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Sansenya S, Payaka A, Mansalai P. Inhibitory Efficacy of Cycloartenyl Ferulate against α-Glucosidase and α-Amylase and Its Increased Concentration in Gamma-Irradiated Rice (Germinated Rice). Prev Nutr Food Sci 2023; 28:170-177. [PMID: 37416788 PMCID: PMC10321442 DOI: 10.3746/pnf.2023.28.2.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 07/08/2023] Open
Abstract
Cycloartenyl ferulate is a derivative of γ-oryzanol with varied biological activity, including diabetes mellitus treatment. This research focused on improving the cycloartenyl ferulate accumulation in germinated rice by gamma irradiation under saline conditions. Moreover, the inhibitory potential of cycloartenyl ferulate against carbohydrate hydrolysis enzymes (α-glucosidase and α-amylase) was investigated through in vitro and in silico techniques. The results revealed that cycloartenyl ferulate increased in germinated rice under saline conditions upon gamma irradiation. A suitable condition for stimulating the highest cycloartenyl ferulate concentration (852.20±20.59 μg/g) in germinated rice was obtained from the gamma dose at 100 Gy and under 40 mM salt concentration. The inhibitory potential of cycloartenyl ferulate against α-glucosidase (31.31±1.43%) was higher than against α-amylase (12.72±1.11%). The inhibition mode of cycloartenyl ferulate against α-glucosidase was demonstrated as a mixed-type inhibition. A fluorescence study confirmed that the cycloartenyl ferulate interacted with the α-glucosidase's active site. A docking study revealed that cycloartenyl ferulate bound to seven amino acids of α-glucosidase with a binding energy of -8.8 kcal/mol and a higher binding potential than α-amylase (-8.2 kcal/mol). The results suggested that the gamma irradiation technique under saline conditions is suitable for stimulating γ-oryzanol, especially cycloartenyl ferulate. Furthermore, cycloartenyl ferulate demonstrated its potential as a candidate compound for blood glucose management in diabetes mellitus treatment.
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Affiliation(s)
- Sompong Sansenya
- Department of Chemistry, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, Pathum Thani 12110, Thailand
| | - Apirak Payaka
- School of Science, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Preecha Mansalai
- Department of Chemistry, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, Pathum Thani 12110, Thailand
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Sansenya S, Payaka A, Mansalai P. Biological activity and inhibition potential against α-glucosidase and α-amylase of 2,4-di-tert-butylphenol from bamboo shoot extract by in vitro and in silico studies. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Sansenya S, Payaka A. Inhibitory potential of phenolic compounds of Thai colored rice (Oryza sativa L.) against α-glucosidase and α-amylase through in vitro and in silico studies. J Sci Food Agric 2022; 102:6718-6726. [PMID: 35620810 DOI: 10.1002/jsfa.12039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/30/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND This study investigated the inhibitory efficiency of phenolic compounds content methyl vanillate, syringic acid and vanillic acid against α-glucosidase and α-amylase. The phenolic compound contents of 10 Thai colored rice cultivars were also determined, and the relationship between the inhibitory efficiency of colored rice extract with methyl vanillate, syringic acid and vanillic acid was evaluated. RESULTS The results revealed that the inhibition efficiency of methyl vanillate, syringic acid and vanillic acid was higher against α-glucosidase than against α-amylase. Inhibitory activity of vanillic acid against α-glucosidase and α-amylase was highest, with IC50 of 0.100 ± 0.01 and 0.130 ± 0.02 mmol L-1 , respectively. Docking study showed strong binding by three hydrogen bonds