text:
dy and G. V. R. Saimadhukar and T. Karunakar and B. Rajeshwar Rao},
	date-added = {2021-06-15 11:12:27 -0400},
	date-modified = {2021-07-25 21:17:44 -0400},
	doi = {10.20959/wjpps20216-19055},
	journal = {WORLD JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES},
	pages = {1479-1486},
	title = {COMPUTATIONAL STUDY ON THE ELECTRONIC STRUCTURE OF METHICILLIN ZWITTERIONS BY AUSTIN MODEL-1 METHOD},
	volume = {10},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.20959/wjpps20216-19055}}

@article{Fujimoto:2021vb,
	abstract = {Cytochrome P450 (CYPs) are oxidoreductases distributed in various tissues in plants and animals. Among the CYP families, CYP3A is the most abundant in vivo, particularly in humans, and it is involved in the metabolism of many drugs. It is crucial to measure CYP3A activity for both pharmaceuticals and agrochemicals because inhibition or induction of this enzyme can seriously affect the occurrence of toxicity or efficacy. In the present study, a novel fluorescent probe, 6-(2,5-bis(trifluoromethyl)benzyloxy)-9-(4-methoxy-2-methylphenyl)-3H-xanthen-3-one (BMX, quantum efficiency: 21{\%}), was designed and synthesized. The design was done by photoinduced electron transfer strategy. BMX was specifically metabolized only using CYP3A to generate 2-Me-4-MeO TokyoGreen (quantum efficiency: 85{\%}), resulting in strong fluorescence in the presence of CYP3A isozymes. Protein assays using recombinant human, rat, and mouse CYP isozymes demonstrated the selective metabolism of BMX and production of fluorescence only by CYP3A in all species.},
	author = {Fujimoto, Keiichi and Takeuchi, Hayato and Takaku, Tomoyuki and Abe, Jun and Harada, Koichiro},
	da = {2021/06/10/},
	date-added = {2021-06-15 11:11:38 -0400},
	date-modified = {2021-06-15 11:11:38 -0400},
	doi = {https://doi.org/10.1016/j.bmcl.2021.128195},
	isbn = {0960-894X},
	journal = {Bioorganic \& Medicinal Chemistry Letters},
	keywords = {CYP3A; fluorescent prove; photoinduced electron transfer (PeT)},
	pages = {128195},
	title = {Designing a novel photoinduced electron transfer-based small-molecule fluorescent probe specific for CYP3A isozymes},
	ty = {JOUR},
	url = {https://www.sciencedirect.com/science/article/pii/S0960894X21004224},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0960894X21004224},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.bmcl.2021.128195}}

@article{D1CP01116B,
	abstract = {Nanomaterials possess a wide range of potential applications due to their novel properties and exceptionally high activity as a result of their large surface to volume ratios compared to bulk matter. The active surface may present both advantage and risk when the nanomaterials interact with living organisms. As the overall biological impact of nanomaterials is triggered and mediated by interactions at the bio--nano interface{,} an ability to predict those from the atomistic descriptors{,} especially before the material is produced{,} can present enormous advantage for the development of nanotechnology. Fast screening of nanomaterials and their variations for specific biological effects can be enabled using computational materials modelling. The challenge lies in the range of scales that needs to be crossed from the material-specific atomistic representation to the relevant length scales covering typical biomolecules (proteins and lipids). In this work{,} we present a systematic multiscale approach that allows one to evaluate crucial interactions at the bionano interface from the first principles without any prior information about the material and thus establish links between the details of the nanomaterials structure to protein--nanoparticle interactions. As an example{,} an advanced computational characterization of titanium dioxide nanoparticles (6 different surfaces of rutile and anatase polymorphs) has been performed. We computed characteristics of the titanium dioxide interface with water using density functional theory for electronic density{,} used these parameters to derive an atomistic force field{,} and calculated adsorption energies for essential biomolecules on the surface of titania nanoparticles via direct atomistic simulations and coarse-grained molecular dynamics. Hydration energies{,} as well as adsorption energies for a set of 40 blood proteins are reported.},
	annote = {cite-code},
	author = {Rouse, Ian and Power, David and Brandt, Erik G. and Schneemilch, Matthew and Kotsis, Konstantinos and Quirke, Nick and Lyubartsev, Alexander P. and Lobaskin, Vladimir},
	date-added = {2021-06-15 11:10:06 -0400},
	date-modified = {2021-06-15 11:10:11 -0400},
	doi = {10.1039/D1CP01116B},
	journal = {Phys. Chem. Chem. Phys.},
	pages = {-},
	publisher = {The Royal Society of Chemistry},
	title = {First principles characterisation of bio--nano interface},
	url = {http://dx.doi.org/10.1039/D1CP01116B},
	year = {2021},
	Bdsk-Url-1 = {http://dx.doi.org/10.1039/D1CP01116B}}

@article{GRZYBEK2021120435,
	abstract = {The K-ZnxCo3-xO4 catalyst supported on α-Al2O3 for N2O decomposition was investigated in terms of its resistance towards typical contaminants (O2, H2O, and NO) present in the nitric acid plant tail gases. The catalyst synthesized in laboratory-scale was thoroughly characterized by means of X-ray μ-tomography, XRF, XRD, and SEM/TEM/EDX. The impact of contaminants such as O2, H2O, and NO on the N2O conversion of the catalyst was examined and quantified by kinetic and thermodynamic modeling. The mechanism of inhibition involving local (active site blocking) and global (modification of the spinel electronic properties by electrophilic NOx adspecies) effects was proposed. The strongest inhibition of NO was associated with its facile reactivity with surface O intermediates produced during N2O decomposition. The resultant NO2 and NO3 surface adducts are stable at the catalyst surface up to 550 $\,^{\circ}$C. For the pilot catalyst, the effect of contamination was the same in nature as for the laboratory sample, however, the observed quantitative differences were associated with the changes in the shape of the spinel nanocrystals constituting the catalyst active phase. The obtained results provide rationales for designing and preparation of the robust deN2O catalyst with enhanced resistivity to poisoning.},
	annote = {no-calc},
	author = {G. Grzybek and J. Grybo{\'s} and P. Indyka and J. Janas and K. Ciura and B. Leszczy{\'n}ski and F. Zasada and A. Kotarba and Z. Sojka},
	date-added = {2021-06-12 18:27:02 -0400},
	date-modified = {2021-06-12 18:27:31 -0400},
	doi = {https://doi.org/10.1016/j.apcatb.2021.120435},
	issn = {0926-3373},
	journal = {Applied Catalysis B: Environmental},
	keywords = {Cobalt catalyst, NO decomposition, Inhibiting effect, Kinetic modeling, Thermodynamics},
	pages = {120435},
	title = {Evaluation of the inhibiting effect of H2O, O2, and NO on the performance of laboratory and pilot K-ZnxCo3-xO4 catalysts supported on α-Al2O3 for low-temperature N2O decomposition},
	url = {https://www.sciencedirect.com/science/article/pii/S0926337321005610},
	volume = {297},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0926337321005610},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.apcatb.2021.120435}}

@article{Jin:2021tc,
	abstract = {Aeromonas hydrophila is a gram-negative bacterium and the major causative agent of the fish disease motile aeromonad septicemia (MAS). It uses N-acyl-homoserine lactone (AHL) quorum sensing signals to coordinate biofilm formation, motility, and virulence gene expression. The AHL signaling pathway is therefore considered to be a therapeutic target against pathogenic A. hydrophila infection. In A. hydrophila, AHL autoinducers biosynthesis are specifically catalyzed by an ACP-dependent AHL synthase AhyI using the precursors SAM and acyl-ACP. Our previously reported AhyI was heterologously expressed in E. coli, which showed the production characteristics of medium-long chain AHLs. This contradicted the prevailing understanding that AhyI was only a short-chain C4/C6-HSL synthase.},
	author = {Jin, Lei and Bao, Jingjiao and Chen, Yu and Yang, Wenge and Du, Wenyi},
	da = {2021/06/08},
	date-added = {2021-06-12 18:25:46 -0400},
	date-modified = {2021-06-12 18:25:46 -0400},
	doi = {10.1186/s12866-021-02244-9},
	id = {Jin2021},
	isbn = {1471-2180},
	journal = {BMC Microbiology},
	number = {1},
	pages = {173},
	title = {Structural insights into acyl-ACP selective recognition by the Aeromonas hydrophila AHL synthase AhyI},
	ty = {JOUR},
	url = {https://doi.org/10.1186/s12866-021-02244-9},
	volume = {21},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1186/s12866-021-02244-9}}

@article{Okadome-Valencia:2021wg,
	annote = {no-access},
	author = {Okadome Valencia, Hubert and Wang, Busheng and Frapper, Gilles and Rohl, Andrew Lloyd},
	booktitle = {Journal of Computational Chemistry},
	da = {2021/06/07},
	date = {2021/06/07},
	date-added = {2021-06-12 18:23:21 -0400},
	date-modified = {2021-06-12 18:23:25 -0400},
	doi = {https://doi.org/10.1002/jcc.26697},
	isbn = {0192-8651},
	journal = {Journal of Computational Chemistry},
	journal1 = {Journal of Computational Chemistry},
	journal2 = {J Comput Chem},
	keywords = {computational chemistry; GDIS; USPEX; VASP; visualization software},
	m3 = {https://doi.org/10.1002/jcc.26697},
	month = {2021/06/12},
	n2 = {Abstract A popular first principles simulation code, the Vienna Ab initio Simulation Package (VASP), and a crystal structure prediction (CSP) package, the Universal Structure Predictor: Evolutionary Xtallography (USPEX) have been integrated into the GDIS visualization software. The aim of this integration is to provide users with a unique and simple interface through which most of the steps of a typical crystal optimization or prediction work. This involved, for the latter, not only setting up a CSP calculation with complete support for the latest version of USPEX, but also displaying the many structure results by linking each structure geometry and its energy via interactive graphics. For the optimization part, any structure displayed by GDIS can now be the starting point for VASP calculations, with support for its most commonly used parameters. Atomic and electronic structures can be displayed as well as dynamic properties such as total energy, force, volume, and pressure for each ionic step. It is not only possible to start calculations from the GDIS visualization software, using an in-place task manager, but a running calculation can also be followed, allowing a greater control of the simulation process. The GDIS software is available under the GNU public license in its second version.},
	number = {n/a},
	publisher = {John Wiley \& Sons, Ltd},
	title = {New developments in the GDIS simulation package: Integration of VASP and USPEX},
	ty = {JOUR},
	url = {https://doi.org/10.1002/jcc.26697},
	volume = {n/a},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1002/jcc.26697}}

@article{Shen:2021ts,
	annote = {cite-code},
	author = {Shen, Sida and Butrin, Arseniy and Doubleday, Peter F. and Melani, Rafael D. and Beaupre, Brett A. and Tavares, Mauricio T. and Ferreira, Glaucio M. and Kelleher, Neil L. and Moran, Graham R. and Liu, Dali and Silverman, Richard B.},
	booktitle = {Journal of the American Chemical Society},
	da = {2021/06/07},
	date = {2021/06/07},
	date-added = {2021-06-12 18:20:32 -0400},
	date-modified = {2021-06-12 18:20:39 -0400},
	doi = {10.1021/jacs.1c02456},
	isbn = {0002-7863},
	journal = {Journal of the American Chemical Society},
	journal1 = {J. Am. Chem. Soc.},
	m3 = {doi: 10.1021/jacs.1c02456},
	month = {06},
	publisher = {American Chemical Society},
	title = {Turnover and Inactivation Mechanisms for (S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase},
	ty = {JOUR},
	url = {https://doi.org/10.1021/jacs.1c02456},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/jacs.1c02456}}

