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60c741f3f96a004d91286534 | 10.26434/chemrxiv.8198795.v1 | XPS of Cold Pressed Multilayered and Freestanding Delaminated 2D Thin Films of Mo2TiC2Tz and Mo2Ti2C3Tz (MXenes) | <p>MXenes, transition metal carbides that are synthesized from the top down by etching of their 3D parent layered solids, the MAX phases, are the latest family of the two-dimensional solids discovered. When the A layers – mostly Al – are etched they are replaced by surface terminations, T<sub>z</sub> mainly comprised of O-, OH- and F-terminations. One of the few techniques capable of quantifying these surface terminations is X-ray photoelectron spectroscopy, XPS. Herein, we undertook an XPS study of the out-of-plane ordered MXenes, Mo<sub>2</sub>TiC<sub>2</sub>T<sub>z</sub> and Mo<sub>2</sub>Ti<sub>2</sub>C<sub>3</sub>T<sub>z</sub>, in both multilayered, ML, cold pressed and delaminated thin film forms. The harsh conditions needed to etch these MAX phases into MLs, results in their partial oxidation. The hydroxide used to delaminate the MLs results in further oxidation and a reduction in the F-content. In all cases, etching resulted in a decrease in the Ti to Mo ratio implying that the former atoms are selectively etched. In all but the ML Mo<sub>2</sub>TiC<sub>2</sub>T<sub>z</sub> case, the Mo to C ratio was also reduced. It follows that the loss of Ti also results in the loss of C atoms. With the exception of the ML Mo<sub>2</sub>Ti<sub>2</sub>C<sub>3</sub>T<sub>z</sub> case, the number of termination moles per formula unit, z, was > 2, which is energetically unfavorable and thus unlikely. However, if one assumes that not all of the O signal is coming from terminations but rather from O atoms that replace C atoms in the MX blocks, then z ≈ 2. This work is an important step in quantifying and understanding the effects of etching on terminations and structure in these Mo and Ti-based MXenes. </p> | Joseph Halim; Kevin Cook; Per Eklund; johanna Rosen; Michel W. Barsoum | Thin Films; Nanostructured Materials - Nanoscience; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741f3f96a004d91286534/original/xps-of-cold-pressed-multilayered-and-freestanding-delaminated-2d-thin-films-of-mo2ti-c2tz-and-mo2ti2c3tz-m-xenes.pdf |
60dc76e99bb5dd14778fa0ea | 10.26434/chemrxiv-2021-ts8g9-v2 | Will the Chemical Probes Please Stand Up? | This work provides a uniquely comprehensive and comparative overview of chemical probe sources and targets. This will be maintained and expanded for experts and non-informaticions seeking chemical probes to use in their work. We have analysed 940 experimental and 3,670 calculated probe candidates. Together these have evidence of specific binding for 796 human proteins across the target classes. We have flagged unsuitable (i.e. potentially misleading and resource-wasting) compounds from both probe groups. Compared to ChEMBL approved drugs, probes tend to be larger and more complex structures. | Ctibor Škuta; Christopher Southan; Petr Bartunek | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2021-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dc76e99bb5dd14778fa0ea/original/will-the-chemical-probes-please-stand-up.pdf |
60c73f45337d6c76fde264fb | 10.26434/chemrxiv.6712826.v2 | Intercalation of First Row Transition Metals inside Covalent-Organic Frameworks (COF): a Strategy to Fine Tune the Electronic Properties of Porous Crystalline Materials | <div>Covalent organic frameworks (COFs) have emerged as an important class of nano-porous crystalline materials with many potential applications. They are intriguing platforms for the design of porous skeletons with special functionality at the molecular level. However, despite their extraordinary properties, it is difficult to control their electronic properties, thus hindering the potential implementation in electronic devices. A new form of nanoporous material, COFs intercalated with first row transition metal is proposed to address this fundamental drawback - the lack of electronic tunability. Using first-principles calculations, we have designed 31 new COF materials <i>in-silico</i> by intercalating all of the first row transition metals (TMs) with boroxine-linked and triazine-linked COFs: COF-TM-x (where TM=Sc-Zn and x=3-5). This is a significant addition considering that only 187 experimentally COFs structures has been reported and characterized so far. We have investigated their structure and electronic properties. Specifically, we predict that COF's band gap and density of states (DOSs) can be controlled by intercalating first row transition metal atoms (TM: Sc - Zn) and fine tuned by the concentration of TMs. We also found that the $d$-subshell electron density of the TMs plays the main role in determining the electronic properties of the COFs. Thus intercalated-COFs provide a new strategy to control the electronic properties of materials within a porous network. This work opens up new avenues for the design of TM-intercalated materials with promising future applications in nanoporous electronic devices, where a high surface area coupled with fine-tuned electronic properties are desired.</div> | Srimanta Pakhira; Jose Mendoza-Cortes | Nanostructured Materials - Materials; Coordination polymers; Computational Chemistry and Modeling; Theory - Computational; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f45337d6c76fde264fb/original/intercalation-of-first-row-transition-metals-inside-covalent-organic-frameworks-cof-a-strategy-to-fine-tune-the-electronic-properties-of-porous-crystalline-materials.pdf |
60c740e5337d6c532be267ae | 10.26434/chemrxiv.7878185.v1 | Plasmonic Stamps Fabricated by Gold Dewetting on PDMS for Catalyzing Hydrosilylation on Silicon Surfaces | <div>In this work plasmonic stamps are harnessed to drive surface chemistry on silicon. The plasmonic stamps were prepared by sputtering gold films on PDMS, followed by thermal annealing to dewet the gold and form gold nanoparticles. By changing the film thickness of the sputtered gold, the approximate size and shape of these gold nanoparticles can be changed, leading to a shift of the optical absorbance maximum of the plasmonic stamp, from 535 nm to 625 nm. Applying the plasmonic stamp to a Si(111)-H surface using 1-dodecene as the ink, illumination with green light results in covalent attachment of 1-dodecyl groups to the surface. Of the dewetted gold films on PDMS used to make the plasmonic stamps, the thinnest three (5.0, 7.0, 9.2 nm) resulted in the most effective plasmonic stamps for hydrosilylation. The thicker stamps had lower efficacy due to the increased fraction of non-spherical particles, which have lower-energy LSPRs that are not excited by green light. Since the electric field generated by the LSPR should be very local, hydrosilylation on the silicon surface should only take place within close proximity of the gold particles on the plasmonic stamps.To complement AFM imaging of the hydrosilylated silicon surfaces, galvanic displacement of gold(III) salts on the silicon was carried out and the samples imaged by SEM - the domains of hydrosilylated alkyl chains would be expected to block the deposition of gold. The bright areas of metallic gold surround dark spots, with the sizes and spacing of these dark spots increasing with the size of the gold particles on the plasmonic stamps. These results underline the central role played by the LSPR in driving the hydrosilylation on silicon surfaces, mediated with plasmonic stamps.</div> | Jillian Buriak; Chengcheng Rao; Erik Luber; Brian Olsen | Nanocatalysis - Catalysts & Materials; Nanofabrication; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e5337d6c532be267ae/original/plasmonic-stamps-fabricated-by-gold-dewetting-on-pdms-for-catalyzing-hydrosilylation-on-silicon-surfaces.pdf |
679142aa6dde43c908d71c25 | 10.26434/chemrxiv-2025-qfgsd | In silico exploration of metabolite-derived soft materials using a chemical reaction network: what is possible? | Future soft materials and polymer chemistries will require innovative non-petroleum sourcing pathways to thrive in a sustainable economy. While leveraging microbial metabolites derived from biological feedstocks possesses high potential in many avenues of chemical development, the applicability of this paradigm to the specifics of soft materials chemistry is unclear. Here, we construct a chemical reaction network based on databases of common microbial metabolites and the USPTO reaction set to examine what is possible in the chemical space of metabolite-derived chemistries of relevance to soft materials. We observe that the accessible chemical space of our chemical reaction network possesses strong microbe-specific chemical diversity, and that this space saturates rapidly within three synthetic steps applied to the original microbial metabolites. Importantly, we show that the chemical space accessible from metabolite precursors possesses significant overlap with existing petrochemical building blocks, known and proposed synthetically feasible polymer monomers, and the chemical space of common organic semiconductors, and redox active materials. The biases induced by the metabolite and reaction databases that parameterize our reaction network are analyzed as a function of chemical functional groups, and pathways towards broader sets of chemistries and reactions are outlined. This work introduces a computational framework for exploring a novel paradigm of soft materials discovery with the potential to accelerate the identification of soft materials relevant to metabolic engineering targets and non-petroleum sourcing pathways for existing soft materials. | Shruti Iyer; Nicholas Jackson | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Natural Products; Petrochemicals; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679142aa6dde43c908d71c25/original/in-silico-exploration-of-metabolite-derived-soft-materials-using-a-chemical-reaction-network-what-is-possible.pdf |