and four hydrogen bonds between vanillic acid with the amino acid in the binding site of α-glucosidase and α-amylase, respectively. Inhibition modes of these phenolic compounds were defined as a mixed type inhibition against α-glucosidase. Highest phenolic compound contents of methyl vanillate, syringic acid and vanillic acid were obtained from methanol extracts of all rice cultivars. The methanol extracts of all colored rice cultivars such as Khao Leum Pua also showed the highest inhibition potential against α-glucosidase and α-amylase. The results indicated that these phenolic compound contents were closely related to the inhibition potential of colored rice extracts against α-glucosidase and α-amylase. CONCLUSION Our results suggest that rice, especially colored rice cultivars, has the source of phenolic compounds. Moreover, the phenolic compounds had the greatest source of natural inhibitor against α-glucosidase and α-amylase. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Sompong Sansenya
- Department of Chemistry, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, Pathum Thani, Thailand
| | - Apirak Payaka
- School of Science, Walailak University, Nakhon Si Thammarat, Thailand
- Research Group in Applied, Computational and Theoretical Science (ACTS), Walailak University, Nakhon Si Thammarat, Thailand
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Chaniad P, Chukaew A, Payaka A, Phuwajaroanpong A, Techarang T, Plirat W, Punsawad C. Antimalarial potential of compounds isolated from Mammea siamensis T. Anders. flowers: in vitro and molecular docking studies. BMC Complement Med Ther 2022; 22:266. [PMID: 36224571 PMCID: PMC9554980 DOI: 10.1186/s12906-022-03742-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/25/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
Background: The emergence of antimalarial drug resistance encourages the search for new antimalarial agents. Mammea siamensis belongs to the Calophyllaceae family, which is a medicinal plant that is used in traditional Thai preparations. The hexane and dichloromethane extracts of this plant were found to have potent antimalarial activity. Therefore, this study aimed to isolate active compounds from M. siamensis flowers and evaluate their antimalarial potential and their interactions with Plasmodium falciparum lactate dehydrogenase (PfLDH). Methods: The compounds from M. siamensis flowers were isolated by chromatographic techniques and evaluated for their antimalarial activity against chloroquine (CQ)-resistant P. falciparum (K1) strains using a parasite lactate dehydrogenase (pLDH) assay. Interactions between the isolated compounds and the PfLDH enzyme were investigated using a molecular docking method. Results: The isolation produced the following thirteen compounds: two terpenoids, lupeol (1) and a mixture of β-sitosterol and stigmasterol (5); two mammea coumarins, mammea A/AA cyclo D (6) and mammea A/AA cyclo F (7); and nine xanthones, 4,5-dihydroxy-3-methoxyxanthone (2), 4-hydroxyxanthone (3), 1,7-dihydroxyxanthone (4), 1,6-dihydroxyxanthone (8), 1-hydroxy-5,6,7-trimethoxyxanthone (9), 3,4,5-trihydroxyxanthone (10), 5-hydroxy-1-methoxyxanthone (11), 2-hydroxyxanthone (12), and 1,5-dihydroxy-6-methoxyxanthone (13). Compound 9 exhibited the most potent antimalarial activity with an IC50 value of 9.57 µM, followed by 10, 1, 2 and 13 with IC50 values of 15.48, 18.78, 20.96 and 22.27 µM, respectively. The molecular docking results indicated that 9, which exhibited the most potent activity, also had the best binding affinity to the PfLDH enzyme in terms of its low binding energy (-7.35 kcal/mol) and formed interactions with ARG109, ASN140, and ARG171. Conclusion: These findings revealed that isolated compounds from M. siamensis flowers exhibited antimalarial activity. The result suggests that 1-hydroxy-5,6,7-trimethoxyxanthone is a possible lead structure as a potent inhibitor of the PfLDH enzyme.
