scholarly journals Binding energies and sticking coefficients of H2 on crystalline and amorphous CO ice

2021 ◽  
Vol 648 ◽  
pp. A84
Author(s):  
G. Molpeceres ◽  
V. Zaverkin ◽  
N. Watanabe ◽  
J. Kästner
Keyword(s):  
Binding Energy ◽  
Binding Sites ◽  
Density Functional ◽  
Binding Energies ◽  
Model Systems ◽  
Ab Initio Molecular Dynamics ◽  
Residence Times ◽  
Wide Range ◽  
Sticking Coefficients ◽  
Ice Phase

Context. Molecular hydrogen (H2) is the most abundant interstellar molecule and plays an important role in the chemistry and physics of the interstellar medium. The interaction of H2 with interstellar ices is relevant for several processes (e.g., nuclear spin conversion and chemical reactions on the surface of the ice). To model surface processes, quantities such as binding energies and sticking coefficients are required. Aims. We provide sticking coefficients and binding energies for the H2/CO system. These data are absent in the literature so far and could help modelers and experimentalists to draw conclusions on the H2/CO interaction in cold molecular clouds. Methods. Ab initio molecular dynamics simulations, in combination with neural network potentials, were employed in our simulations. Atomistic neural networks were trained against density functional theory calculations on model systems. We sampled a wide range of H2 internal energies and three surface temperatures. Results. Our results show that the binding energy for the H2/CO system is low on average, − 157 K for amorphous CO and −266 K for crystalline CO. This carries several implications for the rest of the work. H2 binding to crystalline CO is stronger by 109 K than to amorphous CO, while amorphous CO shows a wider H2 binding energy distribution. Sticking coefficients are never unity and vary strongly with surface temperature, but less so with ice phase, with values between 0.95 and 0.17. With the values of this study, between 17 and 25% of a beam of H2 molecules at room temperature would stick to the surface, depending on the temperature of the surface and the ice phase. Residence times vary by several orders of magnitude between crystalline and amorphous CO, with the latter showing residence times on the order of seconds at 5 K. H2 may diffuse before desorption in amorphous ices, which might help to accommodate it in deeper binding sites. Conclusions. Based on our results, a significant fraction of H2 molecules will stick on CO ice under experimental conditions, even more so under the harsh conditions of prestellar cores. However, with the low H2–CO binding energies, residence times of H2 on CO ice before desorption are too short to consider a significant population of H2 molecules on pure CO ices. Diffusion is possible in a time window before desorption, which might help accommodate H2 on deeper binding sites, which would increase residence times on the surface.

scholarly journals Tuning the electronic structure of Ag-Pd alloys to enhance performance for alkaline oxygen reduction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
José A. Zamora Zeledón ◽  
Michaela Burke Stevens ◽  
G. T. Kasun Kalhara Gunasooriya ◽  
Alessandro Gallo ◽  
Alan T. Landers ◽  
...  
Keyword(s):  
Metal Binding ◽  
Precious Metal ◽  
Metal Content ◽  
Density Functional ◽  
Binding Energies ◽  
Intrinsic Activity ◽  
Energy Technologies ◽  
Highly Active ◽  
Wide Range ◽  
Precious Metal Content

AbstractAlloying is a powerful tool that can improve the electrocatalytic performance and viability of diverse electrochemical renewable energy technologies. Herein, we enhance the activity of Pd-based electrocatalysts via Ag-Pd alloying while simultaneously lowering precious metal content in a broad-range compositional study focusing on highly comparable Ag-Pd thin films synthesized systematically via electron-beam physical vapor co-deposition. Cyclic voltammetry in 0.1 M KOH shows enhancements across a wide range of alloys; even slight alloying with Ag (e.g. Ag0.1Pd0.9) leads to intrinsic activity enhancements up to 5-fold at 0.9 V vs. RHE compared to pure Pd. Based on density functional theory and x-ray absorption, we hypothesize that these enhancements arise mainly from ligand effects that optimize adsorbate–metal binding energies with enhanced Ag-Pd hybridization. This work shows the versatility of coupled experimental-theoretical methods in designing materials with specific and tunable properties and aids the development of highly active electrocatalysts with decreased precious-metal content.