@article{Bezerra:2021wf,
	author = {Bezerra, Fabricio Maest{\'a} and Carvalho Cotre, Dayane Samara de and Plath, Andr{\'e} and Firmino, Helen Beraldo and Lima, Miliane Aparecida de and Lis, Manuel and Samulewski, Rafael Block and Mois{\'e}s, Murilo Pereira},
	booktitle = {Textile Research Journal},
	date = {2021/06/09},
	date-added = {2021-06-12 18:19:42 -0400},
	date-modified = {2021-06-12 18:19:49 -0400},
	doi = {10.1177/00405175211022624},
	isbn = {0040-5175},
	journal = {Textile Research Journal},
	journal1 = {Textile Research Journal},
	m3 = {doi: 10.1177/00405175211022624},
	month = {2021/06/12},
	n2 = {Dyes are complex molecules that can sometimes cause damage to the aquatic environment and harm human health. They are often not completely removed from effluent by the usual treatments; therefore, efforts have been made to increase their exhaustion from dyeing through chemical and physical processes. In this context, the use of ?-cyclodextrin (?-CD) as dyeing auxiliary agent promotes the reduction of harmful products, also increasing the color intensity of the fabric. In this paper, ?-CD was used as a complexing agent to dye polyamide (PA) using the dye C.I. Disperse Yellow 211 (DY211) in order to improve dye exhaustion and color intensity using the ?-CD:DY211 complex. The conventional dyeing process and ?-CD:DY211 dyeing process by exhaustion were compared, and adsorption kinetics, isotherms, and the coloristic intensity were evaluated. The chemical shifts in the FTIR spectra and the thermal stability evidenced the formation of the ?-CD:DY211 complex. Regarding dyeing kinetics and isotherm, the pseudo-first-order model was the most appropriate to describe the process, while Nernst isotherm was the one that best represented the adsorption results. Categorically, the samples dyed with the ?-CD:DY211 complex obtained higher coloristic intensity in comparison with the conventional process. With this evidence, it is possible to conclude that cyclodextrin is a suitable replacement for environmentally harmful textile aides without adding further steps into the dyeing process or the need for additional equipment.},
	pages = {00405175211022624},
	publisher = {SAGE Publications Ltd STM},
	title = {β-Cyclodextrin: Disperse yellow 211 complexes improve coloristic intensity of polyamide dyed knits},
	ty = {JOUR},
	url = {https://doi.org/10.1177/00405175211022624},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1177/00405175211022624}}

@article{Wang:2021uf,
	annote = {cite-code, cite-model},
	author = {Wang, Lun and Zheng, Yunhua and Li, Dan and Yang, Jianhong and Lei, Lei and Yan, Wei and Zheng, Wei and Tang, Minghai and Shi, Mingsong and Zhang, Ruijia and Cai, Xiaoying and Ni, Hengfan and Ma, Xu and Li, Na and Hong, Feng and Ye, Haoyu and Chen, Lijuan},
	booktitle = {Journal of Medicinal Chemistry},
	da = {2021/06/03},
	date = {2021/06/03},
	date-added = {2021-06-07 16:46:05 -0400},
	date-modified = {2021-06-07 16:46:18 -0400},
	doi = {10.1021/acs.jmedchem.0c01961},
	isbn = {0022-2623},
	journal = {Journal of Medicinal Chemistry},
	journal1 = {J. Med. Chem.},
	m3 = {doi: 10.1021/acs.jmedchem.0c01961},
	month = {06},
	publisher = {American Chemical Society},
	title = {Design, Synthesis, and Bioactivity Evaluation of Dual-Target Inhibitors of Tubulin and Src Kinase Guided by Crystal Structure},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acs.jmedchem.0c01961},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acs.jmedchem.0c01961}}

@article{Nazarov:2021vy,
	abstract = {Room-temperature phosphorescence (RTP) of arenes, naphthalene-d8 and phenanthrene, in complexes with β-cyclodextrin (βCD) in the presence of a third component, tert-butylbenzene or p-tert-butyltoluene, providing the appearance of long-lived arene RTP, has been studied. The RTP lifetimes τph of naphthalene-d8 in the naphthalene-d8--βCD--tert-butylbenzene and naphthalene-d8--βCD--p-tert-butyltoluene complexes in the presence of oxygen are 14 and 4.8 s, respectively, and increase up to 16.4 and 6.6 s after oxygen removal. The rate constants of the phosphorescence quenching in these complexes are 34.4 and 76 L mol−1 s−1, respectively, indicating a high degree of naphthalene-d8 isolation from oxygen in the supramolecular system based on βCD. The highest value of τph for phenanthrene in the phenanthrene--βCD--tert-butylbenzene complex in the presence of oxygen is 2.4 s. The RTP decay in the presence of oxygen is always the superposition of two exponents, which is the general property of such three-component complexes, and indicates the presence of two types of phosphorescing complexes. The proposed structures of the complexes have been calculated by the quantum-chemistry method. The mechanism of the arene RTP quenching by oxygen is discussed with the use of the calculated structures of the complexes.},
	annote = {cite-code},
	author = {Nazarov, V. B. and Avakyan, V. G. and Alfimov, M. V.},
	da = {2021/05/01},
	date-added = {2021-06-07 16:45:30 -0400},
	date-modified = {2021-06-07 16:45:36 -0400},
	doi = {10.1134/S0018143921020090},
	id = {Nazarov2021},
	isbn = {1608-3148},
	journal = {High Energy Chemistry},
	number = {3},
	pages = {193--202},
	title = {Long-Lived Room-Temperature Phosphorescence of Arene--Beta-Cyclodextrin--Hydrocarbon Complexes in the Presence of Oxygen},
	ty = {JOUR},
	url = {https://doi.org/10.1134/S0018143921020090},
	volume = {55},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1134/S0018143921020090}}

@article{Polik:2021tt,
	annote = {no-calc, no-access},
	author = {Polik, William F. and Schmidt, J. R.},
	booktitle = {WIREs Computational Molecular Science},
	da = {2021/06/02},
	date = {2021/06/02},
	date-added = {2021-06-07 16:44:07 -0400},
	date-modified = {2021-06-07 16:44:13 -0400},
	doi = {https://doi.org/10.1002/wcms.1554},
	isbn = {1759-0876},
	journal = {WIREs Computational Molecular Science},
	journal1 = {WIREs Computational Molecular Science},
	journal2 = {WIREs Comput Mol Sci},
	keywords = {chemistry education; electronic structure; visualization},
	m3 = {https://doi.org/10.1002/wcms.1554},
	month = {2021/06/07},
	n2 = {Abstract WebMO is a web-based interface for all major quantum chemistry programs. WebMO uses a server?client architecture that installs on a single server or cluster computer and provides access to state-of-the-art computational chemistry programs from a standard web browser. The web interface provides a 3-D molecular editor, pre-defined calculations types, job submission and monitoring, visualization of results, and user management tools. Barriers to using state-of-the-art computational chemistry in teaching and research are minimized through WebMO's universal accessibility, its intuitive and uniform interface to all programs, no software to install on client computers, and support for multiple users with a single instance. Applications of WebMO throughout the undergraduate curriculum are provided. The extensible open-architecture design allows for collaboration among educators, researchers, quantum chemistry program developers, and the WebMO interface developers. This article is categorized under: Computer and Information Science > Visualization Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry},
	number = {n/a},
	pages = {e1554},
	publisher = {John Wiley \& Sons, Ltd},
	title = {WebMO: Web-based computational chemistry calculations in education and research},
	ty = {JOUR},
	url = {https://doi.org/10.1002/wcms.1554},
	volume = {n/a},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1002/wcms.1554}}

@article{antibiotics10060659,
	abstract = {Bacterial infections that do not respond to current treatments are increasing, thus there is a need for the development of new antibiotics. Series of 20 N-substituted quaternary salts of cinchonidine (CD) and their quasi-enantiomer cinchonine (CN) were prepared and their antimicrobial activity was assessed against a diverse panel of Gram-positive and Gram-negative bacteria. All tested compounds showed good antimicrobial potential (minimum inhibitory concentration (MIC) values 1.56 to 125.00 μg/mL), proved to be nontoxic to different human cell lines, and did not influence the production of reactive oxygen species (ROS). Seven compounds showed very strong bioactivity against some of the tested Gram-negative bacteria (MIC for E. coli and K. pneumoniae 6.25 μg/mL; MIC for P. aeruginosa 1.56 μg/mL). To establish a connection between antimicrobial data and potential energy surfaces (PES) of the compounds, activity/PES models using principal components of the disc diffusion assay and MIC and data towards PES data were built. An extensive machine learning procedure for the generation and cross-validation of multivariate linear regression models with a linear combination of original variables as well as their higher-order polynomial terms was performed. The best possible models with predicted R2(CD derivatives) = 0.9979 and R2(CN derivatives) = 0.9873 were established and presented. This activity/PES model can be used for accurate prediction of activities for new compounds based solely on their potential energy surfaces, which will enable wider screening and guided search for new potential leads. Based on the obtained results, N-quaternary derivatives of Cinchona alkaloids proved to be an excellent scaffold for further optimization of novel antibiotic species.},
	annote = {cite-code, cite-model},
	article-number = {659},
	author = {Rami{\'c}, Alma and Sko{\v c}ibu{\v s}i{\'c}, Mirjana and Od{\v z}ak, Renata and {\v C}ipak Ga{\v s}parovi{\'c}, Ana and Milkovi{\'c}, Lidija and Mikeli{\'c}, Ana and Sovi{\'c}, Karlo and Primo{\v z}i{\v c}, Ines and Hrenar, Tomica},
	date-added = {2021-06-07 16:42:51 -0400},
	date-modified = {2021-06-07 16:42:57 -0400},
	doi = {10.3390/antibiotics10060659},
	issn = {2079-6382},
	journal = {Antibiotics},
	number = {6},
	pubmedid = {34073082},
	title = {Antimicrobial Activity of Quasi-Enantiomeric Cinchona Alkaloid Derivatives and Prediction Model Developed by Machine Learning},
	url = {https://www.mdpi.com/2079-6382/10/6/659},
	volume = {10},
	year = {2021},
	Bdsk-Url-1 = {https://www.mdpi.com/2079-6382/10/6/659},
	Bdsk-Url-2 = {https://doi.org/10.3390/antibiotics10060659}}

@article{Shi:2021vo,
	annote = {cite-model},
	author = {Shi, Mingsong and Zhao, Min and Wang, Lun and Liu, Kongjun and Li, Penghui and Liu, Jiang and Cai, Xiaoying and Chen, Lijuan and Xu, Dingguo},
	date-added = {2021-06-07 16:39:31 -0400},
	date-modified = {2021-06-07 16:41:22 -0400},
	doi = {10.1039/D1CP00717C},
	isbn = {1463-9076},
	journal = {Physical Chemistry Chemical Physics},
	journal1 = {Phys. Chem. Chem. Phys.},
	m3 = {10.1039/D1CP00717C},
	n2 = {Salt inducible kinase 2 (SIK2) is a calcium/calmodulin-dependent protein kinase-like kinase that is implicated in a variety of biological phenomena, including cellular metabolism, growth, and apoptosis. SIK2 is the key target for various cancers, including ovarian, breast, prostate, and lung cancers. Although potent inhibitors of SIK2 are being developed, their binding stability and functional role are not presently known. In this work, we studied the detailed interactions between SIK2 and four of its inhibitors, HG-9-91-01, KIN112, MRT67307, and MRT199665, using molecular docking, molecular dynamics simulation, binding free energy calculation, and interaction fingerprint analysis. Intermolecular interactions revealed that HG-9-91-01 and KIN112 have stronger interactions with SIK2 than those of MRT199665 and MRT67307. The key residues involved in binding with SIK2 are conserved among all four inhibitors. Our results explain the detailed interaction of SIK2 with its inhibitors at the molecular level, thus paving the way for the development of targeted efficient anti-cancer drugs.},
	pages = {--},
	publisher = {The Royal Society of Chemistry},
	title = {Exploring the stability of inhibitor binding to SIK2 using molecular dynamics simulation and binding free energy calculation},
	ty = {JOUR},
	url = {http://dx.doi.org/10.1039/D1CP00717C},
	year = {2021},
	Bdsk-Url-1 = {http://dx.doi.org/10.1039/D1CP00717C}}

