scholarly journals Atomic Control of Active Site Ensembles in Ordered Alloys to Enhance Hydrogenation Selectivity

2021 ◽  
Author(s):  
Anish Dasgupta ◽  
Hoaran He ◽  
Rushi Gong ◽  
Shun-Li Shang ◽  
Eric Zimmerer ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Functional Theory ◽  
Ethane Conversion ◽  
Precise Control ◽  
Atom Manipulation ◽  
Catalytic Sites ◽  
Ordered Alloys ◽  
Ethylene Selectivity

Abstract Intermetallic compounds offer unique opportunities for atom-by-atom manipulation of catalytic ensembles through precise stoichiometric control. The [Pd, (M), Zn] γ-brass phase allows for controlled synthesis of Pd-M-Pd catalytic sites (M = Zn, Pd, Cu, Ag and Au) isolated in an inert Zn matrix. These multi-atom heteronuclear active sites are catalytically distinct from Pd single atoms and fully coordinated Pd. We quantify the unexpectedly large effect of active site composition (i.e., identity of M atom in Pd-M-Pd sites) on ethylene selectivity during acetylene semi-hydrogenation. Subtle stoichiometric control demonstrates Pd-Pd-Pd sites are active for ethylene hydrogenation, whereas Pd-Zn-Pd sites show no measurable ethylene to ethane conversion. Agreement between experimental and density functional theory predicted activities and selectivities demonstrates precise control of Pd-M-Pd active site composition. The diversity and well-defined structure of intermetallics can be utilized to design active sites assembled with atomic-level precision.

On the role of lysine in the active site Ser-X-X-Lys region of penicillin-recognizing enzymes

2010 ◽  
Vol 88 (1) ◽  
pp. 1-4
Author(s):  
Saul Wolfe ◽  
Kiyull Yang
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Basis Set ◽  
Penicillin G ◽  
Hydroxyl Group ◽  
Functional Theory ◽  
One Step ◽  
Optimized Geometries

Using Autodock, docking of penicillin G to the crystal structures of penicillin-recognizing enzymes leads to an alignment in the active site Ser-X-X-Lys region consisting of the serine hydroxyl group, the terminal amino group of lysine, a second hydroxyl group, and the N–C=O of the β-lactam. This alignment is consistent with the notion that acylation of the serine hydroxyl group proceeds by a one-step cooperative mechanism in which C–O bond formation and proton transfer to the β-lactam nitrogen take place through a heteroatom bridge. For the cooperative ring opening of penam by two molecules of methanol and one molecule of methylamine or one molecule of water, density functional theory with the B3LYP DFT gradient-corrected functional and the 6–31G(d) basis set reproduces the alignment seen in the docked structures. Methylamine lowers the barrier calculated at MP2/6–31G(d) from the DFT-optimized geometries by 3 kcal/mol; water increases the barrier by 4 kcal/mol. The function of the conserved lysine in the active sites of penicillin-recognizing enzymes is therefore to catalyze the formation of an acyl enzyme by a cooperative mechanism.

scholarly journals A Unique Ru-N4-P Coordinated Structure Synergistically Waking Up the Nonmetal P Active Site for Hydrogen Production

Research ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Chuanqiang Wu ◽  
Shiqing Ding ◽  
Daobin Liu ◽  
Dongdong Li ◽  
Shuangming Chen ◽  
...  
Keyword(s):  
Hydrogen Evolution ◽  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Highly Efficient ◽  
Catalytic Sites ◽  
Catalytically Active ◽  
Doped Graphene ◽  
Waking Up

Numerous experiments have demonstrated that the metal atom is the active center of monoatomic catalysts for hydrogen evolution reaction (HER), while the active sites of nonmetal doped atoms are often neglected. By combining theoretical prediction and experimental verification, we designed a unique ternary Ru-N4-P coordination structure constructed by monodispersed Ru atoms supported on N,P dual-doped graphene for highly efficient hydrogen evolution in acid solution. The density functional theory calculations indicate that the charge polarization will lead to the most charge accumulation at P atoms, which results in a distinct nonmetallic P active sites with the moderate H∗ adsorption energy. Notably, these P atoms mainly supply highly efficient catalytic sites with ultrasmall absorption energy of 0.007 eV. Correspondingly, the Ru-N4-P demonstrated outstanding HER performance not only in an acidic condition but also in alkaline environment. Notably, the performance of Ru-NPC catalyst at high current is even superior to the commercial Pt/C catalysts, whether in acidic or alkaline medium. Our in situ synchrotron radiation infrared spectra demonstrate that a P-Hads intermediate is continually emerging on the Ru-NPC catalyst, actively proving the nonmetallic P catalytically active site in HER that is very different with previously reported metallic sites.

