text:
/science/article/pii/S019701862100067X},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.neuint.2021.105021}}

@article{Coro-Bermello:2021vz,
	abstract = {Chagas disease is a serious health problem in Central and South America for which effective treatment is not currently available. This illness is caused by the protozoa Trypanosoma cruzi, a species that relies on a thiol-based metabolism to regulate oxidative stress. Trypanothione reductase enzyme plays a central role in the metabolic pathway of the parasite. In this work, a virtual screening of a library of novel thiadiazine derivatives against trypanothione reductase using molecular docking was performed. Four different series of hybrid ligands having in the structure one or two peptoid moieties (series I and II) or the tetrazole ring (series III and IV) were considered. An ad hoc numerical index called poses ratio was introduced to interpret the results of the docking analysis and to establish relevant structure-interaction relationships. In addition, six binding modes were found for the ligands with the highest populated conformational clusters after applying contact-based analysis. The most regular and relevant were binding modes I and II, found mainly for ligands from series I. A subsequent molecular docking on human glutathione reductase enzyme allowed to assess the possible cytotoxicity of the ligands towards human cells. A selective binding profile was found for ligands with interactions in the Hydrophobic cleft, the spermidine and the Z subsites inside the active site of trypanothione reductase. At the end of the study, new thiadiazine-based compounds were identified as plausible candidates to selectively inhibit the parasitic enzyme.},
	annote = {cite-code, cite-model},
	author = {Coro-Bermello, Julieta and L{\'o}pez-Rodr{\'\i}guez, Ernesto R. and Alfonso-Ramos, Javier E. and Alonso, Dayana and Ojeda-Carralero, Gerardo M. and Prado, Gustavo A. and Moreno-Castillo, Elena},
	da = {2021/02/25},
	date-added = {2021-04-18 19:08:40 -0400},
	date-modified = {2021-04-18 19:09:19 -0400},
	doi = {10.1007/s42452-021-04375-0},
	id = {Coro-Bermello2021},
	isbn = {2523-3971},
	journal = {SN Applied Sciences},
	number = {3},
	pages = {376},
	title = {Identification of novel thiadiazin derivatives as potentially selective inhibitors towards trypanothione reductase from Trypanosoma cruzi by molecular docking using the numerical index poses ratio Pr and the binding mode analysis},
	ty = {JOUR},
	url = {https://doi.org/10.1007/s42452-021-04375-0},
	volume = {3},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1007/s42452-021-04375-0}}

@article{ARSHAD2021104707,
	abstract = {1-(adamantane-1-carbonyl-3-(1-naphthyl)) thiourea (C22H24N2OS (4), was synthesized by the reaction of freshly prepared adamantane-1-carbonyl chloride from corresponding acid (3) with ammonium thiocyanate in 1:1 M ratio in dry acetone to afford the adamantane-1-carbonyl isothiocyanate (2) in situ followed by treatment with 1-naphthyl amine (3). The structure was established by elemental analyses, FTIR, 1H, 13C NMR and mass spectroscopy. The molecular and crystal structure were determined by single crystal X-ray analysis. It belongs to triclinic system P − 1 space group with a = 6.7832(5) {\AA}, b = 11.1810(8) {\AA}, c = 13.6660(10) {\AA}, α = 105.941(6)$\,^{\circ}$, β = 103.730(6)$\,^{\circ}$, γ = 104.562(6)$\,^{\circ}$, Z = 2, V = 910.82(11) {\AA}3. The naphthyl group is almost planar. In the crystal structure, intermolecular CH···O hydrogen bonds link the molecules into centrosymmetric dimers, enclosing R22(14) ring motifs, while the intramolecular NH···O hydrogen bonds enclose S(6) ring motifs, in which they may be effective in the stabilization of the structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H {\ldots} H (59.3%), H {\ldots} C/C {\ldots} H (19.8%) and H {\ldots} S/S {\ldots} H (10.1%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. DFT, molecular docking and urease inhibition studies revealed stability and electron withdrawing nature of 4 as compared to DNA base pairs and residues of urease. The DNA binding results from docking, UV-- visible spectroscopy, and viscosity studies indicated significant binding of 4 with the DNA via intercalation and groove binding. Further investigation of the compound was done on hepatocellular carcinoma; Huh-7 cell line as well as normal human embryonic kidney; Hek-293 cell line. The compound showed significant cytotoxic activity against Huh-7 cells in comparison to normal Hek-293 cells indicating selective cytotoxicity towards cancer cells.},
	annote = {no-access},
	author = {Nasima Arshad and Aamer Saeed and Fouzia Perveen and Rabail Ujan and Shahid I. Farooqi and Pervaiz {Ali Channar} and Ghulam Shabir and Hesham R. El-Seedi and Aneela Javed and Maham Yamin and Michael Bolte and Tuncer H{\"o}kelek},
	date-added = {2021-04-18 19:08:14 -0400},
	date-modified = {2021-04-18 19:08:19 -0400},
	doi = {https://doi.org/10.1016/j.bioorg.2021.104707},
	issn = {0045-2068},
	journal = {Bioorganic Chemistry},
	keywords = {Adamantanyl thiourea, X-ray, Hirshfeld surface analysis, DNA binding, Urease inhibition, Anticancer potential},
	pages = {104707},
	title = {Synthesis, X-ray, Hirshfeld surface analysis, exploration of DNA binding, urease enzyme inhibition and anticancer activities of novel adamantane-naphthyl thiourea conjugate},
	url = {https://www.sciencedirect.com/science/article/pii/S0045206821000833},
	volume = {109},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0045206821000833},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.bioorg.2021.104707}}

@article{https://doi.org/10.1002/qua.26665,
	abstract = {Abstract A set of the characteristics calculated using any quantum chemical method can be attributed to local electronic structure, which may change for each atom in complex systems. Related average values can give poor characteristics because different atom fractions with different surroundings may have different electronic characteristics poorly corresponding to the average values. The aim of this work is to show that the distribution functions of atomic charges, as well as chemical shifts and molecular orbital energies, can be considered as a set of simple tools for easy analysis of complex systems within the scope of nonlocal characteristics describing whole systems. The approach efficiency and analysis adequacy depend on appropriateness of molecular and cluster models used. The systems with dozens or hundreds of molecules and solid nanoparticles of almost real sizes (>40 units, >2 nm) or calculated with periodic boundary conditions and expanded cells give more adequate nonlocal characteristics than much smaller systems with several molecules and small clusters (<10 units, <1 nm) can give.},
	annote = {cite-code, cite-model},
	author = {Gun'ko, Vladimir M.},
	date-added = {2021-04-18 19:04:25 -0400},
	date-modified = {2021-04-18 22:46:42 -0400},
	doi = {https://doi.org/10.1002/qua.26665},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.26665},
	journal = {International Journal of Quantum Chemistry},
	keywords = {atomic charge distribution function, cluster approach, functionalized silica, interfacial water layer, periodic boundary conditions},
	pages = {e26665},
	title = {Atomic charge distribution functions as a tool to analyze electronic structure of molecular and cluster systems},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26665},
	year = {2021},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26665},
	Bdsk-Url-2 = {https://doi.org/10.1002/qua.26665}}

@article{Song:2021vk,
	abstract = {The aroma of peach fruit is predominantly determined by the accumulation of γ-decalactone and ester compounds. A previous study showed that the biosynthesis of these aroma compounds in peach fruit is catalyzed by PpAAT1, an alcohol acyltransferase. In this work, we investigated the key active site residues responsible for γ-decalactone and ester biosynthesis. A total of 14 candidate amino acid residues possibly involved in internal esterification and 9 candidate amino acid residues possibly involved in esterification of PpAAT1 were assessed via site-directed mutagenesis. Analyses of the in vitro enzyme activities of PpAAT1 and its site-directed mutant proteins (PpAAT1-SMs) with different amino acid residue mutations as well as the contents of γ-decalactone in transgenic tobacco leaves and peach fruits transiently expressing PpAAT1 and PpAAT1-SMs revealed that site-directed mutation of H165 in the conserved HxxxD motif led to lost enzymatic activity of PpAAT1 in both internal esterification and its reactions, whereas mutation of the key amino acid residue D376 led to the total loss of γ-decalactone biosynthesis activity of PpAAT1. Mutations of 9 and 7 other amino acid residues also dramatically affected the enzymatic activity of PpAAT1 in the internal esterification and esterification reactions, respectively. Our findings provide a biochemical foundation for the mechanical biosynthesis of γ-decalactone and ester compounds catalyzed by PpAAT1 in peach fruits, which could be used to guide the molecular breeding of new peach species with more favorable aromas for consumers.},
	annote = {cite-code},
	author = {Song, Zhi-Zhong and Peng, Bin and Gu, Zi-Xia and Tang, Mei-Ling and Li, Bei and Liang, Mei-Xia and Wang, Li-Min and Guo, Xiao-Tong and Wang, Jian-Ping and Sha, Yu-Fen and Zhang, Hong-Xia},
	da = {2021/02/01},
	date-added = {2021-04-18 19:02:25 -0400},
	date-modified = {2021-04-18 19:03:42 -0400},
	doi = {10.1038/s41438-021-00461-x},
	id = {Song2021},
	isbn = {2052-7276},
	journal = {Horticulture Research},
	number = {1},
	pages = {32},
	title = {Site-directed mutagenesis identified the key active site residues of alcohol acyltransferase PpAAT1 responsible for aroma biosynthesis in peach fruits},
	ty = {JOUR},
	url = {https://doi.org/10.1038/s41438-021-00461-x},
	volume = {8},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1038/s41438-021-00461-x}}

@article{doi:10.1080/07391102.2021.1878058,
	annote = {mozyme, cite-model, cite-code},
	author = {Elton Jos{\'e} Ferreira Chaves and Luiz Eduardo Gomes da Cruz and It{\'a}cio Queiroz Mello Padilha and Carlos Henrique Silveira and Demetrius Ant{\^o}nio Machado Araujo and Gerd Bruno Rocha},
	date-added = {2021-04-18 18:57:41 -0400},
	date-modified = {2021-04-18 18:59:00 -0400},
	doi = {10.1080/07391102.2021.1878058},
	eprint = {https://doi.org/10.1080/07391102.2021.1878058},
	journal = {Journal of Biomolecular Structure and Dynamics},
	note = {PMID: 33526002},
	number = {0},
	pages = {1-19},
	publisher = {Taylor & Francis},
	title = {Discovery of RTA ricin subunit inhibitors: a computational study using PM7 quantum chemical method and steered molecular dynamics},
	url = {https://doi.org/10.1080/07391102.2021.1878058},
	volume = {0},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1080/07391102.2021.1878058}}

@article{CAI2021338505,
	abstract = {Gibberellins (GAs) play crucial roles in plant growth and development, and their regulatory functions rely on complex metabolic networks and signaling pathways. Therefore, the exploration of GAs metabolic network is of great importance. However, limited GAs have been found in given plant species, which makes it difficult to comprehensively study the GAs metabolic network. Herein, a structure-guided strategy for GAs screening based on liquid chromatography--mass spectrometry analysis assisted by chemical isotope labeling (CIL-LC-MS) was developed. In the proposed strategy, N,N-dimethyl ethylenediamine (DMED) and its isotopologue d4-DMED were used to label GAs. In light of the characteristic fragmentation patterns exhibited by the labeled GAs, four principles were summarized to screen the potential GAs from plant tissues. Subsequently, the MS/MS fragmentation behavior and qualitative structure-retention relationship (QSRR) model were employed to assist in deciphering structures of GA candidates. With this strategy, thirty potential GAs were screened out and identified from five plant species. Seven of them were confirmed by the authentic standards. Twenty-two of them have not been reported before in the five plant species used in this study, including thirteen that have been reported in other plant species and nine that have never been reported in any plant species. Noteworthily, a total of nine potential GAs were speculated to be novel 16, 17-double hydrated GAs, which indicated that the 16, 17-double hydration may be a ubiquitous metabolic pathway of GAs in plants. This study was the first attempt to establish a structure-guided screening strategy for GAs. Our findings have enriched the GA species in plants and expanded the GAs family, which may be helpful for study of the metabolic pathway and physiological function of GAs.},
	annote = {no-access},
	author = {Wen-Jing Cai and Chen Zeng and Xiao-Yun Zhang and Tiantian Ye and Yu-Qi Feng},
	date-added = {2021-04-18 18:56:56 -0400},
	date-modified = {2021-04-18 18:57:04 -0400},
	doi = {https://doi.org/10.1016/j.aca.2021.338505},
	issn = {0003-2670},
	journal = {Analytica Chimica Acta},
	keywords = {Gibberellins, Isotope labeling, Liquid chromatography, Mass spectrometry, Qualitative structure-retention relationship, Qualitative structure--guided screening strategy},
	pages = {338505},
	title = {A Structure--Guided Screening Strategy for the Discovery and Identification of Potential Gibberellins from Plant Samples Using Liquid Chromatography--Mass Spectrometry assisted by Chemical Isotope Labeling},
	url = {https://www.sciencedirect.com/science/article/pii/S0003267021003317},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0003267021003317},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.aca.2021.338505}}

