Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

Birger Dittrich; Jens Lübben; Stefan Mebs; Armin Wagner; Peter Luger; Ralf Flaig

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Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

机译：通过包括估计的氢ADP和与中子和QM / MM基准相比，通过单晶X射线衍射到氢原子的精确粘合长度。与中子和QM / MM基准相比

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Amino acid structures are an ideal test set for method-development studies in crystallography. High-resolution X-ray diffraction data for eight previously studied genetically encoding amino acids are provided, complemented by a non-standard amino acid. Structures were re-investigated to study a widely applicable treatment that permits accurate X-H bond lengths to hydrogen atoms to be obtained: this treatment combines refinement of positional hydrogenatom parameters with aspherical scattering factors with constrained "TLS+INV" estimated hydrogen anisotropic displacement parameters (H-ADPs). Tabulated invariom scattering factors allow rapid modeling without further computations, and unconstrained Hirshfeld atom refinement provides a computationally demanding alternative when database entries are missing. Both should incorporate estimated H-ADPs, as free refinement frequently leads to over-parameterization and non-positive definite H-ADPs irrespective of the aspherical scattering model used. Using estimated H-ADPs, both methods yield accurate and precise X-H distances in best quantitative agreement with neutron diffraction data (available for five of the test-set molecules). This work thus solves the last remaining problem to obtain such results more frequently. Density functional theoretical QM/MM computations are able to play the role of an alternative benchmark to neutron diffraction.

机译：氨基酸结构是用于晶体学中的方法显影研究的理想测试。提供了先前研究的八个遗传编码氨基酸的高分辨率X射线衍射数据，由非标准氨基酸互补。重新研究结构以研究广泛适用的处理，允许获得氢原子的精确XH键长度：该处理结合了具有受约束的“TLS + INV”估计氢极性位移参数（H. -ADPS）。制表的不变散射因子允许快速建模而无需进一步计算，并且不受约束的HIRSHFELD原子细化在缺少数据库条目时提供了计算要求苛刻的替代方案。两者都应该包含估计的H-ADP，因为无论使用的非球面散射模型如何，自由细化经常导致过度参数化和非正面明确的H-ADP。使用估计的H-ADP，两种方法都可以在与中子衍射数据的最佳定量协议（可用于五个测试集分子中的最佳定量协议中屈服精确且精确X-H距离。因此，这项工作解决了最后剩余的问题，以更频繁地获得此类结果。密度功能理论QM / mm计算能够扮演替代基准到中子衍射的作用。

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来源
《Chemistry: A European journal》 |2017年第19期|共10页
作者
Birger Dittrich; Jens Lübben; Stefan Mebs; Armin Wagner; Peter Luger; Ralf Flaig;
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作者单位

Heinrich-Heine Universit?t Düsseldorf Institut für Anorganische Chemie und Strukturchemie Material- und Strukturforschung Geb-ude: 26.42 Universit?tsstra?e 1 40225 Düsseldorf (Germany);

Heinrich-Heine Universit?t Düsseldorf Institut für Anorganische Chemie und Strukturchemie Material- und Strukturforschung Geb-ude: 26.42 Universit?tsstra?e 1 40225 Düsseldorf (Germany);

Institut für Chemie und Biochemie-Anorganische Chemie der Freien Universit?t Berlin 14195 Berlin (Germany);

Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0DE (UK);

Institut für Chemie und Biochemie-Anorganische Chemie der Freien Universit?t Berlin 14195 Berlin (Germany);

Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0DE (UK);

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原文格式 PDF
正文语种 eng
中图分类应用化学;
关键词
amino acids; density functional theory; neutron diffraction; structure elucidation; X-ray diffraction;

机译：氨基酸;密度函数理论;中子衍射;结构阐明;X射线衍射;

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1. Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks [J] . Birger Dittrich, Jens Lübben, Stefan Mebs, Chemistry: A European journal . 2017,第19期

机译：通过包括估计的氢ADP和与中子和QM / MM基准相比，通过单晶X射线衍射到氢原子的精确粘合长度。与中子和QM / MM基准相比
2. Accurate molecular structures and hydrogen bonding in two polymorphs of ortho-acetamidobenzamide by single-crystal neutron diffraction. [J] . Leech CK, Barnett SA, Shankland K, Acta Crystallographica, Section B. Structural Science . 2006,第5期

机译：通过单晶中子衍射通过单晶中子衍射两种邻乙酰氨基甲酰胺的两种多晶型物的精确分子结构和氢键合。
3. Investigation of nuclear quantum effect on the hydrogen bonds of ammonium dihydrogen phosphate using single-crystal neutron diffraction and theoretical modelling [J] . RAJUL RANJAN CHOUDHURY, R CHITRA Pramana . 2018,第4期

机译：单晶中子衍射和理论模型研究核量子效应对磷酸二氢铵氢键的影响
4. Structural Studies of Hydrogen Storage Alloys using X-ray/Neutron Diffraction and Total Scattering [C] . Yumiko Nakamura, Hyunjeong Kim, Saishun Yamazaki, MRS spring meeting . 2012

机译：X射线/中子衍射和总散射的储氢合金结构研究
5. A neutron diffraction study of hydrogen bonding in copper-substituted melanterites and their dehydration products. [D] . Anderson, Jennifer Lynn. 2002

机译：对铜取代的黑变石及其脱水产物中氢键的中子衍射研究。
6. Accurate Bond Lengths to Hydrogen Atoms from Single‐Crystal X‐ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks [O] . Priv.‐Doz. Dr. Birger Dittrich, Jens Lübben, Dr. Stefan Mebs, -1

机译：通过包括估计的氢ADP以及与中子和QM / MM基准的比较得出单晶X射线衍射与氢原子的准确键长
7. Hydrogen maleate salts: precise and accurate determination of the hydrogen atom position in short hydrogen bonds using X-ray diffraction at extremely low temperatures [O] . Simon Grabowsky, Lorraine Andrade Malaspina, Magdalena Woinska, 2016

机译：马来酸盐盐：在极低温度下使用X射线衍射在短氢键中精确和精确测定氢原子位置
8. Analyzing carboxylic acid and amine-nitro hydrogen-bond geometry in the cocrystal of 4-aminobenzoic acid and 3,5-dinitrobenzoic acid by use of 298 K X-ray and 15 K neutron diffraction [R] . Frankenbach, G. M., Etter, M. C., Schultz, A. J., 1993

机译：利用298 K X射线和15 K中子衍射分析4-氨基苯甲酸和3,5-二硝基苯甲酸共晶中的羧酸和胺 - 硝基氢键几何结构

Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

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