| Kishida Ryo | Last modified date：2023.11.28 |
Assistant Professor /
Department of Dental Science /
Faculty of Dental Science
Papers
| 1. | Janice Lay Tin Tan, Masaya Shimabukuro, Ryo Kishida, Kunio Ishikawa, Fabrication and histological evaluation of ant-nest type porous carbonate apatite artificial bone using polyurethane foam as a porogen, Journal of Biomedical Materials Research : Part B - App Biomater in press, https://doi.org/10.1002/jbm.b.35173, 111, 560-567, 2022.09. |
| 2. | Koichiro Hayashi, Toshiki Yanagisawa, Masaya Shimabukuro, Ryo Kishida, Kunio Ishikawa, Gear-shaped carbonate apatite granules with a hexagonal macropore for rapid bone regeneration, Computational and Structural Biotechnology Journal, 10.1016/j.csbj.2023.03.053, 21, 2514-2523, 2023.04. |
| 3. | Koichiro Hayashi, Toshiki Yanagisawa, Ryo Kishida, Kunio Ishikawa, Effects of scaffold shape on bone regeneration: Tiny shape differences affect the entire system., ACS Nano, https://doi.org/10.1021/acsnano.2c03776, 16, 8, 11755-11768, 2022.07. |
| 4. | Koichiro Hayashi, Ryo Kishida, Akira Tsuchiya, Kunio Ishikawa, Channel aperture characteristics of carbonate apatite honeycomb scaffolds affect ingrowths of bone and fibrous tissues in vertical bone augmentation, Bioenginnering, https://doi.org/10.3389/fbioe.2022.825831, 9, 627, 2022.10. |
| 5. | Maab Elsheikh, Ryo Kishida, Koichiro Hayashi, Akira Tsuchiya, Masaya Shimabukuro, Kunio Ishikawa, Effects of pore interconnectivity on bone regeneration in carbonate apatite blocks, Regenerative Biomaterials, 10.1093/rb/rbac010, 9, 9, 2022.04, Porous architecture in bone substitutes, notably the interconnectivity of pores, is a critical factor for bone ingrowth. However, controlling the pore interconnectivity while maintaining the microarchitecture has not yet been achieved using conventional methods, such as sintering. Herein, we fabricated a porous block using the crystal growth of calcium sulfate dihydrate, and controlled the pore interconnectivity by limiting the region of crystal growth. The calcium sulfate dihydrate blocks were transformed to bone apatite, carbonate apatite (CO3Ap) through dissolution–precipitation reactions. Thus, CO3Ap blocks with 15% and 30% interconnected pore volumes were obtained while maintaining the microarchitecture: they were designated as CO3Ap-15 and CO3Ap-30, respectively. At 4 weeks after implantation in a rabbit femur defect, new bone formed throughout CO3Ap-30, whereas little bone was formed in the center region of CO3Ap-15. At 12 weeks after implantation, a large portion of CO3Ap-30 was replaced with new bone and the boundary with the host bone became blurred. In contrast, CO3Ap-15 remained in the defect and the boundary with the host bone was still clear. Thus, the interconnected pores promote bone ingrowth, followed by replacement of the material with new bone. These findings provide a useful guide for designing bone substitutes for rapid bone regeneration. <p></p>. |
| 6. | Pery Freitas, Ryo Kishida, Koichiro Hayashi, Akira Tsuchiya, Masaya Shimabukuro, Kunio Ishikawa, Fabrication and histological evaluation of porous carbonate apatite blocks using disodium hydrogen phosphate crystals as a porogen and phosphatization accelerator, Journal of Biomedical Materials Research Part A, 10.1002/jbm.a.37374, 110, 6, 1278-1290, 110, 6, 1278-1290, 2022.02. |
| 7. | Ryo Kishida, Maab Elsheikh, Koichiro Hayashi, Akira Tsuchiya, Kunio Ishikawa, Fabrication of highly interconnected porous carbonate apatite blocks based on the setting reaction of calcium sulfate hemihydrate granules, Ceramics International, 10.1016/j.ceramint.2021.03.324, 47, 14, 19856-19863, 47, 19856, 2021.04, [URL], Interconnected porous carbonate apatite (CO3Ap) blocks that emulate cancellous bone have potential as an alternative to autografts. The present study aimed to evaluate the feasibility of fabricating a block via a stepwise compositional transformation to CO3Ap through dissolution-precipitation reactions of an interconnected porous calcium sulfate dihydrate (CSD) block, which was obtained by the setting reaction of calcium sulfate hemihydrate (CSH) granules. Exposure of the CSH granules to water resulted in a setting reaction. However, the gaps between