ChemRxiv : the preprint server for chemistry最新文献

{"title":"Lowering the C-H Bond Activation Barrier of Methane Using SAC@Cu(111): A Periodic DFT Investigations","authors":"M. Bhati, J. Dhumal, Kavita Joshi","doi":"10.33774/chemrxiv-2021-zfrcn","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-zfrcn","url":null,"abstract":"Methane has long captured the world's spotlight for being the simplest and yet one of the most notorious hydrocarbon. Exploring its potential to be converted into value added products has raised a compelling interest. In the present work, we have studied the efficiency of Single-Atom Catalysts (SACs) for methane activation employing Density Functional Theory (DFT). The Climbing Image-Nudged Elastic Bond (CI-NEB) method is used in tandem with the Improved Dimer (ID) method to determine the minimum energy pathway for the first C-H bond dissociation of methane. Our study reported that the transition-metal doped Cu(111) surfaces enhance adsorption, activate C-H bond, and reduce activation barrier for first C-H bond cleavage of methane. The results suggest Ru/Co/Rh doped Cu(111) as promising candidates for methane activation with minimal activation barrier and less endothermic reaction. For these SACs, the calculated activation barriers for first C-H bond cleavage are 0.17 eV, 0.24 eV, and 0.26 eV respectively, which is substantially lower than 1.13 eV, the activation barrier for Cu(111).","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41600515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thermoresponsive hydrogels for atmospheric water vapor harvesting","authors":"P. Cherukupally, Boyuan Hao, Zhongshen Zhang, Daryl R. Williams","doi":"10.33774/chemrxiv-2021-vmf6c","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-vmf6c","url":null,"abstract":"Currently, freshwater scarcity is a global challenge that is threatening four billion people across the world. To satisfy people’s increasing freshwater demand, harvesting atmospheric water from the air could be an alternative way. This work developed copolymer P(NIPAM-co-15%BzDMA) hydrogels to harvest atmospheric water vapor. Two methods were investigated to improve its adsorption performance: decreasing synthesis temperature below the LCST and copolymerizing with the optimum amount of quaternary ammonium salt (QAS). We found these two methods can effectively improve the water vapor uptake. After copolymerizing NIPAM with 15% QAS at 20°C, the water vapor uptake could be increased by almost 20% to 232 mg/g at 20°C and P/P0 of 0.75 compared with pure PNIPAM prepared at 60°C (194 mg/g). The significant increase can be attributed to the more uniform porous structure and the hygroscopicity of QAS. After coating PNIPAM onto the PESPU sponge skeleton, the PESPU-PNIPAM_60 could adsorb 180 mg/g gas water at 20°C and P/P0 of 0.75, and the modified sponges inherit the switchable wettability from PNIPAM. This research provides polymer processing parameters and their character for harvesting water vapor from the air with hydrogels.","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44200329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Charge Induced Chi(3) Susceptibility in Interfacial Nonlinear Optical Spectroscopy Beyond the Bulk Aqueous Contributions: The Case for Silica/Water Interface","authors":"Hui Wang, Xiao-Hua Hu, Hongfei Wang","doi":"10.33774/chemrxiv-2021-stnt5","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-stnt5","url":null,"abstract":"The electric field induced (EFI) bulk Chi(3) contribution to the second harmonic generation (SHG) signal from charged interfaces was discovered and applied to study the interfacial chemistry of various charged interfaces three decades ago. For both the buried fused silica/water interface and the exposed charged monolayer covered air/water interface, such bulk Chi(3) contribution was all attributed to the Chi(3) term of the polarized water molecules near the charged interfaces. The puzzling experimental observation of the more than one-order of magnitude difference of the EFISHG intensity between the fully charged silica/water interface and the charged molecular covered air/water interface was generally overlooked in the EFISHG literature. Nevertheless, this significant signal difference suggests additional source for the Chi(3) contribution at the fully charged silica/water interface other than the polarized water molecules as in the case of charged monolayer covered air/water interface. In this report, we re-examine the treatment of the Chi(3) mechanism at the charged silica/water interface by including the contributions from the bulk silica using proper boundary condition and image charge distributions for the change screening effects inside bulk silica phase. We show that the Chi(3) contribution from the bulk silica is in similar form as that of the aqueous bulk phase, and it is with more than one-order of magnitude and with opposite sign. The treatment reported here can be extended to other charged interfaces.","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46765072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Binding methylarginines and methyllysines as free amino acids: a comparative study of multiple supramolecular host classes","authors":"Zoey Warmerdam, B. Kamba, M. Le, T. Schrader, L. Isaacs, P. Bayer, F. Hof","doi":"10.33774/chemrxiv-2021-2b4bj","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-2b4bj","url":null,"abstract":"Methylated free amino acids are an important class of targets for host-guest chemistry that have recognition properties distinct from those of methylated peptides and proteins. We present comparative binding studies for three different host classes that are each studied with multiple methylated arginines and lysines to determine fundamental structure-function relationships. The hosts studied are all anionic and include three calixarenes, two acyclic cucurbiturils, and two cleft-like hosts. We determined the binding association constants for a panel of methylated amino acids using indicator displacement assays. The calixarene hosts show