60c75240469df41e0ff44b27 | 10.26434/chemrxiv.13273310.v1 | Completion of Partial Reaction Equations | We present a deep-learning model for inferring missing molecules in reaction equations. Such an algorithm features multiple interesting behaviors. First, it can infer the necessary reagents and solvents in chemical transformations specified only in terms of main compounds, as often resulting from retrosynthetic analyses. The completion with necessary reagents ensures that reaction equations are compatible with deep-learning models relying on a complete reaction specification. Second, it can cure existing datasets by detecting missing compounds, such as reagents that are essential for given classes of reactions. Finally, this model is a generalization of models for forward reaction prediction and retrosynthetic analysis, as both can be formulated in terms of incomplete reaction equations. We illustrate that a single trained model, based on the transformer architecture and acting on reaction SMILES strings, can address all three points.<br /><br />Workshop paper at the Machine Learning for Molecules Workshop at NeurIPS 2020.<br /> | Alain C. Vaucher; Philippe Schwaller; Teodoro Laino | Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75240469df41e0ff44b27/original/completion-of-partial-reaction-equations.pdf |
6206bca10c0bf0490ee66ce3 | 10.26434/chemrxiv-2022-lvfn8 | Rationalizing the regioselectivity of substituted phenols from the FERMO concept: stereoelectronic effects on protonation and functionalization | The relative extent of protonation in oxygen and carbon atoms and the position of protonation in carbons depend on several factors. We seek to locate the frontier molecular orbitals involved in the protonation reactions of substituted phenols using the FERMO concept through the MOLPROJ software, to compare the computational results with experimental NMR data obtained in the literature. We evaluate computationally the stereo-electronic effects that govern reactions of aromatic electrophilic substitution using an experimental study as an example. The MOLPROJ returned a percentage of correct answers of approximately 86% in the protonation sites. The experimental results on the protonation sites were rationalized in terms of stereoelectronic effects. | Teodorico Ramalho; Daniel Leal; Leticia Braga | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6206bca10c0bf0490ee66ce3/original/rationalizing-the-regioselectivity-of-substituted-phenols-from-the-fermo-concept-stereoelectronic-effects-on-protonation-and-functionalization.pdf |
6771fa71fa469535b93332c1 | 10.26434/chemrxiv-2024-4hgb0 | NO tablet: autonomous generation of therapeutic
nitric oxide in air through redox-promoted CO2 adsorption | Inhaled nitric oxide (iNO) is a powerful therapy for the treatment of various cardiopulmonary and respiratory diseases. However, access to iNO therapy is often limited by the necessity of cumbersome gas tanks and/or elaborate gas blending apparatus. Here, we report a lightweight, inexpensive, and maintenance-free tablet that autonomously generates a therapeutic quantity of NO in air. The tablet is composed of a thimble filter paper containing a powdery mixture of nitrite (NO2‒)-type layered double hydroxide (NLDH) and ascorbic acid loaded on silica gel (AASiO2). NLDH by itself generates trace amounts of NO in the air due to the left-shifting of the protonation equilibrium of NO2‒ by aerial CO2 and H2O (2[NO2‒]LDH + CO2 + H2O ⇌ 2HNO2↑ + [CO32‒]LDH), which is followed by disproportionation of 2HNO2 to NO, NO2 and H2O. In contrast, it was found that the protonation equilibrium can be shifted to the right side when volatile acid products (HNO2 and NO2) are readily converted to neutral NO over the AASiO2 reductant. Based on this, even a single tablet (containing 0.30 g NLDH and 0.90 g AASiO2) generates 5~20 ppm NO at 0.5 L/min for 24 h, which is sufficient to be useful for the relief of severe hypoxia caused by persistent pulmonary hypertension of the newborn (PPHN). Moreover, the tablet can be activated by exhaled breath for high-dose iNO therapy (80~180 ppm for several hours), revealing its potential utility for treating viral pneumonia. The NO tablet can be stored stably over long periods at ambient temperature in a gas barrier bag, and has the potential to break the logistical, financial, and operational barriers that have long existed to the widespread implementation of iNO therapy. | Shinsuke Ishihara; Jan Labuta; Jonathan Hill; Takashi Nakanishi; Manabu Kakinohana; Nobuo Iyi | Biological and Medicinal Chemistry; Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Solid State Chemistry; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6771fa71fa469535b93332c1/original/no-tablet-autonomous-generation-of-therapeutic-nitric-oxide-in-air-through-redox-promoted-co2-adsorption.pdf |
60c749b7842e650db4db2dbe | 10.26434/chemrxiv.12091962.v1 | Generation and Reactivity of a NiIII2(μ-1,2-peroxo) Complex | Ni-based oxide materials are promising candidates for catalyzing
the oxygen evolution reaction. The detailed mechanism of water splitting in
these systems has been of interest with a goal of understanding the
intermediate species vital for catalytic activity. A potential intermediate
species prior to release of oxygen is a bridging Ni<sup>III</sup><sub>2</sub>(<i>μ</i>-1,2-peroxo)
complex. However, Ni<sub>2</sub>(<i>μ</i>-1,2-peroxo) complexes are rare in
general and are unknown with oxidation states higher than Ni<sup>II</sup>.
Herein, we report the isolation of such an unusual high-valent species in a Ni<sup>III</sup><sub>2</sub>(<i>μ</i>-1,2-peroxo)
complex, which has been characterized using single-crystal X-ray diffraction
and X-ray absorption, NMR, and UV-vis spectroscopies. In addition, treatment
with excess tetrabutylammonium chloride results in regeneration of the
precursor Ni–Cl
species, implicating the reversible release of oxygen or a
reactive oxygen species. Taken together, this suggests that Ni<sup>III</sup><sub>2</sub>(<i>μ</i>-1,2-peroxo)
species are accessible and may be viable intermediates during the oxygen
evolution reaction. | Norman Zhao; Alexander S. Filatov; Jiaze Xie; Ethan A. Hill; John Anderson | Bonding; Coordination Chemistry (Inorg.); Ligands (Inorg.); Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749b7842e650db4db2dbe/original/generation-and-reactivity-of-a-ni-iii2-1-2-peroxo-complex.pdf |
64be21ebb053dad33ac8fe86 | 10.26434/chemrxiv-2023-5718q | Catalytic Friedel–Crafts Reactions of Unactivated Secondary Alcohols: Site-Selective ortho-Alkylation of Phenols | A combination of catalytic ZnCl2 and catalytic CSA enables the first site-selective Friedel–Crafts alkylation of phenolic derivatives with unactivated secondary alcohols. This catalysis favors ortho-selectivity even in the absence of steric influence. Through kinetics and density functional theory, we propose a mechanism where zinc and CSA function to scaffold both the phenolic and alcohol precursors, predisposing them for ortho-alkylation. | Aaron Pan; Viviene Nguyen; Lorraine Rangel; Charlene Fan; Kevin Kou | Organic Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2023-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64be21ebb053dad33ac8fe86/original/catalytic-friedel-crafts-reactions-of-unactivated-secondary-alcohols-site-selective-ortho-alkylation-of-phenols.pdf |
636912e3bef5d4a46149c8d1 | 10.26434/chemrxiv-2022-18nrc-v2 | Active site imprinting on Ti oxocluster metal-organic framework for the photocatalytic hydrogen release from formic acid | On-board hydrogen release from liquid organic carriers is a process that can make feasible the use of H2 as transportation fuel. Formic acid is considered as one of the most convenient liquid hydrogen organic carriers, since it can be easily obtained from CO2, it is water soluble and it makes unnecessary to recover the H2-depleted byproducts. Compared to the more conventional thermal catalytic decomposition of formic acid, the use of light in combination with a photocatalyst has been much less explored. Herein, we report a new paradigm in MOF photocatalysis that is the use of a microporous titanium oxocluster based metal-organic framework (Ti-MOF) endowed by formate-imprinted active sites, namely MIP-177_LT (MIP stands for Materials from Institute of Porous Materials of Paris, LT for Low Temperature), as a highly efficient photocatalyst for H2 release from formic acid without the need to neutralize acidity or the use sacrificial agents or noble metals. Noteworthy, a quantum efficiency of 22 % has been determined for the photocatalytic H2 release that is highly remarkable for a non-toxic noble metal-free photocatalyst. | Alberto García-Baldoví; Raquel Del Angel; Georges Mouchaham; Shanping Liu; Dong Fan; Guillaume Maurin; Sergio Navalón; Christian Serre; Hermenegildo Garcia | Catalysis; Energy; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636912e3bef5d4a46149c8d1/original/active-site-imprinting-on-ti-oxocluster-metal-organic-framework-for-the-photocatalytic-hydrogen-release-from-formic-acid.pdf |
6478e79be64f843f412a424a | 10.26434/chemrxiv-2023-435mj | Dimer interface destabilization of photodissociative Dronpa driven by asymmetric monomer dynamics | Photoswitchable Dronpa (psDronpa) is a unique member of the fluorescent protein family that can undergo reversible photoinduced switching between fluorescent and dark states and has recently been engineered into a dimer (pdDronpaV) that can dissociate and reassociate as part of its photoswitchable pathway. However, the specific details of the protein structure-function relationship of the dimer interface, along with how the dimer proteins interact with each other upon chromophore isomerization, are not yet clear. Classical molecular dynamics simulations were performed on psDronpa as monomers and dimers as well as the pdDronpaV dimer and with cis/trans chromophore structures. Analysis of the cis and trans isomers of the chromophore illustrated key differences between their interaction with residues in the protein in both the monomer and dimer forms of psDronpa. The chromophore was found to interact with water solvent uniquely in both monomeric and dimeric systems. Examination of the psDronpa dimer showed nonidentical chromophore interactions between the domains, indicating domain directional favoring. Examination of the trans form of pdDronpaV illuminated the importance of hydrogen bonding between the monomeric domains in maintaining their association as well as illustrating the motion of dissociation of the domains. This discovery offers important information for possible future mutations of pdDronpaV that might be made to accelerate dissociation. | Christina H. McCulley; Alice R. Walker | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6478e79be64f843f412a424a/original/dimer-interface-destabilization-of-photodissociative-dronpa-driven-by-asymmetric-monomer-dynamics.pdf |
