Pub Date : 2023-10-19DOI: 10.1142/s2737416523420139
A Arunkumar
A new generation of metal-free organic dyes with a range of donor (D1) and acceptors (A1-A3) were designed and examined for dye-sensitized solar cells (DSSCs) based on (3a) dye as a literature. Triphenylamine (TPA), thiophene ([Formula: see text] and 2-cyanoacrylic acid groups each perform the roles of an acceptor (A), donor (D) and spacer in order to produce a D-[Formula: see text]-A system. To investigate the intramolecular charge transfer (ICT), electronic distribution, ultra-violet visible (UV–Vis) absorption wavelengths, molecular electrostatic potential (MEP) and photovoltaic (PV) parameters of the D1 and A1–A3 molecules, density functional theory (DFT) and time-dependent DFT (TD-DFT) were used. The classification of the tunable donor D1 and A1–A3 determines the PV performance of the dye molecules. Results show that the A2 dye replacement group increases the performance of PV cells via red-shifting absorption spectra. Also, when compared to 3a, A2 dye have lower energy gap ([Formula: see text] and superior UV–Vis spectra that cover the full visible range. These results demonstrate the viability of molecular tailoring as an approach to improve D-[Formula: see text]-A sensitizer proposal for efficient DSSCs fabrication.
{"title":"Computational Study on D-π-A-based Electron Donating and Withdrawing Effect of Metal-Free Organic Dye Sensitizers for Efficient Dye-Sensitized Solar Cells","authors":"A Arunkumar","doi":"10.1142/s2737416523420139","DOIUrl":"https://doi.org/10.1142/s2737416523420139","url":null,"abstract":"A new generation of metal-free organic dyes with a range of donor (D1) and acceptors (A1-A3) were designed and examined for dye-sensitized solar cells (DSSCs) based on (3a) dye as a literature. Triphenylamine (TPA), thiophene ([Formula: see text] and 2-cyanoacrylic acid groups each perform the roles of an acceptor (A), donor (D) and spacer in order to produce a D-[Formula: see text]-A system. To investigate the intramolecular charge transfer (ICT), electronic distribution, ultra-violet visible (UV–Vis) absorption wavelengths, molecular electrostatic potential (MEP) and photovoltaic (PV) parameters of the D1 and A1–A3 molecules, density functional theory (DFT) and time-dependent DFT (TD-DFT) were used. The classification of the tunable donor D1 and A1–A3 determines the PV performance of the dye molecules. Results show that the A2 dye replacement group increases the performance of PV cells via red-shifting absorption spectra. Also, when compared to 3a, A2 dye have lower energy gap ([Formula: see text] and superior UV–Vis spectra that cover the full visible range. These results demonstrate the viability of molecular tailoring as an approach to improve D-[Formula: see text]-A sensitizer proposal for efficient DSSCs fabrication.","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135667431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-19DOI: 10.1142/s2737416523410041
A S Aruna, K R Remesh Babu, K Deepthi
The global spread of COVID-19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan in December 2019, created a massive health crisis, and disrupted the world economy. Much research has been conducted to discover drugs, develop vaccines, and find repurposable drugs against the disease. Computational drug repurposing, the process of determining new uses for approved drugs through computational techniques, becomes an effective solution to fight the COVID-19 pandemic. This study aims to investigate and prioritize potential drugs against SARS-CoV-2 through an integrated network-based approach. We propose an ensemble approach based on network inference and inductive matrix completion (NIMCVDA) for virus–drug association prediction to identify antivirals against COVID-19. We constructed a heterogeneous drug–virus network using intra-similarities of virus genomic sequences and drug chemical structures and existing associations between viruses and drugs. A network inference method is used to infer missing drug–virus edges. Based on this, existing drug–virus association matrix is reconstructed. Finally, more accurate association scores between drugs and viruses are computed using the inductive matrix completion algorithm. The proposed method achieved an AUC of 0.9020 on five-fold cross-validation and 0.8786 on leave-one-out cross-validation. We compared the performance of the model with related approaches. In addition, we carried out case studies on the top-predicted drugs and implemented our model with other datasets to verify prediction performance. Our work prioritized repurposable drugs to battle with COVID-19 epidemic. The cross-validation results and case studies illustrate that the top-predicted drugs are strong candidates for further biological tests.
