 publications

Strong N−H⋅⋅⋅O Hydrogen Bonding in a Model Compound of the Catalytic Triad in Serine Proteases

Strong N−H⋅⋅⋅O Hydrogen Bonding in a Model Compound of the Catalytic Triad in Serine Proteases

Crystal structures, atomic vibration, and disorder of the type-I thermoelectric clathratesBa8Ga16Si30,<

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

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