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

scholarly journals Hybrid Dynamic Pharmacophore Models as Effective Tools to Identify Novel Chemotypes for Anti-TB Inhibitor Design: A Case Study With Mtb-DapB

2020 ◽  
Vol 8 ◽  
Author(s):  
Chinmayee Choudhury ◽  
Anshu Bhardwaj
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Chemical Space ◽  
Pharmacophore Model ◽  
Model Systems ◽  
Receptor Interaction ◽  
Hybrid Molecules ◽  
Wide Range ◽  
Binding Pockets ◽  
Pharmacophore Models

Antimicrobial resistance (AMR) is one of the most serious global public health threats as it compromises the successful treatment of deadly infectious diseases like tuberculosis. New therapeutics are constantly needed but it takes a long time and is expensive to explore new biochemical space. One way to address this issue is to repurpose the validated targets and identify novel chemotypes that can simultaneously bind to multiple binding pockets of these targets as a new lead generation strategy. This study reports such a strategy, dynamic hybrid pharmacophore model (DHPM), which represents the combined interaction features of different binding pockets contrary to the conventional approaches, where pharmacophore models are generated from single binding sites. We have considered Mtb-DapB, a validated mycobacterial drug target, as our model system to explore the effectiveness of DHPMs to screen novel unexplored compounds. Mtb-DapB has a cofactor binding site (CBS) and an adjacent substrate binding site (SBS). Four different model systems of Mtb-DapB were designed where, either NADPH/NADH occupies CBS in presence/absence of an inhibitor 2, 6-PDC in the adjacent SBS. Two more model systems were designed, where 2, 6-PDC was linked to NADPH and NADH to form hybrid molecules. The six model systems were subjected to 200 ns molecular dynamics simulations and trajectories were analyzed to identify stable ligand-receptor interaction features. Based on these interactions, conventional pharmacophore models (CPM) were generated from the individual binding sites while DHPMs were created from hybrid-molecules occupying both binding sites. A huge library of 1,563,764 publicly available molecules were screened by CPMs and DHPMs. The screened hits obtained from both types of models were compared based on their Hashed binary molecular fingerprints and 4-point pharmacophore fingerprints using Tanimoto, Cosine, Dice and Tversky similarity matrices. Molecules screened by DHPM exhibited significant structural diversity, better binding strength and drug like properties as compared to the compounds screened by CPMs indicating the efficiency of DHPM to explore new chemical space for anti-TB drug discovery. The idea of DHPM can be applied for a wide range of mycobacterial or other pathogen targets to venture into unexplored chemical space.

scholarly journals A self-adjusting platinum surface for acetone hydrogenation

2020 ◽  
Vol 117 (7) ◽  
pp. 3446-3450 ◽  
Author(s):  
Benginur Demir ◽  
Thomas Kropp ◽  
Keishla R. Rivera-Dones ◽  
Elise B. Gilcher ◽  
George W. Huber ◽  
...  
Keyword(s):  
Reaction Kinetics ◽  
Density Functional ◽  
Surface Coverage ◽  
Binding Energies ◽  
Microkinetic Modeling ◽  
Reaction Conditions ◽  
Platinum Surface ◽  
Kinetics Parameters ◽  
Supported Platinum Catalysts ◽  
Wide Range

We show that platinum displays a self-adjusting surface that is active for the hydrogenation of acetone over a wide range of reaction conditions. Reaction kinetics measurements under steady-state and transient conditions at temperatures near 350 K, electronic structure calculations employing density-functional theory, and microkinetic modeling were employed to study this behavior over supported platinum catalysts. The importance of surface coverage effects was highlighted by evaluating the transient response of isopropanol formation following either removal of the reactant ketone from the feed, or its substitution with a similarly structured species. The extent to which adsorbed intermediates that lead to the formation of isopropanol were removed from the catalytic surface was observed to be higher following ketone substitution in comparison to its removal, indicating that surface species leading to isopropanol become more strongly adsorbed on the surface as the coverage decreases during the desorption experiment. This phenomenon occurs as a result of adsorbate–adsorbate repulsive interactions on the catalyst surface which adjust with respect to the reaction conditions. Reaction kinetics parameters obtained experimentally were in agreement with those predicted by microkinetic modeling when the binding energies, activation energies, and entropies of adsorbed species and transition states were expressed as a function of surface coverage of the most abundant surface intermediate (MASI, C3H6OH*). It is important that these effects of surface coverage be incorporated dynamically in the microkinetic model (e.g., using the Bragg–Williams approximation) to describe the experimental data over a wide range of acetone partial pressures.