@article{Gupta:2021ui,
	annote = {cite-model},
	author = {Gupta, Bramha and Ambekar, Rushikesh S. and Tromer, Raphael M. and Ghosal, Partha Sarathi and Sinha, Rupal and Majumder, Abhradeep and Kumbhakar, Partha and Ajayan, P. M. and Galvao, Douglas S. and Gupta, Ashok Kumar and Tiwary, Chandra Sekhar},
	date-added = {2021-06-07 16:38:46 -0400},
	date-modified = {2021-06-07 16:38:52 -0400},
	doi = {10.1039/D1RA03097C},
	journal = {RSC Advances},
	journal1 = {RSC Adv.},
	m3 = {10.1039/D1RA03097C},
	n2 = {The impact of micro and nanoplastic debris on our aquatic ecosystem is among the most prominent environmental challenges we face today. In addition, nanoplastics create significant concern for environmentalists because of their toxicity and difficulty in separation and removal. Here we report the development of a 3D printed moving bed water filter (M-3DPWF), which can perform as an efficient nanoplastic scavenger. The enhanced separation of the nanoplastics happens due to the creation of a charged filter material that traps the more surface charged nanoparticles selectively. Synthetic contaminated water from polycarbonate waste has been tested with the filter, and enhanced nanoplastic removal has been achieved. The proposed filtration mechanism of surface-charge based water cleaning is further validated using density function theory (semi-empirical) based simulation. The filter has also shown good structural and mechanical stability in both static and dynamic water conditions. The field suitability of the novel treatment system has also been confirmed using water from various sources, such as sea, river, and pond. Our results suggest that the newly developed water filter can be used for the removal of floating nanoparticles in water as a robust advanced treatment system.},
	number = {32},
	pages = {19788--19796},
	publisher = {The Royal Society of Chemistry},
	title = {Development of a schwarzite-based moving bed 3D printed water treatment system for nanoplastic remediation},
	ty = {JOUR},
	url = {http://dx.doi.org/10.1039/D1RA03097C},
	volume = {11},
	year = {2021},
	Bdsk-Url-1 = {http://dx.doi.org/10.1039/D1RA03097C}}

@article{Perez-Mellor:2021vs,
	abstract = {The role of stereochemical factors on the structure and the fragmentation paths of the protonated cyclic dipeptide cyclo histidine--phenylalanine is studied under ion traps conditions by combining tandem mass spectrometry, laser spectroscopy, quantum chemical calculations and chemical dynamics simulations. Vibrational spectroscopy obtained by Infrared Multiple Photon Dissociation (IRMPD) reveals a small difference between the two diastereomers, c-{\$}{\$}{$\backslash$}hbox {\{}LLH{\}}\^{}{\{}+{\}}{\$}{\$}and c-{\$}{\$}{$\backslash$}hbox {\{}LDH{\}}\^{}{\{}+{\}}{\$}{\$}, arising mainly from ancillary CH...{\$}{\$}{$\backslash$}uppi {\$}{\$}interactions. In contrast, there is a strong influence of the residues chirality on the collision-induced dissociation (CID) processes. Chemical dynamics simulations rationalize this effect and evidence that proton mobility takes place, allowing isomerization to intermediate cyclic structures that are different for c-{\$}{\$}{$\backslash$}hbox {\{}LLH{\}}\^{}{\{}+{\}}{\$}{\$}and c-{\$}{\$}{$\backslash$}hbox {\{}LDH{\}}\^{}{\{}+{\}}{\$}{\$}, resulting in different barriers to proton mobility. This effect is related to the protonation of the imidazole ring. It contrasts with the minute stereochemical effects observed for other cyclic dipeptides in which the proton is borne by an amide CO.},
	annote = {cite-code, cite-model},
	author = {P{\'e}rez-Mellor, Ariel and Le Barbu-Debus, Katia and Lepere, Valeria and Alata, Ivan and Spezia, Riccardo and Zehnacker, Anne},
	da = {2021/05/31},
	date-added = {2021-06-05 22:18:23 -0400},
	date-modified = {2021-06-05 22:18:28 -0400},
	doi = {10.1140/epjd/s10053-021-00173-w},
	id = {P{\'e}rez-Mellor2021},
	isbn = {1434-6079},
	journal = {The European Physical Journal D},
	number = {6},
	pages = {165},
	title = {Structure and collision-induced dissociation of the protonated cyclo His-Phe dipeptide: mechanistic studies and stereochemical effects},
	ty = {JOUR},
	url = {https://doi.org/10.1140/epjd/s10053-021-00173-w},
	volume = {75},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1140/epjd/s10053-021-00173-w}}

@article{CHAMKINA2021123929,
	abstract = {Four dendrimers of the first and second generations containing rigid polyphenylene interior and flexible ferrocenyl-terminated alkyl arms (CH2)m(C5H4)Fe(C5H5) (m = 6, 11) were synthesized by combining two types of ``click'' reactions: Diels-Alder and copper-catalyzed azide-alkyne cycloaddition reactions. The resulting compounds were characterized by NMR spectroscopy, gel permeation chromatography, and cyclic voltammetry (CV). CVs of the dendrimers show a single chemically reversible wave. In contrast to wholly aromatic redox-active dendrimers, a combination of rigid polyphenylene interior with flexible alkylferrocenyl periphery provides an electrochemically reversible redox process. The dendrimers exhibit strong adsorption onto the Pt electrode upon oxidation, thus providing fabrication of stable modified electrodes coated with a second-generation dendrimer.},
	annote = {cite-code, cite-model},
	author = {Elena S. Chamkina and Aleksandr A. Chamkin and Zinaida B. Shifrina},
	date-added = {2021-06-05 22:16:24 -0400},
	date-modified = {2021-06-05 22:16:42 -0400},
	doi = {https://doi.org/10.1016/j.polymer.2021.123929},
	issn = {0032-3861},
	journal = {Polymer},
	keywords = {Ferrocenyl polyphenylene dendrimer, Click chemistry, Electrochemical reversibility},
	pages = {123929},
	title = {The flexibility of periphery enhances the electrochemical reversibility of ferrocenyl-terminated polyphenylene dendrimers},
	url = {https://www.sciencedirect.com/science/article/pii/S0032386121005528},
	volume = {228},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0032386121005528},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.polymer.2021.123929}}

@article{Tykol:2021vg,
	author = {Tykol, Andrew J. and Rodriguez, F. A. and Thomas, J. C. and Petersen, E. L.},
	booktitle = {Combustion Science and Technology},
	date = {2021/06/01},
	date-added = {2021-06-05 22:12:34 -0400},
	date-modified = {2021-06-05 22:12:39 -0400},
	doi = {10.1080/00102202.2021.1928093},
	isbn = {0010-2202},
	journal = {Combustion Science and Technology},
	journal1 = {null},
	m3 = {doi: 10.1080/00102202.2021.1928093},
	month = {06},
	pages = {1--18},
	publisher = {Taylor \& Francis},
	title = {Burning Rate Characterization of Guanidine Nitrate and Basic Copper Nitrate Gas Generants with Metal Oxide Additives},
	ty = {JOUR},
	url = {https://doi.org/10.1080/00102202.2021.1928093},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1080/00102202.2021.1928093}}

@article{Kubba:2021vi,
	abstract = {A newly derivative of oxazolidin-5- one namely {$[$}2-(2-biphenyl-4-yl-imidazo {$[$}1,2-a{$]$} pyridine-3-yl)-3-(4-nitro-phenyl)-oxazolidin-5-one (BIPNO5){$]$} was examined as an corrosion inhibitor for carbon steel surface. Quantum mechanical method of Density Functional Theory (DFT) with (B3LYP (6-311++G (2d, 2p)) level of theory was used to calculate the minimize structure, physical properties and inhibition chemical parameters, in vacuum and two solvents (DMSO and H2O), all at equilibrium geometry. The results indicated that the new derivative could adsorb on the surface of carbon steel through the heteroatom, showing that the new inhibitor has good corrosion inhibition performance.},
	annote = {gui=chem3d},
	author = {Kubba, Rehab Majed and Al-Joborry, Nada Mohammed},
	date = {2021/05/30},
	date-added = {2021-06-05 22:11:47 -0400},
	date-modified = {2021-06-05 22:11:56 -0400},
	doi = {10.24996/ijs.2021.62.5.1},
	journal = {Iraqi Journal of Science},
	journal1 = {eijs},
	month = {2021/06/06},
	number = {5},
	pages = {1396-1403},
	se = {Chemistry},
	title = {Theoretical study of a new oxazolidine -5- one derivative as a corrosion inhibitor for carbon steel surface},
	ty = {JOUR},
	url = {https://ijs.uobaghdad.edu.iq/index.php/eijs/article/view/2134},
	volume = {62},
	year = {2021},
	Bdsk-Url-1 = {https://ijs.uobaghdad.edu.iq/index.php/eijs/article/view/2134},
	Bdsk-Url-2 = {https://doi.org/10.24996/ijs.2021.62.5.1}}

@article{Friederich:2021up,
	abstract = {The choice of simulation methods in computational materials science is driven by a fundamental trade-off: bridging large time- and length-scales with highly accurate simulations at an affordable computational cost. Venturing the investigation of complex phenomena on large scales requires fast yet accurate computational methods. We review the emerging field of machine-learned potentials, which promises to reach the accuracy of quantum mechanical computations at a substantially reduced computational cost. This Review will summarize the basic principles of the underlying machine learning methods, the data acquisition process and active learning procedures. We highlight multiple recent applications of machine-learned potentials in various fields, ranging from organic chemistry and biomolecules to inorganic crystal structure predictions and surface science. We furthermore discuss the developments required to promote a broader use of ML potentials, and the possibility of using them to help solve open questions in materials science and facilitate fully computational materials design.},
	annote = {cite-code, no-calc},
	author = {Friederich, Pascal and H{\"a}se, Florian and Proppe, Jonny and Aspuru-Guzik, Al{\'a}n},
	da = {2021/06/01},
	date-added = {2021-06-01 11:43:35 -0400},
	date-modified = {2021-06-01 11:43:40 -0400},
	doi = {10.1038/s41563-020-0777-6},
	id = {Friederich2021},
	isbn = {1476-4660},
	journal = {Nature Materials},
	number = {6},
	pages = {750--761},
	title = {Machine-learned potentials for next-generation matter simulations},
	ty = {JOUR},
	url = {https://doi.org/10.1038/s41563-020-0777-6},
	volume = {20},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1038/s41563-020-0777-6}}

@article{JIANG2021101066,
	abstract = {Upregulating the susceptibility of cancer cells to ferroptosis is crucial to upgrade anti-cancer efficiency of ferroptosis drug system. At present, optimizing the sensitizer for ferroptosis with expected mechanism and improved transport via facile nanocarriers still heavily rely on serendipitous discovery and repetitious assignment. Herein, we employ the tannic acid (TA)-templated silicon nanoparticle as nanocore to descend the lysosome-controlled disintegratable Fe3+@erastin@rapamycin micelles (REFSM) to identify rapamycin as a ferroptosis sensitizer through autophagy-dependent/independent pathways. The as-prepared REFSM dissociates responding to the acidic condition and enzyme system of lysosomes, permitting Fe3+ and erastin release to irritate ferroptosis, which is reinforced by released rapamycin via irritating ferritinophagy and lipophagy, and suppressing HIF-1α. The rapamycin-reinforced ferroptosis is demonstrated to be specific to H2O2-overloaded cancer cells. Moreover, the introduction of rapamycin reduces the positive charge of micelle and improves its distribution in tumors. Both the controllable dissociation and the improved charge of REFSM ensure its anti-cancer efficiency at trace amount of erastin (0.3 mg kg−1) and rapamycin (2.2 mg kg−1) and minimize the systematic toxicity. This archetypical template provides a versatile platform for rapamycin as sensitizer to enhance ferroptosis by displaying its multiple pharmacological mechanism, controlling its release and improving its distribution in vivo.},
	annote = {no-access},
	author = {Renting Jiang and Xin Li and Dun Hu and Min Zhu and Di Zhou and Mengying Yuan and Xin Hu and Shengdan Nie and Jiajia Liu and Haoyue Xiang and Hua Yang and Yi Zhang and Shan Wang},
	date-added = {2021-06-01 11:39:42 -0400},
	date-modified = {2021-06-01 11:39:47 -0400},
	doi = {https://doi.org/10.1016/j.apmt.2021.101066},
	issn = {2352-9407},
	journal = {Applied Materials Today},
	keywords = {Micelle, Ferroptosis, Ferric ions, Rapamycin, Autophagy},
	pages = {101066},
	title = {Rapamycin-reinforced ferroptosis assisted by a lysosome-controlled disintegratable micelle in autophagy-dependent/independent manners},
	url = {https://www.sciencedirect.com/science/article/pii/S2352940721001311},
	volume = {23},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S2352940721001311},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.apmt.2021.101066}}