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Affiliation(s)
- Prapaporn Chaniad
- grid.412867.e0000 0001 0043 6347School of Medicine, Walailak University, 80160 Nakhon Si Thammarat, Thailand ,grid.412867.e0000 0001 0043 6347Research Center in Tropical Pathobiology, Walailak University, 80160 Nakhon Si Thammarat, Thailand
| | - Arnon Chukaew
- grid.444195.90000 0001 0098 2188Chemistry Department, Faculty of Science and Technology, Suratthani Rajabhat University, 84100 Surat Tani, Thailand
| | - Apirak Payaka
- grid.412867.e0000 0001 0043 6347School of Science, Walailak University, 80160 Nakhon Si Thammarat, Thailand
| | - Arisara Phuwajaroanpong
- grid.412867.e0000 0001 0043 6347School of Medicine, Walailak University, 80160 Nakhon Si Thammarat, Thailand
| | - Tachpon Techarang
- grid.412867.e0000 0001 0043 6347School of Medicine, Walailak University, 80160 Nakhon Si Thammarat, Thailand ,grid.412867.e0000 0001 0043 6347Research Center in Tropical Pathobiology, Walailak University, 80160 Nakhon Si Thammarat, Thailand
| | - Walaiporn Plirat
- grid.412867.e0000 0001 0043 6347School of Medicine, Walailak University, 80160 Nakhon Si Thammarat, Thailand
| | - Chuchard Punsawad
- grid.412867.e0000 0001 0043 6347School of Medicine, Walailak University, 80160 Nakhon Si Thammarat, Thailand ,grid.412867.e0000 0001 0043 6347Research Center in Tropical Pathobiology, Walailak University, 80160 Nakhon Si Thammarat, Thailand
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Sansenya S, Payaka A. Inhibition potential of volatile compounds from Thai rice cultivars against acetylcholinesterase through
in vitro
and docking studies. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.17249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Sompong Sansenya
- Department of Chemistry Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi Pathum Thani Thailand
| | - Apirak Payaka
- School of Science, Walailak University Nakhon Si Thammarat Thailand
- Research Group in Applied, Computational and Theoretical Science (ACTS), Walailak University Nakhon Si Thammarat Thailand
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Tantapakul C, Suthiphasilp V, Payaka A, Chaiyosang B, Harding DJ, Phuphong W, Tontapha S, Laphookhieo S. Derrisrobustones A-D, isoflavones from the twig extract of Derris robusta (DC.) Benth. and their α-glucosidase inhibitory activity. Phytochemistry 2022; 198:113168. [PMID: 35331731 DOI: 10.1016/j.phytochem.2022.113168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Three previously undescribed isoflavones, derrisrobustones A-C, and a previously undescribed natural isoflavone, derrisrobustone D, along with eight known isoflavones, were isolated from the twig extract of Derris robusta (DC.) Benth. All structures were identified by extensive spectroscopic analysis. Derrisrobustones A-C were obtained as scalemic mixtures and were resolved by chiral HPLC. The (1″R, 2″R) absolute configuration of (+)-derrisrobustone B was established by single-crystal X-ray crystallography using Cu Kα radiation. The absolute configurations of derrisrobustones A and C were determined by analysis of experimental and calculated ECD data. All compounds were evaluated for their α-glucosidase inhibitory activity. Of these, derrubone displayed the best α-glucosidase inhibitory activity with an IC50 value of 64.2 μM.
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Affiliation(s)
- Cholpisut Tantapakul
- The Research Unit of Natural Product Utilization, School of Science, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Virayu Suthiphasilp
- Center of Chemical Innovation for Sustainability (CIS) and School of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai, 57100, Thailand
| | - Apirak Payaka
- School of Science, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Boonyanoot Chaiyosang
- Natural Products Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - David J Harding
- Functional Materials and Nanotechnology Center of Excellence, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Worrapong Phuphong
- The Research Unit of Natural Product Utilization, School of Science, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Sarawut Tontapha
- Institute of Nanomaterials Research and Innovation for Energy, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Surat Laphookhieo
- Center of Chemical Innovation for Sustainability (CIS) and School of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai, 57100, Thailand; Medicinal Plant Innovation Center of Mae Fah Luang University, Chiang Rai, 57100, Thailand.
