Crystal Structure Analysis of Four 2-Pyridineformamide Thiosemicarbazone Derivatives Using Non-Spherical Atomic Form Factors

IF 0.4 4区化学 Q4 CRYSTALLOGRAPHY

Journal of Chemical Crystallography Pub Date : 2025-01-02 DOI:10.1007/s10870-024-01037-y

Bhushan Shakya, Kuldeep Mahiya, Ramina Maharjan Shrestha, Hari Bhakta Oli, Paras Nath Yadav

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Abstract

The crystal structures of four 2-pyridineformamide thiosemicarbazone derivatives viz, (Z, Z’)-4-methyl-N’-(morpholine-4-carbonothioyl)picolinohydrazonamide (1), (Z, Z’)-4-methyl-N’-(thiomorpholine-4-carbonothioyl) picolinohydrazonamide (2), (Z, Z’)-6-methyl-N’-(thiomorpholine-4-carbonothioyl)picolinohydrazonamide (3) and (Z, Z’)-N’-(azepane-1-carbonothioyl)-4-methylpicolinohydrazonamide (4) has been determined by single crystal X-ray diffraction analysis. Combined quantum mechanical methods (ORCA) and computation of non-spherical scattering form factors (NoSpherA2) were used for the refinement with anisotropic hydrogen atoms. The results of using independent atom model (IAM) and Hirshfield atom refinement (HAR) method based R2SCAN/ def2-TZVP functional were compared. All compounds show an improvement in the model after HAR refinement compared to independent atom model (IAM). There is a significant decrease in the residual factors with the use of anisotropic hydrogen refinement. HAR refinement provides a clearer understanding of electron delocalization, lone pairs, and the accumulation and depletion of electron density. The information obtained came from standard resolution single crystal X-ray diffraction data, indicating that high-quality structural analysis can now be performed without the need for neutron or synchrotron facilities.

Graphical Abstract

Structural studies of four 2-pyridineformamide thiosemicarbazone derivatives using non-spherical atomic form factors

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用非球形原子形因子分析4种2-吡啶甲酰胺硫代氨基脲衍生物的晶体结构

用单晶x射线衍射法测定了4种2-吡啶甲酰胺硫代氨基脲衍生物（Z, Z′）-4-甲基- n′-（硫代氨基-4-羰基）picolinohydrazonamide(1)、（Z, Z′）-4-甲基- n′-（硫代氨基-4-羰基）picolinohydrazonamide(2)、（Z, Z′）-6-甲基- n′-（硫代氨基-4-羰基）picolinohydrazonamide(3)和（Z, Z′）- n′-（氮代烷-1-羰基）-4-甲基picolinohydrazonamide(4)的晶体结构。结合量子力学方法（ORCA）和计算非球面散射形状因子（NoSpherA2）对各向异性氢原子进行细化。比较了独立原子模型（IAM）和基于R2SCAN/ def2-TZVP泛函的Hirshfield原子细化（HAR）方法的结果。与独立原子模型（IAM）相比，所有化合物经过HAR改进后的模型都有改善。采用各向异性氢精炼后，残余因子显著降低。HAR的改进提供了对电子离域、孤对和电子密度的积累和消耗的更清晰的理解。获得的信息来自标准分辨率单晶x射线衍射数据，表明现在可以在不需要中子或同步加速器设施的情况下进行高质量的结构分析。用非球形原子形因子研究4个2-吡啶甲酰胺硫代氨基脲衍生物的结构

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来源期刊

Journal of Chemical Crystallography 化学-光谱学

CiteScore

1.50

自引率

12.50%

发文量

审稿时长

6.3 months

期刊介绍： Journal of Chemical Crystallography is an international and interdisciplinary publication dedicated to the rapid dissemination of research results in the general areas of crystallography and spectroscopy. Timely research reports detail topics in crystal chemistry and physics and their relation to problems of molecular structure; structural studies of solids, liquids, gases, and solutions involving spectroscopic, spectrometric, X-ray, and electron and neutron diffraction; and theoretical studies.