@article{JOSHI2021121066,
	abstract = {In the ultra-high resolution mass spectrometric analysis of processed petroleums (fossil materials), we observed species with ultra-low hydrogen content (e.g. H/C ratio from 0.1 to 0.4). Some of the observed chemical formula (C20-40H10) can be rationalized by the known corannulene-based peri-condensed Polycyclic Aromatic Hydrocarbons (PAHs). Other formulas (such as C20-40H8, C20-40H6 and C20-40H4) cannot be rationalized with any known structures. We proposed highly curved non-planar PAHs involving multiple connected five member aromatic rings. These structures do not obey the isolated pentagon rule (IPR). The stabilities of the proposed structures were evaluated by density functional theory. Strain energies were calculated based on hypothetical isodesmic conversion of planar structures to the curved non-planar structures. Results showed that the strain energies of the proposed structures are lower than that of fullerenes of the same carbon number, confirming stabilities of the non-IPR structures. The low hydrogen content species are likely formed in the thermal and/or catalytic cracking of the petroleums. They are possible intermediate molecules on the path toward the formation of fullerenes (buckyballs) and other nano-carbon materials},
	annote = {no-calc},
	author = {Yogesh V. Joshi and Anthony S. Mennito and Stephen H. Brown and Kuangnan Qian},
	date-added = {2021-06-01 11:39:10 -0400},
	date-modified = {2021-06-01 11:39:14 -0400},
	doi = {https://doi.org/10.1016/j.fuel.2021.121066},
	issn = {0016-2361},
	journal = {Fuel},
	pages = {121066},
	title = {Ultra-low hydrogen content bowl-shaped polycyclic aromatic hydrocarbons in petroleum},
	url = {https://www.sciencedirect.com/science/article/pii/S0016236121009455},
	volume = {301},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0016236121009455},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.fuel.2021.121066}}

@article{Lafuente:2021wj,
	annote = {cite-code},
	author = {Lafuente, Marta and De Marchi, Sarah and Urbiztondo, Miguel and Pastoriza-Santos, Isabel and P{\'e}rez-Juste, Ignacio and Santamar{\'\i}a, Jes{\'u}s and Mallada, Reyes and Pina, Mar{\'\i}a},
	booktitle = {ACS Sensors},
	da = {2021/05/27},
	date = {2021/05/27},
	date-added = {2021-06-01 11:35:39 -0400},
	date-modified = {2021-06-01 11:35:48 -0400},
	doi = {10.1021/acssensors.1c00178},
	journal = {ACS Sensors},
	journal1 = {ACS Sens.},
	m3 = {doi: 10.1021/acssensors.1c00178},
	month = {05},
	publisher = {American Chemical Society},
	title = {Plasmonic MOF Thin Films with Raman Internal Standard for Fast and Ultrasensitive SERS Detection of Chemical Warfare Agents in Ambient Air},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acssensors.1c00178},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acssensors.1c00178}}

@article{Bargavi:ef3014,
	abstract = {Three isatin derivatives, namely, 1-allyl-3-hy{\-}droxy-3-(6-oxo{\-}cyclo{\-}hex-1-en-1-yl)indolin-2-one, C${\sb 17}$H${\sb 17}$NO${\sb 3}$, 1-ethyl-3-hy{\-}droxy-3-(6-oxo{\-}cyclo{\-}hex-1-en-1-yl)indolin-2-one, C${\sb 16}$H${\sb 17}$NO${\sb 3}$, and 5-bromo-3-hy{\-}droxy-1-methyl-3-(6-oxo{\-}cyclo{\-}hex-1-en-1-yl)indolin-2-one, C${\sb 15}$H${\sb 14}$BrNO${\sb 3}$, were synthesized, crystallized by the slow-evaporation technique, characterized by ${\sp 1}$H and ${\sp 13}$C NMR spectroscopy, and analysed by the single-crystal X-ray diffraction (XRD) method. Quantum chemical parameters, such as the energy of the highest occupied mol{\-}ecular orbital, energy of the lowest unoccupied mol{\-}ecular orbital, energy gap, electronic energy, ionization potential, chemical potential, global hardness, global softness and electrophilicity index, were calculated. The druglikeness and bioactivity scores of the com{\-}pounds were calculated. The activities of these isatin derivatives against bacterial strains, such as {\it Eschericia coli}, {\it Proteus vulgaris}, {\it Shigella flexneri}, {\it Staphylococcus aureus} and {\it Micrococcus luteus}, and the fungal strain {\it Aspergillus niger}, were determined using the well-diffusion assay method. Mol{\-}ecular docking studies were carried out to predict the binding mode of the isatin com{\-}pounds with the penicillin binding protein enzyme and to identify the inter{\-}actions between the enzyme and the ligands under study.},
	annote = {cite-code},
	author = {Bargavi, Srinivasan and Gouthaman, Siddan and Sugunalakshmi, Madurai and Lakshmi, Srinivasakannan},
	date-added = {2021-06-01 11:31:33 -0400},
	date-modified = {2021-06-01 11:33:04 -0400},
	doi = {10.1107/S2053229621004940},
	journal = {Acta Crystallographica Section C},
	keywords = {isatin derivatives, spectroscopy, crystal structure, quantum chemical calculations, druglikeness, bioactivity score, antimicrobial, molecular docking},
	month = {Jun},
	number = {6},
	pages = {299--311},
	title = {{Synthesis, spectroscopic investigation, crystal structure analysis, quantum chemical study, biological activity and mol{\-}ecular docking of three isatin derivatives}},
	url = {https://doi.org/10.1107/S2053229621004940},
	volume = {77},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1107/S2053229621004940}}

@article{no-bib5,
	annote = {cite-code},
	author = {Anil Kumar Soni1 and Gajendra Pal Singh and Vishnu Kumar Sahu},
	date-added = {2021-06-01 11:25:26 -0400},
	date-modified = {2021-06-01 11:26:45 -0400},
	doi = {10.4236/ojapps.2021.115041},
	journal = {Open Journal of Applied Sciences},
	title = {Prediction of Antagonistic Activity of β-Carboline and Its Derivatives Using Topological Descriptors},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.4236/ojapps.2021.115041}}

@article{SANTOS2021130171,
	abstract = {The present work aims to develop electroanalytical strategies for separating and quantifying one of the most important biothiols, the reduced glutathione (GSH), based on developing and applying a new and selective magnetic molecular imprinted polymer (mag-MIP). This magnetic-supported polymer was synthesized by precipitation, using GSH as a template, having acrylamide as the functional monomer and trimethylolpropane trimethacrylate as a cross-linking agent. These materials' morphological and physical characteristics were investigated by scanning electron microscope, Fourier transform infrared, and vibrating sample magnetometry. Physicochemical parameters, such as adsorption capacity, were obtained and compared with the respective mag-NIP, which are control polymers without the selective cavity. After all characterizations, mag-MIP and mag-NIP were evaluated on magnetic graphite-epoxy composite (m-GEC) electrodes. The characteristics of the obtained sensors were investigated by cyclic voltammetry and differential pulse voltammetry. After optimizing experimental and operational conditions, a linear response for the concentration of GSH, in the range of 1 to 1400 μmol/L, with low detection and quantification limits of 7 and 20 nmol/L, respectively, were obtained. The GSH levels in mice liver samples were measured by electrochemical and spectrophotometric techniques to compare the method's effectiveness. A high correlation between them and a low relative error of 1.06% were obtained, indicating the good functionality of the proposed sensor.},
	annote = {no-access},
	author = {Ana Caroline Ferreira Santos and Orlando R.P. {de Ara{\'u}jo} and Fabiana A. Moura and Sabir Khan and Auro A. Tanaka and Ant{\^o}nio Euz{\'e}bio G. Santana and Maria Isabel Pividori and Maria del Pilar Taboada-Sotomayor and Mar{\'\i}lia O.F. Goulart},
	date-added = {2021-05-29 16:52:00 -0400},
	date-modified = {2021-05-29 16:52:06 -0400},
	doi = {https://doi.org/10.1016/j.snb.2021.130171},
	issn = {0925-4005},
	journal = {Sensors and Actuators B: Chemical},
	keywords = {Biothiols, magnetic molecular imprinted polymer, electrochemical sensor, electroanalysis, liver tissue},
	pages = {130171},
	title = {Development of magnetic nanoparticles modified with new molecularly imprinted polymer (MIPs) for selective analysis of glutathione},
	url = {https://www.sciencedirect.com/science/article/pii/S0925400521007401},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0925400521007401},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.snb.2021.130171}}

@article{UPPULADINNE2021107945,
	abstract = {In the present study, five novel LNA based antisense modifications have been proposed. A conformational search was carried out using TANGO, followed by geometry optimization using MOPAC. Based on their electronic energies the most stable conformation for each modification was identified. Further, DFT based full geometry optimization on the most stable conformations at the gas phase B3LYP/631-G(d,p) using Gaussin03 and single point energy calculations on the optimized structures at the solvent phase B3LYP/6-311G(d,p) level of theory were done to derive their quantum chemical descriptors using the Gaussian09. A comparison of global reactivity descriptors confirmed that the LNA based modifications were the most reactive. Base-pair stability was recorded by observing the binding energies and base-pairing conformations of modified GC base pairs at the B3LYP/6-311G(d,p) level of theory. Molecular dynamics simulations have been performed at the oligomer duplex level by incorporating individual modifications on 20-mer RNA-RNA duplexes using AMBER16. Free energy calculations of duplex structures suggested that incorporation of A2 modification into the RNA-RNA duplex increased the duplex binding affinity similar to LNA. Whereas, the A3 modification showed less binding compared to LNA but improved binding compared to MOE. This computational approach using quantum chemical methods may be very useful to propose better modifications than the existing ones before performing the experiments in the area of antisense technology.},
	annote = {no-access},
	author = {Mallikarjunachari V.N. Uppuladinne and Dikshita Dowerah and Uddhavesh B. Sonavane and Suvendra Kumar Ray and Ramesh C. Deka and Rajendra R. Joshi},
	date-added = {2021-05-29 16:51:36 -0400},
	date-modified = {2021-05-29 16:51:42 -0400},
	doi = {https://doi.org/10.1016/j.jmgm.2021.107945},
	issn = {1093-3263},
	journal = {Journal of Molecular Graphics and Modelling},
	keywords = {Antisense modifications, LNA, conformational search, TANGO, Quantum Calculations, DFT, global descriptors, MD Simulations},
	pages = {107945},
	title = {Structural Insight into Locked Nucleic Acid based Novel Antisense Modifications: A DFT calculations at monomer and MD simulations at oligomer level},
	url = {https://www.sciencedirect.com/science/article/pii/S1093326321001169},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S1093326321001169},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.jmgm.2021.107945}}

