It excites me discovering the "secrets of the Creator", which may provide a speck of contribution to humankind.

(arranged based on author list, then year of publication)



Quantum and Atomic Scale Materials Modeling in the Philippines: Status, Challenges, and Recommendations


R.L. Arevalo, KIMIKA 31 (2020) 56.


The computational materials modeling and simulation research landscape in the Philippines is explored to identify the problem areas and challenges faced by the experts in this field, thereby gaining insights for policy recommendations towards advancing this field in the country. The identified problem areas based on a survey administered to sixteen expert-respondents include the inadequate computational infrastructure, issues on funding, problems with students, administrative and teaching assignments, and lack of collaborations with the industry. Based on these results, policy recommendations were formulated, which include a proposed framework for an integrated computational and experimental approach in the national research and development agenda, enhancement of the national computing facility, amendment of the procurement law, dedicated funding for computational science, establishment of a junior research fellowship and an organized materials modeling community, and development of regional niches for computational materials science.



Adsorption of CH4 and SO2 on Unsupported Pd1−xMxO(101) Surface


R.L. Arevalo, S.M. Aspera, R.E. Otadoy, H. Nakanishi, H. Kasai, Catalysis Letters 150 (2020) 1870. 


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.



Sulfation of a PdO(101) methane oxidation catalyst: mechanism revealed by first principles calculations


R.L. Arevalo, S.M. Aspera, H. Nakanishi, Catalysis Science and Technology 9 (2019) 232.


PdO efficiently catalyzes the oxidation of methane but suffers tremendously from sulfur poisoning that lowers its catalytic activity. In this work, first principles calculations were performed to reveal the mechanism of PdO(101) sulfation and how the active sites for methane activation are altered upon the formation of SOy (y = 2 to 4) species on the surface. The results suggest that under typical experimental conditions with a high O2/SO2 gas ratio, the formation of SO4-decorated PdO(101) is favored and contributes significantly to the poisoning of PdO(101) as it blocks the coordinatively unsaturated Pd atoms that were identified to play a crucial role in the activation of methane. At a low temperature regime, SO2 oxidation forming SO3 and SO4 species is highly exothermic via the Eley–Rideal and Langmuir–Hinshelwood mechanisms but is limited by the high activation barrier for O2 dissociation. On the other hand, the Mars–van Krevelen mechanism has low exothermicity but provides facile elementary steps. From these results, insights into the design of PdO-based sulfur poisoning-resistant methane oxidation catalysts were drawn.



Adsorption of carbohydrazide on Au(111) and Au3Ni(111) surfaces


R.L. Arevalo, S.M. Aspera, H. Nakanishi, H. Kasai, S. Yamaguchi, K. Asazawa, Catalysis Letters 148 (2018) 1073.


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.



Tuning methane decomposition on stepped Ni surface: The role of subsurface atoms in catalyst design


R.L. Arevalo, S.M. Aspera, M.C.S. Escano, H. Nakanishi, H. Kasai, Scientific Reports 7 (2017) 139


The decomposition of methane (CH4) is a catalytically important reaction in the production of syngas that is used to make a wide spectrum of hydrocarbons and alcohols, and a principal carbon deposition pathway in methane reforming. Literatures suggest that stepped Ni surface is uniquely selective toward methane decomposition to atomic C, contrary to other catalysts that favor the CH fragment. In this paper, we used dispersion-corrected density functional theory-based first principles calculations to identify the electronic factors that govern this interesting property of stepped Ni surface. We found that the adsorption of atomic C on this surface is uniquely characterized by a 5–coordinated bonding of C with Ni atoms from both the surface and subsurface layers. Comparison with Ru surface indicates the importance of the subsurface atoms of stepped Ni surface on its selectivity toward methane decomposition to atomic C. Interestingly, we found that substituting these subsurface atoms with other elements can dramatically change the reaction mechanism of methane decomposition, suggesting a new approach to catalyst design for hydrocarbon reforming applications.



First principles study of methane decomposition on B5 step-edge type site of Ru surface


R.L. Arevalo, S.M. Aspera, M.C.S. Escano, H. Nakanishi, H. Kasai, Journal of Physics: Condensed Matter 29 (2017) 184001.


