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Astatine-211 (211At or simply At) used as an α particle emitter is currently gaining as treatment method for cancer cells. It must however be attached to a carrier to facilitate the treatment process. Gold nanoparticle is a good candidate that has been used in several tests. Knowing the physics behind the adsorption of astatine on gold nanoparticles would be advantageous in designing a more optimal method for such applications. We therefore performed density functional theory calculation on astatine adsorption on gold (111) surface to understand both the mechanism of astatine bonding with gold and the strength of the bonding. We found the mechanism of adsorption to be the hybridization between the 6p orbital of astatine and the 5d and 6s orbitals of the gold. We also found the adsorption strength of astatine on gold to be -1.43 eV at the fcc hollow site. Both results provide us with a good starting point towards our goal of designing an optimized gold nanoparticle for radiotherapy.

Melinjo seed extract contains melinjo resveratrol compounds that has antioxidant activity. The radical-scavenging sites required for the antioxidant activity, however, is yet to be located. We report a computational study that aims to locate scavenging sites of the simplest resveratrol dimer, gnetin C. We consider the reaction of gnetin C and hydroperoxyl radical energetically with the basis of density-functional calculations, to be compared with the reaction of the resveratrol monomer, trans-resveratrol, and hydroperoxyl radical. The results show that OH group at the para position is the most reactive scavenging site for both molecules. Besides the OH group, gnetin C also provides two CH groups in the furan ring that are favorable as scavenging sites. Therefore, furan ring plays an important role in the scavenging activity, which is contrary to the experimental speculation that propose resorcinol ring. Our study shows the prospect of density-functional calculation for studying the radical-scavenging reaction.

A theoretical study based on density functional theory for H2O dissociation on the metal surface of Pt(111) alloyed simultaneously with Ru and Mo was performed. The determination of the minimum energy path using the climbing image nudged elastic band (CI-NEB) method shows that the dissociation reaction of H2O with this catalyst requires almost no energy cost. This dissociation reaction is not only kinetically favored but also almost thermodynamically neutral and somewhat exothermic. The electronic structure analysis showed that much more charge was released in Mo and was used to bind the adsorbed hydroxyl (OHad). Further analyses of the density of states (DOS) showed that the large number of orbitals that overlap when OH binds to Mo are responsible for the stabilization of the OH-surface bond. The stability of the OHad fragment on the surface is believed to be a descriptor for the dissociation of H2O with an almost spontaneous process.

NO dissociation is an important reaction step in the NO reduction reaction, particularly in the three-way catalyst conversion system for automotive gas exhaust purification. In this study, we used first-principles calculations based on density functional theory to analyze the interaction and dissociation of NO on the PdRuIr ternary alloy. The electronic properties of the atomic combination of the PdRuIr ternary alloy create an effective catalyst that is active for NO dissociation and relatively stable against the formation of volatile RuOx through a weakened O adsorption. This study also shows that for an alloyed system, the strength of NO adsorption may not necessarily predict the dissociation activity. This tendency is observed in the PdRuIr ternary alloy where Ru top is the active site for NO adsorption albeit not an effective site for dissociation. It is presumed that NO dissociation is mediated by its molecular diffusion to active sites for dissociation, which are usually high Ru- and/or Ir-coordinated hollow or bridge sites. These active sites allow high charge transfer from the surface to NO, which fills the NO anti-bonding state and facilitates dissociation. This therefore assumes that the strength of NO molecular adsorption is not a descriptor for NO dissociation on metal alloys but rather the ability of the surface to transfer charge to NO and homogeneity of the strength of adsorption. Furthermore, O adsorption on the ternary alloy, particularly near the Ru sites, is relatively weaker as compared to the pure Ru surface. This weakened O adsorption is attributed to charge re-distribution through alloying, particularly charge transfer from the Ru atom to the Ir and Pd atoms.

