Pub Date : 2020-09-18DOI: 10.1142/s0219633620500340
M. Mehboob, Muhammad Usman Khan, Riaz Hussain, Rafia Fatima, Zobia Irshad, Muhammad Adnan
Herein, we have designed four small molecular donors (SMDs) with Donor–Acceptor–Acceptor (D–A–A) backbone having different acceptor units for highly efficient organic solar cells (OSCs). The specif...
{"title":"Designing of near-infrared sensitive asymmetric small molecular donors for high-efficiency organic solar cells","authors":"M. Mehboob, Muhammad Usman Khan, Riaz Hussain, Rafia Fatima, Zobia Irshad, Muhammad Adnan","doi":"10.1142/s0219633620500340","DOIUrl":"https://doi.org/10.1142/s0219633620500340","url":null,"abstract":"Herein, we have designed four small molecular donors (SMDs) with Donor–Acceptor–Acceptor (D–A–A) backbone having different acceptor units for highly efficient organic solar cells (OSCs). The specif...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2050034"},"PeriodicalIF":2.4,"publicationDate":"2020-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620500340","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48242836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-13DOI: 10.1142/s0219633620500297
S. W. Qader, H. Abdallah, Mstaffa Zahid, L. S. Chua
Acetylcholinesterase (AChE) is a key enzyme enhancing the cognitive disorder, leading to Alzheimer’s disease, and AChE inhibition is a crucial therapeutic mechanism against it. Matricaria recutita ...
{"title":"In vitro Acetylcholinesterase inhibitory activity of polyphenolic compounds identified from Matricaria recutita","authors":"S. W. Qader, H. Abdallah, Mstaffa Zahid, L. S. Chua","doi":"10.1142/s0219633620500297","DOIUrl":"https://doi.org/10.1142/s0219633620500297","url":null,"abstract":"Acetylcholinesterase (AChE) is a key enzyme enhancing the cognitive disorder, leading to Alzheimer’s disease, and AChE inhibition is a crucial therapeutic mechanism against it. Matricaria recutita ...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2050029"},"PeriodicalIF":2.4,"publicationDate":"2020-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620500297","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42425902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-09DOI: 10.1142/s0219633620500364
Waqar Hussain, Arshia Majeed, A. Akhtar, N. Rasool
{"title":"Computational Studies of 3D-QSAR on a Highly Active Series of Naturally Occurring Non-Nucleoside Inhibitors of HIV-1 RT (NNRTI)","authors":"Waqar Hussain, Arshia Majeed, A. Akhtar, N. Rasool","doi":"10.1142/s0219633620500364","DOIUrl":"https://doi.org/10.1142/s0219633620500364","url":null,"abstract":"","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2020-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620500364","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41568629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Human glucokinase (GK) is a potentially attractive target for diabetes, playing a prominent role in the control of glucose homeostasis. Dorzagliatin is the first GK activator (GKA) to enter phase I...
{"title":"Insights into the binding of dorzagliatin with glucokinase: A molecular dynamics simulation","authors":"Wei Liu, Chenhui Yao, Qian Shang, Yuqiang Liu, Changying Liu, Fancui Meng","doi":"10.1142/s0219633620500273","DOIUrl":"https://doi.org/10.1142/s0219633620500273","url":null,"abstract":"Human glucokinase (GK) is a potentially attractive target for diabetes, playing a prominent role in the control of glucose homeostasis. Dorzagliatin is the first GK activator (GKA) to enter phase I...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2050027"},"PeriodicalIF":2.4,"publicationDate":"2020-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620500273","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47707629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-02DOI: 10.1142/s0219633620300013
A. Varandas
Since there is no exact solution for problems in physics and chemistry, extrapolation methods may assume a key role in quantitative quantum chemistry. Two topics where it bears considerable impact ...