65c083d7e9ebbb4db9b29e76 | 10.26434/chemrxiv-2024-fqx3t | Simple Synthesis of Unnatural Amino Acids via Ni/Ag-Electrocatalytic Cross-Coupling | A simple protocol is outlined herein for rapid access to enantiopure unnatural amino acids from trivial glutamate and aspartate precursors. The method relies on Ag/Ni-electrocatalytic decarboxylative coupling and can be rapidly conducted in parallel (24 reactions at a time) to ascertain coupling viability followed by scale-up for the generation of useful quantities of UAAs for exploratory studies. | Gabriele Laudadio; Philipp Neigenfind; Rajesh Chebolu; Vanna D. Blasczak; Shambabu Joseph Madirala; Maximilian D. Palkowitz; Philippe N. Bolduc; Michael C. Nicastri; Ravi Kumar Puthukanoori; Bheema Rao Paraselli; Phil S. Baran | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c083d7e9ebbb4db9b29e76/original/simple-synthesis-of-unnatural-amino-acids-via-ni-ag-electrocatalytic-cross-coupling.pdf |
61636065b564b666867330b0 | 10.26434/chemrxiv-2021-k6tf3 | Finding the Order in Complexity: The Electronic Structure of 14-1-11 Zintl Compounds | Yb14MnSb11 and Yb14MgSb11 have rapidly risen to prominence as high-performing p-type thermoelectric materials for potential deep space power generation. However, the fairly complex crystal structure of 14-1-11 Zintl compounds renders the interpretation of the electronic band structure obscure, making it difficult to chemically guide band engineering and optimization efforts. In this work, we delineate the valence balanced Zintl chemistry of A14MX11 compounds (A = Yb, Ca; M = Mg, Mn, Al, Zn, Cd; X = Sb, Bi) using molecular orbital theory analysis. By analyzing the electronic band structures of Yb14MgSb11 and Yb14AlSb11 , we show that the conduction band minimum is composed of either an antibonding molecular orbital originating from the (Sb3)7− trimer, or a mix of atomic orbitals of A, M, and X. The singly degenerate valence band is comprised of non-bonding Sb p-z orbitals primarily from the Sb atoms in the (MSb4)m- tetrahedra and the of isolated Sb atoms distributed throughout the unit cell. Such a chemical understanding of the electronic structure enables strategies to engineer electronic properties (e.g., the band gap) of A14MX11 compounds. | Yukun Liu; Michael Toriyama; Zizhen Cai; Mengjia Zhao; Fei Liu; G. Jeffrey Snyder | Materials Science; Energy; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61636065b564b666867330b0/original/finding-the-order-in-complexity-the-electronic-structure-of-14-1-11-zintl-compounds.pdf |
60c75927842e65101edb49a6 | 10.26434/chemrxiv.14663448.v1 | Does Filter Aided Sample Preparation (FASP) Provide Sufficient Method Linearity for Quantitative Plant Shotgun Proteomics? | Gel-free LC-based shotgun proteomics represents the current gold standard of proteome analysis due to its outstanding throughput, analytical resolution and reproducibility. Thereby, the efficiency of sample preparation, i.e., protein isolation, solubilization and proteolysis, directly affects the correctness and reliability of quantification, being therefore the bottle neck of shotgun proteomics. The desired performance of the sample preparation protocols can be achieved by application of detergents. However, these ultimately compromise reverse phase chromatographic separation and disrupt electrospray ionization. Filter aided sample preparation (FASP) represents an elegant approach to overcome these limitations. Although this method is comprehensively validated for cell proteomics, its applicability to plants and compatibility with plant-specific protein isolation protocols is still unknown, i.e., no data on linearity of underlying protein quantification methods for plant matrices is available. To fill this gap, we address here the potential of FASP in combination with two protein isolation protocols for quantitative analysis of pea (<i>Pisum sativum</i>) seed and <i>Arabidopsis thaliana</i> leaf proteomes by the shotgun approach. For this, in comprehensive spiking experiments with bovine serum albumin (BSA), we evaluated the linear dynamic range (LDR) of protein quantification in the presence of plant matrices. Further, we addressed the interference of two different plant matrices in quantitative experiments, accomplished with two alternative sample preparation workflows in comparison to conventional FASP-based digestion of cell lysates, considered here as a reference. Our results indicate very good applicability of FASP to quantitative plant proteomics with an only limited impact of the protein isolation technique on the methods overall performance.<br /> | Tatiana Leonova; Christian Ihling; Mohamad Saoud; Robert Rennert; Ludger A. Wessjohann; Andrej Frolov | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75927842e65101edb49a6/original/does-filter-aided-sample-preparation-fasp-provide-sufficient-method-linearity-for-quantitative-plant-shotgun-proteomics.pdf |
60fed3e78804437c0ee3a401 | 10.26434/chemrxiv-2021-1xjbc | Sustainable Polymers Square Table Final Report | This is the final report from a NSF-sponsored Square Table on Sustainable Polymers that brought together a diverse cohort of stakeholders to develop broad-ranging, integrated, and futuristic ideas and strategies in the area of sustainable polymers. The Square Table included emerging and established leaders from a wide range of backgrounds and institutional types such that a clear picture of the key challenges and needs were developed. Over the course of two half-day sessions, a group of more than 50 participants (see Appendix 1) discussed strategies for advancing the science, technology, and more overarching systems associated with sustainable polymers. The Square Table concept provides structure and self-facilitated interactions among stakeholders who do not typically interact with one another to bridge gaps that exist between industry, federal agencies, and academia in an open and unbiased manner. This was accomplished by mixing participants in breakout discussion with guiding questions, followed by reporting back to the group and repeating with a new mix of participants, questions, and discussion points. Select participants that not only contributed to the discussion but also acted as scribes for sub-sessions were essential to help capture the sum of the views, suggestions, and inputs from the participants. In this way, the discussions cut to the root cause of successes and opportunities in a rapid and less biased manner than traditional roundtables or workshops. The Square Table objectives included developing proposed answers to key questions such as (1) What are the critical basic and applied questions that, when addressed together, could improve the possibility for impact in terms of moving fundamental research thrusts and translational efforts? (2) What prevents large-scale, coordinated efforts between industry, academia, and federal agencies? (3) What is needed to help reduce these barriers in terms of data resources, physical infrastructure, and/or workforce training? (4) How can data and advanced modeling approaches be shared in a collaborative way that would allow data-driven science and engineering to be accelerated in a translational sense? (5) What partnerships are needed to foster an environment/culture to realize more sustainable polymer solutions in the future? | Juan de Pablo; Marc Hillmyer; Jeffrey Buenaflor; Daphne Chan; Josh Mysona; Phil Rauscher; Caitlin Sample; Ludwig Schneider | Polymer Science | CC BY NC 4.0 | CHEMRXIV | 2021-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fed3e78804437c0ee3a401/original/sustainable-polymers-square-table-final-report.pdf |
66de74d5cec5d6c1428cd837 | 10.26434/chemrxiv-2024-2rxlx | The oxygen paradox in alkaline zinc-air battery via the competition of an unidentified anodic chemical reduction with cathodic kinetics | Can the fuel in use adversely affect the performance of an energy storage system? Here, oxygen (O2) in zinc-air (O2) battery (ZAB) is shown to impact the anodic process adversely, leading to early cell failure, though its amount limiting can affect the cathodic reaction kinetics. An unexplored chemical reduction process of dissolved O2 on metallic zinc in alkaline medium leading to peroxide radical (O2˙¯) species generation is proven, by electron paramagnetic resonance spectroscopy (EPR) and hydrodynamic voltammetry studies, followed by the formation of ZnO passivation layer on the Zn surface causing cell death. Keeping similar discharge times, early ZnO passivation occurred on the ZAB with its anode kept in an O2 rich environment than in the other one of O2 free environment. A slight modification in the cell design ensuring the limited availability of O2 at anode provided ~5 times extended cyclability (~7 hours to ~35 hours) than the ZAB with no such control leading to enhanced specific capacity. Presence of O2 in the anodic compartment leads to early cell failure from passivating ZnO formation impeding charge transfer. Limiting the O2 transfer from the cathodic side to anodic compartment can extend the cell cyclability and enhance discharge capacity. As alkaline ZABs are proposed for applications ranging from portable hearing aids to mini-grids, with self-discharge from the hydrogen evolution reaction (HER) on metallic Zn as a major roadblock, this study unravels predominant parasitic chemical process by O2 on the Zn surface, highlighting the importance of cathodic O2 crossover inhibition in the alkaline ZAB.
