Structure determination of oxamic acid from laboratory powder X-Ray diffraction data and energy minimization by DFT-D

Analio J. Dugarte-Dugarte, Jacco van de Streek, Antonio M. dos Santos, Luke L. Daemen, Alexander A. Puretzky, Graciela Díaz de Delgado, José Miguel Delgado

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

The structure determination from laboratory X-ray powder diffraction data of oxamic acid, a derivative of the biologically active oxalic acid and the simplest organic acid containing an amide group, is presented in this contribution. An energy minimization analysis by DFT-D was carried out. The structure was determined with the program TALP and refined by the Rietveld method with GSAS-II in space group Cc (No. 9). The final unit-cell parameters are a = 9.4989 (6), b = 5.43796 (9), c = 6.8637 (9) Å β = 107.152 (5)° V = 338.772 (10) Å3, Z = 4. The refinement converged to the figures of merit: Re = 0.01674, Rp = 0.03270, Rwp = 0.05652 and GoF = 3.378 with a good fit between the calculated pattern of the structural model and the experimental pattern. The DFT-D calculations show an excellent reproduction of the experimental structure, validating the correctness of the structure. The non-centrosymmetric nature of the structure was confirmed by SHG measurements. In the crystal structure, the molecules are close to planar and form a complex 2D hydrogen-bonding pattern based on the cyclic amide-acid heterosynthon.

Original languageEnglish
Pages (from-to)310-316
Number of pages7
JournalJournal of Molecular Structure
Volume1177
DOIs
StatePublished - Feb 5 2019

Funding

This work was supported by FONACIT-Venezuela , Grant LAB-97000821 . Avant-garde Materials Simulation is gratefully acknowledged for access to the GRACE software. A portion of this research used resources at the Spallation Neutron Source, which is a DOE Office of Science User Facility operated by the Oak Ridge National Laboratory. The SHG measurements were conducted at the Center for Nanophase Materials Sciences (CNMS), which is a DOE Office of Science User Facility. Access to the Cambridge Structural Database (CSD) was possible through the Frank H. Allen International Research & Education Programme (FAIRE) from the Cambridge Crystallographic Data Centre (CCDC). This work was supported by FONACIT-Venezuela, Grant LAB-97000821. Avant-garde Materials Simulation is gratefully acknowledged for access to the GRACE software. A portion of this research used resources at the Spallation Neutron Source, which is a DOE Office of Science User Facility operated by the Oak Ridge National Laboratory. The SHG measurements were conducted at the Center for Nanophase Materials Sciences (CNMS), which is a DOE Office of Science User Facility.

Keywords

  • DFT-D calculations
  • GSAS-II
  • Oxamic acid
  • SHG measurements
  • Structure determination
  • TALP

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