weak binding that favours the higher methylation states, with the strongest binding observed for trimethyllysine. The acyclic cucurbiturils display stronger binding to the methylated amino acids, and some unique patterns of selectivity. The cleft-like hosts follow two different trends, one shallow host following similar trends to the calixarenes, and the other more closed host binding certain less-methylated amino acids stronger than their per-methylated counterparts. Molecular modeling sheds some light on the different preferences of different hosts. The results identify hosts with selectivities that will be useful for certain biomedical applications. The overall selectivity patterns are explained by a common framework that considers the topology, depth of binding pockets, and functional group participation across all host classes.","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42312690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling Electronic Structure, Magnetic States, and Topological Phenomena in Pristine, Defected, and Strained Ti2N MXene","authors":"Yogendra Limbu, G. C. Kaphle, Alok Lal Karn, N. Shah, D. Paudyal","doi":"10.33774/chemrxiv-2021-90scj","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-90scj","url":null,"abstract":"We unravel the evolution of structural, electronic, magnetic, and topological properties of graphene-like pristine, defected, and strained titanium nitride MXene with different functional groups (-F, -O, -H, and -OH) employing first-principles calculations. The formation and cohesive energies reveal their chemical stability. The MAX phase and defect free functionalized MXenes are metallic in nature except for oxygen terminated one, which is 100% spin polarized half-metallic. Additionally, the bare MXene is nearly half-metallic ferromagnet. The spin-orbit coupling significantly influences the bare MXene possessing band inversion. The strain effect sways the Fermi level thereby shifting it toward lower energy state under compression and toward higher energy state under tensile strain in Ti2NH2. These properties are reversed in Ti2N, Ti2NF2, and Ti2N(OH)2. The half-metallic nature changes to semi-metallic under 1% compression and is completely destroyed under 2% compression. In single vacancy defect, the band structure of Ti2NO2 remarkably transforms from half-metallic to semi-conducting (with large band gap of 1.73 eV) in 12.5% Ti, weakly semi-conducting in 5.5% Ti, and topological semi-metal in 12.5% oxygen. The 25% N defect changes the half-metallic to the metallic with certain topological features. Further, the 12.5% Co substitution in Ti2NO2 preserves the half-metallic character, whereas Mn substitution allows to convert half-metallic into weak semi-metallic preserving ferromagnetic character. However, Cr substitution converts half-metallic ferromagnetic to half-metallic anti-ferromagnetic state. The understanding made here on collective structural stability, and magnetic and topological phenomena in novel 2D MXenes open up their possibility in designing them for synthesis and thereby taking to applications.","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41477904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of the structure and properties of ceramic materials with a rigid system of microfiltration transport pores based on basalt fibers","authors":"Siarhei Besarab, S. Azarov, J. Sauka, E. Petyushik, T. Azarova, A. Drobysh","doi":"10.33774/chemrxiv-2021-46cg5","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-46cg5","url":null,"abstract":"The report provides information on the formation of the structure of porous ceramic materials made of basalt fiber obtained by pressing with subsequent sintering. The phase composition, structure, and properties of ceramics are studied. The relationship between the structure, phase composition, and properties of the ceramic material is established.","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48816744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemoselective nickel-catalyzed coupling through substrate photoexcitation","authors":"Pradipta Das, Eliot F Woods, J. Ly, Jack N. Olding, Kayla F. Presley, Brennan Romanoff, Tod A. Grusenmeyer, E. Weiss, J. Kalow","doi":"10.33774/chemrxiv-2021-8wqv0","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-8wqv0","url":null,"abstract":"Metallaphotoredox catalysis combines the well-established mechanisms of transition-metal-catalyzed cross-coupling reactions with one-electron redox manipulations enabled by light. In most cases, a transition metal or organic dye serves as the photoredox catalyst while a ground-state Pd or Ni catalyst performs the organometallic steps. Cross-coupling mechanisms that rely on direct photoexcitation of a light-absorbing substrate have the potential to access distinct mechanisms and deliver unique selectivity based on the substrate’s excited-state properties. In this report, we describe a photoinduced, Ni-catalyzed Suzuki–Miyaura cross coupling reaction that selectively functionalizes BODIPY chromophores, a versatile class of tunable, bright, photostable fluorophores. Using a bis-iodo BODIPY substrate, the selectivity for mono- vs. bis-arylation was found to be governed by a remote substituent that subtly alters the excited-state properties of the substrate. Consistent with a substrate photoexcitation mechanism, high chemoselectivity is also observed in mixtures of chromophores with distinct excited-state properties. This reaction is compatible with a variety of substituted BODIPY chromophores and boronic acids and esters, enabling the rapid synthesis of unsymmetrically-substituted chromophores.","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44332750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Computationally-Realizable Rigorous Canonical Numbering Algorithm for Chemical Graphs with its Open-Source Implementation in Rust","authors":"Qin Wan","doi":"10.33774/chemrxiv-2021-0l9wx","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-0l9wx","url":null,"abstract":"Canonical numbering of the vertices from a graph