Many chemical reactions that produce a wide range of hydrocarbons and alcohols involve the breaking of C–H bonds in methane. In this paper, we analyzed the decomposition of this molecule on the B5 step-edge type site of Ru surface using first principles calculations based on dispersion-corrected density functional theory. Methane was found to be weakly adsorbed on the surface, characterized by the hybridization of its sp states with Ru–dxz,yz,zz states. Dissociative adsorption is energetically preferred over molecular methane adsorption, resulting in CH fragment. CH is strongly adsorbed on the surface due to the prevalence of low-energy sp–d bonding interaction over the electron-unoccupied anti-bonding states. This highly stable CH requires higher activation barrier for C–H bond cleavage than CH4.



Ru-catalyzed steam methane reforming: Mechanistic study from first principles calculations


R.L. Arevalo, S.M. Aspera, M.C.S. Escaño, H. Nakanishi, H. Kasai, ACS Omega 2 (2017) 1295.


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.



Adsorbate-induced demagnetization: Borohydride on magnetic substrates


R.L. Arevalo, M.C.S. Escaño, A.A.B. Padama, H. Kasai, International Journal of Philippine Science and Technology 9 (2016) 10.


Elucidating the effect of different adsorbates on the magnetic properties of substrates has found useful applications in the design of magnetic devices. In this paper, we show through first principles calculations that the adsorption of borohydride on magnetic substrates (pure 3d or first row transition metals such as Cr, Mn, Fe, Co, and Ni and Au-3d metal alloys) induces the demagnetization of the substrate atoms that directly bind with borohydride. We note a forward shifting of the spin-up and backward shifting of the spin-down components of the metal d band, before and after the adsorption of borohydride, demagnetizing the substrate. The inclusion of spin-polarization in the calculation affects the adsorption energy of borohydride but not its adsorption structure and relative energies on different substrates. Large substrate demagnetization is noted for substrates that promote the strong adsorption of borohydride.



First-principles study of nitric oxide oxidation on Pt(111) versus Pt overlayer on 3d transition metals


R.L. Arevalo, M.C.S. Escaño, H. Kasai, Journal of Vacuum Science and Technology A 33 (2015) 021402.


Catalytic oxidation of NO to NO2 is a significant research interest for improving the quality of air through exhaust gas purification systems. In this paper, the authors studied this reaction on pure Pt and Pt overlayer on 3d transition metals using kinetic Monte Carlo simulations coupled with density functional theory based first principles calculations. The authors found that on the Pt(111) surface, NO oxidation proceeds via the Eley–Rideal mechanism, with O2 dissociative adsorption as the rate-determining step. The oxidationpath via the Langmuir–Hinshelwood mechanism is very slow and does not significantly contribute to the overall reaction. However, in the Pt overlayer systems, the oxidation of NO on the surface is more thermodynamically and kinetically favorable compared to pure Pt. These findings are attributed to the weaker binding of O and NO on the Pt overlayer systems and the binding configuration of NO2 that promotes easier N-O bond formation. These results present insights for designing affordable and efficient catalysts for NO oxidation.



Oxidation of NO on Pt/M (M = Pt, Co, Fe, Mn): A first-principles density functional theory


R.L. Arevalo, K. Oka, H. Nakanishi, H. Kasai, H. Maekawa, K. Osumi, N. Shimazaki, Catalysis Science and Technology 5 (2015) 882.


Platinum is commonly used as a catalyst for the oxidation of NO in exhaust gas purification systems. However, in addition to its high cost, the intrinsic NO + O → NO2 reaction is endothermic and the rate-limiting O2,gas dissociative adsorption is activated on Pt(111). In this paper, we show for the first time that the pseudomorphic Pt monolayer on 3d transition metals promotes a thermodynamically and kinetically favorable NO oxidation compared to pure Pt. Using density functional theory-based first principles calculations, we show that such results are attributed to the weaker binding of O and NO on the bimetallic surfaces and the change of the binding configuration of NO2 into a structure that promotes easier N–O bond formation. These results provide insights into the design of low-cost and efficient catalysts for NO oxidation.



Mechanistic insight into the Au-3d metal alloy-catalyzed borohydride electro-oxidation: From electronic properties to thermodynamics


R.L. Arevalo, M.C.S. Escaño, H. Kasai, , ACS Catalysis 3 (2013) 3031.