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Nanthamathee C, Chantarangkul C, Jakkrawhad C, Payaka A, Dechatiwongse P. Fine-tuning the dye adsorption capacity of UiO-66 by a mixed-ligand approach. Heliyon 2022; 8:e08961. [PMID: 35243081 PMCID: PMC8866059 DOI: 10.1016/j.heliyon.2022.e08961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/12/2021] [Accepted: 02/10/2022] [Indexed: 11/24/2022] Open
Abstract
The mixed ligand synthetic approach offers an alternative to engineering a specific character in metal-organic framework (MOFs) materials. Herein, we synthesized and characterized a well-known prototype zirconium-based-MOF, so-called UiO-66, and its mixed ligand derivatives UiO-66-xATA, where x is mole fraction (0.5, 0.75, and 1.0) and ATA is 2-animoterephthalate. The study investigates whether the dye adsorption capacity can be tuned/enhanced by the ATA ligand substitution into the framework. We found that, at room temperature, UiO-66-0.75ATA shows the highest adsorption capacity toward various dye solutions, including methylene blue (MB), indigo carmine (IC), and congo red (CR). The optimum adsorption conditions in all four materials were in a common trend where their adsorption capacities can be increased with decreasing pH and adsorbent dose, increasing IC concentration, contact time, and temperature. Pseudo-second order kinetics model fits best with their adsorption data, where UiO-66-ATA has the fastest adsorption rate. Langmuir and Freundlich isotherms were found best to describe adsorption behavior in ATA-containing UiO-66 and UiO-66, respectively, where adsorption processes were found to be physisorption. Confirming by thermodynamic studies, the adsorption in all four materials occurred spontaneously, driven by entropy. Computational studies showed ligand to metal charge transfer where the distribution of electron densities was varied with the amount of functionalized ligand. Adsorption mechanism is proposed as a synergistic interplay between electrostatic interaction and hydrogen bonding. The findings in this work broaden the potential strategy to fine-tune the dye adsorption capacity in MOF materials.
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Affiliation(s)
- Chompoonoot Nanthamathee
- Department of Chemistry, School of Science, Walailak University, Nakhon Si Thammarat, 80160, Thailand.,Center of Excellence on Wood and Biomaterials, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | | | - Chanida Jakkrawhad
- Department of Chemistry, School of Science, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Apirak Payaka
- Department of Chemistry, School of Science, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Pongsathorn Dechatiwongse
- Department of Chemical Engineering, School of Engineering and Technology, Walailak University, Nakhon Si Thammarat, 80160, Thailand
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Chaniad P, Mungthin M, Payaka A, Viriyavejakul P, Punsawad C. Antimalarial properties and molecular docking analysis of compounds from Dioscorea bulbifera L. as new antimalarial agent candidates. BMC Complement Med Ther 2021; 21:144. [PMID: 34006257 PMCID: PMC8132342 DOI: 10.1186/s12906-021-03317-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/06/2021] [Indexed: 01/27/2023] Open
Abstract
Background At present, the emergence and spread of antimalarial drug resistance has become a significant problem worldwide. There has been a challenge in searching for natural products for the development of novel antimalarial drugs. Therefore, this study aims to evaluate compounds from Dioscorea bulbifera responsible for antimalarial properties and investigate potential interactions of the compounds with Plasmodium falciparum lactate dehydrogenase (PfLDH), an essential glycolytic enzyme in the parasite’s life cycle. Methods An in vitro study of antimalarial activity against chloroquine (CQ)-resistant Plasmodium falciparum (K1 strain) and CQ-sensitive P. falciparum (3D7 strain) was performed using the 3H-hypoxanthine uptake inhibition method. The cytotoxic effects of the pure compounds were tested against Vero cells using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The interactions of the compounds with the PfLDH active site were additionally investigated using a molecular docking method. Results Quercetin (6) exhibited the highest antimalarial activity against the P. falciparum K1 and 3D7 strains, with IC50 values of 28.47 and 50.99 μM, respectively. 2,4,3′,5′-Tetrahydroxybibenzyl (9), 3,5-dimethoxyquercetin (4) and quercetin-3-O-β-D-galactopyranoside (14) also possessed antimalarial effects against these two strains of P. falciparum. Most pure compounds were nontoxic against Vero cells at a concentration of 80 μg/ml, except for compound 9, which had a cytotoxic effect with a CC50 value of 16.71 μM. The molecular docking results indicated that 9 exhibited the best binding affinity to the PfLDH enzyme in terms of low binding energy (− 8.91 kcal/mol) and formed strong hydrogen bond interactions with GLY29, GLY32, THR97, GLY99, PHE100, THR101 and ASN140, amino acids as active sites. In addition, 6 also possessed remarkable binding affinity (− 8.53 kcal/mol) to PfLDH by interacting with GLY29, ILE31, ASP53, ILE54, THR97 and THR101. Conclusion Quercetin is a major active compound responsible for the antimalarial activity of D. bulbifera and is an inhibitor of PfLDH. These findings provide more evidence to support the traditional use of D. bulbifera for malaria treatment. Structural models of its interactions at the PfLDH active site are plausibly useful for the future design of antimalarial agents.