@article{ANDINI2021111222,
	abstract = {Isothiocyanates (ITCs) derived from Brassicaceae are potential food preservatives. Their antimicrobial ac-tivity is strongly influenced by their subclass and side chain. This is the first quantitative structure-activity relationships (QSAR) study of ITCs as antibacterials. Twenty-six ITCs covering 9 subclasses were tested against Escherichia coli and Bacillus cereus. Minimum inhibitory concentration (MIC) and growth inhibitory response (GIR) were determined and used to develop QSAR models. MIC of the most active ITCs was 6.3--9.4 μg/mL. The QSAR models were validated with leave-one-out cross validation. The proposed models had a good fit (R2adj 0.86--0.93) and high internal predictive power (Q2adj 0.80--0.89). Partial charge, polarity, reactivity, and shape of ITCs were key physicochemical properties underlying antibacterial activity of ITCs. Furthermore, ITC compositions and antibacterial activity of Sinapis alba, Brassica napus, B. juncea, B. oleracea, and Camelina sativa extracts were determined, after myrosinase treatment. B. oleracea ITC-rich extract showed promising activity (MIC 750--1000 μg/mL) against both bacteria. C. sativa ITC-rich extract showed promising activity (MIC 188 μg/mL) against B. cereus. The QSAR models successfully predicted activity of the extracts based on ITC compositions. The models are useful to predict antibacterial activity of new ITCs and ITC-rich mixtures. Brassicaceae ITC-rich extracts are promising natural food preservatives.},
	annote = {qsar, gui=moe},
	author = {Silvia Andini and Carla Araya-Cloutier and Bianca Lay and Gijs Vreeke and Jos Hageman and Jean-Paul Vincken},
	date-added = {2021-04-18 15:42:20 -0400},
	date-modified = {2021-04-18 15:43:03 -0400},
	doi = {https://doi.org/10.1016/j.lwt.2021.111222},
	issn = {0023-6438},
	journal = {LWT},
	keywords = {Crucifer, Electrophile, Glucosinolate, Natural food preservative, Quantitative structure-activity relationship},
	pages = {111222},
	title = {QSAR-based physicochemical properties of isothiocyanate antimicrobials against gram-negative and gram-positive bacteria},
	url = {https://www.sciencedirect.com/science/article/pii/S0023643821003753},
	volume = {144},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0023643821003753},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.lwt.2021.111222}}

@article{WU2021145277,
	abstract = {Halobenzoquinones (HBQs) are emerging unregulated drinking water disinfection byproducts (DBPs) that are more toxic than regulated DBPs. This study aimed to determine the distribution and formation of HBQs in drinking water from water treatment plants in China, compare their chronic cytotoxicity and their induction of chromosomal damage in Chinese hamster ovary cells, and analyze the correlation of HBQ toxicity with their physicochemical parameters. Two HBQs, 2,6-dichloro-1,4-benzoquinone (2,6-DCBQ) and 2,6-dibromo-1,4-benzoquinone (2,6-DBBQ), were detected in finished water and tap water in China. The concentrations were in the ranges of <2.6--19.70 ng/L for 2,6-DCBQ and <0.38--1.8 ng/L for 2,6-DBBQ. Chemical oxygen demand and residual chlorine were positively correlated with HBQ formation. The HBQ concentration was lower in a drinking water treatment plant using chlorine dioxide. High Ca2+ in tap water decreased the HBQ level. The rank order of HBQ by cytotoxicity was 2-chloro-1,4-benzoquinone > 2,3-diiodo-1,4-benzoquinone > 2,6-diiodo-1,4-benzoquinone > 2,6-dibromo-1,4-benzoquinone > 2,5-dibromo-1,4-benzoquinone > 2,5-dichloro-1,4-benzoquinone > 2,6-dichloro-1,4-benzoquinone > tetrachloro-1,4-benzoquinone > 2,3,6-trichloro-1,4-benzoquinone, and for their genotoxicity, 2,5-dichloro-1,4-benzoquinone > 2,6-dichloro-1,4-benzoquinone > 2,3-diiodo-1,4-benzoquinone > 2,6-diiodo-1,4-benzoquinone > tetrachloro-1,4-benzoquinone > 2,5-dibromo-1,4-benzoquinone > 2,6-dibromo-1,4-benzoquinone > 2,3,6-trichloro-1,4-benzoquinone. The cytotoxicity of six dihalo-HBQs was negatively correlated with the octanol-water partition coefficient (r = −0.971, P < 0.05), molar refractivity (r = −0.956, P < 0.05), energy of the highest occupied molecular orbital (EHOMO) (r = −0.943, P < 0.05), and polar surface area (r = −0.829, P < 0.05). The genotoxicity of these three pairs of dihalo-HBQ isomers followed the same order as their EHOMO values. This study reveals the occurrence and formation of HBQs in drinking water in China and systematically evaluates the chromosomal damage caused by nine HBQs in mammalian cells.},
	author = {Huan Wu and Kunling Long and Yujie Sha and Du Lu and Ying Xia and Yan Mo and Qiyuan Yang and Weiwei Zheng and Mengting Yang and Xiao Wei},
	date-added = {2021-04-18 15:40:26 -0400},
	date-modified = {2021-04-18 15:40:26 -0400},
	doi = {https://doi.org/10.1016/j.scitotenv.2021.145277},
	issn = {0048-9697},
	journal = {Science of The Total Environment},
	keywords = {Halobenzoquinones, Drinking water, Disinfection byproducts, Occurrence, Formation, Toxicity},
	pages = {145277},
	title = {Occurrence and toxicity of halobenzoquinones as drinking water disinfection byproducts},
	url = {https://www.sciencedirect.com/science/article/pii/S0048969721003430},
	volume = {770},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0048969721003430},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.scitotenv.2021.145277}}

@article{D0RA09418H,
	abstract = {Ru(ii) complexes have attracted increasing attention as promising antitumor agents for their relatively low toxicity{,} high affinity to DNA molecules{,} and correlation with multiple targets. Meanwhile{,} quinolones are synthetic antibacterial agents widely used in the clinical practice. In this paper{,} two novel Ru(ii) complexes coordinated by levofloxacin (LOFLX){,} [Ru(bpy)2(LOFLX)]·2ClO4 (1){,} and [Ru(dmbpy)2(LOFLX)]·2ClO4 (2) (bpy = 2{,}2′-bipyridine{,} dmbpy = 4{,}4′-dimethyl-2{,}2′-bipyridine) were synthesized with high efficiency under microwave irradiation and characterized by ESI-MS{,} 1H NMR{,} and 13C NMR. The binding behavior of these complexes with double-strand calf thymus DNA(CT-DNA) was investigated using spectroscopy{,} molecular docking{,} and density functional theory calculations. Results showed that 2 exhibited higher binding affinity than 1 and LOFLX. Further studies showed that 2 could induce the G2/M phase arrest of A549 cells via DNA damage. In summary{,} these results indicated that 2 could be developed as a potential anticancer agent in treatment of lung cancer through the induction of cell cycle arrest at G2/M phase by triggering DNA damage.},
	annote = {dubious},
	author = {Liu, Ruotong and Yuan, Chanling and Feng, Yin and Qian, Jiayi and Huang, Xiaoting and Chen, Qiutong and Zhou, Shuyuan and Ding, Yin and Zhai, Bingbing and Mei, Wenjie and Yao, Liangzhong},
	date-added = {2021-04-18 15:40:03 -0400},
	date-modified = {2021-04-18 15:40:07 -0400},
	doi = {10.1039/D0RA09418H},
	issue = {8},
	journal = {RSC Adv.},
	pages = {4444-4453},
	publisher = {The Royal Society of Chemistry},
	title = {Microwave-assisted synthesis of ruthenium(ii) complexes containing levofloxacin-induced G2/M phase arrest by triggering DNA damage},
	url = {http://dx.doi.org/10.1039/D0RA09418H},
	volume = {11},
	year = {2021},
	Bdsk-Url-1 = {http://dx.doi.org/10.1039/D0RA09418H}}

@article{Datar:2021vu,
	annote = {cite-code, cite-model},
	author = {Datar, Archit and Witman, Matthew and Lin, Li-Chiang},
	booktitle = {The Journal of Physical Chemistry C},
	da = {2021/02/25},
	date = {2021/02/25},
	date-added = {2021-04-18 15:37:18 -0400},
	date-modified = {2021-04-18 15:37:31 -0400},
	doi = {10.1021/acs.jpcc.0c11082},
	isbn = {1932-7447},
	journal = {The Journal of Physical Chemistry C},
	journal1 = {J. Phys. Chem. C},
	m3 = {doi: 10.1021/acs.jpcc.0c11082},
	month = {02},
	number = {7},
	pages = {4253--4266},
	publisher = {American Chemical Society},
	title = {Improving Computational Assessment of Porous Materials for Water Adsorption Applications via Flat Histogram Methods},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acs.jpcc.0c11082},
	volume = {125},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acs.jpcc.0c11082}}

@article{10.1093/bib/bbab073,
	abstract = {{Metabolomics, the comprehensive study of the metabolome, and lipidomics---the large-scale study of pathways and networks of cellular lipids---are major driving forces in enabling personalized medicine. Complicated and error-prone data analysis still remains a bottleneck, however, especially for identifying novel metabolites. Comparing experimental mass spectra to curated databases containing reference spectra has been the gold standard for identification of compounds, but constructing such databases is a costly and time-demanding task. Many software applications try to circumvent this process by utilizing cutting-edge advances in computational methods---including quantum chemistry and machine learning---and simulate mass spectra by performing theoretical, so called in silico fragmentations of compounds. Other solutions concentrate directly on experimental spectra and try to identify structural properties by investigating reoccurring patterns and the relationships between them. The considerable progress made in the field allows recent approaches to provide valuable clues to expedite annotation of experimental mass spectra. This review sheds light on individual strengths and weaknesses of these tools, and attempts to evaluate them---especially in view of lipidomics, when considering complex mixtures found in biological samples as well as mass spectrometer inter-instrument variability.}},
	annote = {no-access},
	author = {Krettler, Christoph A and Thallinger, Gerhard G},
	date-added = {2021-04-18 15:35:59 -0400},
	date-modified = {2021-04-18 15:36:56 -0400},
	doi = {10.1093/bib/bbab073},
	eprint = {https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbab073/37084843/bbab073.pdf},
	issn = {1477-4054},
	journal = {Briefings in Bioinformatics},
	month = {03},
	note = {bbab073},
	title = {{A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics}},
	url = {https://doi.org/10.1093/bib/bbab073},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1093/bib/bbab073}}