the granules were clogged, preventing the fabrication of interconnected porous structures. Removing the water in the gaps using filter paper was beneficial in avoiding gap clogging and in fabricating interconnected porous CSD blocks. Although the CSD blocks transformed into CaCO3 blocks, which maintained the interconnected porous structure through a dissolution-precipitation reaction in a Na2CO3 solution, their mechanical strength was quite low (diametral tensile strength: DTS = 75 kPa). In contrast, a CaCO3 block with a much greater mechanical strength (DTS = 0.98 MPa) was fabricated when a calcium sulfate anhydrous block made via the heat treatment of the CSD block was used as a precursor. The CaCO3 block transformed into a CO3Ap block (DTS = 2.1 MPa), maintaining the interconnected porous structure through a dissolution-precipitation reaction when immersed in a Na2HPO4 solution. The CO3Ap block had macropores initiated by the gaps between the granules and micropores created by the setting reaction of CSH granules and the dissolution-precipitation reactions to form CO3Ap. The results obtained in the present study demonstrate that this method is useful for fabricating interconnected porous CO3Ap blocks.. |
| 8. | Ryo Kishida, Shosuke Ito, Manickam Sugumaran, Ryan Lacdao Arevalo, Hiroshi Nakanishi, Hideaki Kasai, Density Functional Theory-Based Calculation Shed New Light on the Bizarre Addition of Cysteine Thiol to Dopaquinone, International Journal of Molecular Sciences, 10.3390/ijms22031373, 22, 1373, 22(3), 1373, 2021.01, [URL], 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).. |
| 9. | Ryo Kishida, Shosuke Ito, Manickam Sugumaran, Ryan Lacdao Arevalo, Hiroshi Nakanishi, Hideaki Kasai, Density Functional Theory-Based Calculation Shed New Light on the Bizarre Addition of Cysteine Thiol to Dopaquinone, International Journal of Molecular Sciences, 10.3390/ijms22031373, 22, 3, 1373-1373, 2021.01, 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).. |
| 10. | Koichiro Hayashi, Ryo Kishida, Akira Tsuchiya, Kunio Ishikawa, Granular honeycombs composed of carbonate apatite, hydroxyapatite, and β-tricalcium phosphate as bone graft substitutes: Effects of composition on bone formation and maturation, ACS Applied Bio Materials, 3, 1787-1795, 2020.02. |
| 11. | Koichiro Hayashi, Ryo Kishida, Akira Tsuchiya, Kunio Ishikawa, Carbonate apatite micro-honeycombed blocks generate bone marrow-like tissues as well as bone, Advanced Biosystems, 3, 1900140, 2019.09. |
| 12. | Koichiro Hayashi, Ryo Kishida, Akira Tsuchiya, Kunio Ishikawa, Honeycomb blocks composed of carbonate apatite, β-tricalcium phosphate, and hydroxyapatite for bone regeneration: effects of composition on biological responses, Materials Today Bio, 4, 100031, 2019.09, Synthetic scaffolds exhibiting bone repair ability equal to that of autogenous bone are required in the fields of orthopedics and dentistry. A suitable synthetic bone graft substitute should induce osteogenic differentiation of mesenchymal stem cells, osteogenesis, and angiogenesis. In this study, three types of honeycomb blocks (HCBs), composed of hydroxyapatite (HAp), β-tricalcium phosphate (TCP), and carbonate apatite (CO3Ap), were fabricated, and the effects of HCB composition on bone formation and maturation were investigated. The HC structure was selected to promote cell penetration and tissue ingrowth. HAp and β-TCP HCBs were fabricated by extrusion molding followed by sintering. The CO3Ap HCBs were fabricated by extrusion molding followed by sintering and dissolution-precipitation reactions. These HCBs had similar macroporous structures: all harbored uniformly distributed macropores (∼160 μm) that were regularly arrayed and penetrated the blocks unidirectionally. Moreover, the volumes of macropores were nearly equal (∼0.15 cm3/g). The compressive strengths of CO3Ap, HAp, and β-TCP HCBs were 22.8 ± 3.5, 34.2 ± 3.3, and 24.4 ± 2.4 MPa, respectively. Owing to the honeycomb-type macroporous structure, the compressive strengths of these HCBs were higher than those of commercial scaffolds with intricate three-dimensional or unidirectional macroporous structure. Notably, bone maturation was markedly faster in CO3Ap HCB grafting than in β-TCP and