Recent theoretical and experimental findings have motivated the use of 3d transition metals as alloying elements to improve the performance of Au for the electro-oxidation of borohydride. In this paper, we provide mechanistic insights into the electrochemical oxidation of borohydride on pure Au and Au-3d alloys (Au3M with M = Cr, Mn, Fe, Co, Ni) using first principles calculations. We found that the initial oxidative adsorption of borohydride is the least exothermic among the elementary reactions considered for the complete eight-electron oxidation process. Interestingly, Au-3d metal alloy surfaces promote this oxidation step at a lower electrode potential compared to pure Au due the enhanced stability of borohydride on these alloy surfaces. The most negative borohydride oxidation potential is achieved by M = Co, followed by Fe, Ni, Mn, and Cr in order of increasing electrode potential. Subsequent to the initial oxidative adsorption of borohydride, the dehydrogenations of BH3*, BH2OH*, and BH(OH)2* are endothermic on pure Au at very low potentials. However, these activated and possibly limiting elementary reaction steps are more exothermic on Au-3d alloys than on pure Au. Following the adsorption of borohydride on the surface, all elementary reaction steps for the complete electro-oxidation process proceed downhill in energy at a lower electrode potential on Au-3d alloys than on pure Au.



Computational mechanistic study of borohydride electrochemical oxidation on Au3Ni(111)


R.L. Arevalo, M.C.S. Escaño, H. Kasai, The Journal of Physical Chemistry C 117 (2013) 3818.


Au-3d metal alloys have recently gained interest for use as anode catalysts for direct borohydride fuel cells since these are less expensive than pure Au and exhibit desirable properties for borohydride oxidation. In this paper, a mechanistic study on the electrochemical oxidation of borohydride on Au3Ni(111) using first principles calculations based on spin-polarized density functional theory is presented. A reaction energy diagram showing the free energies of possible elementary surface-bound species on Au3Ni(111) as a function of electrode potential is constructed to show the favorable reaction path for a complete eight-electron oxidation of borohydride. As compared to pure Au, the adsorption of borohydride is favorable on Au3Ni(111) at lower potential due to the greater stability of borohydride on this surface, which is attributed to the upshift of the derived antibonding states of the BH4-sp and Au3Ni-d interaction with respect to pure Au. At a potential of −0.44 V vs NHE and T = 300 K, all subsequent elementary reaction steps for the complete oxidation of borohydride are downhill in energy with B(OH)3,ads as the highly favored final adsorbed species. The overall oxidation is limited by the initial adsorption of borohydride on the surface since it requires the highest electrode potential requirement among all electrochemical steps considered. Calculation of the dehydrogenation barrier of borohydride provides significant evidence that a more favorable elementary reaction on Au3Ni(111) as compared to Au(111) also leads to a lower reaction barrier.



Structure and stability of borohydride on Au(111) and Au3M (M = Cr, Mn, Fe, Co, Ni)


R.L. Arevalo, M.C.S. Escaño, A.Y-S. Wang, H. Kasai, Dalton Transactions 42 (2013) 770.


We study the adsorption of borohydride on Au and Au-based alloys (Au3M with M = Cr, Mn, Fe, Co, and Ni) using first-principles calculations based on spin-polarized density functional theory. Favorable molecular adsorption and greater adsorption stability compared to pure Au are achieved on Au3M alloys. For these alloys, there is an emergence of unoccupied states in the surface d band around the Fermi level with respect to the fully occupied d band of pure Au. Thus, the derived antibonding state of the sp–d interaction is upshifted and becomes unoccupied compared to pure Au. The B–H bond elongation of the adsorbed borohydride on these alloy surfaces points to the role of surface-parallel (dxy and dx2−y2 states) components of the d-band of the alloying metal M, most pronouncedly in the cases of M = Co or Ni. On the alloy surfaces, B binds directly with the alloying metal, unlike in the case of pure Au where the surface bonding is through the H atoms. These results pose relevant insights into the design of Au-based anode catalysts for the direct borohydride fuel cell.



Structure dependence of Pt4 electronic properties


R.L. Arevalo, H. Kishi, A.A.B. Padama, J.L.V. Moreno, H. Kasai, , Journal of Physics: Condensed Matter 25 (2013) 222001. (IOP Select Article)


We show through first-principles calculations that the electronic properties of Pt4 clusters can be tuned by adsorption on substrates with different electronic valence characters. Pt clusters exhibit a metallic character on γ-Al2O3(111) and insulator properties on CaZrO3(001). The noted difference indicates the role of the electronic valence states of the substrate atoms that directly bond with Pt.