Quantum dynamics calculation, performed on top of density functional theory (DFT)-based total energy calculations, show dynamical quantum filtering via enhanced scattering of para-H2 on SrTiO3(001). We attribute this to the strongly orientation-dependent (electrostatic) interaction potential between the H2 (induced) quadrupole moment and the surface electric field gradient of ionic SrTiO3(001). These results suggest that ionic surfaces could function as a scattering/filtering media to realize rotationally state-resolved H2. This could find significant applications not only in H2 storage and transport, but also in realizing materials with pre-determined characteristic properties.

A study on the molecular adsorption of a water (H2O) monomer on Pt alloy surfaces with binary Pt-Ru and Pt-Mo and ternary Pt-Ru-Mo surface models was conducted. Some calculations of the interaction between a H2O monomer and the Pt surface were also done for reference. This study is based on density functional theory (DFT) with periodic models and aims to understand the H2O adsorption mechanism. In Pt, Pt-Ru, and Pt-Mo surfaces, H2O preferably adsorbs via an oxygen atom in a flat configuration at the top sites of Pt, Ru, Mo, respectively. However, on the ternary Pt-Ru-Mo surface, the adsorption configuration has the most inclined H2O structure relative to the surface. The results showed that the binding energy of H2O/Pt-Ru-Mo > H2O/Pt-Mo > H2O/Pt-Ru > H2O/Pt. The adsorption mechanism was then clarified by charge transfer and natural bonding. The charge transfer from the surface to the adsorbate is observed in all models, with the greatest charge transfer occurring on the surface of Pt doped with two Mo atoms. This is probably due to the fact that oxygen can attract the most charge on Mo, because the difference in electronegativity is greatest. The calculation results also show that Ru is the most hydrophilic metal for oxygen. However, since the adsorption structure is parallel to the surface, hydrogen (H) is also more sensitive to receive the charge. Subsequently, the most acceptable reason for the most stable adsorption for H2O/Pt-Ru-Mo is that the inclined structure yields the most orbitals hybridization at the H2O's highest occupied molecular orbital (HOMO). This drives the interaction by forming bonding states at the lowest energy and anti-bonding states at the highest energy.

PdO is known to efficiently catalyze the oxidation of methane but suffers tremendously from sulfur poisoning that lowers its catalytic activity. In this paper, dispersion-corrected density functional theory based first principles calculations were performed to systematically screen the metal impurities M (where M is a transition metal) on a Pd1−xMxO catalyst that promote the desired adsorption energies for CH4 and SO2 to gain insights into the design of sulfation-resistant PdO-based methane oxidation catalysts. Specific Pd1−xMxO(101) catalyst was identified to thermodynamically avoid surface sulfation while maintaining the active sites for methane activation at typical experimental conditions. Results indicate a potential route of tuning the catalytic property of PdO by the introduction of a surface metal impurity.

CO2 hydrogenation to methanol on small size Pdx clusters (x = 7, 9 and 13) has been studied using density functional theory calculations. It has been found that in contrast to metallic Pd system, these small Pdx clusters can interact well with CO2 molecule. CO2 molecule can be adsorbed with a bidendate configuration on the Pdx clusters. The formation of CO2 bidendate adsorption configuration facilitates the first step of CO2 hydrogenation reaction on the clusters. The energy profiles for formate pathway and reverse water gas shift + CO hydrogenation pathways on Pdx clusters are quite similar with Cu(111) surface, except for the first and last hydrogenation steps where the Pdx clusters have lower activation energies. This improvement causing the Pdx clusters to have a tolerable turn over frequencies values. In general, the usage of Pd in the form of small size cluster can improve the catalytic performance of metallic Pd for the CO2 hydrogenation to methanol because small size Pd cluster can act not only as an H2 dissociation center but also as a CO2 hydrogenation center.

This study aimed to investigate the transport mechanisms of ions during forward-osmosis-driven (FO-driven) dewatering of microalgae using molecular dynamics (MD) simulations. The dynamical and structural properties of ions in FO systems of varying NaCl or MgCl2 draw solution (DS) concentrations were calculated and correlated. Results indicate that FO systems with higher DS concentration caused ions to have lower hydration numbers and higher coordination numbers leading to lower diffusion coefficients. The higher hydration number of Mg2+ ions resulted in significantly lower ionic permeability as compared to Na+ ions at all concentrations (p = 0.002). The simulations also revealed that higher DS concentrations led to higher accumulation of ions in the membrane. This study provides insights on the proper selection of DS for FO systems.