{"title":"Extrapolation in quantum chemistry: Insights on energetics and reaction dynamics","authors":"A. Varandas","doi":"10.1142/s0219633620300013","DOIUrl":"https://doi.org/10.1142/s0219633620300013","url":null,"abstract":"Since there is no exact solution for problems in physics and chemistry, extrapolation methods may assume a key role in quantitative quantum chemistry. Two topics where it bears considerable impact ...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2030001"},"PeriodicalIF":2.4,"publicationDate":"2020-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620300013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41751589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-01DOI: 10.1142/s0219633619300015
Mahesh Koirala, E. Alexov
Computational chemistry offers variety of tools to study properties of biological macromolecules. These tools vary in terms of levels of details from quantum mechanical treatment to numerous macroscopic approaches. Here, we provide a review of computational chemistry algorithms and tools for modeling the effects of genetic variations and their association with diseases. Particular emphasis is given on modeling the effects of missense mutations on stability, conformational dynamics, binding, hydrogen bond network, salt bridges, and pH-dependent properties of the corresponding macromolecules. It is outlined that the disease may be caused by alteration of one or several of above-mentioned biophysical characteristics, and a successful prediction of pathogenicity requires detailed analysis of how the alterations affect the function of involved macromolecules. The review provides a short list of most commonly used algorithms to predict the molecular effects of mutations as well.
{"title":"Computational chemistry methods to investigate the effects caused by DNA variants linked with disease","authors":"Mahesh Koirala, E. Alexov","doi":"10.1142/s0219633619300015","DOIUrl":"https://doi.org/10.1142/s0219633619300015","url":null,"abstract":"Computational chemistry offers variety of tools to study properties of biological macromolecules. These tools vary in terms of levels of details from quantum mechanical treatment to numerous macroscopic approaches. Here, we provide a review of computational chemistry algorithms and tools for modeling the effects of genetic variations and their association with diseases. Particular emphasis is given on modeling the effects of missense mutations on stability, conformational dynamics, binding, hydrogen bond network, salt bridges, and pH-dependent properties of the corresponding macromolecules. It is outlined that the disease may be caused by alteration of one or several of above-mentioned biophysical characteristics, and a successful prediction of pathogenicity requires detailed analysis of how the alterations affect the function of involved macromolecules. The review provides a short list of most commonly used algorithms to predict the molecular effects of mutations as well.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619300015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46462212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-01DOI: 10.1142/s0219633620500145
M. Ganesan, S. Paranthaman
Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] and [Formula: see text] dihedral angles, [Formula: see text] varies significantly in sheet structure. This is due to the absence of intermolecular hydrogen bond (H-bond) interactions in sheets considered in this study. Our calculations show that the conformational transition of helix/coil to sheet or vice-versa is due to the floppiness of the amino acid residues. This is observed from the Ramachandran map of the studied secondary structures. Further, it is noted that the intramolecular H-bond interactions play a significant role in the conformational transition of secondary structures of A[Formula: see text].
{"title":"Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study","authors":"M. Ganesan, S. Paranthaman","doi":"10.1142/s0219633620500145","DOIUrl":"https://doi.org/10.1142/s0219633620500145","url":null,"abstract":"Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] and [Formula: see text] dihedral angles, [Formula: see text] varies significantly in sheet structure. This is due to the absence of intermolecular hydrogen bond (H-bond) interactions in sheets considered in this study. Our calculations show that the conformational transition of helix/coil to sheet or vice-versa is due to the floppiness of the amino acid residues. This is observed from the Ramachandran map of the studied secondary structures. Further, it is noted that the intramolecular H-bond interactions play a significant role in the conformational transition of secondary structures of A[Formula: see text].","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2050014"},"PeriodicalIF":2.4,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620500145","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42604933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-01DOI: 10.1142/s0219633620020034
Minghui Li
{"title":"Editorial: Special Issue on Computational Chemistry and Diseases","authors":"Minghui Li","doi":"10.1142/s0219633620020034","DOIUrl":"https://doi.org/10.1142/s0219633620020034","url":null,"abstract":"","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2002003"},"PeriodicalIF":2.4,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620020034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49516312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-01DOI: 10.1142/s0219633620410035
Vidhyanand Mahase, Adebiyi Sobitan, C. Johnson, Farion Cooper, Yixin Xie, Lin Li, S. Teng
Hereditary spastic paraplegias (HSPs) are a genetically heterogeneous collection of neurodegenerative disorders categorized by progressive lower-limb spasticity and frailty. The complex HSP forms are characterized by various neurological features including progressive spastic weakness, urinary sphincter dysfunction, extra pyramidal signs and intellectual disability (ID). The kinesin superfamily proteins (KIFs) are microtubule-dependent molecular motors involved in intracellular transport. Kinesins directionally transport membrane vesicles, protein complexes, and mRNAs along neurites, thus playing important roles in neuronal development and function. Recent genetic studies have identified kinesin mutations in patients with HSPs. In this study, we used the computational approaches to investigate the 40 missense mutations associated with HSP and ID in KIF1A and KIF5A. We performed homology modeling to construct the structures of kinesin–microtubule binding domain and kinesin–tubulin complex. We applied structure-based energy calculation methods to determine the effects of missense mutations on protein stability and protein–protein interaction. The results revealed that the most of disease-causing mutations could change the folding free energy of kinesin motor domain and the binding free energy of kinesin–tubulin complex. We found that E253K associated with ID in KIF1A decrease the protein stability of kinesin motor domains. We showed that the HSP mutations located in kinesin–tubulin complex interface, such as K253N and R280C in KIF5A, can destabilize the kinesin–tubulin complex. The computational analysis provides useful information for understanding the roles of kinesin mutations in the development of ID and HSPs.