A theoretical study of the structure and stability of borohydride on 3d transition metals


R.L. Arevalo, M.C.S. Escaño, E. Gyenge, H. Kasai, , Surface Science 606 (2012) 1954.


The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s–dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.



First principles study on the adsorption and dehydrogenation of borohydride on Mn(111)


R.L. Arevalo, M.C.S. Escaño, H. Kasai, , e-Journal of Surface Science and Nanotechnology 9 (2011) 257.


The mechanism of adsorption and dehydrogenation of borohydride (BH4) on Mn(111) is explored through first principles calculations within Density Functional Theory (DFT). It is found that the preferred sites for adsorption are the bridge site wherein the adsorbate dissociates resulting to BH2,ads+2Hads (“ads” means in the adsorbed state on the surface) fragments characterized by the competing dzz and dxz,yz interactions of the Mn-d states of the surface with the H-s and B-p states of the adsorbate, and the fcc hollow site wherein the adsorption is molecular. Water molecule is formed when a hydroxyl radical bonds with hydrogen atom on top of an initially adsorbed borohydride. It passes through a metastable state, then an intermediate state and finally the most stable state.



DFT and cluster model investigation on the adhesion of polyethylene terephthalate on metals


R.L. Arevalo, R.F. Pobre, e-Journal of Surface Science and Nanotechnology 9 (2011) 251.


We investigate the adhesion mechanism of metal atoms (Al, Cu Ag, Au and Pt) on polyethylene terephthalate (PET) using Density Functional Theory (DFT) and cluster models. The structural geometry of the basic unit of PET is optimized then a metal atom is made to approach this structure at different orientations while calculating the total energy of the system under B3LYP functional. Results show that Al atom binds strongly when oriented linear to C=O at a distance of 1.80 Å. Orbital population analysis indicates that the good adhesion of Al at this orientation is due to the interaction of pz orbital of free oxygen in the carbonyl group and py orbital of Al atom. Binding is strongest for Al atom, followed by Pt, Cu, Ag, and Au, in decreasing order of adhesive strength. 



Vanadium doped polyoxometalate: induced active sites and increased hydrogen adsorption


S.M. Aspera, R.L. Arevalo, H. Nakanishi, H. Kasai, S. Sekine, H. Kawai, Journal of Physics: Condensed Matter 32 (2020) 195001.


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 four 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.




First principles study of surface stability and segregation of PdRuRh ternary metal alloy system


S.M. Aspera, R.L. Arevalo, H. Nakanishi, H. Kasai, Surface Science 671 (2018) 51.


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.



First principles calculation of transition metal binary alloys: Phase stability and surface effect


S.M. Aspera, R.L. Arevalo, K. Shimizu, R. Kishida, K. Kojima, N.H. Linh, H. Nakanishi, H. Kasai, Journal of Electronic Materials 46 (2017) 3776.


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.



A theoretical study on the adsorption of CO2 on CuO(110) surface


J.L.V. Moreno, R.L. Arevalo, M.C.S. Escano, A.A.B. Padama, H. Kasai, Journal of Physical Society of Japan 84 (2015) 015003.


The adsorption of CO2 on CuO(110) was investigated using density functional theory calculations. The CO2 molecule adsorbs on top of an unsaturated Cu atom with a titled configuration. The low adsorption energy and minimal charge transfer confirm the physisorption character of the adsorption process. Unlike pure copper, the more reactive behavior towards CO2 of copper oxides makes them useful for applications such as the photocatalytic reduction of CO2.



Electrocatalysis of borohydride: a review of density functional theory approach combined with experimental verification


M.C.S. Escano, R.L. Arevalo, E. Gyenge, H. Kasai, Journal of Physics: Condensed Matter 26 (2014) 353001.


The electrocatalysis of borohydride oxidation is a complex, up-to-eight-electron transfer process, which is essential for development of efficient direct borohydride fuel cells. Here we review the progress achieved by density functional theory (DFT) calculations in explaining the adsorption of BH4− on various catalyst surfaces, with implications for electrocatalyst screening and selection. Wherever possible, we correlate the theoretical predictions with experimental findings, in order to validate the proposed models and to identify potential directions for further advancements.



First-principles study of borohydride adsorption properties on osmium nanoparticles and surfaces: Understanding facet, size effects and local sites


M.C.S. Escaño, R.L. Arevalo, E. Gyenge, H. Kasai, Catalysis Science & Technology 4 (2014) 1301.