@article{BALACHANDRAN2021,
	abstract = {Mosquitoes are medically important insects worldwide. They serve as a primary vector for transmitting several major diseases like dengue and chikungunya, chiefly spread through Aedes aegypti, a prominent mosquito vector. The present study focused on evaluating the inhibitory effect of natural alkaloids on the acetylcholinesterase present in Ae. aegypti using molecular docking studies. A total of 25 different alkaloids were selected as ligands and their docking ability with an Acetylcholinesterase 1 (AChE1) recept or found in Ae. aegypti was performed by AutoDock. Results indicated that alpha-solanine had the best fit into the AChE1 binding pocket with a minimum binding energy of -8.13 kJ/mol. Among the different alkaloids tested, it is suggested that alpha-solanine would serve as the best inhibitor of AChE1 in Ae. aegypti.},
	annote = {no-access},
	author = {Chellapandian Balachandran and Sankarappan Anbalagan and Chithan Kandeepan and Natarajan {Arun Nagendran} and Manickkam Jayakumar and Elsayed {Fathi Abd_Allah} and Abdulaziz A. Alqarawi and Abeer Hashem and Kathirvelu Baskar},
	date-added = {2021-05-29 16:50:38 -0400},
	date-modified = {2021-05-29 16:50:43 -0400},
	doi = {https://doi.org/10.1016/j.aspen.2021.05.011},
	issn = {1226-8615},
	journal = {Journal of Asia-Pacific Entomology},
	keywords = {Vector Mosquito, Natural polymers, , Acetylcholinesterase},
	title = {Molecular Docking Studies of Natural Alkaloids as Acetylcholinesterase (AChE1) Inhibitors in Aedes aegypti},
	url = {https://www.sciencedirect.com/science/article/pii/S122686152100073X},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S122686152100073X},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.aspen.2021.05.011}}

@article{Vajaravel:2021wf,
	annote = {no-access},
	author = {Vajaravel, Manikandan and Karuppannan, Srinivasan},
	booktitle = {Crystal Research and Technology},
	da = {2021/05/25},
	date = {2021/05/25},
	date-added = {2021-05-29 16:49:37 -0400},
	date-modified = {2021-05-29 16:49:47 -0400},
	doi = {https://doi.org/10.1002/crat.202000223},
	isbn = {0232-1300},
	journal = {Crystal Research and Technology},
	journal1 = {Crystal Research and Technology},
	journal2 = {Crystal Research and Technology},
	keywords = {attachment energy; cocrystals; Hirshfeld surfaces; hydrogen bonds; phase transition; single crystal X-ray diffraction},
	m3 = {https://doi.org/10.1002/crat.202000223},
	month = {2021/05/29},
	n2 = {Abstract A new cocrystal comprising two pharmaceutically important molecules methyl-4-hydroxybenzoate (p-MHB) (C8H8O3) and carbonyl diamide (urea) {$[$}CO(NH2)2{$]$} is crystallized together for the first time through restricted solvent evaporation method at ambient conditions. The single crystal X-ray diffraction analysis shows that the engineered cocrystal p-MHB:urea (1:1) (C9H12N2O4) crystallizes in monoclinic system with centrosymmetric space group C12/c1. The internal structure analysis shows that the urea molecule with its unique ability forms hydrogen bonding network throughout the cocrystal system. Different orientations of the identified synthons form the networks via supramolecular connections such as C═O?H─O and C═O?N─H. Correlation between the internal molecular configurations in the unit cell, protruding molecular groups on different growth faces, and attachment energies of different crystal planes is studied. The Hirshfeld surface analysis shows that the higher percentage of overall interactions between the carbon and oxygen atoms at the outer surfaces of the cocrystal induces further incorporation of molecular aggregation and crystal growth. The 2D finger print plots infer that about 90.9{\%} of the overall interactions are mainly due to the H bonds. Differential scanning calorimetry analysis reveals that the grown cocrystal undergoes an observable phase transition at 105.65 $\,^{\circ}$C prior to its melting endotherm that peaks at 110.29 $\,^{\circ}$C.},
	number = {n/a},
	pages = {2000223},
	publisher = {John Wiley \& Sons, Ltd},
	title = {Formation of a New Cocrystal Methyl-4-hydroxybenzoate:Urea and Its Structural and Thermal Properties},
	ty = {JOUR},
	url = {https://doi.org/10.1002/crat.202000223},
	volume = {n/a},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1002/crat.202000223}}

@article{YANEZ2021111764,
	abstract = {Cocoa beans contain antioxidant molecules with the potential to inhibit type 2 coronavirus (SARS-CoV-2), which causes a severe acute respiratory syndrome (COVID-19). In particular, protease. Therefore, using in silico tests, 30 molecules obtained from cocoa were evaluated. Using molecular docking and quantum mechanics calculations, the chemical properties and binding efficiency of each ligand was evaluated, which allowed the selection of 5 compounds of this series. The ability of amentoflavone, isorhoifolin, nicotiflorin, naringin and rutin to bind to the main viral protease was studied by means of free energy calculations and structural analysis performed from molecular dynamics simulations of the enzyme/inhibitor complex. Isorhoifolin and rutin stand out, presenting a more negative binding ΔG than the reference inhibitor N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-l-valyl-N~1~-((1R,2Z)−4-(benzyloxy)−4-oxo-1-{[(3R)−2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide (N3). These results are consistent with high affinities of these molecules for the major SARS-CoV-2. The results presented in this paper are a solid starting point for future in vitro and in vivo experiments aiming to validate these molecules and /or test similar substances as inhibitors of SARS-CoV-2 protease.},
	annote = {cite-code, cite-model},
	author = {Osvaldo Ya{\~n}ez and Manuel Isa{\'\i}as Osorio and Carlos Areche and Alejandro Vasquez-Espinal and Jessica Bravo and Ang{\'e}lica Sandoval-Aldana and Jos{\'e} M. P{\'e}rez-Donoso and Fernando Gonz{\'a}lez-Nilo and Maria Jo{\~a}o Matos and Edison Osorio and Olimpo Garc{\'\i}a-Beltr{\'a}n and William Tiznado},
	date-added = {2021-05-26 23:51:17 -0400},
	date-modified = {2021-05-26 23:51:50 -0400},
	doi = {https://doi.org/10.1016/j.biopha.2021.111764},
	issn = {0753-3322},
	journal = {Biomedicine & Pharmacotherapy},
	keywords = {, Antioxidant, Bioflavonoids, SARS-CoV-2, Molecular dynamics, DFT},
	pages = {111764},
	title = {Theobroma cacao L. compounds: Theoretical study and molecular modeling as inhibitors of main SARS-CoV-2 protease},
	url = {https://www.sciencedirect.com/science/article/pii/S0753332221005461},
	volume = {140},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0753332221005461},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.biopha.2021.111764}}

@article{SHUI2021104957,
	abstract = {The present study aimed to assess the impact of sodium new houttuyfonate (SNH) on growth and biofilm formation of Streptococcus mutans, and the combinatorial effects of SNH with cariostatic agents. The effects of SNH on S. mutans planktonic cultures were assessed by growth curve assay. The effects of SNH on S. mutans biofilm and extracellular polysaccharides (EPS) production were observed via crystal violet (CV) assay, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay, colony-forming unit (CFU) counting assay, scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Quantitative real-time polymerase chain reaction (qPCR) was applied to investigate the regulatory effects of SNH on the expression of virulence genes of S. mutans. Checkerboard microdilution assay was performed to investigate the combinatorial effects of SNH with two common cariostatic agents. SNH acted as an inhibitor on planktonic cell growth, biofilm formation and EPS production of S. mutans. SNH also downregulated the expression of gtfBCD and comDE systems and exhibited synergism with chlorhexidine (CHX). In conclusion, this study indicated a possibility for SNH to become an anticaries agents by its antimicrobial activity and synergistic effects with CHX against S. mutans.},
	annote = {no-access},
	author = {Yusen Shui and Qingsong Jiang and Xiaoying Lyu and Liang Wang and Yongwang lin and Qizhao Ma and Tao Gong and Jumei Zeng and Ran Yang and Yuqing Li},
	date-added = {2021-05-25 22:25:32 -0400},
	date-modified = {2021-05-25 22:25:45 -0400},
	doi = {https://doi.org/10.1016/j.micpath.2021.104957},
	issn = {0882-4010},
	journal = {Microbial Pathogenesis},
	keywords = {Antimicrobial, Antibiofilm, Natural compound, Sodium new houttuyfonate,},
	pages = {104957},
	title = {Inhibitory effects of sodium new houttuyfonate on growth and biofilm formation of Streptococcus mutans},
	url = {https://www.sciencedirect.com/science/article/pii/S0882401021002291},
	volume = {157},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0882401021002291},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.micpath.2021.104957}}

@article{https://doi.org/10.1002/minf.202100028,
	abstract = {Abstract The COVID-19 pandemic caused by the SARS-CoV-2 has mobilized scientific attention in search of a treatment. The cysteine-proteases, main protease (Mpro) and papain-like protease (PLpro) are important targets for antiviral drugs. In this work, we simulate the interactions between the Mpro and PLpro with Ebselen, its metabolites and derivatives with the aim of finding molecules that can potentially inhibit these enzymes. The docking data demonstrate that there are two main interactions between the thiol (−SH) group of Cys (from the protease active sites) and the electrophilic centers of the organoselenium molecules, i. e. the interaction with the carbonyl group (O=C{\ldots}SH) and the interaction with the Se moiety (Se{\ldots}SH). Both interactions may lead to an adduct formation and enzyme inhibition. Density Functional Theory (DFT) calculations with Ebselen indicate that the energetics of the thiol nucleophilic attack is more favorable on Se than on the carbonyl group, which is in accordance with experimental data (Jin et al. Nature, 2020, 582, 289--293). Therefore, organoselenium molecules should be further explored as inhibitors of the SARS-CoV-2 proteases. Furthermore, we suggest that some metabolites of Ebselen (e. g. Ebselen diselenide and methylebselenoxide) and derivatives ethaselen and ebsulfur should be tested in vitro as inhibitors of virus replication and its proteases.},
	annote = {cite-model, cite-code},
	author = {Nogara, Pablo Andrei and Omage, Folorunsho Bright and Bolzan, Gustavo Roni and Delgado, C{\'a}ssia Pereira and Aschner, Michael and Orian, Laura and Teixeira Rocha, Jo{\~a}o Batista},
	date-added = {2021-05-25 22:24:48 -0400},
	date-modified = {2021-05-25 22:24:59 -0400},
	doi = {https://doi.org/10.1002/minf.202100028},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/minf.202100028},
	journal = {Molecular Informatics},
	keywords = {COVID-19, protease, organoselenium, docking, DFT},
	number = {n/a},
	title = {In silico Studies on the Interaction Between Mpro and PLpro From SARS-CoV-2 and Ebselen, its Metabolites and Derivatives},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/minf.202100028},
	volume = {n/a},
	year = {2021},
	Bdsk-Url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/minf.202100028},
	Bdsk-Url-2 = {https://doi.org/10.1002/minf.202100028}}

@article{doi:10.1246/cl.210272,
	abstract = { It was found that D-π-A pyrazinium dye exhibits a specific solvatochromism in halogenated solvents: the ICT-based photoabsorption bands of D-π-A pyrazinium dye in halogenated solvents appears at a wavelength longer than those of non-halogenated solvents. The influences of halogenated and non-halogenated solvents on the ICT-based photoabsorption band of D-π-A pyrazinium dye were investigated based on 1H NMR measurements as well as semi-empirical molecular calculations. Herein we propose that the specific solvatochromism of dyes in halogenated solvents is termed organohalogenochromism (OHC). },
	annote = {no-access},
	author = {Higashino, Taiki and Ooyama, Yousuke},
	date-added = {2021-05-25 22:23:31 -0400},
	date-modified = {2021-05-25 22:23:57 -0400},
	doi = {10.1246/cl.210272},
	eprint = {https://doi.org/10.1246/cl.210272},
	journal = {Chemistry Letters},
	number = {0},
	pages = {null},
	title = {Organohalogenochromism (OHC) of Dyes: D-π-A Pyrazinium Dye},
	url = {https://doi.org/10.1246/cl.210272},
	volume = {0},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1246/cl.210272}}