| Subhra R. Pattanayak; Pallavi Thakur; Tharangattu N. Narayanan | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66de74d5cec5d6c1428cd837/original/the-oxygen-paradox-in-alkaline-zinc-air-battery-via-the-competition-of-an-unidentified-anodic-chemical-reduction-with-cathodic-kinetics.pdf |
661d62e991aefa6ce19eb726 | 10.26434/chemrxiv-2024-7lbzl | Electrochemical Control of Strong Coupling of CdSe Exciton-Polaritons in Plasmonic Cavities | This work reports in-situ (active) electrochemical control over the coupling strength between semiconducting nanoplatelets and a plasmonic cavity. We found that by applying a reductive bias to an Al nanoparticle lattice working electrode, the number of CdSe nanoplatelet emitters that can couple to the cavity is decreased. Strong coupling can be reversibly recovered by discharging the lattice at oxidative potentials relative to the conduction band edge reduction potential of the emitters. By correlating the number of electrons added or removed with the measured coupling strength, we identified that loss and recovery of strong coupling is likely hindered by side processes that trap and/or inhibit electrons from populating the nanoplatelet conduction band. These findings demonstrate tunable, external control of strong coupling and offer prospects to tune selectivity in chemical reactions. | Nathan Sinai; Christian Dones Lassalle; Jennica Kelm; Shreya Patel; Sang-Min Park; Max J. H. Tan; Teri Odom; Jillian Dempsey | Physical Chemistry; Nanoscience; Plasmonic and Photonic Structures and Devices; Electrochemistry - Mechanisms, Theory & Study; Optics | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d62e991aefa6ce19eb726/original/electrochemical-control-of-strong-coupling-of-cd-se-exciton-polaritons-in-plasmonic-cavities.pdf |
60c746e5f96a000f8d286e26 | 10.26434/chemrxiv.11426946.v1 | Impact of Surface Modification on the Li, Na, and K Intercalation Efficiency and Capacity of Few-Layer Graphene Electrodes | <p>In
a conventional lithium ion battery (LIB), graphite forms the negative electrode
or anode. Although Na is considered one of the most attractive alternatives to
Li, achieving reversible Na intercalation within graphitic materials under
ambient conditions remains a challenge. More efficient carbonaceous anode
materials are desired for developing advanced LIBs and <i>beyond Li-ion</i> battery
technologies. We hypothesized that two-dimensional materials with distinct surface
electronic properties create conditions for ion insertion into few-layer graphene (FLG) anodes.
This is because modification of the electrode/electrolyte interface potentially
modifies the energetics and mechanisms of ion intercalation in the thin bulk of
FLG. Through a first principles calculations; we show that the electronic,
structural, and thermodynamic properties of FLG anodes can be fine-tuned by a
covalent heteroatom substitution at the uppermost layer of the FLG electrode, or
by interfacing FLG with a single-side fluorinated graphene or a Janus-type
hydrofluorographene monolayer. When suitably interfaced with the 2D surface
modifier, the FLG exhibits favorable thermodynamics for the Li<sup>+</sup>, Na<sup>+</sup>,
and K<sup>+</sup> intercalation. Remarkably, the reversible binding of Na
within carbon layers becomes thermodynamically allowed and a large storage
capacity can be achieved for the Na intercalated modified FLG anodes. The
origin of charge-transfer promoted electronic tunability of modified FLGs are rationalized
by various theoretical methods. </p> | Nijamudheen Abdulrahiman; Dipobrato Sarbapalli; Jingshu Hui; Joaquín Rodríguez-López; Jose Mendoza-Cortes | Multilayers; Nanostructured Materials - Nanoscience; Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Power; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746e5f96a000f8d286e26/original/impact-of-surface-modification-on-the-li-na-and-k-intercalation-efficiency-and-capacity-of-few-layer-graphene-electrodes.pdf |
63975cce836ceb4cfc7edb27 | 10.26434/chemrxiv-2022-9twlq-v4 | C—H Activation of Unbiased C(sp3)—H Bonds | The selective functionalization of non-activated C(sp3)—H bonds is a major challenge in chemistry. Here, we have developed an [Au]-catalyzed C(sp3)-H activation of common 1 bromoalkynes into a library of diverse 3D-scaffolds. The reaction was shown to proceed via an unknown before mechanism: a concerted [1,5]-H shift / C—C bond formation involving a gold-stabilized vinylcation-like transition state. The most salient feature of this methodology is the ability to functionalize in a predictable way non-activated C(sp3)—H bonds without any sort of electronic, geometric, or conformational bias. | Rubén Miguélez; Nina Semleit; Carlos Rodríguez-Arias; Pavel Mykhailiuk; José M. González; Gebhard Haberhauer; Pablo Barrio | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63975cce836ceb4cfc7edb27/original/c-h-activation-of-unbiased-c-sp3-h-bonds.pdf |
65806ed666c13817297fc8ce | 10.26434/chemrxiv-2023-q265h | Sustainable Electrosynthesis of Cyclohexanone Oxime through Nitrate Reduction on a Zn-Cu Alloy Catalyst | Cyclohexanone oxime is an important precursor for Nylon-6 and is typically synthesized via the nucleophilic addition-elimination of hydroxylamine with cyclohexanone. Current technologies for hydroxylamine production are, however, not environment-friendly due to the requirement of harsh reaction conditions. Here we report an electrochemical method for the one-pot synthesis of cyclohexanone oxime under ambient conditions with aqueous nitrate as the nitrogen source. A series of Zn-Cu alloy catalysts are developed to drive the electrochemical reduction of nitrate, where the hydroxylamine intermediate formed in the electroreduction process can undergo a chemical reaction with the cyclohexanone present in the electrolyte to produce the corresponding oxime. The best performance is achieved on a Zn93Cu7 electrocatalyst with a 97% yield and a 27% Faradaic efficiency for cyclohexanone oxime at 100 mA/cm2. By analyzing the catalytic activities/selectivities of the different Zn-Cu alloys and conducting in-depth mechanistic studies via in-situ Raman spectroscopy and theoretical calculations, we demonstrate that the adsorption of nitrogen species plays a central role on catalytic performance. Overall, this work provides an attractive strategy to build the C–N bond in oxime and drive sustainable organic synthesis through electrochemical nitrate reduction, while highlighting the importance of controlling surface adsorption for product selectivity in electrosynthesis. | Jonathan Sharp; Anna Ciotti; Hayley Andrews; Shaktiswaran Udayasurian; Max García-Melchor; Tengfei Li | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65806ed666c13817297fc8ce/original/sustainable-electrosynthesis-of-cyclohexanone-oxime-through-nitrate-reduction-on-a-zn-cu-alloy-catalyst.pdf |
678feaef81d2151a022a9f21 | 10.26434/chemrxiv-2025-6wb80-v2 | Chiral Transient Directing Groups for Catalytic Asymmetric Intramolecular Alkene Hydroacylation | We developed a chiral 2-aminopyridine as a co-catalyst with Rh(I) to accomplish highly enantioselective intramolecular alkene hydroacylation reactions (up to 96:4 er). The chiral 2-aminopyridine served dual purposes: a transient directing group for aldehyde C–H activation and the sole source of asymmetry in the transformation. Our chiral transient directing group approach overcame prior limitations in asymmetric hydroacylation reactions, where reactants containing embedded chelating groups were required for success. We demonstrated our method in enantioselective syntheses of two biologically-relevant small molecules. | Parker Staub; Hannah Holst; Nitha Puthalath; Christopher Douglas | Organic Chemistry; Catalysis; Organometallic Chemistry; Stereochemistry; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678feaef81d2151a022a9f21/original/chiral-transient-directing-groups-for-catalytic-asymmetric-intramolecular-alkene-hydroacylation.pdf |