@article{https://doi.org/10.1002/psc.3295,
	abstract = {The red tree frog Litoria rubella from Australia has been studied for several decades showing that their dorsal skin glands secrete a number of small peptides containing a Pro--Trp sequence, known as tryptophyllin L peptides. Although peptides from many genera of Australian frogs have been reported to possess a variety of biological activities, the bioactivities of this peptide family have remained to be discovered. In this study, we investigated the antioxidant potency of a number of tryptophyllin L peptides for the first time using a joint statistical and experimental approach in which predictions based on Gaussian three-dimensional quantitative structure--activity relationship (3D-QSAR) models were employed to guide an in vitro experimental investigation. Two tryptophyllin tripeptides P--W--L (OH) and P--W--L (NH2) were predicted to have the Trolox equivalent antioxidant capacity (TEAC) values of 0.80 and 0.87 μM Trolox/μM peptide, respectively. With those promising results, antioxidant capabilities of five tryptophyllin L peptides with the common core Pro--Trp--Leu were synthesized and subjected to 1,1-diphenyl-2-picrylhydrazyl (DPPH), ferric reducing ability of plasma (FRAP) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical cation (ABTS˙+) radical scavenging assays. The tests indicated that all the tested tryptophyllin L peptides, noticeably S--P--W--L (OH) and F--P--W--L (NH2), are strong ABTS˙+ radical scavengers and moderate scavengers in the other two assays. The results, thus, suggested that the tryptophyllin L peptides are likely to be a part of the skin antioxidant system helping the frog to cope with drastic change in oxygen exposure and humidity, as they inhabit over a large area of Australia with a wide climate variation.},
	annote = {qsar, cite-code},
	author = {Tran, Thi Thanh Nha and Tran, Dinh Phien and Nguyen, Van Cuong and Tran, Thi Dieu Thuan and Bui, Thi Thu Thuy and Bowie, John Hamilton},
	date-added = {2021-04-18 15:34:14 -0400},
	date-modified = {2021-04-18 15:34:27 -0400},
	doi = {https://doi.org/10.1002/psc.3295},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/psc.3295},
	journal = {Journal of Peptide Science},
	keywords = {3D-QSAR, antioxidants, DPPH radical scavenging activity, FRAP, Gaussian-based CoMSIA model, TEAC, tryptophyllin L peptides},
	note = {e3295 PSC-20-0109.R1},
	number = {4},
	pages = {e3295},
	title = {Antioxidant activities of major tryptophyllin L peptides: A joint investigation of Gaussian-based 3D-QSAR and radical scavenging experiments},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/psc.3295},
	volume = {27},
	year = {2021},
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	Bdsk-Url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/psc.3295},
	Bdsk-Url-2 = {https://doi.org/10.1002/psc.3295}}

@article{D1NR00106J,
	abstract = {We report the formation of self-assembled monolayers of a molecular photoswitch (azobenzene-bithiophene derivative{,} AzBT) on cobalt via a thiol covalent bond. We study the electrical properties of the molecular junctions formed with the tip of a conductive atomic force microscope under ultra-high vacuum. The statistical analysis of the current--voltage curves shows two distinct states of the molecule conductance{,} suggesting the coexistence of both the trans and cis azobenzene isomers on the surface. The cis isomer population (trans isomer) increases (decreases) upon UV light irradiation. The situation is reversed under blue light irradiation. The experiments are confronted to first-principle calculations performed on the molecular junctions with the Non-Equilibrium Green{'}s Function formalism combined with Density Functional Theory (NEGF/DFT). The theoretical results consider two different molecular orientations for each isomer. Whereas the orientation does not affect the conductance of the trans isomer{,} it significantly modulates the conductance of the cis isomer and the resulting conductance ON/OFF ratio of the molecular junction. This helps identifying the molecular orientation at the origin of the observed current differences between the trans and cis forms. The ON state is associated to the trans isomer irrespective of its orientation in the junction{,} while the OFF state is identified as a cis isomer with its azobenzene moiety folded upward with respect to the bithiophene core. The experimental and calculated ON/OFF conductance ratios have a similar order of magnitude. This conductance ratio seems reasonable to make these Co--AzBT molecular junctions a good test-bed to further explore the relationship between the spin-polarized charge transport{,} the molecule conformation and the molecule-Co spinterface.},
	annote = {gui=chem3d},
	author = {Thomas, Louis and Arbouch, Imane and Gu{\'e}rin, David and Wallart, Xavier and van Dyck, Colin and M{\'e}lin, Thierry and Cornil, J{\'e}r{\^o}me and Vuillaume, Dominique and Lenfant, St{\'e}phane},
	date-added = {2021-04-18 15:33:20 -0400},
	date-modified = {2021-04-18 15:33:38 -0400},
	doi = {10.1039/D1NR00106J},
	issue = {14},
	journal = {Nanoscale},
	pages = {6977-6990},
	publisher = {The Royal Society of Chemistry},
	title = {Conductance switching of azobenzene-based self-assembled monolayers on cobalt probed by UHV conductive-AFM},
	url = {http://dx.doi.org/10.1039/D1NR00106J},
	volume = {13},
	year = {2021},
	Bdsk-Url-1 = {http://dx.doi.org/10.1039/D1NR00106J}}

@article{LI2021124101,
	abstract = {A novel class of hybrid solvents (mEIP:Tetz) comprising of N-methylated ethylene imine polymer (mEIP) and 1-ethyl-3-methylimidazolium tetrazolate ([Emim][Tetz]) were developed for the highly efficient and reversible capture of SO2. The synergistic interactions rather than simple mixing between mEIP and [Emim][Tetz] were confirmed by Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR) and density functional theory (DFT) calculations. Besides, it was experimentally demonstrated that mEIP:Tetz mixtures exhibited improved kinetics for SO2 absorption, and the production of viscous solids were completely eliminated, compared with using mEIP alone. More significantly, an exceedingly high solubility of 0.308 g SO2·g−1 absorbent in 2mEIP:8Tetz was received for trapping SO2 from simulated flue gas containing 2000 ppm SO2, which was much higher than most of the results reported in previous literatures under the same conditions. Finally, the absorption and desorption mechanisms were proposed according to the results of FTIR and 1H NMR analysis.},
	annote = {cite-code},
	author = {Dan Li and Yong Kang},
	date-added = {2021-04-18 15:29:42 -0400},
	date-modified = {2021-04-18 15:30:02 -0400},
	doi = {https://doi.org/10.1016/j.jhazmat.2020.124101},
	issn = {0304-3894},
	journal = {Journal of Hazardous Materials},
	keywords = {N-methylation, SO capture, Ionic liquids, Hybrid materialsMaterials, Chemical absorbent},
	pages = {124101},
	title = {Significantly promoted SO2 uptake by the mixture of N-methylated ethylene imine polymer and 1-ethyl-3-methylimidazolium tetrazolate},
	url = {https://www.sciencedirect.com/science/article/pii/S0304389420320914},
	volume = {404},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0304389420320914},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.jhazmat.2020.124101}}

@article{LARHRIB2021137841,
	abstract = {Electrolytes are essential constituents for safe and reliable battery performance. Current lithium-ion battery (LIB) systems present an inherent safety problem stemming from the use of metal oxide cathodes, which are oxygen sources, and flammable electrolytes based primarily on organic carbonates. Herein we report a novel non-flammable electrolyte formulated by the addition of 30% wt. of methyltributhylphosphonium Bis(trifluoromethanesulfonyl) imide [Bu3MeP][TFSI] ionic liquid (IL) to a standard electrolyte (SE, ethylene carbonate (EC): ethyl methyl carbonate (EMC) 1:1 wt/wt) + 1M LiPF6). The good physicochemical properties of the IL, (i) mitigate the ignition delay and flammability of the proposed electrolyte and (ii) markedly improve the interfacial resistance of the LiMn2O4//Li and LiNi0.8Co0.15Al0.05O2//Li half-cells. The half-cells' performance indicates that the conveyed hybrid electrolyte (HE) retains a higher portion of its energy density (629 vs. 446 Wh.kg−1 for HE and SE in an NCA//Li half-cell, accordingly). At 60$\,^{\circ}$C, [Bu3MeP] [TFSI] considerably improved the cathode performance in terms of capacity (up to 230 mAh.g−1 for NCA) and coulombic efficiency (>99%).},
	annote = {dubious},
	author = {Badre Larhrib and Georgios Nikiforidis and M{\'e}ri{\`e}m Anouti},
	date-added = {2021-04-18 15:25:39 -0400},
	date-modified = {2021-04-18 15:27:27 -0400},
	doi = {https://doi.org/10.1016/j.electacta.2021.137841},
	issn = {0013-4686},
	journal = {Electrochimica Acta},
	keywords = {Electrolyte, Phosphonium ionic liquid, Flammability, Safety, Lithium-Ion Battery},
	pages = {137841},
	title = {Safe and efficient phosphonium ionic liquid based electrolyte for high-potential LiMn2O4 and LiNi0.8Co0.15Al0.05O2 cathodes for Li-ion batteries},
	url = {https://www.sciencedirect.com/science/article/pii/S0013468621001304},
	volume = {371},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0013468621001304},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.electacta.2021.137841}}

@article{SIGURNJAKBURES2021115885,
	abstract = {Pollutants in real aquatic systems commonly occur as chemical mixtures. Yet, the corresponding risk assessment is still mostly based on information on single-pollutant toxicity, accepting the assumption that pollutant mixtures exhibit additive toxicity effect which is often not the case. Therefore, it is still better to use the experimental approach. Unfortunately, experimental determination of toxicity for each mixture is practically unfeasible. In this study, quantitative structure-activity relationship (QSAR) models for the prediction of toxicity of binary mixtures towards bioluminescent bacteria Vibrio fischeri were developed at three toxicity levels (EC10, EC30 and EC50). For model development, experimentally determined toxicity values of 14 pollutants (pharmaceuticals and pesticides) were correlated with their structural features, applying multiple linear regression together with genetic algorithm. Statistical analysis, internal validation and external validation of the models were carried out. The toxicity is accurately predicted by all three models. EC30 and EC50 values are mostly influenced by geometrical distances between nitrogen and sulfur atoms. Furthermore, the simultaneous presence of oxygen and chlorine atoms in mixture can induce the increase in toxicity. At lower effect levels (EC10), nitrogen atom bonded to different groups has the highest impact on mixture toxicity. Thus, the analysis of the descriptors involved in the developed models can give insight into toxic mechanisms of the binary systems.},
	annote = {qsar, no-access},
	author = {M. {Sigurnjak Bure{\v s}} and {\v S}. Uki{\'c} and M. Cvetni{\'c} and V. Prevari{\'c} and M. Marki{\'c} and M. Rogo{\v s}i{\'c} and H. Ku{\v s}i{\'c} and T. Bolan{\v c}a},
	date-added = {2021-04-18 15:24:54 -0400},
	date-modified = {2021-04-18 15:24:58 -0400},
	doi = {https://doi.org/10.1016/j.envpol.2020.115885},
	issn = {0269-7491},
	journal = {Environmental Pollution},
	keywords = {QSAR, Mixture toxicity, Toxicology, Joint toxicity, Binary mixture},
	pages = {115885},
	title = {Toxicity of binary mixtures of pesticides and pharmaceuticals toward Vibrio fischeri: Assessment by quantitative structure-activity relationships},
	url = {https://www.sciencedirect.com/science/article/pii/S026974912036574X},
	volume = {275},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S026974912036574X},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.envpol.2020.115885}}

@article{Turdybekov:2021tu,
	abstract = {The germacrane-type sesquiterpene lactones tatridin A and B were isolated for the first time during chemical studies of the extract of Lepidolopha karatavica. The structures of the compounds were elucidated using spectral data and X-ray crystal structure analyses (XSAs). Correlations of the XSAs and CD spectra defined the absolute configurations of the molecules. Possible conformational states of 3,8-deoxytatridin A and B were calculated by a quantum chemical method.},
	annote = {cite-model},
	author = {Turdybekov, K. M. and Morozova, O. A. and Ivasenko, S. A. and Makhmutova, A. S. and Turdybekov, D. M. and Adekenov, S. M.},
	da = {2021/01/01},
	date-added = {2021-04-18 15:23:04 -0400},
	date-modified = {2021-04-18 15:23:55 -0400},
	doi = {10.1007/s10600-021-03288-z},
	id = {Turdybekov2021},
	isbn = {1573-8388},
	journal = {Chemistry of Natural Compounds},
	number = {1},
	pages = {83--87},
	title = {Molecular Structure and Absolute Configuration of Tatridin A and B from Lepidolopha karatavica},
	ty = {JOUR},
	url = {https://doi.org/10.1007/s10600-021-03288-z},
	volume = {57},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1007/s10600-021-03288-z}}