{"title":"An ensemble approach for prioritizing antivirals against COVID-19 via heterogeneous network inference-based inductive matrix completion","authors":"A S Aruna, K R Remesh Babu, K Deepthi","doi":"10.1142/s2737416523410041","DOIUrl":"https://doi.org/10.1142/s2737416523410041","url":null,"abstract":"The global spread of COVID-19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan in December 2019, created a massive health crisis, and disrupted the world economy. Much research has been conducted to discover drugs, develop vaccines, and find repurposable drugs against the disease. Computational drug repurposing, the process of determining new uses for approved drugs through computational techniques, becomes an effective solution to fight the COVID-19 pandemic. This study aims to investigate and prioritize potential drugs against SARS-CoV-2 through an integrated network-based approach. We propose an ensemble approach based on network inference and inductive matrix completion (NIMCVDA) for virus–drug association prediction to identify antivirals against COVID-19. We constructed a heterogeneous drug–virus network using intra-similarities of virus genomic sequences and drug chemical structures and existing associations between viruses and drugs. A network inference method is used to infer missing drug–virus edges. Based on this, existing drug–virus association matrix is reconstructed. Finally, more accurate association scores between drugs and viruses are computed using the inductive matrix completion algorithm. The proposed method achieved an AUC of 0.9020 on five-fold cross-validation and 0.8786 on leave-one-out cross-validation. We compared the performance of the model with related approaches. In addition, we carried out case studies on the top-predicted drugs and implemented our model with other datasets to verify prediction performance. Our work prioritized repurposable drugs to battle with COVID-19 epidemic. The cross-validation results and case studies illustrate that the top-predicted drugs are strong candidates for further biological tests.","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135667432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-06DOI: 10.1142/s2737416523500588
Sameena Gul, Shabbir Muhammad, Muhammad Irfan, Tareg M Belali, A. R. Chaudhry, Muhammad Khan
{"title":"Discovery of Potential Natural STAT3 Inhibitors: An in silico Molecular Docking and Molecular Dynamics Study","authors":"Sameena Gul, Shabbir Muhammad, Muhammad Irfan, Tareg M Belali, A. R. Chaudhry, Muhammad Khan","doi":"10.1142/s2737416523500588","DOIUrl":"https://doi.org/10.1142/s2737416523500588","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":"4 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139322164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-04DOI: 10.1142/s2737416523500540
Mahendra Gowdru Srinivasa, Shivakumar, Udaya Kumar, C. Mehta, U. Nayak, B. C. Revanasiddappa
{"title":"In silico studies of (Z)-3-(2-chloro-4-nitrophenyl)-5-(4-nitrobenzylidene)-2-thioxothiazolidin-4-one derivatives as PPAR-α agonist: Design, Molecular Docking, MM-GBSA Assay, Toxicity Predictions, DFT Calculations and MD Simulation Studies","authors":"Mahendra Gowdru Srinivasa, Shivakumar, Udaya Kumar, C. Mehta, U. Nayak, B. C. Revanasiddappa","doi":"10.1142/s2737416523500540","DOIUrl":"https://doi.org/10.1142/s2737416523500540","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49348636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-04DOI: 10.1142/s2737416523500552
Mohammed Muzaffar-Ur-Rehman, Chougule Kishore Suryakant, Ala Chandu, B. K. Kumar, Renuka Parshuram Joshi, Snehal Rajkumar Jadav, Sankaranarayanan Murugesan, Seshadri S. Vasan
{"title":"Molecular docking and dynamics identify potential drugs to be repurposed as SARS-CoV-2 inhibitors","authors":"Mohammed Muzaffar-Ur-Rehman, Chougule Kishore Suryakant, Ala Chandu, B. K. Kumar, Renuka Parshuram Joshi, Snehal Rajkumar Jadav, Sankaranarayanan Murugesan, Seshadri S. Vasan","doi":"10.1142/s2737416523500552","DOIUrl":"https://doi.org/10.1142/s2737416523500552","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47381299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-01DOI: 10.1142/s2737416523500527
Shabnam Ameenudeen, S. Hemalatha
{"title":"Could unfold protein response pathway proteins be a missing link in neuropathic pain and Alzheimer's disease aetiology? - Findings from computational studies","authors":"Shabnam Ameenudeen, S. Hemalatha","doi":"10.1142/s2737416523500527","DOIUrl":"https://doi.org/10.1142/s2737416523500527","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49650214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-01DOI: 10.1142/s2737416523500539
Kaliraj Chandran, Azar Zochedh, Asath Bahadur Sultan, T. Kathiresan
{"title":"Investigation on 5-Isopropyl-2-methylphenol via quantum chemicals, pharmacokinetics, molecular docking and cytotoxicity evaluation against breast cancer","authors":"Kaliraj Chandran, Azar Zochedh, Asath Bahadur Sultan, T. Kathiresan","doi":"10.1142/s2737416523500539","DOIUrl":"https://doi.org/10.1142/s2737416523500539","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42436647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-25DOI: 10.1142/s2737416523500515
Fredrick C. Asogwa, H. Louis, T. Gber, B. K. Isamura, Stephen A. Adalikwua
{"title":"Electronic Structure Property and Disposal Efficiency of 2, 2- dichloropropionic acid Using Metalloid (B, Si, and Ge) Decorated Gallium nano-clusters (Ga12X12 (X=N, O))","authors":"Fredrick C. Asogwa, H. Louis, T. Gber, B. K. Isamura, Stephen A. Adalikwua","doi":"10.1142/s2737416523500515","DOIUrl":"https://doi.org/10.1142/s2737416523500515","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44856243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-25DOI: 10.1142/s2737416523420115
S. A. Adalikwu, H. Louis, Daniel Etiese, Udochukwu G Chukwu, E. Agwamba
{"title":"Density functional theory computation of the electronic, elastic, phonon, X-ray spectroscopy, and the optoelectronic properties of CsXI3 (X: Si, Ge, Sn) halide perovskite materials","authors":"S. A. Adalikwu, H. Louis, Daniel Etiese, Udochukwu G Chukwu, E. Agwamba","doi":"10.1142/s2737416523420115","DOIUrl":"https://doi.org/10.1142/s2737416523420115","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41385668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-25DOI: 10.1142/s273741652341003x
Cibe Chakaravarthy Murali, Selvaraj Kunjiappan, S. Murugesan, Sureshkumar Pandian, T. Kathiresan, K. Sundar
{"title":"Network analysis and in silico molecular modelling of bioactive compounds from Sida cordifolia against NMDA receptor","authors":"Cibe Chakaravarthy Murali, Selvaraj Kunjiappan, S. Murugesan, Sureshkumar Pandian, T. Kathiresan, K. Sundar","doi":"10.1142/s273741652341003x","DOIUrl":"https://doi.org/10.1142/s273741652341003x","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46680433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：