@article{Yang:2021ts,
	annote = {qsar, no-access},
	author = {Yang, Bo and Si, Hongzong and Zhai, Honglin},
	date = {2021-04-01T00:00:00///},
	date-added = {2021-05-25 22:20:19 -0400},
	date-modified = {2021-05-25 22:20:26 -0400},
	journal = {Letters in Drug Design \& Discovery},
	keywords = {gene expression programming; Human african trypanosomiasis; IC50; heuristic method; antitrypanosomal agent; quantitative structure-activity relationship},
	m3 = {doi:10.2174/1570180817999201102200015},
	n2 = {Background: Trypanosomiasis is a widespread zoonotic disease and the existing drugs are not enough to prevent and treat it. <br></br> Objective: This study aimed to build a quantitative structure-activity relationship model by the chemical structures of a class of thiazolidone/thiazolidamide based hybrids. The model was used to screen new antitrypanosomal agents and predict the properties of composite molecules. <br></br> Methods: All compounds were randomly divided into a training set and a test set. A large number of descriptors were calculated by the software, then some of the best descriptors were selected to build the models. The linear model was built by the heuristic method and the nonlinear model was built by gene expression programming method. <br></br> Results: In the heuristic method, the correlation coefficients ,<i>R</i><sup>2</sup>, <i>R</i><sup>2</sup><sub>cv</sub>, <i>F</i> and <i>S</i><sup>2</sup> were 0.581, 0.457, 14.053 and 15.311, respectively. In gene expression programming, the R<sup>2</sup> and S<sup>2</sup> were 0.715, 10.997 in the training set and 0.617, 22.778 in the test set. The results showed that the relative number of S atoms and the minimum bond order of an H atom had a significant positive contribution to IC50. Meanwhile, the relative number of double bonds and the count of hydrogen-bonding acceptor sites had a great negative impact on IC<sub>50</sub>. <br></br> Conclusion: Both the heuristic method and gene expression programming had a good predictive performance. By contrast, the gene expression programming method fitted well with the experimental values and it was expected to be beneficial in the synthesis of new antitrypanosomal drugs.},
	number = {4},
	pages = {406--415},
	title = {QSAR Studies on the IC50 of a Class of Thiazolidinone/Thiazolide Based Hybrids as Antitrypanosomal Agents},
	ty = {ABST},
	url = {https://www.ingentaconnect.com/content/ben/lddd/2021/00000018/00000004/art00011},
	url1 = {https://doi.org/10.2174/1570180817999201102200015},
	volume = {18},
	year = {2021-04-01T00:00:00},
	Bdsk-Url-1 = {https://www.ingentaconnect.com/content/ben/lddd/2021/00000018/00000004/art00011}}

@inproceedings{no-bib4,
	author = {Eloi Alves da Silva Filho and Fabr{\'\i}cio Uliana and Arlan da Silva Gon{\c c}alves},
	booktitle = {Paraffin - Thermal Energy Storage Applications},
	date-added = {2021-05-25 22:10:00 -0400},
	date-modified = {2021-05-25 22:11:08 -0400},
	doi = {10.5772/intechopen.96906},
	title = {News Aspects Theoric and Experimental to Paraffins Compounds},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.5772/intechopen.96906}}

@article{NGOHANNA2021e07032,
	abstract = {A quantitative structure-activity relationship (QSAR) study was conducted using nineteen previously synthesized, and tested 1-aryl-6-hydroxy-1,2,3,4-tetrahydroisoquinolines with proven in vitro activities against Plasmodium falciparum. In order to computationally design and screen potent antimalarial agents, these compounds with known biological activity ranging from 0.697 to 35.978 μM were geometry optimized at the B3LYP/6-311 + G(d,p) level of theory, using the Gaussian 09W software. To calculate the topological differences, the series of the nineteen compounds was superimposed and a hypermolecule obtained with s¯ = 17 and 20 vertices. Other molecular descriptors were considered in order to build a highly predictive QSAR model. These include the minimal topological differences (MTD), LogP, two dimensional polarity surface area (TDPSA), dipole moment (μ), chemical hardness (η), electrophilicity (ω), potential energy (Ep), electrostatic energy (Eele) and number of rotatable bonds (NRB). By using a training set composed of 15 randomly selected compounds from this series, several QSAR equations were derived. The QSAR equations obtained were then used to attempt to predict the IC50 values of 4 remaining compounds in a test (or validation) set. Ten analogues were proposed by a fragment search of a fragment library containing the pharmacophore model of the active compounds contained in the training set. The most active proposed analogue showed a predicted activity within the lower micromolar range.},
	annote = {gui=moe},
	author = {Joelleinsert {Ngo Hanna} and Vincent de Paul N. Nziko and Fidele Ntie-Kang and James A. Mbah and Flavien A.A. Toze},
	date-added = {2021-05-25 22:07:37 -0400},
	date-modified = {2021-05-25 22:07:50 -0400},
	doi = {https://doi.org/10.1016/j.heliyon.2021.e07032},
	issn = {2405-8440},
	journal = {Heliyon},
	keywords = {Gaussian 09W, design, Malaria, , QSAR, Screening},
	number = {5},
	pages = {e07032},
	title = {The use of minimal topological differences to inspire the design of novel tetrahydroisoquinoline analogues with antimalarial activity},
	url = {https://www.sciencedirect.com/science/article/pii/S240584402101135X},
	volume = {7},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S240584402101135X},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.heliyon.2021.e07032}}

@article{Wang:2021ws,
	abstract = {Application of multi-scale modelling workflows to characterise polymorphism in ritonavir with regard to its stability, bioavailability and processing.},
	author = {Wang, Chang and Rosbottom, Ian and Turner, Thomas D. and Laing, Sydney and Maloney, Andrew G. P. and Sheikh, Ahmad Y. and Docherty, Robert and Yin, Qiuxiang and Roberts, Kevin J.},
	da = {2021/05/19},
	date-added = {2021-05-25 22:06:40 -0400},
	date-modified = {2021-05-25 22:06:40 -0400},
	doi = {10.1007/s11095-021-03048-2},
	id = {Wang2021},
	isbn = {1573-904X},
	journal = {Pharmaceutical Research},
	title = {Molecular, Solid-State and Surface Structures of the Conformational Polymorphic Forms of Ritonavir in Relation to their Physicochemical Properties},
	ty = {JOUR},
	url = {https://doi.org/10.1007/s11095-021-03048-2},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1007/s11095-021-03048-2}}

@inproceedings{no-bib3,
	annote = {cite-code, cite-model},
	author = {Taft, C.A. and Canchaya, J.G.S. and dos Santos, J.D. and Silva, J.C.F.},
	booktitle = {Functional Properties of Advanced Engineering Materials and Biomolecules},
	date-added = {2021-05-21 16:58:38 -0400},
	date-modified = {2021-05-21 17:00:44 -0400},
	doi = {10.1007/978-3-030-62226-8_2},
	title = {Review: Simulation Models for Materials and Biomolecules},
	year = {2021},
	Bdsk-File-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxArLi4vLi4vLi4vLi4vRG93bmxvYWRzL1MwMTY3NzMyMjIxMDE3OTJYLmJpYk8RAWoAAAAAAWoAAgAADU1hY2hpbnRvc2ggSEQAAAAAAAAAAAAAAAAAAAAAAABCRAAB/////xVTMDE2NzczMjIyMTAxNzkyWC5iaWIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAD/////AAAAAAAAAAAAAAAAAAQAAgAACiBjdQAAAAAAAAAAAAAAAAAJRG93bmxvYWRzAAACADAvOlVzZXJzOmplbW91c3NhOkRvd25sb2FkczpTMDE2NzczMjIyMTAxNzkyWC5iaWIADgAsABUAUwAwADEANgA3ADcAMwAyADIAMgAxADAAMQA3ADkAMgBYAC4AYgBpAGIADwAcAA0ATQBhAGMAaABpAG4AdABvAHMAaAAgAEgARAASAC5Vc2Vycy9qZW1vdXNzYS9Eb3dubG9hZHMvUzAxNjc3MzIyMjEwMTc5MlguYmliABMAAS8AABUAAgAP//8AAAAIAA0AGgAkAFIAAAAAAAACAQAAAAAAAAAFAAAAAAAAAAAAAAAAAAABwA==},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-030-62226-8_2}}

@article{Borges:2021ub,
	annote = {cite-code},
	author = {Borges, Ricardo M. and Colby, Sean M. and Das, Susanta and Edison, Arthur S. and Fiehn, Oliver and Kind, Tobias and Lee, Jesi and Merrill, Amy T. and Merz, Kenneth M. and Metz, Thomas O. and Nunez, Jamie R. and Tantillo, Dean J. and Wang, Lee-Ping and Wang, Shunyang and Renslow, Ryan S.},
	booktitle = {Chemical Reviews},
	da = {2021/05/12},
	date = {2021/05/12},
	date-added = {2021-05-18 12:14:30 -0400},
	date-modified = {2021-05-18 12:14:36 -0400},
	doi = {10.1021/acs.chemrev.0c00901},
	isbn = {0009-2665},
	journal = {Chemical Reviews},
	journal1 = {Chem. Rev.},
	m3 = {doi: 10.1021/acs.chemrev.0c00901},
	month = {05},
	publisher = {American Chemical Society},
	title = {Quantum Chemistry Calculations for Metabolomics},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acs.chemrev.0c00901},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acs.chemrev.0c00901}}

@article{TUROV2021126844,
	abstract = {It has been assumed that nanoparticle/aggregate/agglomerate structure, texture and surface characteristics of hydrophobic nanosilica AM1 treated with certain amounts of arginine and water may provide better conditions for methane adsorption compared to AM1 alone. Nanosilica and composites are characterized using adsorption, desorption, microscopic, spectroscopic, XRD, SAXS, and quantum chemistry methods. The 1H NMR spectroscopy (at 200-283K) and cryoporometry (T < 273K) methods have been applied to AM1/arginine differently wetted and mechanically treated. The wetted blends have been studied in the methane atmosphere without or with addition of chloroform-d. In mechanically treated wetted blends, arginine (initially crystalline) is nanostructured and amorphous. In the powders wetted at 0.1-0.5 grams of water per gram of dry solids, interaction energy of unfrozen water with nanoparticles depends nonmonotonically on the degree of hydration. The value of the free surface energy is maximal at the hydration of 0.3g/g. Bound water, which partially fills interparticle voids and may remain liquid or forms amorphous ice nanoparticles at lower temperatures, provides enhanced nanoporosity in wetted composites. This is appropriate for the methane adsorption up to 7.3-4.9wt.% at 199-283K.},
	annote = {no-access},
	author = {Vladimir V. Turov and Vladimir M. Gun'ko and Tetyana V. Krupska and Mykola V. Borysenko and Magdalina D. Tsapko and Nataliia V. Guzenko and Mykola T. Kartel},
	date-added = {2021-05-18 12:11:55 -0400},
	date-modified = {2021-05-18 12:12:03 -0400},
	doi = {https://doi.org/10.1016/j.colsurfa.2021.126844},
	issn = {0927-7757},
	journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
	keywords = {Hydrophobic nanosilica, Immobilized arginine, Hydrophobic nanosilica/arginine composite, Bound water, Methane adsorption, Confined space effects},
	pages = {126844},
	title = {Temperature (200-283 K) dependence of methane adsorption onto hydrophobic nanosilica/arginine composite at various hydration},
	url = {https://www.sciencedirect.com/science/article/pii/S0927775721007135},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0927775721007135},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.colsurfa.2021.126844}}