We present the first density functional theory investigation on the adsorption properties of borohydride on Os surfaces and nanoparticles with respect to the effects of facets, size and local sites. We found that the adsorption configuration and the binding energy significantly changed with respect to these factors. On Os surfaces, the most stable adsorbate configuration is molecular on (0001) but dissociated on (100) and (100). For the Os nanoparticles, the preferred configurations on the Os surface are preserved only on the counterpart (0001) and (100) planes and the binding energies are significantly larger due to the presence of vertices/edges. The difference in the structures between the (100) facet of the slab and of the nanoparticle is attributed to very different Os lateral distances. With respect to the nanoparticle size, the adsorbate structure is also preserved but the binding energy increases when the particle size is increased. At various electrode potentials, borohydride oxidative adsorption is less favorable on the ~2.0 nm Os nanoparticles as compared to the Os surface of the same facet due to enhanced solvation at the vertex sites of the former. Finally, using ab initio molecular dynamics, we found that these less coordinated sites of the Os nanoparticles reconstruct significantly with temperature, especially the smaller sized ones. Only when the nanoparticle size is ~2.0 nm do these reconstructions become minimal. These findings present fundamental borohydride adsorption information on nanoparticles and surface facets relevant for modeling/screening of suitable nanostructures of anode catalysts for direct borohydride fuel cells.



Water co-adsorption and electric field effects on borohydride structures on Os(111) by first-principles calculations


M.C.S. Escaño, R.L. Arevalo, E. Gyenge, H. Kasai, Journal of Alloys and Compounds 580 (2013) S6.


Periodic density functional theory calculations are performed to investigate the nature of the BH4ad and its interaction with H2Oad in the presence of homogenous electric field. We observed a significant charge polarity of BH4ad on Os(1 1 1) and such property could explain the electrostatic interaction with water monomer (Had) with its HOH plane parallel to the surface. This interaction changes the BHad molecular structure to BH3ad + Had. In the presence of homogenous electric field, the water co-adsorption effect is reduced due to the stabilization of H2Oad on the surface and the deviation of the O–H bond from the plane, decreasing the electrostatic interaction between BH4ad and H2Oad. These fundamental findings imply accessible control of borohydride structures on an electrode surface, which could be relevant for direct borohydride fuel cell (DBFC) and reversible hydrogen storage/release applications.



Surface compositions of Pt-Pd/Pd(111) alloys in the presence of O and OH during oxygen reduction reaction: A first principles study


B. Chantaramolee, S.M. Aspera, R.L. Arevalo, E.F. Arguelles, R. Kishida, A.A.B. Padama, H. Kasai, H. Nakanishi, Journal of the Physical Society of Japan 88 (2019) 044820.


The surface stability and compositions of catalysts under varied conditions play an important role in its activity and selectivity toward various reactions. In this paper, density functional theory based first principles calculations were used to investigate the stability and compositions of the first two layers of Pt–Pd alloys on Pd substrate under the electrode-potential dependent oxygen reduction conditions. The adsorption of O and OH have different preference surface compositions of Pt:Pd≈50:50Pt:Pd≈50:50 and Pt:Pd≈0:100Pt:Pd≈0:100, respectively. However, at high electrode potential, it is found that O should be dominant adsorbate on the surface. Therefore, the surface composition should favor the Pt:Pd≈50:50Pt:Pd≈50:50. Moreover, this oxygen covered surface is characterized by weakened surface Pt–Pt bonds, which is attributed to the increase in the population of the Pt–Pt antibonding state. These findings support the experimentally observed Pd segregation from the as-prepared Pt/Pd(111) to the composition of Pt:Pd=60:40Pt:Pd=60:40 during ORR.



Effects of introduction of α-carboxylate, N-methyl, and N-formyl groups on intramolecular cyclization of o-quinone amines: Density functional theory-based study


R. Kishida, A.G. Saputro, R.L. Arevalo, H. Kasai, International Journal of Quantum Chemistry 7 (2017) 23.


o‐Quinone amines, which are relevant to various biological processes, can undergo spontaneous intramolecular cyclization (ring closure reaction by amino‐terminated hydrocarbon side chain) that deactivates them toward another possible reactions, that is, thiol binding. Density functional theory‐based calculation is employed for obtaining the potential energy curves along the C-N bond formation in the intramolecular cyclization of various o‐quinone amines, viz., dopaminequinone, dopaquinone, N‐methyl‐dopaminequinone, N‐formyl‐dopaminequinone, and the corresponding methylene‐inserted analogues. The activation barrier is decreased by introduction of α‐carboxylate and N‐methyl group whereas increased by introduction of N‐formyl group. A negative correlation between the activation barriers and the level of highest occupied molecular orbital is pointed out. Furthermore, the methylene‐inserted analogues show decreased activation barriers. This is explained by reduction of steric repulsion in the transition state.