{"title":"Computational analysis of hereditary spastic paraplegia mutations in the kinesin motor domains of KIF1A and KIF5A","authors":"Vidhyanand Mahase, Adebiyi Sobitan, C. Johnson, Farion Cooper, Yixin Xie, Lin Li, S. Teng","doi":"10.1142/s0219633620410035","DOIUrl":"https://doi.org/10.1142/s0219633620410035","url":null,"abstract":"Hereditary spastic paraplegias (HSPs) are a genetically heterogeneous collection of neurodegenerative disorders categorized by progressive lower-limb spasticity and frailty. The complex HSP forms are characterized by various neurological features including progressive spastic weakness, urinary sphincter dysfunction, extra pyramidal signs and intellectual disability (ID). The kinesin superfamily proteins (KIFs) are microtubule-dependent molecular motors involved in intracellular transport. Kinesins directionally transport membrane vesicles, protein complexes, and mRNAs along neurites, thus playing important roles in neuronal development and function. Recent genetic studies have identified kinesin mutations in patients with HSPs. In this study, we used the computational approaches to investigate the 40 missense mutations associated with HSP and ID in KIF1A and KIF5A. We performed homology modeling to construct the structures of kinesin–microtubule binding domain and kinesin–tubulin complex. We applied structure-based energy calculation methods to determine the effects of missense mutations on protein stability and protein–protein interaction. The results revealed that the most of disease-causing mutations could change the folding free energy of kinesin motor domain and the binding free energy of kinesin–tubulin complex. We found that E253K associated with ID in KIF1A decrease the protein stability of kinesin motor domains. We showed that the HSP mutations located in kinesin–tubulin complex interface, such as K253N and R280C in KIF5A, can destabilize the kinesin–tubulin complex. The computational analysis provides useful information for understanding the roles of kinesin mutations in the development of ID and HSPs.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2041003"},"PeriodicalIF":2.4,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620410035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47152518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-08-19DOI: 10.1142/s021963362050025x
Nadjet Deddouche, H. Chemouri
A comparative theoretical study of the kinetics of the Diels–Alder (DA) reaction between empty fullerene (C60) and lithium ion encapsulated fullerene (Li+@C60) with 1,3 cyclohexadiene (C6H8) was ca...
{"title":"Theoretical elucidation of the energy conversion rate in organic photovoltaic cells of the fullerene nanostructure derivatives. A density functional theory study","authors":"Nadjet Deddouche, H. Chemouri","doi":"10.1142/s021963362050025x","DOIUrl":"https://doi.org/10.1142/s021963362050025x","url":null,"abstract":"A comparative theoretical study of the kinetics of the Diels–Alder (DA) reaction between empty fullerene (C60) and lithium ion encapsulated fullerene (Li+@C60) with 1,3 cyclohexadiene (C6H8) was ca...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2050025"},"PeriodicalIF":2.4,"publicationDate":"2020-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s021963362050025x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45488698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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