@article{Berstis:2021vu,
	annote = {cite-code},
	author = {Berstis, Laura and Elder, Thomas and Dixon, Richard and Crowley, Michael and Beckham, Gregg T.},
	booktitle = {ACS Sustainable Chemistry \& Engineering},
	da = {2021/02/01},
	date = {2021/02/01},
	date-added = {2021-04-18 15:21:19 -0400},
	date-modified = {2021-04-18 15:21:27 -0400},
	doi = {10.1021/acssuschemeng.0c04240},
	journal = {ACS Sustainable Chemistry \& Engineering},
	journal1 = {ACS Sustainable Chem. Eng.},
	m3 = {doi: 10.1021/acssuschemeng.0c04240},
	month = {02},
	number = {4},
	pages = {1518--1528},
	publisher = {American Chemical Society},
	title = {Coupling of Flavonoid Initiation Sites with Monolignols Studied by Density Functional Theory},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acssuschemeng.0c04240},
	volume = {9},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acssuschemeng.0c04240}}

@article{ma14030679,
	abstract = {Doping of graphene and a controlled induction of disturbances in the graphene lattice allows the production of numerous active sites for lithium ions on the surface and edges of graphene nanolayers and improvement of the functionality of the material in lithium-ion batteries (LIBs). This work presents the process of introducing boron and fluorine atoms into the structure of the reduced graphene during hydrothermal reaction with boron fluoride tetrahydrofuran (BF3·THF). The described process is a simple, one-step synthesis with little to no side products. The synthesized materials showed an irregular, porous structure, with an average pore size of 3.44--3.61 nm (total pore volume (BJH)) and a multi-layer structure and a developed specific surface area at the level of 586--660 m2/g (analysis of specific surface Area (BET)). On the external surfaces, the occurrence of irregular particles with a size of 0.5 to 10 µm was observed, most probably the effect of doping the graphene structure and the formation of sp3 hybridization defects. The obtained materials show the ability to store electric charge due to the development of the specific surface area. Based on cyclic voltammetry, the tested material showed a capacity of 450--550 mAh/g (charged up to 2.5 V).},
	annote = {gui=scigress},
	article-number = {679},
	author = {Kaczmarek, {\L}ukasz and Balik, Magdalena and Warga, Tomasz and Acznik, Ilona and Lota, Katarzyna and Miszczak, Sebastian and Sobczyk-Guzenda, Anna and Kyzio{\l}, Karol and Zawadzki, Piotr and Wosiak, Agnieszka},
	date-added = {2021-04-18 15:08:01 -0400},
	date-modified = {2021-04-18 15:19:39 -0400},
	doi = {10.3390/ma14030679},
	issn = {1996-1944},
	journal = {Materials},
	number = {3},
	pubmedid = {33540630},
	title = {Functionalization Mechanism of Reduced Graphene Oxide Flakes with BF3·THF and Its Influence on Interaction with Li+ Ions in Lithium-Ion Batteries},
	url = {https://www.mdpi.com/1996-1944/14/3/679},
	volume = {14},
	year = {2021},
	Bdsk-Url-1 = {https://www.mdpi.com/1996-1944/14/3/679},
	Bdsk-Url-2 = {https://doi.org/10.3390/ma14030679}}

@article{10.35848/1347-4065/abf4a2,
	abstract = {Surface potential contrasts were measured for n-type silicon (111) modified with 1-alkene self-assembled monolayers (SAMs) of varying hydrocarbon chain lengths (n = 10 to 20) using Kelvin Probe Force Microscopy (KPFM). Micropatterned SAMs were used in KPFM analysis, with hexadecyl SAM acting as a reference to avoid possible variations due to different KPFM cantilever tips used for analysis. Micropatterning was performed via vacuum ultraviolet (VUV) photolithography at λ = 172 nm. Individual samples were also analyzed by ellipsometry, x-ray photoelectron spectroscopy, static water contact angle tests and atomic force microscopy to determine SAM quality. Surface potential changes observed between the different SAMs were attributed to differences in the dipole moment of the precursor molecules, changes in SAM dielectric properties due to differences in molecular packing, and varying oxygen content at the surface.},
	author = {Maria Carmela Tan Garcia and Toru Utsunomiya and Takashi Ichii and Hiroyuki Sugimura},
	date-added = {2021-04-18 15:06:35 -0400},
	date-modified = {2021-04-18 15:06:52 -0400},
	doi = {10.35848/1347-4065/abf4a2},
	journal = {Japanese Journal of Applied Physics},
	title = {Kelvin probe force microscopy studies on the influence of hydrocarbon chain length on 1-alkene self-assembled monolayers on Si (111)},
	url = {http://iopscience.iop.org/article/10.35848/1347-4065/abf4a2},
	year = {2021},
	Bdsk-Url-1 = {http://iopscience.iop.org/article/10.35848/1347-4065/abf4a2}}

@article{Santra:2021uk,
	annote = {gui=moe},
	author = {Santra, Soumava and Kortagere, Sandhya and Vedachalam, Seenuvasan and Gogoi, Sanjib and Antonio, Tamara and Reith, Maarten E. A. and Dutta, Aloke K.},
	booktitle = {ACS Chemical Neuroscience},
	da = {2021/04/12},
	date = {2021/04/12},
	date-added = {2021-04-18 15:02:39 -0400},
	date-modified = {2021-04-18 15:03:02 -0400},
	doi = {10.1021/acschemneuro.1c00078},
	journal = {ACS Chemical Neuroscience},
	journal1 = {ACS Chem. Neurosci.},
	m3 = {doi: 10.1021/acschemneuro.1c00078},
	month = {04},
	publisher = {American Chemical Society},
	title = {Novel Potent Dopamine--Norepinephrine and Triple Reuptake Uptake Inhibitors Based on Asymmetric Pyran Template and Their Molecular Interactions with Monoamine Transporters},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acschemneuro.1c00078},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acschemneuro.1c00078}}

@article{https://doi.org/10.1002/qua.26441,
	abstract = {Abstract This work investigates possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods for the prediction of standard enthalpy of formation (ΔfHo) through the use of an artificial neural network (ANN) with molecular descriptors. A total of 142 organic compounds with enough structural diversity has been considered in the training set. Standard enthalpy of formation for the selected compounds at the semiempirical PM3 and PM6 quantum chemistry methods is collected from literature and is calculated by using the semiempirical PM7 method in this work. The multiple stepwise regression is first used to screen effective molecular descriptors, which are highly correlated with the error terms of the standard enthalpy of formation compared with experimental values. The obtained seven effective molecular descriptors are then used as input set to establish three 7-11-1 neural network-based correction models to improve the accuracy of SQC methods. By using the developed correction models, the mean absolute errors for ΔfHo of PM3, PM6, and PM7 methods are reduced from 22.36, 18.60, and 17.27 to 9.86, 9.83, and 8.95, respectively, in kJ/mol. Meanwhile, the results of the test set show that the neural network does not have the problem of overfitting. Detailed analysis of the seven effective molecular descriptors indicates that the major source of the correction models is the electron-withdrawing effect. The developed ANN models for the three selected SQC methods provide an efficient method for the quick and accurate prediction of thermodynamic properties.},
	annote = {cite-code, cite-model},
	author = {Wan, Zhongyu and Wang, Quan-De and Liang, Jinhu},
	date-added = {2021-04-18 14:58:28 -0400},
	date-modified = {2021-04-18 15:01:38 -0400},
	doi = {https://doi.org/10.1002/qua.26441},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.26441},
	journal = {International Journal of Quantum Chemistry},
	keywords = {artificial neural network, enthalpy of formation, molecular descriptors, semiempirical quantum chemistry methods},
	number = {2},
	pages = {e26441},
	title = {Accurate prediction of standard enthalpy of formation based on semiempirical quantum chemistry methods with artificial neural network and molecular descriptors},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26441},
	volume = {121},
	year = {2021},
	Bdsk-Url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26441},
	Bdsk-Url-2 = {https://doi.org/10.1002/qua.26441}}

@article{LIU2021118373,
	abstract = {New Particle Formation (NPF) is considered as the dominant source of aerosol particles, influencing the environment and human health tightly. In recent years, valine (VAL) has been identified in field detection in urban areas, which reveals that VAL may play an important role in participating in atmospheric nucleation. However, there have been no categorical reports explaining how VAL participates in the multi-component nucleation with precursor Sulfuric Acid (SA) and the atmospheric organic amine Dimethylamine (DMA) so far. In this paper, quantum chemical calculation and cluster kinetic simulation have been studied to research the nucleation mechanism of (SA)x(DMA)y(VAL)z (0≤x, y, z ≤ 3) system. Structural and thermodynamic analysis at ωB97XD/6-31++G(d, p) theory level and basis set shows that VAL could form various stable structures through hydrogen bonds with SA and DMA, and proton transfer in ternary structure enhances the stability of system. However, in the clusters of SA-DMA-VAL system with large numbers of molecules, there has been steric hindrance between molecules of cluster due to the high proportion of inactive groups in VAL, which insulates the further formation of hydrogen bonds. With regard to the distribution of Gibbs free energy on VAL-DMA grid, the energy decreases rapidly along the diagonal with VAL and DMA in different numbers of SA molecules, predicting possible nucleation path along the diagonal. Besides, there is a synergistic effect of VAL in system SA-DMA-VAL, and VAL tends to replace the role of DMA in the ternary system. Evaporation rate analysis indicates that the ternary system containing SA is more stable. The simulating formation rate of SA-DMA-VAL system compared with the CLOUD experiment at CERN shows that the nucleation potential of SA-DMA-VAL is superior to that of SA-NH3-H2O, but inferior to that of SA-DMA-H2O, inferring that VAL may show more potential in growth processes than the initial nucleation processes in the light of the specific value of formation rate.},
	annote = {no-access},
	author = {Ying Liu and Yi-Rong Liu and Ya-Juan Feng and Teng Huang and Shuai Jiang and Zi-Hang Wang and Hui Cao and Wei Huang},
	date-added = {2021-04-18 14:57:03 -0400},
	date-modified = {2021-04-18 14:57:09 -0400},
	doi = {https://doi.org/10.1016/j.atmosenv.2021.118373},
	issn = {1352-2310},
	journal = {Atmospheric Environment},
	keywords = {Nucleation mechanism, Amino acid, Topological analysis, Evaporation rate, Atmospheric relevance},
	pages = {118373},
	title = {Valine involved sulfuric acid-dimethylamine ternary homogeneous nucleation and its atmospheric implications},
	url = {https://www.sciencedirect.com/science/article/pii/S1352231021001928},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S1352231021001928},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.atmosenv.2021.118373}}