HAp HCB grafting, and the mature bone area percentages for CO3Ap HCBs at postsurgery weeks 4 and 12 were 14.3- and 4.3-fold higher and 7.5- and 1.4-fold higher than those for HAp and β-TCP HCBs, respectively. The differences in bone maturation and formation were probably caused by the disparity in concentrations of calcium ions surrounding the HCBs, which were dictated by the inherent material resorption behavior and mechanism; generally, CO3Ap is resorbed only by osteoclastic resorption, HAp is not resorbed, and β-TCP is rapidly dissolved even in the absence of osteoclasts. Besides the composition, the microporous structure of HC struts, inevitably generated during the formation of HCBs of various compositions, may contribute to the differences in bone maturation and formation.. |
| 13. | Koichiro Hayashi, Ryo Kishida, Akira Tsuchiya, Kunio Ishikawa, Carbonate Apatite Micro-Honeycombed Blocks Generate Bone Marrow-Like Tissues as well as Bone, Advanced Biosystems, 10.1002/adbi.201900140, 3, 12, 1900140, 2019.09, Hematopoietic stem cells form blood cells in bone marrow and reside in niches. Artificial environments that conserve these niches may generate bone marrow. Osteogenesis, angiogenesis, and material resorption must be regulated to create these environments. These processes are controlled by material composition and macro- and microporous structures. Here, three blocks with different micropore structures are fabricated. Carbonate apatite has nearly the same composition as natural human bone and their honeycomb structure facilitates cell penetration and survival. In samples with high microporosity, endosteum-like tissues such as sinusoids form in areas of material resorption and high local calcium concentration. These conditions resemble environments conducive to niche maintenance. Bone marrow-like tissues and megakaryocytes are successfully generated in this environment. Micropore structure is the most critical factor in bone marrow formation; however, the influences of material composition and macropore structure must also be considered. The results of this study may help develop treatments for bone marrow-related diseases and elucidate the components and functions of the hematopoietic stem cell niche.. |
| 14. | Bhume Chantaramolee, Susan Meñez Aspera, Ryan Lacdao Arevalo, Elvis Flaviano Arguelles, Ryo Kishida, Allan Abraham Bustria Padama, Hideaki Kasai, Hiroshi Nakanishi, Surface Compositions of Pt–Pd/Pd(111) Alloys in the Presence of O and OH during Oxygen Reduction Reaction: A First-Principles Study, Journal of Physical Society of Japan, 10.7566/JPSJ.88.044802, 88, 044802-1-044802-8, 2019.05, [URL], 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 approximate to 50:50 and Pt : Pd approximate to 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 approximate to 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 : 40 during ORR.. |
| 15. | Bhume Chantaramolee, Susan Menez Aspera, Ryan Lacdao Arevalo, Elvis Flaviano Arguelles, Ryo Kishida, Allan Abraham Bustria Padama, Hideaki Kasai, Hiroshi Nakanishi, Surface Compositions of Pt-Pd/Pd(111) Alloys in the Presence of O and OH during Oxygen Reduction Reaction: A First-Principles Study, Journal of the Physical Society of Japan, 10.7566/JPSJ.88.044802, 88, 4, 044802, 2019.04, 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 approximate to 50:50 and Pt : Pd approximate to 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 approximate to 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 : 40 during ORR.. |
| 16. | Ryo Kishida, Hideaki Kasai, Cyclic Bond Formation of Rhododendrol-quinone and Dopamine-quinone: Effects of Proton Rearrangement, Journal of the Physical Society of Japan, 10.7566/JPSJ.87.084802, 87, 8, 084802, 2018.08, The synthesis of melanin pigment involves intramolecular cyclic bond formation between benzene ring and side chain moieties of o-quinone as a necessary process for o-quinone conversion into a cyclic catechol, i.e., cyclization. Dopamine (DA)-quinone and rhododendrol (RD)-quinone undergo cyclic C-N and C-O bond formation, respectively. A previous theoretical study revealed that RD-quinone requires hydroxy deprotonation or quinonic protonation for cyclic C-O bond formation. In