npj：異相催化中複雜吸附物構型—圖形表示法探索

異相催化對於可持續能源產生和存儲、精細化學品的合成和食品生產都有重要影響。更好的催化劑的發現需要從原子尺度來加速結構-性能關係的認識。計算能力和資源的迅速發展，使利用密度泛函理論來分析複雜反應化學過程成為可能，例如，多配位基吸附物和高吸附物覆蓋度。然而，要模擬這些複雜的反應化學仍然存在很大挑戰，例如，在低對稱性表面的高吸附物覆蓋度的分析，以及缺乏普適的流程來系統地模擬這些情況。這些問題急需一個有效工具，能夠在眾多不同幾何構型中探測唯一吸附物構型，並且利用這些信息能夠推演更高覆蓋度的構型。

來自美國普度大學的Greeley教授研究團隊，報導了一種基於Python的算法，利用非直接圖形表示來描述給定的異相催化模型系統。這些圖形表示是多分子的，涉及到多種不同類型的原子和價鍵，以及吸附物原子和基底表面之間的多種接觸點（單、雙和三配位基）。這些圖形表示用來探測唯一的吸附物構型和催化劑表面的吸附位點。而且，這些圖形表示還可以確定和比較低或高覆蓋度唯一構型以及單配位基和多配位基幾何構型。這一方法模擬進一步與進化算法相結合，能夠系統地估計低對稱性表面上的高覆蓋度模型。另外，最近鄰相互作用的估計等設計原則可以用來簡化大量樣品空間。作者利用這一策略演示了Pt3Sn(111)梯田表面吸附NO的覆蓋度依賴相圖分析和反應中間物丙炔(CHCCH3*)吸附在PtIn(021)臺階表面時吸附能與唯一最小能構型的確定。這種基於圖形的方法在異相催化領域構建了一種新的圖形理論，能夠自動、快速地篩選與吸附物相互作用的多種表面接觸點組合，而且可以拓展到多種原子模型應用。

該文近期發表於npj Computational Materials 6: 79 (2020)，英文標題與摘要如下，點擊https://www.nature.com/articles/s41524-020-0345-2可以自由獲取論文PDF。

Graph theory approach to determine configurationsof multidentate and high coverage adsorbatesfor heterogeneous catalysis

Siddharth Deshpande, Tristan Maxson& Jeffrey Greeley

Heterogeneous catalysts constitute a crucial component of many industrial processes, and to gain an understanding of the atomicscale features of such catalysts, ab initio density functional theory is widely employed. Recently, growing computational power haspermitted the extension of such studies to complex reaction networks involving either high adsorbate coverages or multidentateadsorbates, which bind to the surface through multiple atoms. Describing all possible adsorbate configurations for such systems,however, is often not possible based on chemical intuition alone. To systematically treat such complexities, we present ageneralized Python-based graph theory approach to convert atomic scale models into undirected graph representations. Theserepresentations, when combined with workflows such as evolutionary algorithms, can systematically generate high coverageadsorbate models and classify unique minimum energy multidentate adsorbate configurations for surfaces of low symmetry,including multi-elemental alloy surfaces, steps, and kinks. Two case studies are presented which demonstrate these capabilities;first, an analysis of a coverage-dependent phase diagram of absorbate NO on the Pt3Sn(111) terrace surface, and second, aninvestigation of adsorption energies, together with identifying unique minimum energy configurations, for the reactionintermediate propyne (CHCCH3*) adsorbed on a PdIn(021) step surface. The evolutionary algorithm approach reproduces highcoverage configurations of NO on Pt3Sn(111) using only 15% of the number of simulations required for a brute force approach.Furthermore, the screening of potentially hundreds of multidentate adsorbates is shown to be possible without humanintervention. The strategy presented is quite general and can be applied to a spectrum of complex atomic systems.