@article{WEI2021153378,
	abstract = {Background
In our previous study, we demonstrated the hepatoprotective effect of Herpetospermum pedunculosum in cholestatic rats. A bioassay-guided study also led to the identification and isolation of a lignan, dihydrodiconiferyl alcohol (DA) from the seeds of H. pedunculosum.
Purpose
To investigate whether DA could alleviate cholestasis and determine the mechanisms underlying such action.
Methods
Male Sprague-Dawley (SD) rats were administered with DA (10, 20 or 40 mg/kg) intragastrically once daily for 7 days prior to treatment with α-naphthylisothiocyanate (ANIT) (60 mg/kg). We then evaluated the levels of a range of serum indicators, determined bile flow, and carried out histopathological analyses. Western blotting was then used to investigate the levels of inflammatory mediators and the Farnesoid X Receptor (FXR), proteins involved in the downstream biosynthesis of bile acids, and a range of transport proteins. Molecular docking was used to simulate the interaction between DA and FXR. Cell viability of human hepatocytes (L-02) cells was determined by MTT. Then, we treated guggulsterone-inhibited L-02 cells, Si-FXR L-02 cells, and FXR-overexpression cells with the FXR agonist GW4064 (6 μM) or DA (25, 50 and 100 μM) for 24 h before detecting gene and protein expression by RT-PCR and western blotting, respectively.
Results
DA significantly attenuated ANIT-induced cholestasis in SD rats by reducing liver function indicators in the serum, increasing bile flow, improving the recovery of histopathological injuries in the liver, and by alleviating pro-inflammatory cytokines in the liver. DA also increased the expression levels of FXR and altered the levels of downstream proteins in the liver tissues, thus indicating that DA might alleviate cholestasis by regulating the FXR. Molecular docking simulations predicted that DA was as an agonist of FXR. In vitro mechanical studies further showed that DA increased the mRNA and protein expression levels of FXR, Small Heterodimer Partner 1/2, Bile Salt Export Pump, Multidrug Resistance-associated Protein 2, and Na+/taurocholate Co-transporting Polypeptide, in both guggulsterone-inhibited and Si-FXR L-02 cells. Moreover, DA enhanced the mRNA and protein expression of FXR, and its downstream genes and proteins, in L-02 cells containing an FXR-overexpression plasmid.
Conclusion
DA may represent an effective agonist for FXR has significant therapeutic potential for the treatment of cholestatic liver injury.},
	annote = {no-access},
	author = {Xiaodong Wei and Yingxiong Ma and Zhaoyue Dong and Guowei Wang and Xiaozhong Lan and Zhihua Liao and Min Chen},
	date-added = {2021-04-18 14:54:48 -0400},
	date-modified = {2021-04-18 14:55:14 -0400},
	doi = {https://doi.org/10.1016/j.phymed.2020.153378},
	issn = {0944-7113},
	journal = {Phytomedicine},
	keywords = {, Dehydrodiconiferyl alcohol, Cholestasis, α-naphthylisothiocyanate, Farnesoid X receptor},
	pages = {153378},
	title = {Dehydrodiconiferyl alcohol, a lignan from Herpetospermum pedunculosum, alleviates cholestasis by activating pathways associated with the farnesoid X receptor},
	url = {https://www.sciencedirect.com/science/article/pii/S0944711320302099},
	volume = {80},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0944711320302099},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.phymed.2020.153378}}

@article{molecules26072098,
	abstract = {(1) Background: Data accuracy plays a key role in determining the model performances and the field of metabolism prediction suffers from the lack of truly reliable data. To enhance the accuracy of metabolic data, we recently proposed a manually curated database collected by a meta-analysis of the specialized literature (MetaQSAR). Here we aim to further increase data accuracy by focusing on publications reporting exhaustive metabolic trees. This selection should indeed reduce the number of false negative data. (2) Methods: A new metabolic database (MetaTREE) was thus collected and utilized to extract a dataset for metabolic data concerning glutathione conjugation (MT-dataset). After proper pre-processing, this dataset, along with the corresponding dataset extracted from MetaQSAR (MQ-dataset), was utilized to develop binary classification models using a random forest algorithm. (3) Results: The comparison of the models generated by the two collected datasets reveals the better performances reached by the MT-dataset (MCC raised from 0.63 to 0.67, sensitivity from 0.56 to 0.58). The analysis of the applicability domain also confirms that the model based on the MT-dataset shows a more robust predictive power with a larger applicability domain. (4) Conclusions: These results confirm that focusing on metabolic trees represents a convenient approach to increase data accuracy by reducing the false negative cases. The encouraging performances shown by the models developed by the MT-dataset invites to use of MetaTREE for predictive studies in the field of xenobiotic metabolism.},
	annote = {cite-model, cite-code, qsar},
	article-number = {2098},
	author = {Mazzolari, Angelica and Sommaruga, Luca and Pedretti, Alessandro and Vistoli, Giulio},
	date-added = {2021-04-18 14:53:39 -0400},
	date-modified = {2021-04-18 14:54:03 -0400},
	doi = {10.3390/molecules26072098},
	issn = {1420-3049},
	journal = {Molecules},
	number = {7},
	title = {MetaTREE, a Novel Database Focused on Metabolic Trees, Predicts an Important Detoxification Mechanism: The Glutathione Conjugation},
	url = {https://www.mdpi.com/1420-3049/26/7/2098},
	volume = {26},
	year = {2021},
	Bdsk-Url-1 = {https://www.mdpi.com/1420-3049/26/7/2098},
	Bdsk-Url-2 = {https://doi.org/10.3390/molecules26072098}}

@article{TSAPLEV2021112967,
	abstract = {Earlier, we reported our finding of the fluorescence emission derived from the triple-deprotonated form of curcumin (Cur3--) in dimethyl sulfoxide (DMSO) in the presence of NaOH. Herein, we disclose the results of the studies on the luminescent properties of Cur3-- in the presence of LiOH, NaOH and KOH, which are indicative of the cation-dependent behavior of the Cur3-- fluorescence excitation and the emission spectra. The fluorescence quantum yield in the presence of LiOH and NaOH significantly increases compared to that of neutral curcumin. Studying the fluorescence polarization properties revealed that the observed increase in the quantum yield is accounted for by the decreased rate of the nonradiative excited-state deactivation. We assume that the origin of the cation-dependent fluorescence properties refers to the formation of coordination bonds between the alkali metal cations and the oxygen atoms of the β-diketone (keto-enol) group of curcumin, which is substantiated by the experimental results and supported by the semiempirical modeling.},
	annote = {no-access},
	author = {Yurii B. Tsaplev and Viktoria A. Lapina and Aleksei V. Trofimov},
	date-added = {2021-04-18 14:52:53 -0400},
	date-modified = {2021-04-18 14:52:58 -0400},
	doi = {https://doi.org/10.1016/j.jphotochem.2020.112967},
	issn = {1010-6030},
	journal = {Journal of Photochemistry and Photobiology A: Chemistry},
	keywords = {Curcumin, Alkaline, Dimethyl sulfoxide, Fluorescence, Cationochromism},
	pages = {112967},
	title = {Fluorescence of curcumin in alkaline dimethyl sulfoxide and the effects of alkali metal cations on it},
	url = {https://www.sciencedirect.com/science/article/pii/S1010603020307644},
	volume = {405},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S1010603020307644},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.jphotochem.2020.112967}}

@article{PERES2021113266,
	abstract = {A new material formed by graphene oxide and a perylene diimide derivate was successfully synthesized and applied for photocatalytic degradation of methylene blue (MB). The perylene diimide was modified with APTES in a simple chemical method to force excimer formation. The new material showed to be capable of stabilizing the electron/ hole pair initiated by perylene diimides excimers formed after excitation in the visible range. Theoretical calculations show that the structures in which GO is perpendicular to the perylene core are more prompt to form the anion radical than pure GO, indicating that perpendicular excimers could play an important role in stabilizing electrons. This way, efficient removal of 90 % of methylene blue was observed since the mechanism of photodegradation of a dye depends on the efficient separation and mobility of carriers.},
	annote = {no-access},
	author = {Rayana Martins Peres and Josu{\'e} S.B. Forero and Rodrigo Jos{\'e} Corr{\^e}a},
	date-added = {2021-04-18 14:50:59 -0400},
	date-modified = {2021-04-18 14:51:12 -0400},
	doi = {https://doi.org/10.1016/j.jphotochem.2021.113266},
	issn = {1010-6030},
	journal = {Journal of Photochemistry and Photobiology A: Chemistry},
	keywords = {Graphene oxide, Perylene diimide, Methylene blue, Excimer, Charge separation},
	pages = {113266},
	title = {Tuning the graphene oxide chemistry by excimer formation: The stabilization of electron/hole pair on sp2 surface},
	url = {https://www.sciencedirect.com/science/article/pii/S1010603021001386},
	volume = {414},
	year = {2021},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S1010603021001386},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.jphotochem.2021.113266}}

@article{Zhang:2021vw,
	annote = {gui=lumpac},
	author = {Zhang, Yonghong and Thor, Waygen and Wong, Ka-Leung and Tanner, Peter A.},
	booktitle = {The Journal of Physical Chemistry C},
	da = {2021/04/08},
	date = {2021/04/08},
	date-added = {2021-04-18 14:45:21 -0400},
	date-modified = {2021-04-18 14:45:28 -0400},
	doi = {10.1021/acs.jpcc.1c00158},
	isbn = {1932-7447},
	journal = {The Journal of Physical Chemistry C},
	journal1 = {J. Phys. Chem. C},
	m3 = {doi: 10.1021/acs.jpcc.1c00158},
	month = {04},
	number = {13},
	pages = {7022--7033},
	publisher = {American Chemical Society},
	title = {Determination of Triplet State Energy and the Absorption Spectrum for a Lanthanide Complex},
	ty = {JOUR},
	url = {https://doi.org/10.1021/acs.jpcc.1c00158},
	volume = {125},
	year = {2021},
	year1 = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1021/acs.jpcc.1c00158}}

@article{Chen:2021tp,
	annote = {cite-model},
	author = {Chen, Cheng-Yu and Lee, Woonghee and Renhowe, Paul A. and Jung, Joon and Montfort, William R.},
	booktitle = {Protein Science},
	date-added = {2021-04-18 14:43:45 -0400},
	date-modified = {2021-04-23 17:56:40 -0400},
	doi = {https://doi.org/10.1002/pro.4005},
	isbn = {0961-8368},
	journal = {Protein Science},
	journal1 = {Protein Science},
	journal2 = {Protein Science},
	keywords = {drug binding; guanylate cyclase; H-NOX; nitric oxide; NMR; solution structure},
	m3 = {https://doi.org/10.1002/pro.4005},
	n2 = {Abstract Heme-nitric oxide/oxygen binding (H-NOX) domains bind gaseous ligands for signal transduction in organisms spanning prokaryotic and eukaryotic kingdoms. In the bioluminescent marine bacterium Shewanella woodyi (Sw), H-NOX proteins regulate quorum sensing and biofilm formation. In higher animals, soluble guanylyl cyclase (sGC) binds nitric oxide with an H-NOX domain to induce cyclase activity and regulate vascular tone, wound healing and memory formation. sGC also binds stimulator compounds targeting cardiovascular disease. The molecular details of stimulator binding to sGC remain obscure but involve a binding pocket near an interface between H-NOX and coiled-coil domains. Here, we report the full NMR structure for CO-ligated Sw H-NOX in the presence and absence of stimulator compound IWP-051, and its backbone dynamics. Nonplanar heme geometry was retained using a semi-empirical quantum potential energy approach. Although IWP-051 binding is weak, a single binding conformation was found at the interface of the two H-NOX subdomains, near but not overlapping with sites identified in sGC. Binding leads to rotation of the subdomains and closure of the binding pocket. Backbone dynamics are similar across both domains except for two helix-connecting loops, which display increased dynamics that are further enhanced by compound binding. Structure-based sequence analyses indicate high sequence diversity in the binding pocket, but the pocket itself appears conserved among H-NOX proteins. The largest dynamical loop lies at the interface between Sw H-NOX and its binding partner as well as in the interface with the coiled coil in sGC, suggesting a critical role for the loop in signal transduction.},
	number = {2},
	pages = {448--463},
	publisher = {John Wiley \& Sons, Ltd},
	title = {Solution structures of the Shewanella woodyi H-NOX protein in the presence and absence of soluble guanylyl cyclase stimulator IWP-051},
	ty = {JOUR},
	url = {https://doi.org/10.1002/pro.4005},
	volume = {30},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.1002/pro.4005}}