64f9cca7b6ab98a41c035618 | 10.26434/chemrxiv-2023-24tmj | New Genetically Engineered Derivatives of Antibacterial Darobac-tins Underpin their Potential for Antibiotic Development | Biosynthetic engineering of bi–cyclic darobactins, which selectively seal the lateral gate of the outer membrane pro-tein BamA, lead to highly active analogues which are up to 128–fold more potent against critical and clinically relevant Gram–negative pathogens compared to their native counterparts. Because of their excellent antibacterial activity, darobactins represent one of the most promising new antibiotic classes of the last decades. Here we present a series of structure-driven biosynthetic modifications of our current frontrunner, darobactin 22 (D22), to investigate modifica-tions at the understudied positions 2, 4 and 5 of the darobactin heptapeptide for their impact on bioactivity. Novel darobactins were found highly active against critical pathogens from the WHO priority list. Antibacterial activity data were corroborated by determination of the dissociation constants KD with BamA beta barrel. The most promising de-rivatives, D22 and D69, were subjected to ADMET profiling, showing high metabolic and plasma stability and low plasma protein binding. We further evaluated D22 and D69 for bioactivity against multidrug–resistant clinical isolates and found them to have low to submicromolar activity. | Carsten E. Seyfert; Alison V. Müller; Danica J. Walsh; Joy Birkelbach; Andreas M. Kany; Christoph Porten; Biao Yuan; Daniel Krug; Jennifer Herrmann; Thomas C. Marlovits; Anna K. H. Hirsch; Rolf Müller | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f9cca7b6ab98a41c035618/original/new-genetically-engineered-derivatives-of-antibacterial-darobac-tins-underpin-their-potential-for-antibiotic-development.pdf |
66df52e112ff75c3a1e2d611 | 10.26434/chemrxiv-2024-vnj32-v2 | Gold Nanorods Grant an ON-OFF Control over the Kinetics of the Z-E Isomerization of Azobenzene-Based Photoswitch via Thermoplasmonic Effect | Proper formulation of systems containing plasmonic and photochromic units, such as gold nanoparticles and azobenzene derivatives, yields materials and interfaces with synergic functionalities. Moreover, gold nanoparticles are known to accelerate the Z-E isomerization of azobenzene molecules in the dark. However, very little is known about the light-driven, plasmon-assisted Z-E isomerization of azobenzene compounds. Additionally, most of the azobenzene-gold hybrids are prepared with nanoparticles of small, isotropic shapes and azobenzene ligands covalently linked to the surface of nanostructures. Herein, a formulation of a novel system combining azobenzene derivative, gold nanorods, and cellulose nanofibers is proposed. The system's structural integrity relies on electrostatic interactions among components instead of covalent linkage. Cellulose, a robust scaffold, maintains the material's functionality in water and enables monitoring of the material's plasmonic-photochromic properties upon irradiation and at elevated temperatures without gold nanorods' aggregation. Experimental evidence supported by statistical analysis suggests that the optical properties of plasmonic nanometal enable indirect control over the Z-E isomerization of the photochromic component with near-infrared irradiation by triggering the thermoplasmonic effect. The proposed hybrid material's dual plasmonic-photochromic functionality, versatility, and ease of processing render a convenient starting point for further advanced azobenzene-related research and 3D printing of macroscopic light-responsive structures. | Nina Tarnowicz-Staniak; Mateusz Staniak; Marta Dudek; Marek Grzelczak; Katarzyna Matczyszyn | Materials Science; Catalysis; Nanoscience; Dyes and Chromophores; Nanocatalysis - Catalysts & Materials; Nanocatalysis - Reactions & Mechanisms | CC BY 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66df52e112ff75c3a1e2d611/original/gold-nanorods-grant-an-on-off-control-over-the-kinetics-of-the-z-e-isomerization-of-azobenzene-based-photoswitch-via-thermoplasmonic-effect.pdf |
6797c546fa469535b910f384 | 10.26434/chemrxiv-2025-s99f0 | Scalable Hyperpolarized MRI Enabled by Ace-SABRE of [1-13C]Pyruvate | Hyperpolarized (HP) MRI using [1-13C]pyruvate is emerging as a promising molecular imaging approach. Among hyperpolarization methods, Signal Amplification By Reversible Exchange (SABRE) is attractive because SABRE polarizes the substrates directly in room-temperature solutions avoiding complex hardware. Most SABRE experiments have historically been performed in methanol, a relatively toxic and difficult to remove solvent. Here we first demonstrate the use of a acetone-water-solvent system (Ace-SABRE) to provide hyperpolarized [1-13C]pyruvate with up to 40% polarization, then implement a solvent processing protocol to achieve injectable solutions, and lastly demonstrate HP in vivo spectroscopy and imaging using the Ace-SABRE platform to showcase metabolic tracking in a hepatocellular carcinoma (HCC) tumor as well as HP-MRI, both in direct comparison to dissolution dynamic nuclear polarization (d-DNP) experiments. The Ace-SABRE technique promises faster adoption of SABRE hyperpolarization in biological experiments, overall lowering the barriers to entry for HP-NMR and HP-MRI. | Stephen McBride; Megan Pike; Erica Curran; Alexander Zavriyev; Bukola Adebesin; Luke Tucker; Jared Harzan; Ishani Senanayake; Mustapha Abdulmojeed; Franziska Theiss; Sheng Shen; Thomas Boele; Simon Duckett; Boyd Goodson; Matthew Rosen; Eduard Chekmenev; Hong Yuan; Carlos Dedesma; Terence Gade; Stephen Kadlecek; Thomas Theis; Patrick TomHon | Physical Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6797c546fa469535b910f384/original/scalable-hyperpolarized-mri-enabled-by-ace-sabre-of-1-13c-pyruvate.pdf |
64a5a22f9ea64cc1677e2702 | 10.26434/chemrxiv-2023-21vt3 | Nontrivial Impact of Relative Humidity on Organic
New Particle Formation from Ozonolysis of cis-3-Hexenyl Acetate | The impact of relative humidity (RH) on organic new particle formation (NPF) from ozonolysis of biogenic volatile organic compounds (BVOCs) remains an area of active
debate. Previous reports provide contradictory results indicating both depression and enhancement of NPF under conditions of high RH. Herein we report on the impact of RH on NPF from dark ozonolysis of cis-3-hexenyl acetate (CHA), a green-leaf volatile (GLV) emitted by vegetation. We
show that RH inhibits NPF by this BVOC, essentially shutting it down at RH levels > 1 %. While the mechanism for inhibition of NPF remains unclear, we demonstrate that it is likely not due to increased losses of CHA to the humid chamber walls. New oxidation products dominant under
humid conditions were identified that, based on estimated vapor pressures (VPs), should enhance NPF; however, it is possible that the vapor phase concentration of these low volatility products is not sufficient to initiate NPF. Furthermore, reaction of C3-excited state Criegee intermediates (CIs) with water may lead to the formation of small carboxylic acids that do not contribute to NPF. This
hypothesis is supported by experiments with quaternary O3 + CHA + α-pinene + RH systems, which showed decreases in total α-pinene-derived NPF at ~ 0% RH and subsequent recovery at elevated RH. | Austin Flueckiger; Christopher Snyder; Giuseppe Petrucci | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a5a22f9ea64cc1677e2702/original/nontrivial-impact-of-relative-humidity-on-organic-new-particle-formation-from-ozonolysis-of-cis-3-hexenyl-acetate.pdf |
60c73fddbb8c1a9c7f3d9c40 | 10.26434/chemrxiv.7499288.v1 | Quaternary Centers via Ni-Catalyzed Cross-Coupling of Tertiary Carboxylic Acids and Aryl Zinc Reagents | <div>
<div>
<div>
<p>This work bridges a gap in the cross-coupling of aliphatic
redox-active esters with aryl zinc reagents. Previously limited to
primary, secondary and specialized tertiary centers, a new protocol
has been devised to enable the coupling of general tertiary systems
using Ni-catalysis. The scope of this operationally simple method is
broad and can be used to simplify the synthesis of medicinally
relevant motifs bearing quaternary centers.