this study, the theoretical model was extended to an (H2O)(n)-quinone interacting system (n = 3, 4) so that protonation and deprotonation governed by H2O molecules are incorporated. Density functional theory (DFT)-based simulation showed that RD-quinone can undergo proton-rearrangement-assisted cyclic C-O bond formation with a moderate barrier height which is still higher than that for DA-quinone cyclic bond formation. The DFT-based simulation also showed that both DA-quinone and RD-quinone can undergo proton-rearrangement-assisted C-O bond formation for the addition of water with slightly higher activation energies than those of cyclic bond formation. The obtained mechanism is markedly different from that for DA-quinone, which can sequentially undergo the cyclic C-N bond formation and proton rearrangement.. |
| 17. | Ryo Kishida, Hideaki Kasai, Cyclic bond formation of rhododendrol-quinone and dopamine-quinone: effects of proton rearrangement, Journal of Physical Society of Japan, 10.7566/JPSJ.87.084802, 87, 084802-1-084802-5, 2018.07, [URL], The synthesis of melanin pigment involves intramolecular cyclic bond formation between benzene ring and side chain moieties of o-quinone as a necessary process for o-quinone conversion into a cyclic catechol, i.e., cyclization. Dopamine (DA)-quinone and rhododendrol (RD)-quinone undergo cyclic C-N and C-O bond formation, respectively. A previous theoretical study revealed that RD-quinone requires hydroxy deprotonation or quinonic protonation for cyclic C-O bond formation. In this study, the theoretical model was extended to an (H2O)(n)-quinone interacting system (n = 3, 4) so that protonation and deprotonation governed by H2O molecules are incorporated. Density functional theory (DFT)-based simulation showed that RD-quinone can undergo proton-rearrangement-assisted cyclic C-O bond formation with a moderate barrier height which is still higher than that for DA-quinone cyclic bond formation. The DFT-based simulation also showed that both DA-quinone and RD-quinone can undergo proton-rearrangement-assisted C-O bond formation for the addition of water with slightly higher activation energies than those of cyclic bond formation. The obtained mechanism is markedly different from that for DA-quinone, which can sequentially undergo the cyclic C-N bond formation and proton rearrangement.. |
| 18. | Ryo Kishida, Adhitya Gandaryus Saputro, Ryan Lacdao Arevalo, Hideaki Kasai, Effects of introduction of α-carboxylate, N-methyl, and N-formyl groups on intramolecular cyclization of o-quinone amines: Density functional theory-based study, International Journal of Quantum Chemistry, 10.1002/qua.25445, 117, 23, e25445-1-e25445-9, 2017.12, [URL], 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 alpha-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.. |
| 19. | Ryo Kishida, Adhitya Gandaryus Saputro, Ryan Lacdao Arevalo, Hideaki Kasai, Effects of introduction of alpha-carboxylate, N-methyl, and N-formyl groups on intramolecular cyclization of o-quinone amines: Density functional theory-based study, International Journal of Quantum Chemistry, 10.1002/qua.25445, 117, 23, e25445, 2017.12, 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 alpha-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.. |
| 20. | Susan Meñez Aspera, Ryan Lacdao Arevalo, Koji Shimizu, Ryo Kishida, Kazuki Kojima, Nguyen Hoang Linh, Hiroshi Nakanishi, Hideaki Kasai, First Principles Calculations of Transition Metal Binary Alloys: Phase Stability and Surface Effects, Journal of Electronic Materials, 10.1007/s11664-017-5402-3, 46, 6, 3776-3783, 2017.06, [URL], 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.. |
| 21. | Ryo Kishida, Hideaki Kasai, Susan Menez Aspera, Ryan Lacdao Arevalo, Hiroshi Nakanishi, Branching Reaction in Melanogenesis: The Effect of Intramolecular Cyclization on Thiol Binding, Journal of Electronic Materials, 10.1007/s11664-017-5299-x, 46, 6, 3784-3788, 2017.06, 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.. |
| 22. | Susan Meez Aspera, Ryan Lacdao Arevalo, Koji Shimizu, Ryo Kishida, Kazuki Kojima, Nguyen Hoang Linh, Hiroshi Nakanishi, Hideaki Kasai, First Principles Calculations of Transition Metal Binary Alloys: Phase Stability and Surface Effects, Journal of Electronic Materials, 10.1007/s11664-017-5402-3, 46, 6, 3776-3783, 2017.06, 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.. |