Two types of melanin pigments, brown to black eumelanin and yellow to reddish brown pheomelanin, are biosynthesized through a branched reaction, which is associated with the key intermediate dopaquinone (DQ). In the presence of l-cysteine, DQ immediately binds to the –SH group, resulting in the formation of cysteinyldopa necessary for the pheomelanin production. l-Cysteine prefers to bond with aromatic carbons adjacent to the carbonyl groups, namely C5 and C2. Surprisingly, this Michael addition takes place at 1,6-position of the C5 (and to some extent at C2) rather than usually expected 1,4-position. Such an anomaly on the reactivity necessitates an atomic-scale understanding of the binding mechanism. Using density functional theory-based calculations, we investigated the binding of l-cysteine thiolate (Cys–S−) to DQ. Interestingly, the C2–S bonded intermediate was less energetically stable than the C6–S bonded case. Furthermore, the most preferred Cys–S−-attacked intermediate is at the carbon-carbon bridge between the two carbonyls (C3–C4 bridge site) but not on the C5 site. This structure allows the Cys–S− to migrate onto the adjacent C5 or C2 with small activation energies. Further simulation demonstrated a possible conversion pathway of the C5–S (and C2–S) intermediate into 5-S-cysteinyldopa (and 2-S-cysteinyldopa), which is the experimentally identified major (and minor) product. Based on the results, we propose that the binding of Cys–S− to DQ proceeds via the following path: (i) coordination of Cys–S− to C3–C4 bridge, (ii) migration of Cys–S− to C5 (C2), (iii) proton rearrangement from cysteinyl –NH3+ to O4 (O3), and (iv) proton rearrangement from C5 (C2) to O3 (O4).

The biosynthetic pathway of melanin is branched into pheomelanogenesis and eumelanogenesis at the stage of dopaquinone conversion. In the presence of intracellular thiols such as cysteine, dopaquinone binds to the sulfhydryl group of thiols, whereas under lower concentration of thiols dopaquinone spontaneously undergoes intramolecular cyclization through the alanyl side chain. The binding of cysteine produces cysteinyldopa necessary for pheomelanogenesis, whereas the cyclized product, cyclodopa further transforms into eumelanin. In this chapter, we introduce computational studies for cyclization and thiol binding for dopaquinone and structurally similar o-quinones with the emphasis on the competitive behavior between the two reactions. As a result, remarkable charge redistributions were observed during cyclization and thiol binding. From this point of view, the HOMO and LUMO levels of o-quinone are pointed out as important factors affecting the reactivity and the competition between the two reactions. Furthermore, a mechanistic issue of thiol binding is also discussed based on the atomic-scale simulation results, which showed the presence of unusual reaction intermediate. Our approach clarifies branched reactions of dopaquinone and resembling o-quinones from atomic nuclei and electrons world.

Summarizing our findings, we give concluding remarks and future perspectives. One of next challenges will be to unveil quantum effects of atomic nuclei in melanogenesis. While the classical description of atomic nuclei is sufficient for most scenarios, certain phenomena require quantum mechanical description of both atomic nuclei and electrons.

In this study, we performed density functional theory based calculations to determine the effect of the size of Cu

The recognized importance on the studies of alloyed materials is due to the high possibility of forming designer materials that caters to different applications. In any reaction and application, the stability and configuration of the alloy combination are important. In this study, we analyzed the surface stability and segregation of ternary metal alloy system PdRuRh through first principles calculation using density functional theory (DFT). We considered the possibility of forming phases as observed in the binary combinations of elements, i.e., completely miscible, and separating phases. With that, the model we analyzed for the ternary metal alloy slabs considers forming complete atomic miscibility, segregation of each component, and segregation of one component with mixing of the two other. Our results show that for the ternary combination of Pd, Rh and Ru, the Pd atoms have high tendency to segregate at the surface, while due to the high tendency of Ru and Rh to mix, core formation of a mixed RuRh is possible. Also, we determined that the trend of stability in the binary alloy system is a good determinant of stability in the ternary alloy system.