@article{MALTSEV2021105792,
	abstract = {A study on the anxiolytic activity of the new derivatives of 11-dialkylaminoethyl-2,3,4,5-tetrahydrodiazepino[1,2-a]benzimidazole, containing privileged scaffolds of benzodiazepine and benzimidazole in their structure, was conducted. The cytotoxic properties of low levels of six compounds were preliminary determined in vitro using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide test. The screening of these substances for anxiolytic activity was conducted using elevated plus maze (EPM) test in vivo, and DAB-21 was found to be the most active compound. The acute toxicity of DAB-21 was determined as less toxic than that of diazepam. The dose-dependent effect of the most active compound revealed a minimum dose of 1.26 mg/kg, which resulted in the maximum counterphobic effect. The effect of DAB-21 was superior in a number of tests compared with that of diazepam, which indicated a high level of tranquilizing activity for DAB-21. The results of in silico docking analysis suggest that DAB-21 should have a slightly lower anxiolytic activity than diazepam, but should exhibit greater specific affinity for the benzodiazepine site of the GABAA receptor, in comparison with its GABA-binding site. The interaction between DAB-21 and flumazenil in terms of EPM verifies the GABAergic mechanism of action of DAB-21. Our results highlight the potential of 11-dialkylaminomethyl-2,3,4,5-tetrahydrodiazepino[1,2-a]benzimidazoles as promising compounds in the search for new highly effective anxiolytics.},
	annote = {no-access},
	author = {Dmitriy V. Maltsev and Alexander A. Spasov and Dmitriy S. Yakovlev and Pavel M. Vassiliev and Maria O. Skripka and Mikhail V. Miroshnikov and Kira T. Sultanova and Andrey N. Kochetkov and Lyudmila N. Divaeva and Tatyana A. Kuzmenko and Anatolii S. Morkovnik},
	date-added = {2021-04-18 14:37:56 -0400},
	date-modified = {2021-04-18 14:38:11 -0400},
	doi = {https://doi.org/10.1016/j.ejps.2021.105792},
	issn = {0928-0987},
	journal = {European Journal of Pharmaceutical Sciences},
	keywords = {DAB-21, diazepino[1,2-a]benzimidazole, privileged scaffolds, neuropsychotropic activity, anxiolytic, HepG2 cell line},
	pages = {105792},
	title = {Searching for new anxiolytic agents among derivatives of 11-dialkylaminoethyl-2,3,4,5-tetrahydrodiazepino[1,2-a]benzimidazole},
	url = {https://www.sciencedirect.com/science/article/pii/S0928098721000944},
	volume = {161},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0928098721000944},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.ejps.2021.105792}}

@article{JUNG2021131763,
	abstract = {It has been known that the enantioselectivity of the chiral Lewis base-catalyzed, SiCl4-promoted kinetic resolution of α,β-dichloro cis-vinyl epoxide is highly influenced by the configuration of the distal β-chlorine-bearing stereocenter. In this report, the precise nature of this unusual remote stereocontrol was investigated both experimentally and theoretically. Upon examination of a substrate that has an alkyl group in place of the β-chlorine substituent, the spatial location of major catalyst-substrate interaction was determined. Subsequently, through computational analysis of transition states, the steric repulsion by the β-substituents as well as the additional C--H/π hydrogen bond by the alkyl substituent were proposed as the crucial stereo-determining factors.},
	annote = {cite-code},
	author = {Jungi Jung and Mugeon Song and Jun-Ho Choi and Won-jin Chung},
	date-added = {2021-04-18 14:36:07 -0400},
	date-modified = {2021-04-18 14:36:23 -0400},
	doi = {https://doi.org/10.1016/j.tet.2020.131763},
	issn = {0040-4020},
	journal = {Tetrahedron},
	keywords = {Epoxide opening, Kinetic resolution, Lewis base catalysis, Silicon tetrachloride, C--H/π hydrogen bond},
	pages = {131763},
	title = {Mechanistic investigation on the remote stereocontrol in the chiral Lewis base-catalyzed, SiCl4-promoted kinetic resolution of chlorinated cis-vinyl epoxides},
	url = {https://www.sciencedirect.com/science/article/pii/S0040402020309984},
	volume = {77},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0040402020309984},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.tet.2020.131763}}

@article{BANFI2021,
	author = {Banfi, Felipe Finger AND Krombauer, Gabriela Camila AND Fonseca, Amanda Luisa da AND Nunes, Renata Rachide AND Andrade, Silmara Nunes AND Rezende, Millena Alves de AND Chaves, Mariana Helena AND Mon\~A\S\~A\poundso Filho, Evaldo dos Santos AND Taranto, Alex Guterres AND Rodrigues, Domingos de Jesus AND Vieira J\~A\textordmasculinenior, Gerardo Magela AND Castro, Whocely Victor de AND Varotti, Fernando de Pilla AND Sanchez, Bruno Antonio Marinho},
	date-added = {2021-04-18 14:34:54 -0400},
	date-modified = {2021-04-18 14:35:09 -0400},
	doi = {10.1590/1678-9199-jvatitd-2020-0073},
	issn = {1678-9199},
	journal = {{Journal of Venomous Animals and Toxins including Tropical Diseases}},
	language = {en},
	month = {00},
	publisher = {scielo},
	title = {{Dehydrobufotenin extracted from the Amazonian toad Rhinella marina (Anura: Bufonidae) as a prototype molecule for the development of antiplasmodial drugs}},
	url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992021000100301&nrm=iso},
	volume = {27},
	year = {2021},
	Bdsk-Url-1 = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992021000100301&nrm=iso}}

@article{FLISZARNYUL2021115945,
	abstract = {SZV 1287 is our novel multi-target analgesic, which seems to be a promising drug candidate for the treatment of neuropathic pain. Therefore, the drug development process has been started in 2016. Since the pharmacokinetic characterization of a drug candidate is essential and albumin binding of drugs can strongly affect their pharmacokinetic properties, herein we provided the detailed investigation and characterization of the interaction of SZV 1287 and its known metabolites with serum albumin. In a preliminary animal study, we demonstrated the appearance of SZV 1287, oxaprozin, L 2799, L 2805, and L 2811 in the circulation after the per os administration of the parent compound to rats. Then albumin-ligand interactions were examined employing fluorescence spectroscopy, affinity chromatography, ultrafiltration, ultracentrifugation, and molecular modeling. Finally, we tested the potential species dependent differences in the albumin binding of SZV 1287, employing human, bovine, porcine, and rat serum albumins. Our results demonstrated that SZV 1287 and its metabolites form highly stable complexes with albumin (Ka = 105 to 106 L/mol). Furthermore, SZV 1287 occupies Sudlow's Site II on human serum albumin. Therefore, it is reasonable to hypothesize that SZV 1287-albumin interaction is an important issue regarding the pharmacokinetics of this drug candidate.},
	annote = {cite-code, cite-model, gui=maestro},
	author = {Eszter Flisz{\'a}r-Ny{\'u}l and Zelma Faisal and Violetta Mohos and Di{\'a}na Derd{\'a}k and Be{\'a}ta Lemli and Tam{\'a}s K{\'a}lai and Cec{\'\i}lia S{\'a}r and Bal{\'a}zs Z. Zsid{\'o} and Csaba Het{\'e}nyi and {\'A}d{\'a}m I. Horv{\'a}th and Zsuzsanna Helyes and Ruth Deme and D{\'o}ra Bogd{\'a}n and Andrea Czompa and P{\'e}ter M{\'a}tyus and Mikl{\'o}s Po{\'o}r},
	date-added = {2021-04-18 14:32:29 -0400},
	date-modified = {2021-04-18 14:32:59 -0400},
	doi = {https://doi.org/10.1016/j.molliq.2021.115945},
	issn = {0167-7322},
	journal = {Journal of Molecular Liquids},
	keywords = {SZV 1287, Oxaprozin, Serum albumin, Albumin-ligand interaction, Pharmacokinetics},
	pages = {115945},
	title = {Interaction of SZV 1287, a novel oxime analgesic drug candidate, and its metabolites with serum albumin},
	url = {https://www.sciencedirect.com/science/article/pii/S0167732221006723},
	volume = {333},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0167732221006723},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.molliq.2021.115945}}

@article{BONI2021117444,
	abstract = {Nanostructured polyelectrolyte complexes (nano PECs) based on biopolymers are an important technological strategy to target drugs to the action and/or absorption site in a more effective way. In this work, computational studies were performed to predict the ionization, spatial arrangement and interaction energies of chitosan (CS), hyaluronic acid (HA), and hypromellose phthalate (HP), for the design of nano PEC carriers for methotrexate (MTX). The optimal pH range (5.0--5.5) for preparing nano PECs was selected by experimental and computational methodologies, favoring the polymers interactions. CS, HA, HP and MTX addition order was also rationalized, maximizing their interactions and MTX entrapment. Spherical nano-sized particles (256--575 nm, by dynamic light scattering measurement) with positive surface charge (+25.5 to +29.2 mV) were successfully prepared. The MTX association efficiency ranged from 20 to 32 %. XRD analyses evidenced the formation of a new material with an organized structure, in relation to raw polymers.},
	annote = {cite-code},
	author = {Fernanda Isadora Boni and Beatriz Stringhetti Ferreira Cury and Nat{\'a}lia Noronha Ferreira and Deiver Alessandro Teixeira and Maria Palmira Daflon Gremi{\~a}o},
	date-added = {2021-04-18 14:29:02 -0400},
	date-modified = {2021-04-18 14:29:29 -0400},
	doi = {https://doi.org/10.1016/j.carbpol.2020.117444},
	issn = {0144-8617},
	journal = {Carbohydrate Polymers},
	keywords = {Hyaluronic acid, Hypromellose phthalate, Methotrexate, Quantum chemical calculations, Semi-empirical parametric method level, Nanometric polyelectrolyte complex},
	pages = {117444},
	title = {Computational and experimental approaches for chitosan-based nano PECs design: Insights on a deeper comprehension of nanostructure formation},
	url = {https://www.sciencedirect.com/science/article/pii/S0144861720316179},
	volume = {254},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0144861720316179},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.carbpol.2020.117444}}

@incollection{SCIOR2021205,
	abstract = {Medicinal chemists without practical molecular modeling experience are invited to practice simple docking simulations of small organic molecules into biomolecular targets. These targets are proteins such as enzymes, receptors, or ion channels in common cases, but can also be DNA or RNA or combinations thereof. Of note, the target is sometimes also referred to as macromolecule or biopolymer in the docking programs. In-house knowledge has been acquired over the last decade or so and is disclosed here to train users to practice docking on personal computers. This guide shows how to combine Autodock Vina with Autodock Tools, Swiss PDB Viewer, and Vega ZZ to prepare the input data and analyze the output data after docking. Special attention is drawn to include aspects, rarely laid open, about file management, input data preparation, and solving problems in a do-it-yourself manner. Pharmaceutical or medicinal chemistry knowledge is expected, while the practitioner is introduced step by step into the practical work of computational molecular docking simulations. The recommended way to use this chapter is to read through it first and then go into practical mode to carry out the docking simulation.},
	annote = {no-access},
	author = {Thomas Scior},
	booktitle = {Molecular Docking for Computer-Aided Drug Design},
	date-added = {2021-04-18 14:28:02 -0400},
	date-modified = {2021-04-18 14:28:31 -0400},
	doi = {https://doi.org/10.1016/B978-0-12-822312-3.00003-5},
	editor = {Mohane S. Coumar},
	isbn = {978-0-12-822312-3},
	keywords = {Binding site, Docking, Free software, Input data preparation, Ligand, Molecular data formats, Pitfalls, Receptor, Tutorial, User guide, Virtual screening, Workarounds},
	pages = {205-227},
	publisher = {Academic Press},
	title = {Chapter 10 - Do It Yourself---Dock It Yourself: General Concepts and Practical Considerations for Beginners to Start Molecular Ligand--Target Docking Simulations},
	url = {https://www.sciencedirect.com/science/article/pii/B9780128223123000035},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/B9780128223123000035},
	Bdsk-Url-2 = {https://doi.org/10.1016/B978-0-12-822312-3.00003-5}}