has been a challenging open issue for decades not only in the domain of graph theory but also in the cheminformatic applications. This paper presents an efficient, fast and rigorous approach for canonical numbering and symmetry perception as the first workable solution with theoretical completeness. The methodology is composed of a set of algorithms including extendable representation of vertex, high-performance sorting and graph reduction, etc. The canonical numbering of vertices can be generated in a short time through the novel vertex representation method. Furthermore, a new concept of graph reduction decreases the amount of computation to determine constitutional symmetry of complex graphs into the range of hardware capability. An open-source version of algorithms overall is implemented in Rust thanks to the features of safety, performance and robust abstraction of this modern programming language. The results of experiments on more than 2 million molecules from ChEMBL database has been given at the end.","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47305492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel dynamic residue network analysis approaches to study homodimeric allosteric modulation in SARS-CoV-2 Mpro and in its evolutionary mutations","authors":"Olivier Sheik Amamuddy, Rita Afriyie Baoteng, Victor Barozi, D. Nyamai, Ozlem Tastan Bishop","doi":"10.33774/chemrxiv-2021-7thm1","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-7thm1","url":null,"abstract":"The rational search for allosteric modulators and the allosteric mechanisms of these modulators in the presence of evolutionary mutations, including resistant ones, is a relatively unexplored field. Here, we established novel in silico approaches and applied to SARS-CoV-2 main protease (Mpro). First, we identified six potential allosteric modulators (SANC00302, SANC00303, SANC00467, SANC00468, SANC00469, SANC00630) from the South African Natural Compounds Database (SANCDB) bound to the allosteric pocket of Mpro that we determined in our previous work. We also checked the stability of these compounds against Mpro of laboratory strain HCoV-OC43 and identified differences due to residue changes between the two proteins. Next, we focused on understanding the allosteric effects of these modulators on each protomer of the reference Mpro protein, while incorporating the symmetry problem in the functional homodimer. In general, asymmetric behavior of multimeric proteins is not commonly considered in computational analysis. We introduced a novel combinatorial approach and dynamic residue network (DRN) analysis algorithms to examine patterns of change and conservation of critical nodes, according to five independent criteria of network centrality (betweenness centrality (BC), closeness centrality (CC), degree centrality (DC), eigencentrality (EC) and katz centrality (KC)). The relationships and effectiveness of each metric in characterizing allosteric behavior were also investigated. We observed highly conserved network hubs for each averaged DRN metric on the basis of their existence in both protomers in the absence and presence of all ligands, and we called them persistent hubs (residues 17, 111, 112 and 128 for averaged BC; 6, 7, 113, 114, 115, 124, 125, 126, 127 and 128 for averaged CC; 36, 91, 146, 150 and 206 for averaged DC; 7, 115 and 125 for EC; 36, 125 and 146 for KC). We also detected ligand specific signal changes some of which were in or around functional residues (i.e. chameleon switch PHE140). Using EC persistent hubs and ligand introduced hubs we identified a residue communication path between allosteric binding site and catalytic site. Finally, we examined the effects of the mutations on the behavior of the protein in the presence of selected potential allosteric modulators and investigated the ligand stability. The hit compounds showed various levels of stability in the presence of SARS-CoV-2 Mpro mutations, being most stable in A173V, N274D and R279C, and least stable in R60C, N151D V157I, C160S and A255V. SANC00468 was the most stable compound in the 43 mutant protein systems. We further used DRN metric analysis to define cold spots as being those regions that are least impacted, or not impacted, by mutations. One crucial outcome of this study was to show that EC centrality hubs form an allosteric communication path between the allosteric ligand binding site to the active site going through the interface residues of Domain I and II; and","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48250752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-Macromolecular Level Imaging of a Hydrogel Structure","authors":"R. Kiyama, T. Nonoyama, Sedlacik Tomas, H. Jinnai, J. Gong","doi":"10.33774/chemrxiv-2021-x1s5k","DOIUrl":"https://doi.org/10.33774/chemrxiv-2021-x1s5k","url":null,"abstract":"Hydrogels are promising materials for several applications, including cell scaffolds and artificial load-bearing substitutes (cartilages, ligaments, tendons, etc.). Direct observation of the nanoscale polymer network of hydrogels is essential in understanding its properties. However, imaging of individual network strands at the molecular level is not achieved yet due to the lack of suitable methods. Herein, for the first time, we developed a novel mineral-staining method and network fixation method for transmission electron microscopy observation to visualize the hydrogel network in its unperturbed conformation with nanometer resolution. Surface network observation indicates that the length of surface dangling chains, which play a major role in friction and wetting, can be estimated from the gel mesh size. Moreover, bulk observations reveals a hierarchical formation mechanism of gel heterogeneity. These observations have the great potential to advance gel science by providing comprehensive perspective that link bulk gel properties with nanoscale.","PeriodicalId":72565,"journal":{"name":"ChemRxiv : the preprint server for chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44913152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}