scholarly journals Active sites for tandem reactions of CO2 reduction and ethane dehydrogenation

2018 ◽  
Vol 115 (33) ◽  
pp. 8278-8283 ◽  
Author(s):  
Binhang Yan ◽  
Siyu Yao ◽  
Shyam Kattel ◽  
Qiyuan Wu ◽  
Zhenhua Xie ◽  
...  
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Raw Materials ◽  
Co2 Reduction ◽  
Tandem Reactions ◽  
In Situ Characterization ◽  
Functional Theory ◽  
Ethane Dehydrogenation ◽  
Ethylene Selectivity

Ethylene (C2H4) is one of the most important raw materials for chemical industry. The tandem reactions of CO2-assisted dehydrogenation of ethane (C2H6) to ethylene creates an opportunity to effectively use the underutilized ethane from shale gas while mitigating anthropogenic CO2 emissions. Here we identify the most likely active sites over CeO2-supported NiFe catalysts by using combined in situ characterization with density-functional theory (DFT) calculations. The experimental and theoretical results reveal that the Ni–FeOx interfacial sites can selectively break the C–H bonds and preserve the C–C bond of C2H6 to produce ethylene, while the Ni–CeOx interfacial sites efficiently cleave all of the C–H and C–C bonds to produce synthesis gas. Controlled synthesis of the two distinct active sites enables rational enhancement of the ethylene selectivity for the CO2-assisted dehydrogenation of ethane.

Investigation of YIG’s Active Site Using Density Functional Theory

2017 ◽  
Vol 888 ◽  
pp. 76-80
Author(s):  
Wan Fahmin Faiz Wan Ali ◽  
Maslinda Kamarudin ◽  
Norazharuddin Shah Abdullah ◽  
Zainal Arifin Ahmad
Keyword(s):  
Density Functional Theory ◽  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Density Of State ◽  
Yttrium Iron ◽  
Functional Theory ◽  
Energy Substitution ◽  
Phase Diversity ◽  
Iron Garnet

Numerous materials characteristic including yttrium iron garnet (YIG) are directly dependent on its crystal structure; phase diversity. However, only a few examination of energy and its mechanism at atomistic scales was reported. In this article, a density functional theory (DFT) based calculations have been carried out to study electronic properties of cubic Y3Fe5O12 (YIG) at its known active sites; (0,0,4), (2,2,4) and (2,2,4). The density of state (DOS) these sites were presented at-19 eV to-14 eV for lower valance band and-6 eV to 0 for upper valance band. Both (0,0,4) and (0,2,4) planes shows highest possibility of cation substitution since the energy substitution are the lowest (~40 KeV). (2,2,4) plane composed of O-O interaction in which would contribute to the oxygen vacancy.

scholarly journals Study on the adsorption selection of CH$$_4$$ on CuO (110) versus (111) surfaces: a density functional theory study

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Long Lin ◽  
Linwei Yao ◽  
Shaofei Li ◽  
Zhengguang Shi ◽  
Kun Xie ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Adsorption Capacity ◽  
Active Sites ◽  
Density Functional ◽  
Oxygen Vacancies ◽  
Density Functional Theory Calculations ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Strong Adsorption ◽  
Selection Of

AbstractFinding the active sites of suitable metal oxides is a key prerequisite for detecting CH$$_4$$ 4 . The purpose of the paper is to investigate the adsorption of CH$$_4$$ 4 on intrinsic and oxygen-vacancies CuO (111) and (110) surfaces using density functional theory calculations. The results show that CH$$_4$$ 4 has a strong adsorption energy of −0.370 to 0.391 eV at all site on the CuO (110) surface. The adsorption capacity of CH$$_4$$ 4 on CuO (111) surface is weak, ranging from −0.156 to −0.325 eV. In the surface containing oxygen vacancies, the adsorption capacity of CuO surface to CH$$_4$$ 4 is significantly stronger than that of intrinsic CuO surface. The results indicate that CuO (110) has strong adsorption and charge transfer capacity for CH$$_4$$ 4 , which may provide experimental guidance.