@article{LAMANNA2021113547,
	abstract = {Herein we investigated the structural and cellular effects ensuing from the cyclization of a potent inhibitor of JAK2 as mimetic of SOCS1 protein, named PS5. The introduction of un-natural residues and a lactam internal bridge, within SOCS1-KIR motif, produced candidates that showed high affinity toward JAK2 catalytic domain. By combining CD, NMR and computational studies, we obtained valuable models of the interactions of two peptidomimetics of SOCS1 to deepen their functional behaviors. Notably, when assayed for their biological cell responses mimicking SOCS1 activity, the internal cyclic PS5 analogues demonstrated able to inhibit JAK-mediated tyrosine phosphorylation of STAT1 and to reduce cytokine-induced proinflammatory gene expression, oxidative stress generation and cell migration. The present study well inserts in the field of low-molecular-weight proteomimetics with improved longtime cellular effects and adds a new piece to the puzzled way for the conversion of bioactive peptides into drugs.},
	annote = {no-access},
	author = {Sara {La Manna} and Laura Lopez-Sanz and Susana Bernal and Sara Fortuna and Flavia A. Mercurio and Marilisa Leone and Carmen Gomez-Guerrero and Daniela Marasco},
	date-added = {2021-05-18 12:09:19 -0400},
	date-modified = {2021-05-18 12:09:24 -0400},
	doi = {https://doi.org/10.1016/j.ejmech.2021.113547},
	issn = {0223-5234},
	journal = {European Journal of Medicinal Chemistry},
	keywords = {Mimetic peptides, Cytokine signaling, JAK/STAT, SOCS1, Oxidative stress, Inflammation},
	pages = {113547},
	title = {Cyclic mimetics of Kinase-Inhibitory Region of Suppressors of Cytokine Signaling 1: progress toward novel anti-inflammatory therapeutics},
	url = {https://www.sciencedirect.com/science/article/pii/S0223523421003962},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0223523421003962},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.ejmech.2021.113547}}

@article{LIU2021117200,
	abstract = {As the ubiquitous active components in aquatic environment, low molecular weight organic acids (LMWOAs) have great influence on the environmental behaviors of contaminants. This research was focused on the effect of different LMWOAs including 11 aliphatic acids and 7 aromatic acids on the photodegradation kinetics of tetracycline (TC), and the development of quantitative structure-activity relationship (QSAR) model. Results showed that TC photodegradation in the presence of LMWOAs fitted pseudo-first-order photolysis kinetics, and the observed photolysis rate constant (kobs) varied from 0.077 to 0.331 h-1. The QSAR model was developed by partial-least-squares (PLS) with using a sequential approach with 25 theoretical molecular descriptors. Four descriptors including ELUMO-EHOMO, ELUMO, CCR and Qmax were found to mechanistically and statistically affect kobs, and the standardized QSAR model was: The high cross validated regression coefficient (Qcum2, 0.898) and high correlation coefficient (R2, 0.908) indicated significantly goodness-of-fit and high robustness of the model. The predicted and observed values with high agreement in the defined applicability domain featured accuracy and feasibility of model. This work provided a robust predictive method for estimating the TC photodegradation in the presence of different structure LMWOAs.},
	annote = {no-access},
	author = {Fei Liu and Fang Liu and Xiao Qian and Xianjian Zhu and Yansha Lou and Xinhui Liu and Baoshan Cui and Junhong Bai},
	date-added = {2021-05-18 11:54:41 -0400},
	date-modified = {2021-05-18 11:54:45 -0400},
	doi = {https://doi.org/10.1016/j.envpol.2021.117200},
	issn = {0269-7491},
	journal = {Environmental Pollution},
	keywords = {Photodegradation, Tetracycline, QSAR model, LMWOAs},
	pages = {117200},
	title = {Quantitatively modeling of tetracycline photodegradation in low molecular weight organic acids under simulated sunlight irradiation},
	url = {https://www.sciencedirect.com/science/article/pii/S026974912100782X},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S026974912100782X},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.envpol.2021.117200}}

@inproceedings{no-bib2,
	annote = {cite-code, qsar},
	author = {Kar, S. and Roy, J.K. and Leszczynski, J.},
	booktitle = {Development of Solar Cells. Challenges and Advances in Computational Chemistry and Physics, vol 32},
	date-added = {2021-05-18 11:52:21 -0400},
	date-modified = {2021-05-18 11:54:09 -0400},
	doi = {10.1007/978-3-030-69445-6_7},
	title = {Application of QSPR Modeling in Designing and Prediction of Power Conversion-Efficient Solar Cell},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-3-030-69445-6_7}}

@article{no-bib,
	author = {Carlos A Ortiz-Mahecha and William A Agudelo and Manuel A Patarroyo and Manuel E Patarroyo and Carlos F Su{\'a}rez},
	date-added = {2021-05-18 11:47:25 -0400},
	date-modified = {2021-05-18 11:48:49 -0400},
	doi = {10.1093/bib/bbab171},
	journal = {Briefings in Bioinformatics},
	title = {MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1093/bib/bbab171}}

@article{doi:10.1080/07391102.2021.1924271,
	annote = {mozyme, cite-model, cite-code},
	author = {Rafael E. O. Rocha and Elton J. F. Chaves and Pedro H. C. Fischer and Leon S. C. Costa and Igor Barden Grillo and Luiz E. G. da Cruz and Fabiana C. Guedes and Carlos H. da Silveira and Marcus T. Scotti and Alex D. Camargo and Karina S. Machado and Adriano V. Werhli and Rafaela S. Ferreira and Gerd B. Rocha and Leonardo H. F. de Lima},
	date-added = {2021-05-16 14:05:43 -0400},
	date-modified = {2021-05-16 14:06:43 -0400},
	doi = {10.1080/07391102.2021.1924271},
	eprint = {https://doi.org/10.1080/07391102.2021.1924271},
	journal = {Journal of Biomolecular Structure and Dynamics},
	note = {PMID: 33970798},
	number = {0},
	pages = {1-21},
	publisher = {Taylor & Francis},
	title = {A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers},
	url = {https://doi.org/10.1080/07391102.2021.1924271},
	volume = {0},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1080/07391102.2021.1924271}}

@article{no-auto-citation,
	annote = {no-calc},
	author = {Mohamad Nurul Azmi and Tan Aik Sian and Munirah Suhaimi and Muhamad Noor Alfarizal Kamarudin and Mohd Fadzli Md Din and Mohd Azlan Nafiah and Noel F. Thomas and Habsah Abdul Kadir and Khalijah Awang},
	date-added = {2021-05-16 14:01:54 -0400},
	date-modified = {2021-05-16 14:05:03 -0400},
	doi = {https://doi.org/10.21315/jps2021.32.1.6},
	journal = {Journal of Physical Science},
	pages = {69-89},
	title = {Synthesis of Indolostilbenes via FeCl3-promoted Oxidative Cyclisation and their Biological Effects on NG108-15 Cell Viability and H2O2-induced Cytotoxicity},
	volume = {32},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.21315/jps2021.32.1.6}}

@article{Yang:2021wf,
	annote = {cite-model},
	author = {Yang, Ye and Liu, Ling and Wang, Huixian and Zhang, Xiuhui},
	booktitle = {The Journal of Physical Chemistry A},
	da = {2021/05/10},
	date = {2021/05/10},
	date-added = {2021-05-16 13:56:27 -0400},
	date-modified = {2021-05-16 13:56:35 -0400},
	doi = {10.1021/acs.jpca.1c02113},
	isbn = {1089-5639},
	journal = {The Journal of Physical Chemistry A},
	journal1 = {J. Phys. Chem. A},
	m3 = {doi: 10.1021/acs.jpca.1c02113},
	month = {05},
	publisher = {American Chemical Society},
	title = {Molecular-Scale Mechanism of Sequential Reaction of Oxalic Acid with SO3: Potential Participator in Atmospheric Aerosol Nucleation},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acs.jpca.1c02113},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acs.jpca.1c02113}}

@article{Zeng:2021ug,
	abstract = {A three-descriptor quantitative structure--activity/toxicity relationship (QSAR/QSTR) model was developed for the skin permeability of a sufficiently large data set consisting of 274 compounds, by applying support vector machine (SVM) together with genetic algorithm. The optimal SVM model possesses the coefficient of determination R2 of 0.946 and root mean square (rms) error of 0.253 for the training set of 139 compounds; and a R2 of 0.872 and rms of 0.302 for the test set of 135 compounds. Compared with other models reported in the literature, our SVM model shows better statistical performance in a model that deals with more samples in the test set. Therefore, applying a SVM algorithm to develop a nonlinear QSAR model for skin permeability was achieved.},
	annote = {gui=chem3d},
	author = {Zeng, Ruolan and Deng, Jiyong and Dang, Limin and Yu, Xinliang},
	da = {2021/05/12},
	date-added = {2021-05-16 13:55:56 -0400},
	date-modified = {2021-05-16 13:56:04 -0400},
	doi = {10.1038/s41598-021-89587-5},
	id = {Zeng2021},
	isbn = {2045-2322},
	journal = {Scientific Reports},
	number = {1},
	pages = {10076},
	title = {Correlation between the structure and skin permeability of compounds},
	ty = {JOUR},
	url = {https://doi.org/10.1038/s41598-021-89587-5},
	volume = {11},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1038/s41598-021-89587-5}}

@article{Zhang:2021wz,
	abstract = {Brominated disinfection byproducts (Br-DBPs) are formed during the disinfection process of water containing bromine ions, such as marine aquaculture water. Little attention has been paid to Br-DBPs with anthropogenic chemicals as precursors. This study summarized the sodium hypochlorite (NaClO) oxidation of three frequently used pharmaceuticals, including two antibiotics, norfloxacin (NOR) and sulfamethoxazole (SMX), and the growth hormone estrogen 17β-estradiol (E2). Transformations of the pharmaceuticals were found to be faster in marine aquaculture water than in distilled water. Several Br-DBPs and Cl-DBPs were identified for NOR, SMX, and E2. It was shown that the carboxyl group, piperazine ring, C3, and C8 atoms were the primary reaction sites on NOR. The aniline moiety and S-N bond were identified to be the reaction sites on SMX. The C2, C4, C9, and C16 atoms were the potential reaction centers on E2. Preliminary calculation by QSAR model indicated that the value of logKow significantly increased with an increase in the number of bromine atoms in the Br-DBPs. The results of the bioconcentration factors (BCF) analysis suggested that the bioaccumulation of Br-DBPs were greater than that chlorinated DBPs (Cl-DBPs) in distilled water.},
	author = {Zhang, Yuanyuan and Zhu, Yunjie and Shao, Yanan and Rong, Chuan and Pan, Zihan and Deng, Jie},
	da = {2021/05/09},
	date-added = {2021-05-12 16:20:08 -0400},
	date-modified = {2021-05-12 16:20:08 -0400},
	doi = {10.1007/s11356-021-14161-5},
	id = {Zhang2021},
	isbn = {1614-7499},
	journal = {Environmental Science and Pollution Research},
	title = {Toxicity of disinfection byproducts formed during the chlorination of sulfamethoxazole, norfloxacin, and 17β-estradiol in the presence of bromide},
	ty = {JOUR},
	url = {https://doi.org/10.1007/s11356-021-14161-5},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1007/s11356-021-14161-5}}

@inbook{Thomas2021,
	abstract = {This chapter deals with the historical and theoretical analysis of crosslinked polyethylene (XLPE). The chapter is divided into three sections, the first section dealing with the historical developments in XLPE. This part depicted a historical picture of invention, the necessity of invention and finally its establishment as various XLPE products. Here gives a detailed discussion about the emergence of XLPE as the insulation cables, which is the most recognized application of XLPE and also other applications of XLPE like hip arthroplasty. The second section is a more in-depth presentation of classical and quantum mechanical theories behind the computational analysis. The final picture describes how various methods of computational studies in XLPE molecule parameterization and crosslinking reactions. This chapter is coverage of fundamentals in computational chemistry and a survey of most widely used force fields and software's for simulation of polymer systems. Also, references to the theories used in the atomic simulation of the study of XLPE. Theoretical aspects of the mechanism of electrical treeing and UV radiation crosslinking process of polyethylene (PE) suggest some voltage stabilizers, antioxidants and crosslinkers for the future process of an efficient XLPE cable operating in high voltage.},
	address = {Singapore},
	annote = {gui=chem3d},
	author = {Thomas, Minu Elizabeth and Vidya, Rajamani and Thomas, Jince and Ahmad, Zakiah},
	booktitle = {Crosslinkable Polyethylene: Manufacture, Properties, Recycling, and Applications},
	date-added = {2021-05-12 00:45:14 -0400},
	date-modified = {2021-05-12 00:46:33 -0400},
	doi = {10.1007/978-981-16-0514-7_2},
	editor = {Thomas, Jince and Thomas, Sabu and Ahmad, Zakiah},
	isbn = {978-981-16-0514-7},
	pages = {17--40},
	publisher = {Springer Singapore},
	title = {Historical and Theoretical Background of XLPE},
	url = {https://doi.org/10.1007/978-981-16-0514-7_2},
	year = {2021},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {https://doi.org/10.1007/978-981-16-0514-7_2}}