@article{moorthy2021silico,
	annote = {qsar, no-access},
	author = {Moorthy, Narayana Subbiah HN},
	date-added = {2021-04-18 14:25:22 -0400},
	date-modified = {2021-04-18 14:26:16 -0400},
	doi = {10.2174/1570180817999200818155601},
	journal = {Letters in Drug Design \& Discovery},
	number = {1},
	pages = {93--103},
	publisher = {Bentham Science Publishers},
	title = {In Silico Based Structural and Fingerprint Analysis of Structurally Diverse AT1 inhibitors},
	volume = {18},
	year = {2021},
	Bdsk-Url-1 = {https://doi.org/10.2174/1570180817999200818155601}}

@article{ZHU2021115213,
	abstract = {In this study, the dynamic behavior, geometric structure, electron density parameters and infrared spectra for toluene(T)-water(W) systems were calculated using molecular dynamics simulation, quantum chemistry calculation and wavefunction analysis. Dynamic simulations demonstrate that there are three interaction ways, Hw{\ldots}πT, Hw{\ldots}CT and Ow{\ldots}CT, in TW system, and due to these interactions, each toluene can form 5~10H-bonds with water molecules, indicating that the toluene are easy to form H-bonds with H2O particularly at low temperature, while high temperature is harmful for that. Analyses of the TWn(n=1--10) cluster by quantum chemistry calculations and wavefunction analysis indicate that HW{\ldots}πT is primarily responsible for the stabilization of TWna(n=1--2), while OW{\ldots}HT is primarily responsible for the stabilization of TWna (n=3--10). In addition, Hw{\ldots}πT, Hw{\ldots}CT and Ow{\ldots}CT show the dispersion and electrostatic nature. Furthermore, the degeneracy and delocalization of free OH and donor O-H modes are changed due to the formation of Hw{\ldots}πT, Hw{\ldots}CT and Ow{\ldots}CT. The results displayed here have potential application prospects for the development of molecular recognition systems involving aromatic interactions.},
	annote = {no-access},
	author = {Tingting Zhu and Ping Ning and Zezhi Chen},
	date-added = {2021-04-18 14:19:36 -0400},
	date-modified = {2021-04-18 14:19:44 -0400},
	doi = {https://doi.org/10.1016/j.molliq.2020.115213},
	issn = {0167-7322},
	journal = {Journal of Molecular Liquids},
	keywords = {Toluene-HO(=1--10), Weak interaction, Spectroscopic, Electron density},
	pages = {115213},
	title = {Structures and spectroscopic properties of low-energy candidate structures for toluene-(H2O)n (n=1--10) clusters},
	url = {https://www.sciencedirect.com/science/article/pii/S0167732220374559},
	volume = {326},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0167732220374559},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.molliq.2020.115213}}

@article{D0FO03059G,
	abstract = {Gout is a common inflammatory arthritis associated with various comorbidities{,} such as cardiovascular disease and metabolic syndrome. Xanthine oxidase inhibitors (XOIs) have emerged as effective substances to control gout. Much attention has been given to the search for natural XOIs. In this study{,} a molecular database of natural XOIs was created for modeling purposes. Quantitative structure--activity relationship models were developed by combining various machine learning approaches and three descriptor pools. The models revealed several features of XOIs{,} including hydrophobicity and steric molecular structures. Experimental results showed the xanthine oxidase (XO) inhibitory activity of predicted compounds. Vanillic acid was identified as a promising new XOI candidate{,} with an IC50 of 0.593 μg mL−1. The functions of hydrogen bonds and hydrophobic interactions in XO activity inhibition were confirmed by molecular docking. This study fills knowledge gaps pertaining to the discovery of natural XOIs and to the interaction mechanisms between XOIs and XO.},
	annote = {qsar, gui=moe},
	author = {Zhou, Qian and Yin, Jia-Yi and Liang, Wei-Yue and Chen, Dong-Mei and Yuan, Qing and Feng, Bao-long and Zhang, Ying-Hua and Wang, Yu-Tang},
	date-added = {2021-04-18 14:17:01 -0400},
	date-modified = {2021-04-18 14:17:11 -0400},
	doi = {10.1039/D0FO03059G},
	issue = {4},
	journal = {Food Funct.},
	pages = {1580-1589},
	publisher = {The Royal Society of Chemistry},
	title = {Various machine learning approaches coupled with molecule simulation in the screening of natural compounds with xanthine oxidase inhibitory activity},
	url = {http://dx.doi.org/10.1039/D0FO03059G},
	volume = {12},
	year = {2021},
	Bdsk-Url-1 = {http://dx.doi.org/10.1039/D0FO03059G}}

@article{CHETTRI2021101043,
	abstract = {The hydrogen storage capacity of Boron Nitride nanosheet has been performed by using density functional theory (DFT). All the structural and electronic properties of a monolayer BN nanosheet are in well agreement with the previously reported results. Out of the four possible adsorption sites, centre is the most favourable adsorption site for H2 molecule with binding energy ∼0.212 eV/H2. We have proceeded our calculations considering this adsorption site. The calculated direct band gap within GGA and HSE for pristine h-BN monolayer are found to be 4.669 eV and 5.63 eV, respectively. In our calculation the Hydrogen storage capacity of BN nanosheet was found to be 6.7 wt.% well within benchmark value (6.0%) with an average adsorption energy of (∼0.128 eV/H2). Bader analysis revealed that the charge transfer from BN nanosheet to the H2 molecule is very low (0.004--0.065∣ e ∣) leading to weak binding of the H2 molecule. The calculated desorption temperature was found to be low due to low average adsorption energy of the H2 molecule. Also, upon increasing the number of H2 molecule adsorption a feeble tuning of the band gap has been observed due to the contribution of the 1s orbital of H2 molecule.},
	annote = {no-access},
	author = {B. Chettri and P.K. Patra and Nguyen N. Hieu and D.P. Rai},
	date-added = {2021-04-18 14:13:21 -0400},
	date-modified = {2021-04-18 14:13:28 -0400},
	doi = {https://doi.org/10.1016/j.surfin.2021.101043},
	issn = {2468-0230},
	journal = {Surfaces and Interfaces},
	keywords = {, DFT, Adsorption energy, Weight percentage},
	pages = {101043},
	title = {Hexagonal boron nitride (h-BN) nanosheet as a potential hydrogen adsorption material: A density functional theory (DFT) study},
	url = {https://www.sciencedirect.com/science/article/pii/S2468023021001206},
	volume = {24},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S2468023021001206},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.surfin.2021.101043}}

@article{CHHETRI2021129178,
	abstract = {Four novel ionic liquid tagged azo-azomethine derivatives (L1-L4) have been prepared by the condensation reaction of azo-coupled ortho-vaniline precursor with amino functionalised imidazole derivative and the synthesized derivatives (L1-L4) have been characterized by different analytical and spectroscopic techniques. Molecular docking studies were carried out to ascertain the inhibitory action of studied ligands (L1-L4) against the Main Protease (6LU7) of novel coronavisrus (COVID-19). The result of the docking of L1-L4 showed a significant inhibitory action against the Main protease (Mpro) of SARS-CoV-2 and the binding energy (ΔG) values of the ligands (L1-L4) against the protein 6LU7 have found to be −7.7 Kcal/mole (L1), −7.0 Kcal/mole (L2), −7.9 Kcal/mole (L3), and −7.9 Kcal/mole (L4).The efficiency of the ligands has been compared with the FDA approved and clinically trial drugs such as remdesivir, Chloroquin and Hydroxychloroquin and native ligand N3 of main protease 6LU7 to ascertain the inhibitory potential of the studied ligands (L1-L4) against the protein 6LU7. Pharmacokinetic properties (ADME) of the ligands (L1-L4) have also been studied.},
	annote = {no-access},
	author = {Abhijit Chhetri and Sailesh Chettri and Pranesh Rai and Biswajit Sinha and Dhiraj Brahman},
	date-added = {2021-04-18 14:12:51 -0400},
	date-modified = {2021-04-18 14:12:56 -0400},
	doi = {https://doi.org/10.1016/j.molstruc.2020.129178},
	issn = {0022-2860},
	journal = {Journal of Molecular Structure},
	keywords = {Azo imidazole, Molecular docking, Binding energy, SARS-CoV-2 M, Pharmacokinetics, Remdesivir, Chloroquin, Hydroxychloroquin},
	pages = {129178},
	title = {Exploration of inhibitory action of Azo imidazole derivatives against COVID-19 main protease (Mpro): A computational study},
	url = {https://www.sciencedirect.com/science/article/pii/S002228602031499X},
	volume = {1224},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S002228602031499X},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.molstruc.2020.129178}}

@article{AJAYEOBA2021130275,
	abstract = {Three aroylhydrazones, acetophenone-Benzoylhydrazone (I), p-hydroxy-acetophenone-benzoylhydrazone (II) and p-nitro- acetophenone-benzoylhydrazone (III) have been synthesized and further analyzed with the aid of IR, UV-Vis, and NMR spectroscopic and X-ray Crystallographic techniques. The optimized molecular structures were determined by Density Functional Theory (DFT) using the B3LYP function comprising the 6-311++G (2d, 2p) basis set. The calculated and experimental results for the NMR spectroscopic technique were observed to be consistent. The two reported crystals are monoclinic in the same space group of P21/c. Hirshfeld surface analyses revealed H···H as the most important intermolecular interactions in compounds II and III. The molecular docking of the compounds against three enzymes - aldose reductase, aldehyde reductase, and β-glucosidase were also carried out where compound III displayed the best inhibition of the enzymes with a binding energy of -11.30, -9.58 and -11.10 Kcal mol−1 against aldose reductase, aldehyde reductase, and β- glucosidase respectively.},
	annote = {no-access},
	author = {Temitope A. Ajayeoba and Joseph O. Woods and Ayowole O. Ayeni and Tomilola J. Ajayi and Raji A. Akeem and Eric C. Hosten and Olawale F. Akinyele},
	date-added = {2021-04-18 14:11:24 -0400},
	date-modified = {2021-04-18 14:11:32 -0400},
	doi = {https://doi.org/10.1016/j.molstruc.2021.130275},
	issn = {0022-2860},
	journal = {Journal of Molecular Structure},
	keywords = {Hydrazones, Aldose reductase, DFT, Hirshfeld surface analysis, Molecular docking},
	pages = {130275},
	title = {Synthesis, crystallographic, computational and molecular docking studies of new acetophenone-benzoylhydrazones},
	url = {https://www.sciencedirect.com/science/article/pii/S0022286021004063},
	volume = {1237},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0022286021004063},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.molstruc.2021.130275}}

@article{CHHETRI2021129230,
	abstract = {A series of six novel imidazole anchored azo-imidazole derivatives (L1-L6) have been prepared by the simple condensation reaction of azo-coupled ortho-vaniline precursor with amino functionalised imidazole derivative and the synthesized derivatives (L1-L6) have been characterized by different analytical and spectroscopic techniques. Molecular docking studies were carried out to ascertain the inhibitory action of studied ligands (L1-L6) against the Main Protease (6LU7) of novel coronavirus (COVID-19). The result of the docking of L1-L6 showed a significant inhibitory action against the Main protease (Mpro) of SARS-CoV-2 and the binding energy (ΔG) values of the ligands (L1-L6) against the protein 6LU7 have found to be -7.7 Kcal/mole (L1), -7.4 Kcal/mole (L2), -6.7 Kcal/mole (L3), -7.9 Kcal/mole (L4), -8.1 Kcal/mole (L5) and -7.9 Kcal/mole (L6). Pharmacokinetic properties (ADME) of the ligands (L1-L6) have also been studied.},
	annote = {no-access},
	author = {Abhijit Chhetri and Sailesh Chettri and Pranesh Rai and Dipu Kumar Mishra and Biswajit Sinha and Dhiraj Brahman},
	date-added = {2021-04-18 14:10:48 -0400},
	date-modified = {2021-04-18 14:10:53 -0400},
	doi = {https://doi.org/10.1016/j.molstruc.2020.129230},
	issn = {0022-2860},
	journal = {Journal of Molecular Structure},
	keywords = {ADME, Azo imidazole, Molecular docking, Sars-cov-2, Pharmacokinetics, 6lu7},
	pages = {129230},
	title = {Synthesis, characterization and computational study on potential inhibitory action of novel azo imidazole derivatives against COVID-19 main protease (Mpro: 6LU7)},
	url = {https://www.sciencedirect.com/science/article/pii/S0022286020315507},
	volume = {1225},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0022286020315507},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.molstruc.2020.129230}}

