Home The crystal structure of 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl)isoindolin-2-yl)pentanoic acid, C17H19N3O5
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The crystal structure of 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl)isoindolin-2-yl)pentanoic acid, C17H19N3O5

  • Qing Wang , Yanrong Gao , Hongjuan Tong ORCID logo and Wenqiang Tang ORCID logo EMAIL logo
Published/Copyright: November 15, 2023

Abstract

C17H19N3O5, triclinic, P 1 (no. 2), a = 8.3683(3) Å, b = 9.1873(3) Å, c = 11.3782(4) Å, α = 96.553(1)°, β = 108.368(1)°, γ = 92.429(1)°, V = 821.94(5) Å3, Z = 2, R gt (F) = 0.0450, wR ref (F2) = 0.1175, T = 170 K.

CCDC no.: 2292587

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.12 × 0.08 × 0.05 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.10 mm−1
Diffractometer, scan mode: D8 VENTURE, φ and ω
θmax, completeness: 26.4°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 9545, 3343, 0.049
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 2528
N(param)refined: 227
Programs: Bruker [1], SHELX [2, 3], Olex2 [4]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z Uiso*/Ueq
C1 0.2862 (2) 0.9589 (2) 0.22399 (19) 0.0311 (5)
H1A 0.308889 0.914396 0.148001 0.037*
H1B 0.374918 1.038936 0.268497 0.037*
C2 0.1103 (3) 1.0146 (2) 0.1920 (2) 0.0391 (5)
H2A 0.105517 1.095633 0.255826 0.047*
H2B 0.076876 1.049482 0.109141 0.047*
C3 −0.0021 (2) 0.8796 (2) 0.1915 (2) 0.0358 (5)
H3C −0.097598 0.908077 0.220521 0.043*
H3D −0.047640 0.823651 0.106623 0.043*
C4 0.1134 (2) 0.7896 (2) 0.28104 (17) 0.0261 (4)
C5 0.4231 (2) 0.78458 (19) 0.37368 (16) 0.0225 (4)
C6 0.5601 (2) 0.7746 (2) 0.32857 (18) 0.0287 (4)
H6 0.552054 0.808699 0.251302 0.034*
C7 0.7082 (2) 0.7162 (2) 0.39375 (18) 0.0300 (5)
H7 0.798872 0.710672 0.360405 0.036*
C8 0.7240 (2) 0.6661 (2) 0.50681 (18) 0.0270 (4)
H8 0.823670 0.624865 0.551640 0.032*
C9 0.5885 (2) 0.67854 (19) 0.55227 (17) 0.0227 (4)
C10 0.4404 (2) 0.73710 (19) 0.48870 (16) 0.0212 (4)
C11 0.3249 (2) 0.7415 (2) 0.56653 (16) 0.0237 (4)
H11A 0.300058 0.843520 0.588659 0.028*
H11B 0.217382 0.680921 0.522527 0.028*
C12 0.5774 (2) 0.64364 (19) 0.67298 (17) 0.0221 (4)
C13 0.4279 (2) 0.81687 (19) 0.87301 (16) 0.0209 (4)
C14 0.3728 (2) 0.67029 (19) 0.78794 (16) 0.0206 (4)
H14 0.432252 0.590957 0.833275 0.025*
C15 0.1824 (2) 0.6355 (2) 0.75472 (17) 0.0230 (4)
H15A 0.122669 0.706199 0.700209 0.028*
H15B 0.150455 0.535723 0.707140 0.028*
C16 0.1254 (2) 0.6432 (2) 0.87012 (17) 0.0244 (4)
H16A 0.147842 0.745616 0.912810 0.029*
H16B 0.001865 0.618076 0.842705 0.029*
C17 0.2099 (2) 0.5435 (2) 0.96203 (17) 0.0238 (4)
N1 0.27630 (18) 0.84785 (17) 0.30557 (14) 0.0246 (4)
N2 0.42371 (18) 0.67976 (16) 0.67728 (13) 0.0207 (3)
N3 0.5523 (2) 0.81464 (17) 0.97887 (15) 0.0298 (4)
H3A 0.588989 0.895769 1.031824 0.036*
H3B 0.598233 0.732024 0.996313 0.036*
O1 0.07119 (16) 0.68343 (15) 0.32244 (12) 0.0318 (3)
O2 0.35670 (16) 0.92824 (13) 0.84154 (12) 0.0286 (3)
O3 0.68721 (16) 0.59542 (15) 0.75635 (12) 0.0303 (3)
O4 0.28085 (18) 0.43750 (15) 0.93747 (13) 0.0340 (3)
O5 0.19910 (18) 0.58426 (15) 1.07467 (12) 0.0349 (4)
H5 0.248094 0.526080 1.123532 0.052*

