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使用各种计算方法对堆叠咖啡因二聚体的实验数据进行再现。

Reproduction of experimental data for stacked caffeine dimers using various computational methods.

作者信息

Gutierrez Maria Patricia Sanchez, Jimenez Eduardo Gonzalez, Deriabina Alexandra, Perez Juan Carlos Sanchez, Poltev Valeri

机构信息

Faculty of Physical and Mathematical Sciences, Autonomous University of Puebla (BUAP), Puebla, 72570, Mexico.

出版信息

Sci Rep. 2024 Nov 6;14(1):26906. doi: 10.1038/s41598-024-77372-z.

DOI:10.1038/s41598-024-77372-z
PMID:39505983
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11541902/
Abstract

Reliable description of stacking interaction of aromatic molecules is important for the understanding structure, stability, and functions of biopolymers. The caffeine molecule is an ideal object for this study as the stacking interactions are the preferential ones for self-associations of this hydrophobic molecule without H-bond donor groups. The analysis of anhydrous caffeine crystal structures revealed five types of caffeine stacking dimers. Geometry optimization of these dimers was performed using two molecular mechanics force fields, ab-initio method Møller Plesset of the second order (MP2), and density functional theory (DFT) with different functionals. The comparison of geometric parameters of the caffeine dimers obtained using different theoretical methods with those in crystals enables us to suggest the methods providing the most reliable stacking characteristics. These methods are: the MP2 with Basis Set Superposition Error correction (MP2/CP), Poltev force field, along with PBE0-DH, SCAN and PBE-D3 functionals of DFT. For the methods, which give the dimer interaction energy close to that obtained by MP2/CP method, the evaluated sublimation enthalpy values are shown to be close to the experimental data. Additionally, MP2/CP, Poltev FF and PBE0-DH functional showed to be the methods that describe well both the energy and geometry of the caffeine stacking dimer.

摘要

可靠地描述芳香分子的堆积相互作用对于理解生物聚合物的结构、稳定性和功能至关重要。咖啡因分子是这项研究的理想对象,因为堆积相互作用是这种没有氢键供体基团的疏水分子自缔合的优先相互作用。无水咖啡因晶体结构的分析揭示了五种类型的咖啡因堆积二聚体。使用两种分子力学力场、二阶Møller Plesset从头算方法(MP2)以及具有不同泛函的密度泛函理论(DFT)对这些二聚体进行了几何优化。将使用不同理论方法获得的咖啡因二聚体的几何参数与晶体中的参数进行比较,使我们能够提出提供最可靠堆积特征的方法。这些方法是:具有基组叠加误差校正的MP2(MP2/CP)、波尔捷夫力场,以及DFT的PBE0-DH、SCAN和PBE-D3泛函。对于给出的二聚体相互作用能接近MP2/CP方法所得结果的方法,评估的升华焓值显示与实验数据接近。此外,MP2/CP、波尔捷夫力场和PBE0-DH泛函显示是能够很好地描述咖啡因堆积二聚体的能量和几何结构的方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/af7bacdc7967/41598_2024_77372_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/ec7bb9630a0d/41598_2024_77372_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/e6afda702bad/41598_2024_77372_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/7e93940854eb/41598_2024_77372_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/0704332e7393/41598_2024_77372_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/af7bacdc7967/41598_2024_77372_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/ec7bb9630a0d/41598_2024_77372_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/e6afda702bad/41598_2024_77372_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/7e93940854eb/41598_2024_77372_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/0704332e7393/41598_2024_77372_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7050/11541902/af7bacdc7967/41598_2024_77372_Fig5_HTML.jpg

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