Hydrazine (N2H4) and hydroxyl (OH) coadsorption on the Ni(211) surface is investigated using Density Functional Theory (DFT) based calculations. Effects of the vicinal steps and edges on the stability of various N2H4-OH coadsorption configurations are investigated and compared with the case of individual adsorption of the respective molecules. Stabilizing interaction between N2H4 and OH coadsorbate is found to be mediated by hydrogen-bond. The most stable interaction of N2H4-OH is found perpendicular to the step direction, with N2H4 and OH occupying the terrace and edge sites, respectively. Swapping the position of N2H4 and OH reduce the relative stability. However, placing N2H4 on edge sites stabilizes its cis-conformation with noticeable N - H bond elongation. Finally, N2H4 and OH coadsorption with N2H4 and OH coadsorbed on edge-sites is moderate in terms of overall stability but exhibits the weakest N2H4 coadsorption and longest hydrogen bond interaction distance. Nevertheless, these N2H4-OH coadsorption structures are almost equally accessible thermodynamically due to the relatively small energy differences among them (less than 0.2 eV). In an ideal extended periodic system at specific coverage used in this study, the obtained coadsorption reveals the formation of a chain-like structure between N2H4-OH linked by hydrogen bonds. The results demonstrate the importance of steps and edges in effective formations of hydrogen bond stabilizing N2H4 coadsorption with prospects of promoting proton-transfer-reaction from N2H4 to OH.

Carbohydrazide (CH6N4O) is a potential substitute to hydrazine in fuel cell applications. This paper presents a theoretical study on the adsorption of carbohydrazide on Au(111) and Au3Ni(111) surfaces using first principles calculations based on density functional theory. Results show that without van der Waals correction in the calculations, carbohydrazide weakly physisorbs on Au(111), corroborating the experimentally observed high overpotential requirement for carbohydrazide oxidation on Au catalyst. An enhanced reactivity is observed by alloying Au with Ni due to the emergence of a localized d-band near the Fermi level that interacts strongly with the HOMO of carbohydrazide. On Au3Ni(111), a N–Ni bond between carbohydrazide and the surface is formed, characterized by the hybridization of N–pz and Ni–dzz states. These results pose insights into the use of 3d transition metals as alloying components in enhancing the reactivity of Au catalyst for carbohydrazide oxidation.

We report a novel unshifted Dirac cone in energy and in k-space (pristine-like) for the spin-up electrons of experimentally verified bridge-structure of graphene on Ni(111) using density functional theory with van der Waals corrections. Also, we found that the spin-down electrons exhibit a metallic property. This co-existence of semi-metallic and metallic nature of electrons at the Fermi level can pave a way for effective ultra-thin spin-electronic devices such as memory devices, where different scattering of two spin-configurations of electrons is desired.

We investigated the arrangement of Pd atoms in PdCu(111) when CO, COH, and HCO are introduced as adsorbates, by performing density functional theory (DFT) based calculations. We modeled several Pd alloyed Cu(111) surfaces, i.e., PdCu(111), by substituting small numbers of Cu atoms with Pd atoms in the topmost and subsurface layers of Cu(111). The arrangement of Pd atoms in the presence of adsorbates is evaluated by comparing the energy profiles of adsorbate–PdCu configurations with aggregated and nonaggregated surface and subsurface Pd atoms. In clean PdCu(111) surfaces, the Pd atoms prefer the nonaggregated arrangement. In the presence of the adsorbed molecules, however, we found that the Pd atoms will favor the aggregated configuration. CO and HCO adsorption structures are determined by the coordination of Pd atoms in the topmost layer. Their adsorption energies do not depend on the number of Pd atoms in the topmost layer alone but are also influenced by subsurface Pd atoms. On the other hand, COH is al...