</p>
</div>
</div>
</div> | Phil Baran; Pavel Mykhailiuk; haolin zhang; Rohan R. Merchant; Courtney A. Smith; Tian qin; Tie-Gen Chen | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fddbb8c1a9c7f3d9c40/original/quaternary-centers-via-ni-catalyzed-cross-coupling-of-tertiary-carboxylic-acids-and-aryl-zinc-reagents.pdf |
60c73f9bbb8c1a0a0e3d9bad | 10.26434/chemrxiv.7408748.v1 | Integrated Experimental-Theoretical Approach to Determine Reliable Molecular Reaction Mechanisms on Transition Metal Oxide Surfaces | <p>By
combining experimental and theoretical approaches, we investigate the quantitative
relationship between molecular desorption temperature and binding energy on <i>d</i> and <i>f</i> metal oxide surfaces. We demonstrate how temperature programmed
desorption (TPD) can be used to quantitatively correlate the theoretical surface
chemistry of metal oxides (via on-site Hubbard U correction) to gas surface
interactions for catalytic reactions. For this purpose, both CO and NO
oxidation mechanisms are studied in a step by step reaction process for
perovskite and mullite-type oxides, respectively. Additionally, we show solutions
for over-binding issues found in CO<sub>x</sub>, NO<sub>x</sub>, SO<sub>x</sub>,
and other covalently bonded molecules which must be considered during surface reaction
modeling. This work shows the high reliability of using TPD and density
functional theory (DFT) in conjunction to create accurate surface chemistry
information for a variety of correlated metal oxide materials.</p> | Nickolas Ashburn; yongping zheng; Sampreetha Thampy; Sean Dillon; Yves Chabal; Julia
W. P. Hsu; Kyeongjae Cho | Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Theory - Computational; Heterogeneous Catalysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9bbb8c1a0a0e3d9bad/original/integrated-experimental-theoretical-approach-to-determine-reliable-molecular-reaction-mechanisms-on-transition-metal-oxide-surfaces.pdf |
636a9c4233f73330b0df125e | 10.26434/chemrxiv-2022-s1qj9 | Week-long operation of electrochemical aptamer sensors: New insights into self-assembled monolayer degradation mechanisms and solutions for stability in biofluid at body temperature | Conventional wisdom suggests that widely-utilized self-assembled alkylthiolate monolayers on gold are too unstable to last more than several days when exposed to complex fluids such as raw serum at body temperature. Demonstrated here is that these monolayers can not only last at least one week under such harsh conditions, but that significant applied value can be captured for continuous electrochemical aptamer biosensors. Electrochemical aptamer biosensors provide an ideal tool to investigate monolayer degradation, as aptamer sensors require a tightly-packed monolayer to preserve sensor signal versus background current and readily reveal fouling by albumin and other solutes when operating in biofluids. Week-long operation in serum at 37 ˚C is achieved by: (1) assembling monolayers on gold with roughness that promotes small alkylthiolate monolayer defect sizes; (2) increasing van der Waals interactions between adjacent monolayer molecules to increase the activation energy required for desorption; (3) optimizing electrochemical measurement to decrease both alkylthiolate oxidation and electric-field induced desorption; (4) mitigating fouling by using protective zwitterionic membranes and zwitterion-based blocking layers with antifouling properties. This work further proposes origins and mechanisms of monolayer degradation in a logical stepwise manner that was previously unobservable over multi-day time scales. Several of the observed results are surprising, revealing that short term improvements to sensor longevity (i.e., hours) actually increase sensor degradation in the longer term (i.e., days). The results and underlying insights on mechanisms not only push forward fundamental understanding of stability for self-assembled monolayers, but demonstrate an important milestone for continuous electrochemical aptamer biosensors. | Zach Watkins; Aleksandar Karajić; Thomas Young; Ryan White; Jason Heikenfeld | Analytical Chemistry; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636a9c4233f73330b0df125e/original/week-long-operation-of-electrochemical-aptamer-sensors-new-insights-into-self-assembled-monolayer-degradation-mechanisms-and-solutions-for-stability-in-biofluid-at-body-temperature.pdf |
60c7498af96a0049b2287290 | 10.26434/chemrxiv.9789482.v2 | Green-to-Blue Triplet Fusion Upconversion Sensitized by Anisotropic CdSe Nanoplatelets | <p>Green-to-blue photon upconversion bears great potential in photocatalytic applications. However, current hybrid inorganic-organic upconversion schemes utilizing spherical CdSe nanocrystals are often limited by energetic polydispersity, low quantum yields and an additional tunneling barrier resulting from the necessity of surface-passivating inorganic shells. In this contribution, we introduce anisotropic CdSe nanoplatelets as triplet sensitizers. Here, quantum confinement occurs in only one direction, erasing effects stemming from energetic polydispersity. We investigate the triplet energy transfer from the CdSe nanoplatelets to the surface-bound triplet acceptor 9-anthracene carboxylic acid. We further focus on the influence of nanoplatelet stacking and singlet back transfer on the observed upconversion efficiency. We obtain an upconversion quantum yield of 5.4% at a power density of 11 W/cm<sup>2</sup> using the annihilator 9,10-diphenylanthracene, and a low efficiency threshold <i>I</i><sub>th</sub> of 237 mW/cm<sup>2</sup>. </p> | Zachary A. VanOrman; Alexander S. Bieber; Sarah Wieghold; Lea Nienhaus | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Interfaces; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7498af96a0049b2287290/original/green-to-blue-triplet-fusion-upconversion-sensitized-by-anisotropic-cd-se-nanoplatelets.pdf |
65a701f6e9ebbb4db951c96a | 10.26434/chemrxiv-2024-lp0l6 | Electrically Insulated Catalyst-Ionomer Anode Interfaces towards Durable Alkaline Membrane Electrolyzer | Anion-exchange-membrane water electrolysis (AEMWE) is an emerging technology for scalable hydrogen production. AEMWE has poor durability when operating without supporting electrolyte due to the oxidation of ionomers and membranes in contact with anode oxygen evolution reaction (OER) catalyst. We report a new “passivated” anode architecture for AEMWE where OER catalysts and ionomers are physically separated with a thin film amorphous oxide coating that is electrically insulating but conductive to hydroxide ions. We find that 2–3 nm of HfOx passivation layers show sufficient hydroxide ion transport to minimally limit the cell performance while suppressing ionomer degradation with both Ir (500 mA·cm−2 for 40 h) and CoOx (1.0 A·cm−2 for 100 h) model porous-transport-layer-supported catalysts in AEMWE. This interfacial engineering approach guides electrode design to improve the durability of AEMWE, particularly for systems operating with pure water feed. | Minkyoung Kwak; Kasinath Ojha; Meikun Shen; Shannon W. Boettcher | Energy | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a701f6e9ebbb4db951c96a/original/electrically-insulated-catalyst-ionomer-anode-interfaces-towards-durable-alkaline-membrane-electrolyzer.pdf |
63eb1eacfcfb27a31fc152ae | 10.26434/chemrxiv-2023-jn276 | Heterogeneously Catalyzed Decarbonylation of Thioesters by Supported Nanoparticle Catalysts | This study demonstrated a heterogeneously catalyzed system for decarbonylation of various aryl thioesters to produce thioethers and CO by utilizing CeO2- or hydroxyapatite-supported Ni or Pd nanoparticle catalysts. The Ni catalysts showed high catalytic activity, while the Pd catalysts possessed excellent functional group tolerance. | Takehiro Matsuyama; Takafumi Yatabe; Kazuya Yamaguchi | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eb1eacfcfb27a31fc152ae/original/heterogeneously-catalyzed-decarbonylation-of-thioesters-by-supported-nanoparticle-catalysts.pdf |
60c740e59abda258f1f8bd96 | 10.26434/chemrxiv.7871504.v1 | Low-Cost Molecular Excited States from a State-Averaged Resonating Hartree-Fock Approach | Quantum chemistry methods that describe excited states on the same footing as the ground state are generally scarce. In previous work, Gill et al. (J. Phys. Chem. A 112, 13164 (2008)) and later Sundstrom and Head-Gordon (J. Chem. Phys. 140, 114103 (2014)) considered excited states resulting from a non-orthogonal configuration interaction (NOCI) on stationary solutions of the Hartree–Fock equations. We build upon those contributions and present the state-averaged resonating Hartree–Fock (sa-ResHF) method, which differs from NOCI in that spin-projection and orbital relaxation effects are incorporated from the onset. Our results in a set of small molecules (alanine, formaldehyde, acetaldehyde, acetone, formamide, and ethylene) suggest that sa-ResHF excitation energies are a notable improvement over configuration interaction singles (CIS), at a mean-field computational cost. The orbital relaxation in sa-ResHF, in the presence of a spin-projection operator, generally results in excitation energies that are closer to the experimental values than the corresponding NOCI ones. | Jacob Nite; Carlos A. Jimenez-Hoyos | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e59abda258f1f8bd96/original/low-cost-molecular-excited-states-from-a-state-averaged-resonating-hartree-fock-approach.pdf |