Computational study of Mg insertion into amorphous silicon: advantageous energetics over crystalline silicon for Mg storage

2013 ◽  
Vol 1540 ◽  
Author(s):  
Fleur Legrain ◽  
Oleksandr I. Malyi ◽  
Teck L. Tan ◽  
Sergei Manzhos
Keyword(s):  
Density Functional ◽  
Nearest Neighbor ◽  
Defect Formation ◽  
Crystalline Silicon ◽  
Computational Study ◽  
Binding Energies ◽  
Functional Theory ◽  
Wide Range ◽  
Insertion Sites ◽  
Formation Energies

ABSTRACTWe show in a theoretical density functional theory study that amorphous Si (a-Si) has more favorable energetics for Mg storage compared to crystalline Si (c-Si). Specifically, Mg and Li insertion is compared in a model a-Si simulation cell. Multiple sites for Mg insertion with a wide range of binding energies are identified. For many sites, Mg defect formation energies are negative, whereas they are positive in c-Si. Moreover, while clustering in c-Si destabilizes the insertion sites (by about 0.1/0.2 eV per atom for nearest-neighbor Li/Mg), it is found to stabilize some of the insertion sites for both Li (by up to 0.27 eV) and Mg (by up to 0.35 eV) in a-Si. This could have significant implications on the performance of Si anodes in Mg batteries.

Interaction mechanisms and structural properties of B-, Si-doped C60 fullerenes with 1-formylpiperazine

2016 ◽  
Vol 39 (5-6) ◽  
Author(s):  
Cemal Parlak ◽  
Özgür Alver ◽  
Ponnadurai Ramasami
Keyword(s):  
Electronic Properties ◽  
Density Functional ◽  
Interaction Mechanism ◽  
Potential Interaction ◽  
Binding Energies ◽  
Molecular Structures ◽  
Interaction Mechanisms ◽  
Wide Range ◽  
Si Doped ◽  
Physical And Chemical

AbstractPiperazines and fullerene nanocages are versatile compounds. These are discussed in a wide range of academic work, especially in the field of medicine, and considered for various applications by the pharmaceutical industry. In the present research, the potential interaction mechanisms between B-, Si-doped C60 and 1-formylpiperazine (1-fp) were examined within the framework of density functional theory, along with their optimized molecular structures and electronic properties. The calculated binding energies and various other physical and chemical parameters of 1-fp found in this work in comparison with the Si- and B-doped fullerenes suggest that doping of fullerene nanocage leads to a strong interaction mechanism that alters the chemical and electronic properties of the investigated compounds. This finding can be used as a guide for their further applications.

scholarly journals The investigation of 2D monolayers as potential chelation agents in Alzheimer’s disease

2019 ◽  
Author(s):  
Neha Pavuluru ◽  
Xuan Luo
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Charge Transfer ◽  
Binding Energy ◽  
Amyloid Beta ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Amyloid Beta Protein ◽  
Functional Theory

In this study, we conducted Density Functional Theory calculations comparing the binding energy of the copper- Amyloid-beta complex to the binding energies of potential chelation materials. We used the first-coordination sphere of the truncated high-pH Amyloid-beta protein subject to computational limits. Binding energy and charge transfer calculations were evaluated for copper’s interaction with potential chelators: monolayer boron nitride, monolayer molybdenum disulfide, and monolayer silicene. Silicene produced the highest binding energies to copper, and the evidence of charge transfer between copper and the monolayer proves that there is a strong ionic bond present. Although our three monolayers did not directly present chelation potential, the absolute differences between the binding energies of the silicene binding sites and the Amyloid-beta binding site were minimal proving that further research in silicene chelators may be useful for therapy in Alzheimer’s disease.

scholarly journals Antimony Selenide Crystals Encapsulated within Single Walled Carbon Nanotubes-A DFT Study