@article{BALACHANDAR2021109801,
	abstract = {Azoles such as tetrazole, triazole, pyrazole, and imidazole are considered to be core nitrogen rich structures. 2,6-Dinitro-4-(trifluoromethyl)phenol was treated with imidazole, 3-nitropyrazole, 1,2,4-triazole, 3-amino-1,2,4-triazole, 3,5-diamino-1,2,4-triazole, 5-aminotetrazole, and 5-nitrotriazolone to synthesize acid-base salts using a proton transfer mechanism. The spectroscopic characterization of the synthesized compounds 1--7 was carried out by IR, 1H NMR, 13C NMR, and 19F NMR spectroscopies. Single crystal X-ray diffraction studies of compounds 1 and 3 showed that they possess densities of 1.675 and 1.670 g/cm3, respectively. The detonation properties of all the synthesized compounds were studied using computational software such as the LOTUSES, EXPLO 5, and EXTEC codes. The blast peak over pressure and blast impulse were determined for each compound. The thermal behaviour of the synthesized compounds was analyzed using TGA/DSC thermogram, and each compound was found to exhibit acceptable thermal stability. The performance of the synthesized compounds were found to be high and fit into the category of high-energy-density materials (HEDMs).},
	annote = {no-access},
	author = {Kannan Gajendran Balachandar and Arumugam Thangamani},
	date-added = {2021-05-12 00:41:28 -0400},
	date-modified = {2021-05-12 00:41:35 -0400},
	doi = {https://doi.org/10.1016/j.jfluchem.2021.109801},
	issn = {0022-1139},
	journal = {Journal of Fluorine Chemistry},
	keywords = {High-energy-density materials (HEDMs), Proton transfer mechanism, Organic fluorine, Heat of formation, TGA/DSC, NMR},
	pages = {109801},
	title = {Novel high performance energetic materials of fluorine-containing 2,6-dinitro-4-(trifluoromethyl)phenol derivatives with substituted azoles},
	url = {https://www.sciencedirect.com/science/article/pii/S0022113921000798},
	volume = {247},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0022113921000798},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.jfluchem.2021.109801}}

@article{prepub,
	author = {Bojja Rajeshwar Rao},
	date-added = {2021-05-12 00:39:07 -0400},
	date-modified = {2021-05-12 00:40:39 -0400},
	doi = {10.20959/wjpps20215-18896},
	journal = {WORLD JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES},
	pages = {689-725},
	title = {A CRITICAL REVIEW ON THE COMPUTATIONAL STUDY OF ZWITTERIONS IN BENZYLPENICILLIN TAUTOMERS BY AUSTIN MODEL-1 METHOD},
	volume = {10},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.20959/wjpps20215-18896}}

@article{Takioku:2021vy,
	annote = {gui=chem3d},
	author = {Takioku, Maho and Takamura, Yuta and Fujihara, Michiko and Watanabe, Masaki and Yamada, Shoya and Kawasaki, Mayu and Ito, Sohei and Nakano, Shogo and Kakuta, Hiroki},
	booktitle = {ACS Medicinal Chemistry Letters},
	da = {2021/05/07},
	date = {2021/05/07},
	date-added = {2021-05-12 00:29:17 -0400},
	date-modified = {2021-05-12 00:29:31 -0400},
	doi = {10.1021/acsmedchemlett.1c00201},
	journal = {ACS Medicinal Chemistry Letters},
	journal1 = {ACS Med. Chem. Lett.},
	m3 = {doi: 10.1021/acsmedchemlett.1c00201},
	month = {05},
	publisher = {American Chemical Society},
	title = {Creation of Fluorescent RXR Antagonists Based on CBTF-EE and Application to a Fluorescence Polarization Binding Assay},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acsmedchemlett.1c00201},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acsmedchemlett.1c00201}}

@article{MELCHOR-RODRIGUEZ2021,
	annote = {cite-code, cite-model},
	author = {Melchor-Rodr\~A\-guez, Kenia AND Gaspard, Sarra AND J\~A!`uregui-Haza, Ulises Javier},
	crossref = {10.21577/0100-4042.20170666},
	date-added = {2021-05-12 00:26:40 -0400},
	date-modified = {2021-05-12 00:28:02 -0400},
	doi = {10.21577/0100-4042.20170666},
	issn = {0100-4042},
	journal = {{Qu\~A\-mica Nova}},
	language = {en},
	month = {02},
	pages = {172 - 179},
	publisher = {scielo},
	title = {{CHLORDECONE ADSORPTION ON FUNCTIONALIZED ACTIVATED CARBONS: COMPUTATIONAL CHEMISTRY AS A TOOL FOR UNDERSTANDING THE ADSORPTION PROCESS}},
	url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-40422021000200172&nrm=iso},
	volume = {44},
	year = {2021},
	Bdsk-Url-1 = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-40422021000200172&nrm=iso}}

@article{WU2021120288,
	abstract = {The catalytic hydrogen transfer (CHT) cascade reaction between alcohols and nitro- compounds meets green chemistry yet involves high catalyst requirements. Herein, a hierarchical nano-pyramid structure, in which cobalt single atoms (Co SAs) are deposited on highly dispersed ZnO nanoparticles supported by nitrogen-doped carbon (denoted as Co-ZnO/NC), was designed and obtained through pyrolysis of ZnCo-ZIF. The catalyst exhibited excellent catalytic performance toward the CHT cascade reaction, achieving a high nitrobenzene conversion (94%), imine selectivity (97%), and turnover frequency (8.8 h-1). This nano-pyramid is a state-of-the-art non-noble-metal catalyst and is comparable to noble-metal catalysts. Experimental and DFT results revealed that the Co SAs supported on ZnO reduced the reaction energy barrier of hydroxyl dehydrogenation, the first and rate-determining step in this heterogeneous catalysis. Furthermore, Co-ZnO/NC exhibits good recyclability and universality. Our findings offer a new catalyst for Schiff base synthesis and aid understanding of the roles of Zn in ZIF-derived carbon catalysts.},
	annote = {no-access},
	author = {Chen Wu and Changyan Zhu and Kangkai Liu and Shaowei Yang and Yu Sun and Kai Zhu and Yueling Cao and Sai Zhang and Sifei Zhuo and Min Zhang and Qiuyu Zhang and Hepeng Zhang},
	date-added = {2021-05-09 18:17:52 -0400},
	date-modified = {2021-05-09 18:17:57 -0400},
	doi = {https://doi.org/10.1016/j.apcatb.2021.120288},
	issn = {0926-3373},
	journal = {Applied Catalysis B: Environmental},
	keywords = {Catalytic hydrogen transfer, Cascade reaction, Imine synthesis, MOF-derived carbon material, Single atom catalysis},
	pages = {120288},
	title = {Nano-pyramid-type Co-ZnO/NC for Hydrogen Transfer Cascade Reaction between Alcohols and Nitrobenzene},
	url = {https://www.sciencedirect.com/science/article/pii/S0926337321004148},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0926337321004148},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.apcatb.2021.120288}}

@article{ZHANG2021109814,
	abstract = {The β-glucosidase derived from microorganisms has attracted worldwide interest for their industrial applications, but studies on β-glucosidases from Oenococcus oeni are rare. In this paper, catalytic mechanism of a novel β-glucosidase BGL0224 of Oenococcus oeni SD-2a was explored for the first time by kinetic parameters determination, fluorescence spectroscopy and quenching mechanism analysis, molecular dynamics simulation. The results indicated that BGL0224 had universal catalytic effect on different types of glycoside substrates, but the catalytic efficiencies were different. Fluorescence quenching analysis results suggested that the quenching processes between BGL0224 and seven kinds of substrates were predominated by the static quenching mechanism. A reasonable three-dimensional model of BGL0224 was obtained using the crystal structure of E.coli BglA as a template. The analysis results of molecular simulation (RMSD, Rg, RMSF and hydrogen bonding) showed that the composite system `BGL0224-pNPG' was very stable after 40 ns. The catalytic process of BGL0224 acting on `p-Nitrophenyl β-d-glucopyranoside' conformed to the double displacement mechanism. Two glutamic acid residues `Glu178 and Glu377' played a vital role in the whole catalytic process. Overall, this study gave specific insights on the catalytic mechanism of BGL0224, which was of great significance for developing its potential applications in food industry.},
	annote = {no-access},
	author = {Jie Zhang and Ning Zhao and Junnan Xu and Yiman Qi and Xinyuan Wei and Mingtao Fan},
	date-added = {2021-05-09 18:17:17 -0400},
	date-modified = {2021-05-09 18:17:23 -0400},
	doi = {https://doi.org/10.1016/j.enzmictec.2021.109814},
	issn = {0141-0229},
	journal = {Enzyme and Microbial Technology},
	keywords = {Amino acid, β-Glucosidase, Catalysis, Molecular docking, -NPG, Food industry},
	pages = {109814},
	title = {Exploring the catalytic mechanism of a novel β-glucosidase BGL0224 from Oenococcus oeni SD-2a: Kinetics, spectroscopic and molecular simulation},
	url = {https://www.sciencedirect.com/science/article/pii/S0141022921000727},
	volume = {148},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0141022921000727},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.enzmictec.2021.109814}}

@article{Ghorbani:2021tr,
	abstract = {In this study, we report binding free energy calculations of various drugs-of-abuse to Cucurbit-{$[$}8{$]$}-uril as part of the SAMPL8 blind challenge. Force-field parameters were obtained from force-matching with different quantum mechanical levels of theory. The Replica Exchange Umbrella Sampling (REUS) approach was used with a cylindrical restraint to enhance the sampling of host--guest binding. Binding free energy was calculated by pulling the guest molecule from one side of the symmetric and cylindrical host, then into and through the host, and out the other side (bidirectional) as compared to pulling only to the bound pose inside the cylindrical host (unidirectional). The initial results with force-matched MP2 parameter set led to RMSE of 4.68 {\$}{\$}{\{}{$\backslash$}text{\{}kcal{\}}{\}}/{\{}{$\backslash$}text{\{}mol{\}}{\}}{\$}{\$}from experimental values. However, the follow-up study with CHARMM generalized force field parameters and force-matched PM6-D3H4 parameters resulted in RMSEs from experiment of {\$}{\$}2.65{\$}{\$}and {\$}{\$}1.72 {\{}{$\backslash$}text{\{}kcal{\}}{\}}/{\{}{$\backslash$}text{\{}mol{\}}{\}}{\$}{\$}, respectively, which demonstrates the potential of REUS for accurate binding free energy calculation given a more suitable description of energetics. Moreover, we compared the free energies for the so called bidirectional and unidirectional free energy approach and found that the binding free energies were highly similar. However, one issue in the bidirectional approach is the asymmetry of profile on the two sides of the host. This is mainly due to the insufficient sampling for these larger systems and can be avoided by longer sampling simulations. Overall REUS shows great promise for binding free energy calculations.},
	annote = {cite-code},
	author = {Ghorbani, Mahdi and Hudson, Phillip S. and Jones, Michael R. and Aviat, F{\'e}lix and Meana-Pa{\~n}eda, Rub{\'e}n and Klauda, Jeffery B. and Brooks, Bernard R.},
	da =

license_type: permissive

branch_name: refs/heads/main

extension: bib