1 Source of materials

A mixture of methyl 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl) isoindolin-2-yl)pentanoate (3.6 g, 10 mmol), H2O (10 mL), and sodium hydroxide (1.6 g, 40 mmol) was stirred in tetrahydrofuran (30 mL) at 40 °C for 2 h. The reaction was monitored by thin-layer chromatography. The solution was concentrated and diluted with water, and the pH was adjusted to three by adding hydrochloric acid solution (4 mol/L). The mixture was extracted with ethyl acetate and washed with brine. The organic layer was concentrated under reduced pressure, and the residue was purified by column chromatography using dichloromethane and methanol (15:1, v/v). Crystals of the title compound were obtained by slow evaporation of the aforementioned mixed solution at room temperature after a week.

2 Experimental details

Hydrogen atoms were positioned ideally and refined as riding atoms, with Uiso values set to 1.2 Ueq of the parent atoms. The structure was solved with ShelXT [2] and refined using ShelXL [3] in Olex2 software [4].

3 Comment

Isoindole derivatives are a prominent class of heterocyclic compounds with significant biological activity [5]. To date, numerous research reports have explored the crystal structures of isoindoles, which play a significant role in studying their activity and aiding in the development of new drugs [6], [7], [8], [9], [10], [11].

The crystal structure analysis reveals that a pyrrolidin-2-one group substitutes a hydrogen atom on the phenyl ring within the isoindole framework. Notably, the atoms within the pyrrolidin-2-one moiety exhibit non-coplanar arrangement, exemplified by the dihedral angle of 32.05(19)° for the N1–C1–C2–C3 atoms. Conversely, the atoms within the isoindole moiety demonstrate nearly coplanar alignment, with minimal torsional angles, consistent with previously reported structures [12], [13], [14]. This investigation encompasses a discussion on the crystal packing of the studied compound, revealing that the molecules primarily form stacks through hydrogen bonds. Specifically, two crystallographically dependent N3–H3A⋯O2 bonds and one O5–H5⋯O3 bond are involved in the intermolecular interactions. These hydrogen bonds display angles close to 180° and bond lengths below 2 Å, indicating strong hydrogen bonding interactions.


Corresponding author: Wenqiang Tang, Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xianyang, Shaanxi, China, E-mail:

Funding source: key laboratory of molecular imaging and drug synthesis of Xianyang city

Award Identifier / Grant number: 2021QXNL–PT-0008

Funding source: Natural Science Foundation of Shaanxi Province

Award Identifier / Grant number: 2021SF-386

Funding source: the scientific research plan project of Shaanxi provincial department of education

Award Identifier / Grant number: 21JK0517

Funding source: Shaanxi University Association of Science and Technology Young Talents Lifting Plan Project

Award Identifier / Grant number: 20210313

  1. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was financially supported by the projects of key laboratory of molecular imaging and drug synthesis of Xianyang city (2021QXNL–PT-0008), the Natural Science Foundation of Shaanxi Province (2021SF-386), the scientific research plan project of Shaanxi provincial department of education (21JK0517) and Shaanxi University Association of Science and Technology Young Talents Lifting Plan Project (20210313).

  3. Competing interests: The authors declare no conflicts of interest regarding this article.

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Received: 2023-09-30
Accepted: 2023-11-03
Published Online: 2023-11-15
Published in Print: 2024-02-26

© 2023 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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