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Affiliation(s)
- Prapaporn Chaniad
- School of Medicine, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Apirak Payaka
- School of Science, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Parnpen Viriyavejakul
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Chuchard Punsawad
- School of Medicine, Walailak University, Nakhon Si Thammarat, 80160, Thailand.
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Sansenya S, Payaka A, Wannasut W, Hua Y, Chumanee S. Biological activity of rice extract and the inhibition potential of rice extract, rice volatile compounds and their combination against α‐glucosidase, α‐amylase and tyrosinase. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sompong Sansenya
- Department of Chemistry Faculty of Science and Technology Rajamangala University of Technology Thanyaburi, Pathum Thani12110Thailand
| | - Apirak Payaka
- School of Science Walailak University Nakhon Si Thammarat80160Thailand
- Research Group in Applied, Computational and Theoretical Science (ACTS) Walailak University Nakhon Si Thammarat80160Thailand
| | - Wachirawit Wannasut
- Department of Chemistry Faculty of Science and Technology Rajamangala University of Technology Thanyaburi, Pathum Thani12110Thailand
| | - Yanling Hua
- The Center for Scientific and Technological Equipment Suranaree University of Technology Nakhon Ratchasima30000Thailand
| | - Saowapa Chumanee
- Division of Chemistry Faculty of Science and Technology Phetchabun Rajabhat University Mueang, Phetchabun67000Thailand
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Thubsuang U, Chotirut S, Nuithitikul K, Payaka A, Manmuanpom N, Chaisuwan T, Wongkasemjit S. Oxidative upgrade of furfural to succinic acid using SO 3H-carbocatalysts with nitrogen functionalities based on polybenzoxazine. J Colloid Interface Sci 2020; 565:96-109. [PMID: 31935589 DOI: 10.1016/j.jcis.2020.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 01/01/2020] [Indexed: 12/29/2022]
Abstract
SO3H-carbocatalysts with nitrogen functionalities were prepared using the carbonization of polybenzoxazine derived from four different amines (aniline, ethylenediamine, triethylenetetramine, and tetraethylenepentamine) and then sulfonation. The obtained SO3H-carbocatalysts underwent catalytic testing for furfural oxidation with H2O2 to produce succinic acid. The effects of nitrogen functionalities were reported for the first time. The results showed that all carbon samples exhibited a microporous characteristic with comparable textural properties and contained various nitrogen functionalities (N-6, N-5, N-Q, and N-X). After sulfonation, the SO3H-carbocatalyst prepared from tetraethylenepentamine-based polybenzoxazine had the highest amount of sulfonic acid groups (1.45 mmol g-1) and a high nitrogen content (4.23%), providing a maximum succinic acid yield of 93.0% within a rapid reaction time of 60 min under the optimized conditions. This was higher than from Amberlyst-type catalysts and SO3H-carbocatalyst without nitrogen functionalities and was ascribed to the synergistic activity of the sulfonic acid groups and nitrogen functionalities. The XPS spectra and computational study confirmed that such nitrogen functionalities, especially N-5, are capable of forming hydrogen bonding with furfural, facilitating the formation of an intermediate compound and thereby enhancing the catalytic efficiency. However, after four cycles, the succinic acid yield decreased to 40% due to leaching of the sulfonic acid groups.