| 23. | Ryo Kishida, Hideaki Kasai, Susan Menez Aspera, Ryan Lacdao Arevalo, Hiroshi Nakanishi, Density Functional Theory-Based First Principles Calculations of Rhododendrol-Quinone Reactions: Preference to Thiol Binding over Cyclization, Journal of the Physical Society of Japan, 10.7566/JPSJ.86.024804, 86, 2, 024804, 2017.02, 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.. |
| 24. | Ryo Kishida, Hideaki Kasai, Susan Meñez Aspera, Ryan Lacdao Arevalo, Hiroshi Nakanishi, Density Functional Theory-Based First Principles Calculations of Rhododendrol-Quinone Reactions: Preference to Thiol Binding over Cyclization, Journal of Physical Society of Japan, 10.7566/JPSJ.86.024804, 86, 024804-1-024804-5, 2017.01, [URL], 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.. |
| 25. | Ryo Kishida, Hideaki Kasai, Susan Meñez Aspera, Ryan Lacdao Arevalo, Hiroshi Nakanishi, Branching Reaction in Melanogenesis: The Effect of Intramolecular Cyclization on Thiol Binding, Journal of Electronic Materials, 10.1007/s11664-017-5299-x, 46, 6, 3784-3788, 2017.01, [URL], 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.. |
| 26. | Ryo Kishida, Adhitya Gandaryus Saputro, Hideaki Kasai, Mechanism of dopachrome tautomerization into 5,6-dihydroxyindole-2-carboxylic acid catalyzed by Cu(II) based on quantum chemical calculations, Biochimica et Biophysica Acta, 10.1016/j.bbagen.2014.10.024, 1850, 281-286, 2015.10, [URL], Background: Tautomerization of dopachrome to 5,6-dihydroxyindole-2-carboxylic acid (DHICA) is a biologically crucial reaction relevant to melanin synthesis, cellular antioxidation, and cross-talk among epidermal cells. Since dopachrome spontaneously converts into 5,6-dihydroxyindole (DHI) via decarboxylation without any enzymes at physiologically usual pH, the mechanism of how tautomerization to DHICA occurs in physiological system is a subject of intense debate. A previous work has found that Cu(II) is an important factor to catalyze the tautomerization of dopachrome to DHICA. However, the effect of Cu(II) on the tautomerization has not been clarified at the atomic level.Methods: We propose the reaction mechanism of the tautomerization to DHICA by Cu(II) from density functional theory-based calculation.Results: We clarified that the activation barriers of alpha-deprotonation, beta-deprotonation, and decarboxylation from dopachrome are significantly reduced by coordination of Cu(II) to quinonoid oxygens (5,6-oxygens) of dopachrome, with the lowest activation barrier of beta-deprotonation among them. In contrast to our previous work, in which beta-deprotonation and quinonoid protonation (O5/O6-protonation) were shown to be important to form DHI, our results show that the Cu(II) coordination to quinonoid oxygens inhibits the quinonoid protonation, leading to the preference of proton rearrangement from beta-carbon to carboxylate group but not to the quinonoid oxygens.Conclusion: Integrating these results, we conclude that dopachrome tautomerization first proceeds via proton rearrangement from beta-carbon to carboxylate group and subsequently undergoes alpha-deprotonation to form DHICA.General significance: This study would provide the biochemical basis of DHICA metabolism and the generalized view of dopachrome conversion which is important to understand melanogenesis.. |
| 27. | Ryo Kishida, Adhitya Gandaryus Saputro, Hideaki Kasai, Mechanism of dopachrome tautomerization into 5,6-dihydroxyindole-2-carboxylic acid catalyzed by Cu(II) based on quantum chemical calculations, Biochimica et Biophysica Acta - General Subjects, 10.1016/j.bbagen.2014.10.024, 1850, 2, 281-286, 2015.02, Background: Tautomerization of dopachrome to 5,6-dihydroxyindole-2-carboxylic acid (DHICA) is a biologically crucial reaction relevant to melanin synthesis, cellular antioxidation, and cross-talk among epidermal cells. Since dopachrome spontaneously converts into 5,6-dihydroxyindole (DHI) via decarboxylation without any enzymes at physiologically usual pH, the mechanism of how tautomerization to DHICA occurs in physiological system