@article{MUHAMMAD2021138141,
	abstract = {The effects of outer-cleft aromatic ring mutations Y5A and F124A on the resistivity of a GH11 xylanase (xyn11A) from Bacillus Firmus K1 to the inhibition by highly-concentrated coniferyl alcohols were investigated both in vitro and an in silico, in which coniferyl alcohols tended to aggregate into clusters and induced the inhibition. The mutants displayed a lower inhibition percentage despite the decrease in enzymatic activities due to the mutation-induced conformational changes of xyn11A. The mutants' ability to resist coniferyl alcohols could be explained by the disruption of the coniferyl clusters formed within the binding cleft due to aromatic ring deletions.},
	author = {Auwal Muhammad and Apichet Ngenyoung and Pongsak Khunrae and Thana Sutthibutpong},
	date-added = {2021-04-18 14:08:20 -0400},
	date-modified = {2021-04-18 14:08:20 -0400},
	doi = {https://doi.org/10.1016/j.cplett.2020.138141},
	issn = {0009-2614},
	journal = {Chemical Physics Letters},
	keywords = {Molecular dynamics, Coniferyl alcohol, Xylanase},
	pages = {138141},
	title = {Effects of the outer-cleft aromatic ring deletion on the resistivity of a GH11 xylanase to the lignin-like monolignol aggregates},
	url = {https://www.sciencedirect.com/science/article/pii/S0009261420310514},
	volume = {762},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0009261420310514},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.cplett.2020.138141}}

@article{HARINARAYANAMOORTHY2021104213,
	abstract = {The development of novel bioactive molecules without hERG ion channel blocking activities is one of the important tasks for the drug discovery scientists. Both experimental and in silico techniques are applied for screening/assaying of novel molecules and existing molecules against hERG ion channel to study its cardiotoxicity. Hence, in the present investigation, QSAR and multialgorithm based classification analysis such as Random Forest (RF), Decision Tree (DT), Support Vector Machine (SVM) and Naive Bayesian (BN) were performed on the data set possessed hERG ion channel blocking activity using different variable (MOE-descriptors and MACCS Fingerprints). The models developed with the MLR and the machine learning techniques provided significant results which were confirmed by their acceptable statistical parameter values. Further, the sum of ranking differences (SRDs) calculated for the models showed that the Model 6-MOE, Model 7-MOE, Model 4-SVM, Model 7-SVM and Model 9-SVM are having smaller SRD values and are placed as top ranked models. The MOE-descriptors and the MACCS Fingerprints contributed in these models revealed that the volume-surface area properties, negative charge on the vdW surface area, number of fluorine atom, number of aromatic ring/atoms, less number of oxygen and hydrogen bonding and donor atoms are contributed for the activity. Furthermore the MACCS Fingerprints such as MACCSFP42, MACCSFP85, MACCSFP122 and MACCSFP139 also explain the polarity of the compounds. The structural pattern analysis with the MACCS Fingerprint revealed that the aromatic rings responsible for hydrophobicity, halogen and heteroatoms provide polarity to the compounds and the asymmetric carbon make the compounds are highly flexible. These studies concluded that the derived results can be used for prediction of hERG ion channel blocking activity of novel molecules.},
	annote = {qsar, no-access},
	author = {N.S. {Hari Narayana Moorthy} and Chandrabose Karthikeyan and Elangovan Manivannan},
	date-added = {2021-04-18 14:07:27 -0400},
	date-modified = {2021-04-18 14:08:00 -0400},
	doi = {https://doi.org/10.1016/j.chemolab.2020.104213},
	issn = {0169-7439},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	keywords = {hERG blockers, QSAR, Machine learning, MACCS Fingerprints, MOE-Descriptors, Support vector machine},
	pages = {104213},
	title = {Multi-algorithm based machine learning and structural pattern studies for hERG ion channel blockers mediated cardiotoxicity prediction},
	url = {https://www.sciencedirect.com/science/article/pii/S0169743920306481},
	volume = {208},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0169743920306481},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.chemolab.2020.104213}}

@article{molecules26020421,
	abstract = {Using the GUSAR 2013 program, the quantitative structure–antioxidant activity relationship has been studied for 74 phenols, aminophenols, aromatic amines and uracils having lgk7 = 0.01–6.65 (where k7 is the rate constant for the reaction of antioxidants with peroxyl radicals generated upon oxidation). Based on the atomic descriptors (Quantitative Neighborhood of Atoms (QNA) and Multilevel Neighborhoods of Atoms (MNA)) and molecular (topological length, topological volume and lipophilicity) descriptors, we have developed 9 statistically significant QSAR consensus models that demonstrate high accuracy in predicting the lgk7 values for the compounds of training sets and appropriately predict lgk7 for the test samples. Moderate predictive power of these models is demonstrated using metrics of two categories: (1) based on the determination coefficients R2 (R2TSi, R20, Q2(F1), Q2(F2), RmTSi2¯) and based on the concordance correlation coefficient (CCC)); or (2) based on the prediction lgk7 errors (root mean square error (RMSEP), mean absolute error (MAE) and standard deviation (S.D.)) The RBF-SCR method has been used for selecting the descriptors. Our theoretical prognosis of the lgk7 for 8-PPDA, a known antioxidant, based on the consensus models well agrees with the experimental value measure in the present work. Thus, the algorithms for calculating the descriptors implemented in the GUSAR 2013 program allow simulating kinetic parameters of the reactions underling the liquid-phase oxidation of hydrocarbons.},
	annote = {qsar},
	article-number = {421},
	author = {Khairullina, Veronika and Safarova, Irina and Sharipova, Gulnaz and Martynova, Yuliya and Gerchikov, Anatoly},
	date-added = {2021-04-18 13:55:11 -0400},
	date-modified = {2021-04-18 13:55:17 -0400},
	doi = {10.3390/molecules26020421},
	issn = {1420-3049},
	journal = {Molecules},
	number = {2},
	pubmedid = {33466934},
	title = {QSAR Assessing the Efficiency of Antioxidants in the Termination of Radical-Chain Oxidation Processes of Organic Compounds},
	url = {https://www.mdpi.com/1420-3049/26/2/421},
	volume = {26},
	year = {2021},
	Bdsk-Url-1 = {https://www.mdpi.com/1420-3049/26/2/421},
	Bdsk-Url-2 = {https://doi.org/10.3390/molecules26020421}}

@article{SIN2021111299,
	abstract = {The AEOL series of manganoporphyrins (MnP; AEOL compounds were named by US Aeolus pharmaceuticals) designed as superoxide dismutase mimic are well-known for their powerful catalytic activity to neutralize reactive oxygen and nitrogen species. Reductive oxygen atom cleavage from peroxynitrite (ONOO−) to form NO2 in aqueous solution by some AEOL compounds (AEOL-10113, AEOL-10150, AEOL-11114 and AEOL-11203) was studied by DFT/M06-2X computations with D3 dispersion correction and gCP (geometrical counterpoise correction) for basis set superposition error. DFT computation showed that AEOL-10150 can form the most stable association complex {MnP{\ldots}OONO} among four AEOL models. AEOL-10150 complex with ONOO− has the lowest deformation energy. In AEOL compounds and their association complexes with ONOO−, Mn atom prefered the high spin state (S = 2) to the intermediate spin state (S = 1). Natural bond orbital analysis showed that electron transfer from the most negative oxygen atom in ONOO− to Mn atom in MnP has the biggest interaction energy among all kinds of donor-acceptor interactions between ONOO− and MnP.},
	annote = {no-access},
	author = {Kye-Ryong Sin and Sun-Gyong Ko and Chol-Jin Kim and Tae-Won Maeng and Sung-Jub Choe and Kum-Ryong Ri},
	date-added = {2021-04-18 13:53:15 -0400},
	date-modified = {2021-04-18 13:54:07 -0400},
	doi = {https://doi.org/10.1016/j.jinorgbio.2020.111299},
	issn = {0162-0134},
	journal = {Journal of Inorganic Biochemistry},
	keywords = {Catalytic antioxidant, Metalloporphyrins, Density functional theory, AEOL, Peroxynitrite, Natural bond orbital},
	pages = {111299},
	title = {Reduction of peroxynitrite by some manganoporphyrins of AEOL series: DFT approach with dispersion correction and NBO analysis},
	url = {https://www.sciencedirect.com/science/article/pii/S0162013420303275},
	volume = {214},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0162013420303275},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.jinorgbio.2020.111299}}

@article{JIANG2021116186,
	abstract = {The relationships between the structure and the thermodynamic behavior and the hydrogen bond (HB) interactions in H2O + ionic liquid (IL) systems were systematically investigated for the first time. Imidazolium-based ILs comprising 1-alkyl-3-methylimidazolium cations ([RMIM]+) and various anions such as acetate ([AC]-), thiocyanate ([SCN]-), tetrafluoroborate ([BF4]-), and bis(trifluoromethylsulfonyl)imide ([Tf2N]-) were investigated. The vapor--liquid equilibrium (VLE) of H2O + IL systems was experimentally determined and predicted by the UNIFAC-Lei model. The results demonstrated that the vapor pressure is mainly dependent on the type of anion and increases slightly with an increase in the cation alkyl chain length. Quantum chemistry calculation and wavefunction analysis clearly revealed the relationship between the VLE and the HB interactions. This study provides theoretical guidance for designing and screening task-specific ILs for chemical processes such as gas dehydration and dehumidification.},
	annote = {cite-code},
	author = {Yifan Jiang and Zhenhang Wang and Zhigang Lei and Gangqiang Yu},
	date-added = {2021-04-18 13:46:50 -0400},
	date-modified = {2021-04-18 13:49:38 -0400},
	doi = {https://doi.org/10.1016/j.ces.2020.116186},
	issn = {0009-2509},
	journal = {Chemical Engineering Science},
	keywords = {Ionic liquids, Vapor-liquid equilibrium, Hydrogen bond interaction, UNIFAC-Lei model, Structural effect, Quantum chemistry calculation},
	pages = {116186},
	title = {Structural effects on thermodynamic behavior and hydrogen bond interactions of water--ionic liquid systems},
	url = {https://www.sciencedirect.com/science/article/pii/S0009250920307181},
	volume = {230},
	year = {2021},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0009250920307181},
	Bdsk-Url-2 = {https://doi.org/10.1016/j.ces.2020.116186}}

@article{Gunko:2021wm,
	abstract = {A set of characteristics calculated within the scope of quantum chemistry methods may be assigned to local ones changing from atom to atom in complex systems. Simple averaging of the related values gives rather poor characteristics of the systems because various fractions of certain atoms can have different surrounding and, therefore, different characteristics, which may not correspond to the average one. The aim of this study is searching a more appropriate pathway to transform local characteristics, e.g., atomic charges, into nonlocal ones based on the distribution functions. The distribution functions of atomic charges (CDF) could be considered as a simple tool to analyze nonuniform complex systems since specificity of different fractions of atoms reflects in the CDF shape. As a whole, the approach accuracy and efficiency depend on the quality and appropriateness of molecular and cluster models used, as well as on the quantum chemical methods (ab initio, DFT, and semiempirical) and the basis sets used. Nanosystems with dozens of molecules (clusters

license_type: permissive

branch_name: refs/heads/main

extension: bib