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Affiliation(s)
- Uthen Thubsuang
- School of Engineering and Technology, Walailak University, Nakhon Si Thammarat 80160, Thailand.
| | - Suphawadee Chotirut
- School of Engineering and Technology, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Kamchai Nuithitikul
- School of Engineering and Technology, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Apirak Payaka
- School of Science, Walailak University, Nakhon Si Thammarat 80160, Thailand; Research Group in Applied, Computational and Theoretical Science (ACTS), Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Nicharat Manmuanpom
- The Petroleum and Petrochemical College, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Petrochemical and Materials Technology, Bangkok 10330, Thailand
| | - Thanyalak Chaisuwan
- The Petroleum and Petrochemical College, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Petrochemical and Materials Technology, Bangkok 10330, Thailand
| | - Sujitra Wongkasemjit
- The Petroleum and Petrochemical College, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Petrochemical and Materials Technology, Bangkok 10330, Thailand
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Kodchakorn K, Dokmaisrijan S, Chong WL, Payaka A, Wisitponchai T, Nimmanpipug P, Zain SM, Rahman NA, Tayapiwatana C, Lee VS. GPU Accelerated Molecular Dynamics Simulations for Protein-Protein Interaction of Ankyrin Complex. Integrated Ferroelectrics 2014; 156:137-146. [DOI: 10.1080/10584587.2014.906894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
- Kanchanok Kodchakorn
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supaporn Dokmaisrijan
- Theoretical and Computational Modeling (TCM) Research Group, School of Science, Walailak University, Nakhon Si Thammarat 80161, Thailand
| | - Wei Lim Chong
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Apirak Payaka
- Theoretical and Computational Modeling (TCM) Research Group, School of Science, Walailak University, Nakhon Si Thammarat 80161, Thailand
| | - Tanchanok Wisitponchai
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Piyarat Nimmanpipug
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sharifuddin M. Zain
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Noorsaadah Abd. Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Biomedical Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Vannajan Sanghiran Lee
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
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Payaka A, Yotmanee P, Tongraar A. Characteristics of the “Hypercoordination” of hydroxide (OH−) in water: A comparative study of HF/MM and B3LYP/MM MD simulations. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2013.09.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Dokmaisrijan S, Payaka A, Tantishaiyakul V, Chairat M, Nimmanpipug P, Lee VS. Conformations and spectroscopic properties of laccaic acid A in the gas phase and in implicit water. Spectrochim Acta A Mol Biomol Spectrosc 2013; 105:125-134. [PMID: 23295218 DOI: 10.1016/j.saa.2012.11.105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/26/2012] [Accepted: 11/28/2012] [Indexed: 06/01/2023]
Abstract
Conformations and spectroscopic properties of laccaic acid A (lacA) were studied by means of the experimental and theoretical approaches. The minimum energy conformers of lacA in the gas phase and in implicit water obtained from the B3LYP/6-311G(d,p) calculations displayed the same orientation of the COOH and OH groups on the anthraquinone-based component. The intramolecular hydrogen bonds (H-bonds) formed between the COOH, C=O and OH groups are very strong. In contrast, the orientations of the Ph(OH)CH(2)CH(2)NHCOCH(3) substituent moiety on the anthraquinone-based component in the gas phase and in implicit water are completely different. The substituent prefers to bind with the anthraquinone-based component in the gas phase while it moves away from the anthraquinone-based component in implicit water. The calculated IR spectra of the two lowest-lying energy conformers of lacA in the gas phase fit to the experimental FTIR spectrum. The full assignments of the vibrational modes with the correlated vibrational wavenumbers of those conformers were proposed here, for the first time. The intramolecular H-bond formations in lacA can cause the shift of the vibrational wavenumber for the COOH, C=O, OH and NH groups as compared to the normal vibrations of these groups. The NMR spectra showed that the stabilities of the two lowest-lying energy conformers of lacA in the gas phase are comparable and this is consistent with their computational energies. The UV-Vis spectra of the lowest-lying energy conformers of lacA in implicit water were compared with the experimental UV-Vis spectrum. The calculations suggested that the electronic transition in the visible region involves with the singlet π→π(*) excitation which the electron density transfers to a COOH group on the anthraquinone ring.