is a subject of intense debate. A previous work has found that Cu(II) is an important factor to catalyze the tautomerization of dopachrome to DHICA. However, the effect of Cu(II) on the tautomerization has not been clarified at the atomic level.Methods: We propose the reaction mechanism of the tautomerization to DHICA by Cu(II) from density functional theory-based calculation.Results: We clarified that the activation barriers of alpha-deprotonation, beta-deprotonation, and decarboxylation from dopachrome are significantly reduced by coordination of Cu(II) to quinonoid oxygens (5,6-oxygens) of dopachrome, with the lowest activation barrier of beta-deprotonation among them. In contrast to our previous work, in which beta-deprotonation and quinonoid protonation (O5/O6-protonation) were shown to be important to form DHI, our results show that the Cu(II) coordination to quinonoid oxygens inhibits the quinonoid protonation, leading to the preference of proton rearrangement from beta-carbon to carboxylate group but not to the quinonoid oxygens.Conclusion: Integrating these results, we conclude that dopachrome tautomerization first proceeds via proton rearrangement from beta-carbon to carboxylate group and subsequently undergoes alpha-deprotonation to form DHICA.General significance: This study would provide the biochemical basis of DHICA metabolism and the generalized view of dopachrome conversion which is important to understand melanogenesis. (C) 2014 Elsevier B.V. All rights reserved.. |
| 28. | Ryo Kishida, Yohei Ushijima, Adhitya Gandaryus Saputro, Hideaki Kasai, Effect of pH on elementary steps of dopachrome conversion from first-principles calculation, Pigment Cell & Melanoma Research, 10.1111/pcmr.12256, 27, 5, 734-743, 2014.09, Dopachrome conversion, in which dopachrome is converted into 5,6-dihydroxyindole (DHI) or 5,6-dihydroxyindole-2-carboxylic acid (DHICA) upstream of eumelanogenesis, is a key step in determining the DHI/DHICA monomer ratio in eumelanin, which affects the antioxidant activity. Although the ratio of DHI/DHICA formed and the conversion rate can be regulated depending on pH, the mechanism is still unclear. To clarify the mechanism, we carried out first-principles calculations. The results showed the kinetic preference of proton rearrangement to form quinone methide intermediate via -deprotonation. We also identified possible pathways to DHI/DHICA from the quinone methide. The DHI formation can be achieved by spontaneous decarboxylation after proton rearrangement from carboxyl group to 6-oxygen. -Deprotonation, which leads to DHICA formation, can also proceed with a significantly reduced activation barrier compared with that of the initial dopachrome. Considering the rate of the proton rearrangements in a given pH, we conclude that the conversion is suppressed at acidic pH.. |
| 29. | Ryo Kishida, Yohei Ushijima, Adhitya Gandaryus Saputro, Hideaki Kasai, Effect of pH on elementary steps of dopachrome conversion from first-principles calculation, Pigment Cell and Melanoma Research, 10.1111/pcmr.12256, 27, 734-743, 2014.05, [URL], Dopachrome conversion, in which dopachrome is converted into 5,6-dihydroxyindole (DHI) or 5,6-dihydroxyindole-2-carboxylic acid (DHICA) upstream of eumelanogenesis, is a key step in determining the DHI/DHICA monomer ratio in eumelanin, which affects the antioxidant activity. Although the ratio of DHI/DHICA formed and the conversion rate can be regulated depending on pH, the mechanism is still unclear. To clarify the mechanism, we carried out first-principles calculations. The results showed the kinetic preference of proton rearrangement to form quinone methide intermediate via -deprotonation. We also identified possible pathways to DHI/DHICA from the quinone methide. The DHI formation can be achieved by spontaneous decarboxylation after proton rearrangement from carboxyl group to 6-oxygen. -Deprotonation, which leads to DHICA formation, can also proceed with a significantly reduced activation barrier compared with that of the initial dopachrome. Considering the rate of the proton rearrangements in a given pH, we conclude that the conversion is suppressed at acidic pH.. |
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