A theoretical study of the reactivity of Cu2O(111) surfaces: the case of NO dissociation


H. Kishi, A.A.B. Padama, R.L. Arevalo, J.L.V. Moreno, H. Kasai, M. Taniguchi, M. Uenishi, H. Tanaka, Y. Nishihata, Journal of Physics: Condensed Matter 24 (2012) 262001.

(IOP Select Article and featured in IOP Science Labtalk News)


We compare the electronic properties of Cu(111) and Cu2O(111) surfaces in relation to the dissociation of NO using first principles calculations within density functional theory. We note a well-defined three-fold site on both O- and Cu-terminated Cu2O surfaces which is verified as the active site for the adsorption and dissociation of NO. The interaction of Cu with O atoms results in the forward shifting of the local density of states and formation of unoccupied states above the Fermi level, compared to the fully occupied d band of pure Cu. These results give valuable insights in the realization of a catalyst without precious metal for the dissociation of NO.



NO dissociation on Cu(111) and Cu2O(111) surfaces: a density functional theory based study


A.A.B. Padama, H. Kishi, R.L. Arevalo, J.L.V. Moreno, H. Kasai, M. Taniguchi, M. Uenishi, H. Tanaka, Y. Nishihata, Journal of Physics: Condensed Matter 24 (2012) 175005.


NO dissociation on Cu(111) and Cu2O(111) surfaces is investigated using spin-polarized density functional theory. This is to verify the possibility of using Cu-based catalyst for NO dissociation which is the rate limiting step for the NOx reduction process. The dissociation of molecularly adsorbed NO on the surface is activated for both cases. However, from the reaction path of the NO–Cu2O(111) system, the calculated transition state lies below the reference energy which indicates the possibility of dissociation. For the NO–Cu(111) system, the reaction path shows that NO desorption is more likely to occur. The geometric and electronic structure of the Cu2O(111) surface indicates that the surface Cu atoms stabilize themselves with reference to the O atom in the subsurface. The interaction results in modification of the electronic structure of the surface Cu atoms of Cu2O(111) which greatly affects the adsorption and dissociation of NO. This phenomenon further explains the obtained differences in the dissociation pathways of NO on the surfaces.



Reactivity descriptor for borohydride interaction with metal surfaces


M.C.S. Escaño, E. Gyenge, R.L. Arevalo, H. Kasai, The Journal of Physical Chemistry C 115 (2011) 19883.


First-principles density functional theory calculations were performed to study the adsorption of borohydride (BH4) on close-packed transition-metal surfaces, M(111) (M = Au, Pt, Ir, Os, Ag, Pd, Rh, Ru). A correlation between the relative adsorption energies of BH4ad and the d-band center of the metals is established. In terms of the adsorbate configuration, both molecular (BH4ad) and dissociated (BH4-y,ad + yHad, y = 1, ...,3) structures are possible regardless of the adsorption energy value. On Os, Rh, and Ru surfaces, molecular (i.e., undissociative) adsorption is preferred despite the strong surface binding energy of BH4ad. Orbital-specific analysis of the bonding, points to the role of the dzz and dyz states of the surface metal atoms in determining the final BH4ad configuration on all metals. However, in the presence of H2O molecules, the preference for strong molecular adsorption may be lost because of BH4ad–H2Oad interaction. Using the coadsorption on Os(111) of BH4ad and H2Oad with and without the presence of OHad (generated either by electrosorption of OH– or dissociative water adsorption), the origins of the adsorbate–adsorbate and adsorbate–metal interactions are discussed. Electronic factors to predict the BH4ad conformation on metal catalysts in water environment are proposed.



Density Functional Theory-Based Calculation Shed New Light on the Bizarre Addition of Cysteine Thiol to Dopaquinone


R. Kishida, S. Ito, M. Sugumaran, R.L. Arevalo, H. Nakanishi, H. Kasai, International Journal of Molecular Sciences 22 (2021) 1373. 


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). 