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Affiliation(s)
- Supaporn Dokmaisrijan
- Division of Chemistry, School of Science, Walailak University, Nakhon Si Thammarat 80161, Thailand.
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Tongraar A, Yotmanee P, Payaka A. Characteristics of CO32−–water hydrogen bonds in aqueous solution: insights from HF/MM and B3LYP/MM MD simulations. Phys Chem Chem Phys 2011; 13:16851-60. [DOI: 10.1039/c1cp21802f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Affiliation(s)
- Apirak Payaka
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Michael Rode
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Cembran A, Payaka A, Lin YL, Xie W, Mo Y, Song L, Gao J. A Non-Orthogonal Block-Localized Effective Hamiltonian Approach for Chemical and Enzymatic Reactions. J Chem Theory Comput 2010; 6:2242-2251. [PMID: 20694172 PMCID: PMC2914346 DOI: 10.1021/ct1001686] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The effective Hamiltonian-molecular orbital and valence bond (EH-MOVB) method based on non-orthogonal block-localized fragment orbitals has been implemented into the program CHARMM for molecular dynamics simulations of chemical and enzymatic reactions, making use of semiempirical quantum mechanical models. Building upon ab initio MOVB theory, we make use of two parameters in the EH-MOVB method to fit the barrier height and the relative energy between the reactant and product state for a given chemical reaction to be in agreement with experiment or high-level ab initio or density functional results. Consequently, the EH-MOVB method provides a highly accurate and computationally efficient QM/MM model for dynamics simulation of chemical reactions in solution. The EH-MOVB method is illustrated by examination of the potential energy surface of the hydride transfer reaction from trimethylamine to a flavin cofactor model in the gas phase. In the present study, we employed the semiempirical AM1 model, which yields a reaction barrier that is more than 5 kcal/mol too high. We use a parameter calibration procedure for the EH-MOVB method similar to that employed to adjust the results of semiempirical and empirical models. Thus, the relative energy of these two diabatic states can be shifted to reproduce the experimental energy of reaction, and the barrier height is optimized to reproduce the desired (accurate) value by adding a constant to the off-diagonal matrix element. The present EH-MOVB method offers a viable approach to characterizing solvent and protein-reorganization effects in the realm of combined QM/MM simulations.
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Affiliation(s)
- Alessandro Cembran
- Department of Chemistry, Digital Technology Center and Supercomputing
Institute, University of Minnesota, Minneapolis, MN 55455 And Department of
Chemistry, Western Michigan University Kalamazoo, Michigan 49008
| | - Apirak Payaka
- Department of Chemistry, Digital Technology Center and Supercomputing
Institute, University of Minnesota, Minneapolis, MN 55455 And Department of
Chemistry, Western Michigan University Kalamazoo, Michigan 49008
| | - Yen-lin Lin
- Department of Chemistry, Digital Technology Center and Supercomputing
Institute, University of Minnesota, Minneapolis, MN 55455 And Department of
Chemistry, Western Michigan University Kalamazoo, Michigan 49008
| | - Wangshen Xie
- Department of Chemistry, Digital Technology Center and Supercomputing
Institute, University of Minnesota, Minneapolis, MN 55455 And Department of
Chemistry, Western Michigan University Kalamazoo, Michigan 49008
| | - Yirong Mo
- Department of Chemistry, Digital Technology Center and Supercomputing
Institute, University of Minnesota, Minneapolis, MN 55455 And Department of
Chemistry, Western Michigan University Kalamazoo, Michigan 49008
| | - Lingchun Song
- Department of Chemistry, Digital Technology Center and Supercomputing
Institute, University of Minnesota, Minneapolis, MN 55455 And Department of
Chemistry, Western Michigan University Kalamazoo, Michigan 49008
| | - Jiali Gao
- Department of Chemistry, Digital Technology Center and Supercomputing
Institute, University of Minnesota, Minneapolis, MN 55455 And Department of
Chemistry, Western Michigan University Kalamazoo, Michigan 49008
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Affiliation(s)
- Apirak Payaka
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Michael Rode
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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