scholarly journals Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3631
Author(s):  
Ahmed M. Deghady ◽  
Rageh K. Hussein ◽  
Abdulrahman G. Alhamzani ◽  
Abeer Mera
Keyword(s):  
Density Functional Theory ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Carbonyl Group ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Molecular Docking Study ◽  
Functional Theory

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

Study on adsorption of CO and CO2 by graphene gas sensor

2021 ◽  
pp. 2150154
Author(s):  
Wenchao Tian ◽  
Jiahao Niu ◽  
Wenhua Li ◽  
Xiaohan Liu
Keyword(s):  
Gas Sensors ◽  
Active Sites ◽  
Density Functional ◽  
Gas Adsorption ◽  
Experimental Studies ◽  
Detection Accuracy ◽  
Functional Theory ◽  
Vacancy Defects ◽  
Adsorption Of Co ◽  
Detection Characteristics

The two-dimensional (2D) plane of graphene has many active sites for gas adsorption. It has broad application prospects in the field of MEMS gas sensors. At present, there are many experimental studies on graphene gas sensors, but it is difficult to accurately control various influencing factors in the experiments. Therefore, this paper applies the first principle based on density functional theory to study the adsorption and detection characteristics of graphene on CO and CO2. The first-principles analysis method was used to study the adsorption characteristics and sensitivity of graphene. The results show that the inductive graphene has a sensitivity of 1.55% and 0.77% for CO and CO2, respectively. The Stone–Wales defects and multi-vacancy defects have greatly improved the sensitivity of graphene to CO, which is 35.25% and 4.14%, respectively. Introduction of defects increases the sensitivity of detection of CO and CO2, but also improves the selective gas detection material of these two gases. Thus, the control and selectively introducing defects may improve the detection accuracy of the graphene CO and CO2.

The structure and activity of potassium supported on SBA-15 molecular sieve: Density functional theory study

2014 ◽  
Vol 13 (01) ◽  
pp. 1350076 ◽  
Author(s):  
Bing Liu ◽  
Daxi Wang ◽  
Zhongxue Wang ◽  
Zhen Zhao ◽  
Yu Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Lewis Acid ◽  
Molecular Sieve ◽  
Active Sites ◽  
Density Functional ◽  
Structural Model ◽  
Vibrational Frequencies ◽  
Oxygen Molecule ◽  
Lewis Base ◽  
Functional Theory

The geometries, vibrational frequencies, electronic properties and reactivity of potassium supported on SBA-15 have been theoretically investigated by the density functional theory (DFT) method. The structural model of the potassium supported on SBA-15 was constructed based on our previous work [Wang ZX, Wang DX, Zhao Z, Chen Y, Lan J, A DFT study of the structural units in SBA-15 mesoporous molecular sieve, Comput. Theor. Chem.963, 403, 2011]. This paper is the extension of our previous work. The most favored location of potassium atom was obtained by the calculation of substitution energy. The calculated vibrational frequencies of K /SBA-15 are in good agreement with the experimental results. By analyzing the properties of electronic structure, we found that the O atom of Si - O (2)- K group acts as the Lewis base center and the K atom acts as the Lewis acid center. The reactivity of K /SBA-15 was investigated by calculating the activation of oxygen molecule. The oxygen molecule can be activated by K /SBA-15 with an energy barrier of 103.2 kJ/mol. In the final state, the activated oxygen atoms become new Lewis acid centers, which are predicted to act as the active sites in the catalytic reactions. This study provides a deep insight into the properties of supported potassium catalysts and offers fundamental information for further research.

scholarly journals Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites

2018 ◽  
Vol 115 (48) ◽  
pp. 12124-12129 ◽  
Author(s):  
Benjamin E. R. Snyder ◽  
Max L. Bols ◽  
Hannah M. Rhoda ◽  
Pieter Vanelderen ◽  
Lars H. Böttger ◽  
...  
Keyword(s):  
High Activity ◽  
Active Site ◽  
Active Sites ◽  
High Performance ◽  
Density Functional ◽  
Catalyst Deactivation ◽  
Density Functional Theory Calculations ◽  
Oxidation Catalysis ◽  
Spectroscopic Techniques ◽  
Benzene Hydroxylation

A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates.

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