The continuous threat of increasing CO2 concentration in the atmosphere has altered the carbon balance of our planet causing global climate change. Biological fixation of atmospheric CO2 by unicellular microorganisms such as microalgae is a promising technology pursued extensively by researchers as a means for carbon capture. The study aimed to provide an atomic level of study that will demonstrate the effect of the salinity on the mechanism of CO2 absorption across microalgae lipid bilayer. Molecular dynamics simulations were utilized to calculate the free energies of CO2 molecule as it permeates inside the microalgae cell. In thermodynamics, the transport process of a molecule can be demonstrated through its free energy gradient. Thus, calculating the free energies of CO2 molecule across microalgae lipid bilayer can elucidate the mechanisms of permeation processes. Four microalgae lipid bilayer structures were constructed that contains 128-DPPC (dipalmitoylphosphatidylcholine) lipid bilayer with 3640 water molecules with different NaCl concentrations: 0, 3, 13, and 19 NaCl molecules which correspond to a salinity level of 0, 50, 200, and 300 mM, respectively. The cavity insertion Widom method was used to calculate the free energy of CO2 molecule along the lipid bilayer. The results demonstrated that the salinity does not affect the free energies significantly, thus, it does not hamper CO2 transport across microalgae lipid membrane.

Elucidating the reaction mechanism of steam methane reforming (SMR) is imperative for the rational design of catalysts for efficient hydrogen production. In this paper, we provide mechanistic insights into SMR on Ru surface using first principles calculations based on dispersion-corrected density functional theory. Methane activation (i.e., C–H bond cleavage) was found to proceed via a thermodynamically exothermic dissociative adsorption process, resulting in (CHy + zH)* species (“*” denotes a surface-bound state, and y + z = 4), with C* and CH* being the most stable adsorbates. The calculation of activation barriers suggests that the conversion of C* into O-containing species via C–O bond formation is kinetically slow, indicating that the surface reaction of carbon intermediates with oxygen is a possible rate-determining step. The results suggest the importance of subsequent elementary reactions following methane activation in determining the formation of stable carbon structures on the surface that deactivates the catalyst or the conversion of carbon into O-containing species.

Ab initio study on the viability of calcium decorated silicon carbide nanotube as a hydrogen storage material was conducted. Calcium strongly adsorbs on silicon carbide nanotube (SiCNT) with a significant binding energy of −2.83 eV, thus calcium's low cohesive energy and strong binding with SiCNT may prevent Ca to form clusters with other adsorbates. Bader charge analysis also revealed a charge transfer of 1.45e from Ca to SiCNT resulting to calcium's cationic state, which may induce charge polarization to a nearby molecule such as hydrogen. Hydrogen molecule was then allowed to interact with the calcium adatom where it exhibited charge polarization, induced by the electric field from calcium's positive charge. This resulted to a significant binding energy of −0.22 eV for the first hydrogen molecule. Results reveal that Ca on SiCNT can hold up to 7 hydrogen molecules and can be a promising candidate for a hydrogen storage material.

The phase stability and surface effects on binary transition metal nano-alloy systems were investigated using density functional theory-based first principles calculations. In this study, we evaluated the cohesive and alloying energies of six binary metal alloy bulk systems that sample each type of alloys according to miscibility, i.e., Au-Ag and Pd-Ag for the solid solution-type alloys (SS), Pd-Ir and Pd-Rh for the high-temperature solid solution-type alloys (HTSS), and Au-Ir and Ag-Rh for the phase-separation (PS)-type alloys. Our results and analysis show consistency with experimental observations on the type of materials in the bulk phase. Varying the lattice parameter was also shown to have an effect on the stability of the bulk mixed alloy system. It was observed, particularly for the PS- and HTSS-type materials, that mixing gains energy from the increasing lattice constant. We furthermore evaluated the surface effects, which is an important factor to consider for nanoparticle-sized alloys, through analysis of the (001) and (111) surface facets. We found that the stability of the surface depends on the optimization of atomic positions and segregation of atoms near/at the surface, particularly for the HTSS and the PS types of metal alloys. Furthermore, the increase in energy for mixing atoms at the interface of the atomic boundaries of PS- and HTSS-type materials is low enough to overcome by the gain in energy through entropy. These, therefore, are the main proponents for the possibility of mixing alloys near the surface.