668b0e2fc9c6a5c07a988c07 | 10.26434/chemrxiv-2024-002t5 | Intermolecular Proton Transfer Enabled Reactive CO2 Capture by the Malononitrile Anion | Task-specific ionic liquids employing carbanions represent a new class of ionic liquids for carbon capture. The deprotonated malononitrile carbanion, [CH(CN)2]−, has shown close to equimolar capacity for reactive CO2 capture. Although formation of the [C(CN)2COOH]− carboxylic acid was found to be the final product, how the hydrogen atom on the [CH(CN)2]− carbanion transfers to the carboxylate group as a proton is unclear. In this work, we employ density-functional-theory calculations with an implicit solvation model to investigate the proton transfer mechanisms in forming carboxylic acid from the reaction of the [CH(CN)2]− carbanion with CO2. We find that the intramolecular proton-transfer pathway in [CH(CN)2COO]− to form [C(CN)2COOH]− is unlikely due to the high energy barrier of 152 kJ/mol. Instead, the intermolecular proton transfer pathway between two [CH(CN)2COO]− anions is more feasible to form two molecules of [C(CN)2COOH]−, with a significantly lower activation energy of 50 kJ/mol. Moreover, the [C(CN)2COOH]− dimer is further stabilized by the intermolecular hydrogen bonds of the two -COOH groups in the Z-configuration of the π-conjugated planar geometry. The insight of reactive CO2 capture enabled by intermolecular proton transfer will be useful in designing novel carbanions and ionic liquids for carbon capture and conversion. | Bo Li; Yuqing Fu; Zhenzhen Yang; Sheng Dai; De-en Jiang | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668b0e2fc9c6a5c07a988c07/original/intermolecular-proton-transfer-enabled-reactive-co2-capture-by-the-malononitrile-anion.pdf |
60c757febdbb89f912a3ace3 | 10.26434/chemrxiv.14484621.v1 | Assessing Material Fragility using Nanoscale Incremental Dynamic Analysis | A new methodology to assess material failure subjected to stochastic loads is proposed, titled Nanoscale Incremental Dynamic Analysis (NIDA), which is adopted from performance-based assessment in structural engineering. Using full atomistic molecular dynamics, proof-of-concept simulations produce the material fragility curve of a simple carbon nanotube. | Steven Cranford | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757febdbb89f912a3ace3/original/assessing-material-fragility-using-nanoscale-incremental-dynamic-analysis.pdf |
6126370dac3219f060688bbf | 10.26434/chemrxiv-2021-gsrtp | Validation of the triplet ground state in a persistent derivative of Clar’s hydrocarbon | Triangulene is a prototypical non-Kekulé diradical known as Clar’s hydrocarbon. It is the smallest non-Kekulé graphene fragment comprised of six benzenoid rings fused in a triangular shape. In accordance with Hund’s rule, a triplet ground state is predicted for this hydrocarbon. However, because of its high reactivity, synthesis of a stable or persistent derivative of neutral triangulene to validate this prediction has been an elusive goal for almost 70 years. Herein, we report the synthesis and characterization of the first persistent derivative of triangulene, kinetically stabilized by three sterically demanding substituents installed at the most reactive positions in the centers of the zigzag edges. The triplet ground state of this hydrocarbon is unequivocally confirmed by pulse electron paramagnetic resonance spectroscopy and supported by density functional theory. The realization of a long-sought-after persistent triangulene derivative will motivate the synthesis of analogous open-shell graphene fragments as prospective building blocks of high-spin materials for the newly emerging field of organic spintronics.
| Leoš Valenta; Maximilian Mayländer; Pia Kappeler; Olivier Blacque; Tomáš Šolomek; Sabine Richert; Michal Juríček | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6126370dac3219f060688bbf/original/validation-of-the-triplet-ground-state-in-a-persistent-derivative-of-clar-s-hydrocarbon.pdf |
64ca17de69bfb8925a39d601 | 10.26434/chemrxiv-2023-tw9l1-v2 | Electroreductive Deoxygenative C–H and C–C Bond Formation from Non-Derivatized Alcohols Fueled by Borohydride Oxidation | Alcohols are one of the most common organic compound classes among natural and synthetic products. Thus, methods for direct removal of C–OH groups without the need for wasteful pre-functionalization are of great synthetic interest to unlock the full synthetic potential of the compound class. Herein, electroreductive C–OH bond activation and subsequent deoxygenative C–H and C–C bond formation of benzylic and propargylic alcohols is demonstrated. Experimental and theoretical studies indicate that the reductive C–OH bond cleavage furnishes an open shell intermediate that undergoes a radical-polar crossover to the corresponding carbanion that subsequently undergoes protonation to furnish alkane products. Furthermore, we demonstrate the carbanion can be trapped with CO2 to form arylacetic acids, representing the first example of deoxygenative electrochemical C–C bond formation from non-derivatized alcohols. The cathodic transformations are efficiently balanced by the anodic oxidation of borohydride additives, a strategy that serves as a highly attractive alternative to the use of sacrificial metal anodes. | Piret Villo; Malin Lill; Zainab Alsaman; Adrian Soto Kronberg; Victoria Chu; Guillermo Ahumada; Hemlata Agarwala; Mårten Ahlquist; Helena Lundberg | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca17de69bfb8925a39d601/original/electroreductive-deoxygenative-c-h-and-c-c-bond-formation-from-non-derivatized-alcohols-fueled-by-borohydride-oxidation.pdf |
66e1451451558a15efa83aa8 | 10.26434/chemrxiv-2024-9m6nj | Cyclopalladation of a Covalent Organic Framework for Near-Infrared Light-Driven Photocatalytic Hydrogen Peroxide Production | Covalent organic frameworks (COFs) have been extensively developed as photosensitizers for photocatalytic energy conversion over the past decade. However, current COF photocatalysts have yet to demonstrate the capability to harvest near-infrared (NIR) light (above 760 nm), which constitutes approximately 53% of the solar spectrum, for fuel or chemical conversion. In this work, we introduce a novel post-synthetic functionalization strategy for COFs by incorporating a palladacycle directly into the COF backbone, extending the light absorption of an azobenzene-based COF into the NIR region. This approach enables homogeneous, atomically-distributed Pd functionalization with a high loading amount of 12 wt% and without noticeable formation of Pd nanoparticles. The cyclopalladated COF, TpAzo-CPd, was utilized as a catalyst for photocatalytic hydrogen peroxide production under 810 nm illumination. This study represents the first implementation of COFs for NIR photocatalysis and opens the door to Pd-single-site COF catalysts for a wide range of organic transformations. | Andrés Rodríguez-Camargo; Maxwell W. Terban; Martina Paetsch; Elio A. Rico; Radhika Hirpara; Viola Duppel; Igor Moudrakovski; Martin Etter; Néstor Guijarro; Robert E. Dinnebier; Liang Yao; Bettina V. Lotsch | Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Photocatalysis; Coordination Chemistry (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e1451451558a15efa83aa8/original/cyclopalladation-of-a-covalent-organic-framework-for-near-infrared-light-driven-photocatalytic-hydrogen-peroxide-production.pdf |
6189a93fd828a4577f70c801 | 10.26434/chemrxiv-2021-k7ghz | Expanding the Current Boundaries of Nature-based Modeling and Computing: Chem-Inspiration for Meta-Heuristics | High-throughput methods in science have created a trend to generate massive amount of data that challenge our ability to mine and search through massive information spaces. Thus more efficient and effective solutions for data analysis and optimization are required continuously. The best solutions for many problems-solving approaches in science could have many sources of inspiration coming from diverse natural phenomena. In this context, most Artificial Intelligence (AI) approaches benefit from emulation natural processes for their information processing strategy. Among the AI protocols, meta-heuristic algorithms for learning model and optimization have exploited a number of biological phenomena leading to highly effective search and learning engines. Examples of these processes are the ant colony organization, brain function and genetics among others. The evolution has turned all these biological events in highly efficient procedures, whose basics principles have then provided an excellent ground of new computational algorithms The aim of this report is pave the way to a new class of nature-based meta-heuristic methods which shall be based on diverse chemical and biomolecular systems. We present five examples from different subjects of Chemistry like Organic Chemistry, Chemical Physics and Biomolecules; and introduce how computational models could be inferred from them. Besides, we develop one of these models, in detail, which is based on protein evolution and folding principles. We consider that the wealth of systems and processes related to Chemistry, as those described in the present communication, might boost the development of relevant meta-heuristic and classification algorithms in upcoming years. | Yovani Marrero-Ponce; Yasser B. Ruiz-Blanco; Yuviny Echevarría; Felix Martinez-Rios; Rafael Bello; Carlos Morrel; Ricardo Vivas-Reyes | Theoretical and Computational Chemistry; Physical Chemistry; Artificial Intelligence; Biophysical Chemistry; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6189a93fd828a4577f70c801/original/expanding-the-current-boundaries-of-nature-based-modeling-and-computing-chem-inspiration-for-meta-heuristics.pdf |