Branching reaction in melanogenesis: The effect of intramolecular cyclization on thiol binding


R. Kishida, H. Kasai, S.M. Aspera, R.L. Arevalo, H. Nakanishi, Journal of Electronic Materials 46 (2017) 3784.


With the aid of density functional theory-based first principles calculations, we investigated energetics and electronic structure changes in reactions involving dopaquinone to give insights into the branching behaviors in melanogenesis. The reactions we investigated are the intramolecular cyclization and thiol binding, which are competing with each other. It was found that, in order to accomplish thiol binding, charge transfer of around one electron from thiol to dopaquinone occurs. Furthermore, intramolecular cyclization of dopaquinone increases the lowest unnoccupied molecular orbital level substantially. This result clearly shows prevention of the binding of thiol by intramolecular cyclization.



Density functional theory-based first principles calculations of rhododendrol-quinone reactions: Preference to thiol binding over cyclization


R. Kishida, H. Kasai, S.M. Aspera, R.L. Arevalo, H. Nakanishi, Journal of the Physical Society of Japan 86 (2017) 024804.


Using density functional theory-based first principles calculations, we investigated the changes in the energetics and electronic structures of rhododendrol (RD)-quinone for the initial step of two important reactions, viz., cyclization and thiol binding, to give significant insights into the mechanism of the cause of cytotoxic effects. We found that RD-quinone in the electroneutral structure cannot undergo cyclization, indicating a slow cyclization of RD-quinone at neutral pH. Furthermore, using methane thiolate ion as a model thiol, we found that the oxidized form of the cyclized RD-quinone, namely RD-cyclic quinone, exhibited a reduced binding energy for thiols. However, this reduction of binding energy is clearly smaller than the case of dopaquinone, which is a molecule originally involved in the melanin synthesis. This study clearly shows that RD-quinone has a preference toward thiol bindings than cyclization compared to the case of dopaquinone. Considering that thiol bindings have been reported to induce cytotoxic effects in various ways, the preference toward thiol bindings is an important chemical property for the cytotoxicity caused by RD.



Pt(111)-alloy surfaces for non-activated OOH dissociation


W.T. Cahyanto, M.C. Escaño, H. Kasai, R.L. Arevalo, e-Journal of Surface Science and Nanotechnology 9 (2011) 352.


We present a density functional theory calculation for the adsorption and dissociation of OOH on Pt(111) and Pt(111)-alloy surfaces. We confirmed the theoretical understanding of an activated OOH dissociation on Pt(111) surface and on small Pt clusters. Interestingly, in this work, we found an existence of a “barrierless” OOH dissociation on several Pt-binary and ternary alloy surfaces with Ru and Mo as alloying components: PtRu and PtRuMo. Here, we demonstrate how such reaction proceeds and discuss the role of Ru—O and Mo—O in the spontaneous OOH dissociation in these systems. The reaction energetics of OOH specie is one of the most sought fundamental surface science studies due to its importance in many catalytic and surface reactions such as hydrogen fuel cell.



Rational Synthesis for a Noble Metal Carbide


T. Wakisaka, K. Kusada, D. Wu, T. Yamamoto, T. Toriyama, S. Matsumura, H. Akiba, O. Yamamuro, K. Ikeda, T. Otomo, N. Palina, Y. Chen, L.S.R. Kumara, C. Song, O. Sakata, W. Xie, M. Koyama, Y. Kubota, S. Kawaguchi, R.L. Arevalo, S.M. Aspera, E.F. Arguelles, H. Nakanishi, H. Kitagawa, Journal of the American Chemical Society 142 (2020) 1247.


Transition metal carbides have attractive physical and chemical properties that are much different from their parent metals. Particularly, noble metal carbides are expected to be promising materials for a variety of applications, particularly as efficient catalysts. However, noble metal carbides have rarely been obtained because carbide phases do not appear in noble metal–carbon phase diagrams and a reasonable synthesis method to make noble metal carbides has not yet been established. Here, we propose a new synthesis method for noble metal carbides and describe the first synthesis of rhodium carbide using tetracyanoethylene (TCNE). The rhodium carbide was synthesized without extreme conditions, such as the very high temperature and/or pressure typically required in conventional carbide syntheses. Moreover, we investigated the electronic structure and catalytic activity for the hydrogen evolution reaction (HER). We found that rhodium carbide has much higher catalytic activity for HER than pure Rh. Our study provides a feasible strategy to create new metal carbides to help advance the field of materials science.


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