2009 ◽  
Vol 6 (s1) ◽  
pp. S147-S152 ◽  
Author(s):  
Navaratnarajah Kuganathan
Keyword(s):  
Carbon Nanotubes ◽  
Binding Energy ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Single Walled Carbon Nanotubes ◽  
Binding Energies ◽  
Single Walled Carbon ◽  
Transmission Electron ◽  
Antimony Selenide ◽  
Walled Carbon Nanotubes

The structure and binding energies of antimony selenide crystals encapsulated within single-walled carbon nanotubes are studied using density functional theory. Calculations were performed on the simulated Sb2Se3structure encapsulated within single walled nanotube to investigate the perturbations on the Sb2Se3crystal and tube structure and electronic structure and to estimate the binding energy. The calculated structures are in good agreement with the experimental high resolution transmission electron microscopy images of the Sb2Se3@SWNT. The calculated binding energy shows that larger diameter tube could accommodate the Sb2Se3crystals exothermically. Minimal charge transfer is observed between nanotube and the Sb2Se3crystals.

scholarly journals Giant gate-tunable bandgap renormalization and excitonic effects in a 2D semiconductor

2019 ◽  
Vol 5 (7) ◽  
pp. eaaw2347 ◽  
Author(s):  
Zhizhan Qiu ◽  
Maxim Trushin ◽  
Hanyan Fang ◽  
Ivan Verzhbitskiy ◽  
Shiyuan Gao ◽  
...  
Keyword(s):  
Binding Energy ◽  
Single Layer ◽  
Scanning Tunneling Spectroscopy ◽  
Binding Energies ◽  
Exciton Binding Energy ◽  
Scanning Tunneling ◽  
Full Potential ◽  
2D Semiconductors ◽  
Wide Range ◽  
Excitonic Effects

Understanding the remarkable excitonic effects and controlling the exciton binding energies in two-dimensional (2D) semiconductors are crucial in unlocking their full potential for use in future photonic and optoelectronic devices. Here, we demonstrate large excitonic effects and gate-tunable exciton binding energies in single-layer rhenium diselenide (ReSe2) on a back-gated graphene device. We used scanning tunneling spectroscopy and differential reflectance spectroscopy to measure the quasiparticle electronic and optical bandgap of single-layer ReSe2, respectively, yielding a large exciton binding energy of 520 meV. Further, we achieved continuous tuning of the electronic bandgap and exciton binding energy of monolayer ReSe2 by hundreds of milli–electron volts through electrostatic gating, attributed to tunable Coulomb interactions arising from the gate-controlled free carriers in graphene. Our findings open a new avenue for controlling the bandgap renormalization and exciton binding energies in 2D semiconductors for a wide range of technological applications.

Ab Initio Molecular Dynamics Reveals New Active Sites in Atomically Dispersed Pt1/TiO2 Catalysts

2020 ◽  
Author(s):  
Nicholas Humphrey ◽  
Selin Bac ◽  
Shaama Mallikarjun Sharada
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Active Sites ◽  
Density Functional ◽  
Elevated Temperatures ◽  
Water Gas Shift ◽  
Ab Initio Molecular Dynamics ◽  
Catalytic Surface ◽  
Wide Range ◽  
Water Gas

<div> <div> <div> <p>We present a multi-scale modeling study of atomically dispersed Pt on the (110) surface of rutile TiO2. Using density functional theory (DFT) and ab initio molecular dynamics (AIMD), we probe the dynamic evolution of the catalytic surface at elevated temperatures. We identify metal atom diffusion as well as support atom mobility as important dynamical phenomena that enable the formation of new active sites. Among the eight new dynamically formed sites that are distinct from prior experimental and DFT reports, two sites exhibit anionic, near-linear O−Pt−O configurations. Such configurations are neither intuitive nor easily located using static methods such as DFT. Therefore, DFT alone is not sufficient to obtain a complete, dynamic description of the catalytic surface. Furthermore, the near-linear O−Pt−O sites exhibit CO binding characteristics that are markedly distinct from their parent sites, with possibly higher activity towards CO oxidation and water-gas shift reactions. Based on the wide range of adsorbate affinities exhibited by the DFT and AIMD-generated sites in this study, our aim going forward is to probe site-sensitivity of water-gas shift kinetics with these catalysts. </p> </div> </div> </div>

Sign in / Sign up

Export Citation Format

Share Document