We analyzed the electronic and structural properties of an α-Keggin type molybdenum-based polyoxometalate (POM) [[PMo12O40]3-] and its capacity for reduction reaction via H adsorption using Ab Initio calculations based on density functional theory (DFT). We also determined the change in the electronic properties brought about by vanadium substitutional doping, and its effect on the capacity of POM to adsorb H atom. We found that the optimal substitutional doping of 4 vanadium per one unit of POM is adequate to maintain its structural stability. Furthermore, increasing dopant concentration changes charge redistribution such that it induces charge transfer to an initially less active sites for H adsorption on pristine POM. This may increase the possibility of creating active sites from an initially inert H adsorption sites and allows for a higher density of H adsorption. This phenomenon could be relevant for chemical reactions that initially requires high number of pre-adsorbed H atoms.

The envisioned hydrogen-powered future is gradually taking shape in our time. In many countries around the world, active efforts to decarbonize energy systems have turned hydrogen into the centerpiece of grand master plans for clean and sustainable replacement to fossil fuels. This chapter tackles the current status of hydrogen economy, which provides a scientific, social, and economic perspective of hydrogen economy and its realization in our modern time. It elaborates the importance of research findings on the different aspects—hydrogen production, storage, delivery, and fuel cell—relevant to the realization of a hydrogen economy. It also illustrates the impact of the results of scientific investigations in attaining innovative hydrogen technologies. Lastly, it discusses the current technologies for hydrogen in the context of their implementation following the hydrogen roadmaps of different countries around the world.

As the lightest element, hydrogen is typically used as a test particle to establish the fundamental concepts in surface science and to evaluate surface reactivity and relevant surface processes. Aside from this, hydrogen attracts enormous interests for industrial and technological applications due to its potential use as the key energy carrier in the future. If realized, it will provide an environmental friendly alternative to conventional fossil fuels. This chapter aims to discuss the interaction of hydrogen and other compounds such as methane and water with transition metal surfaces. Also, induced surface reconstructions and induced surface segregations in bimetallic systems will be tackled. Such processes are usually taking place on surfaces in the presence of adsorbates. As much as possible, the role of metal surfaces in hydrogen-related applications will be evaluated based on their reactivities and properties that could possibly bring important ideas to further improve existing technologies that will aid in the realization of hydrogen-based technologies.

Although the classical description of the atomic nuclei is sufficient in most scenarios, certain phenomena require a quantum mechanical treatment to fully grasp the nature of such particles. Since the quantum mechanical features are prominently associated with particles with small masses, hydrogen can exhibit quantum mechanical-based phenomena at relatively high temperatures as compared to other elements. This chapter will discuss various phenomena and applications where the quantum mechanical description of nuclei is vital. It starts with a brief review of the Born-Oppenheimer approximation, a necessary framework to treat the nuclei motions at their electronic ground state. The next two sections then discuss the hydrogen adsorption and hydrogen reaction dynamics on surfaces under the quantum mechanical framework, respectively. The chapter then concludes with a brief review of the measurement methods for hydrogen dynamics on surfaces.

The reaction of atoms or molecules on surfaces is the cornerstone of surface science and is of profound importance in many physical, chemical, and biological phenomena. Understanding the basic mechanism of these surface reactions lay the foundation of sophisticated ideas that give rise to diverse industrial and technological applications that are important in our modern time. This chapter will discuss the mechanism of reactions between atoms or molecules on surfaces from the viewpoint of theory and simulation. The chapter starts with a brief discussion of density functional theory, followed by a review of basic crystallography, and ends with the theory of adsorption, desorption, and scattering. These basic concepts of surface science are indispensable in a more complex and thorough analysis of more complicated systems that will be discussed in the succeeding chapters.

We performed density functional theory (DFT) based calculations to investigate the interaction of CO

A new mechanism beyond charge transfer, spin-orientation dependence of O2 reactivity on a ferromagnetic surface, is presented using first-principles methods. O2 favors the anti-parallel configuration at the transition state and a parallel configuration at distances above and below it. This suggests coupling and is found to originate from the unquenched spin moment of O2.