622e8bcd702f0417d8bb483f | 10.26434/chemrxiv-2022-njzlw | Synthesis and structural properties of a 2D Zn(II) dodecahydroxy-closo-dodecaborate coordination polymer | In this work, we discuss the synthesis and characterization of a 2D coordination polymer composed of a dianionic perhydroxylated boron cluster, [B12(OH)122-], coordinated to Zn(II)—the first example of a transition metal-coordinated [B12(OH)12]2- compound. This material was synthesized via cation exchange from the starting cesium salt and then subjected to rigorous characterizion prior to and after thermal activation. Numerous techniques, including XRD, FTIR, SEM, TGA, and solid-state NMR revealed a 2D coordination polymer composed of sheets of Zn(II) ions intercalated between planes of boron clusters. The as-synthesized material was then evacuated of solvent via thermal treatment, and atomic-level changes from this transformation were elucidated through a combination of 1D and 2D solid-state NMR analyses of 11B and 1H nuclei, suggesting the full removal of coordinated solvent molecules. Evidence also suggested that [B12(OH)122-] can adjust its coordination to Zn(II) in the solid-state through hemilability of its numerous -OH ligands. | Austin Ready; Shona Becwar; Dahee Jung; Emily Schueller; Kierstyn Anderson; Rebecca Kubena; Ram Seshadri; Bradley Chmelka; Alexander Spokoyny | Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Main Group Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622e8bcd702f0417d8bb483f/original/synthesis-and-structural-properties-of-a-2d-zn-ii-dodecahydroxy-closo-dodecaborate-coordination-polymer.pdf |
62f1a15d42ddf532a9b420af | 10.26434/chemrxiv-2022-nr0dm-v2 | Chemoinformatics and Artificial Intelligence Colloquium: Progress and Challenges to Develop Bioactive Compounds | We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15-17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, and non-for-profit organizations. Twelve hundred and ninety students and academics from more than 60 countries. During the meeting, applications, challenges, and opportunities in drug discovery, de novo drug design, ADME-Tox (absorption, distribution, metabolism, excretion and toxicity) property predictions, organic chemistry, peptides, and antibiotic resistance were discussed. The program along with the recordings of all sessions are freely available at https://www.difacquim.com/english/events/2022-colloquium/ | Jürgen Bajorath; Ana L. Chávez-Hernández; Miquel Duran-Frigola; Eli Fernández-de Gortari; Johann Gasteiger; Edgar López-López; Gerald M. Maggiora; José L. Medina-Franco; Oscar Méndez-Lucio; Jordi Mestres; Ramón Alain Miranda-Quintana; Tudor I. Oprea; Fabien Plisson; Fernando D. Prieto-Martínez; Raquel Rodríguez-Pérez; Paola Rondón-Villarreal; Fernanda I. Saldívar-Gonzalez; Norberto Sánchez-Cruz; Marilia Valli | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f1a15d42ddf532a9b420af/original/chemoinformatics-and-artificial-intelligence-colloquium-progress-and-challenges-to-develop-bioactive-compounds.pdf |
60c74df7ee301c9fa3c7a3e7 | 10.26434/chemrxiv.12681761.v1 | Hit-Optimization Using Target-Directed Dynamic Combinatorial Chemistry: Development of Inhibitors of the Anti-Infective Target 1-Deoxy-D-Xylulose-5-Phosphate Synthase | <p>Target-directed dynamic
combinatorial chemistry (tdDCC) enables the identification, as well as
optimization of ligands for un(der)explored targets such as the anti-infective
target 1‑deoxy‑d‑xylulose-5-phosphate synthase (DXS).
We report the unprecedented use of tdDCC to first identify and subsequently
optimize inhibitors of the anti-infective target DXS. Using tdDCC, we were able
to generate acylhydrazone-based inhibitors for DXS. The tailored tdDCC runs
also provided insights into the structure–activity relationship of this novel class
of DXS inhibitors. This approach holds the potential to expedite the drug
discovery process and could be generally applied to a range of biological
targets.</p> | Ravindra P. Jumde; Melissa Guardigni; Robin M. Gierse; Alaa Alhayek; Di Zhu; Zhoor Hamed; Sandra Johannsen; Walid A. M. Elgaher; Jörg Haupenthal; Anna K.H. Hirsch | Combinatorial Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df7ee301c9fa3c7a3e7/original/hit-optimization-using-target-directed-dynamic-combinatorial-chemistry-development-of-inhibitors-of-the-anti-infective-target-1-deoxy-d-xylulose-5-phosphate-synthase.pdf |
60c73f9fbdbb8917c0a3803f | 10.26434/chemrxiv.7460618.v1 | A Coordinative Solubilizer Method to Fabricate Soft Porous Materials from Insoluble Metal-Organic Polyhedra | <p>Porous molecular cages have a characteristic processability arising from their solubility, which allows their incorporation into porous materials. Attaining solubility often requires covalently bound functional groups that are unnecessary for porosity, and which ultimately occupy free volume in the materials and decrease their surface areas. Here, we describe a method that takes advantage of the coordination bonds in metal-organic polyhedra (MOPs) to render insoluble MOPs soluble by reversibly attaching an alkyl-functionalized ligand. We then use the newly soluble MOPs as monomers for supramolecular polymerization reactions, obtaining permanently porous, amorphous polymers with the shape of colloids and gels, which display increased gas uptake in comparison with materials made with covalently functionalized MOPs.</p> | Arnau Carné-Sánchez; Gavin A. Craig; Patrick Larpent; vincent guillerm; Kenji Urayama; Daniel Maspoch; Shuhei Furukawa | Coordination Chemistry (Inorg.); Polymers; Supramolecular Chemistry (Inorg.); Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9fbdbb8917c0a3803f/original/a-coordinative-solubilizer-method-to-fabricate-soft-porous-materials-from-insoluble-metal-organic-polyhedra.pdf |
60c74540567dfec994ec4430 | 10.26434/chemrxiv.9999848.v1 | Terbium(III) Phthalocyaninato Multiple-Decker Complexes in High Oxidation States: Correlation Between Electronic, Structural and Magnetic Properties and Unexpected Triplet Biradical States | <p>Herein
we present a comprehensive study of the highly oxidized species of
multiple-decker complexes composed of Tb(III) and Cd(II) ions and two to five
phthalocyaninato ligands, which are stabilized by electron-donating <i>n</i>-butoxy
chains. Paramagnetic <sup>1</sup>H NMR measurements for the series of triple,
quadruple and quintuple-decker complexes revealed that ligand oxidations lead
to a decrease in magnetic anisotropy, as predicted from <i>ab initio</i> calculations. Unusual paramagnetic shifts were observed
in +2<i>e</i> charged quadruple and quintuple-decker complexes, indicating that
those two species are actually triplet biradicals. The X-ray structural
analysis for the series of oxidized multiple-decker complexes revealed that all
the species show an axial compression induced by the ligand oxidations,
resulting in the bowl-shaped distortion of the ligands, in agreement with
predictions from DFT calculations. Magnetic measurements revealed that the
series of complexes show single-molecule magnet (SMM) properties, which are
controlled by the multi-step redox induced structural changes.</p> | Yoji Horii; Marko Damjanović; M. R. Ajayakumar; Keiichi Katoh; Yasutaka Kitagawa; Liviu Chibotaru; Liviu Ungur; Marta Mas-Torrent; Wolfgang Wernsdorfer; Markus Enders; Jaume Veciana; Masahiro Yamashita | Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74540567dfec994ec4430/original/terbium-iii-phthalocyaninato-multiple-decker-complexes-in-high-oxidation-states-correlation-between-electronic-structural-and-magnetic-properties-and-unexpected-triplet-biradical-states.pdf |
60c73f1b337d6c6980e264b5 | 10.26434/chemrxiv.7235438.v1 | Dual-Catalytic Transition Metal Systems for Functionalization of Unreactive Sites of Molecules | <b>Catalytic reactions occur readily at sites of
starting materials that are both innately reactive and sterically accessible or
that are predisposed by a functional group amenable to direct a catalyst.
However, selective reactions at unbiased sites of substrates remain challenging
and typically require additional pre-activation steps or the use of highly
reactive reagents. Herein, we report dual-catalytic transition metal systems
that merge a reversible activation cycle with a functionalization cycle, together
enabling functionalization of substrates at their inherently unreactive sites.
By engaging the Ru- or Fe-catalyzed equilibrium between an alcohol and an
aldehyde, Pd-catalyzed <i>b</i>-arylation of aliphatic alcohols and
Rh-catalyzed <i>g</i>-hydroarylation
of allylic alcohols were developed. The mild conditions, functional group
tolerance and broad scope of the methodologies (81 examples) demonstrate the
synthetic applicability of the dual-catalytic systems. In a broader context,
this work highlights the potential of the multi-catalytic approach to address
challenging transformations to circumvent the multi-step procedures and the use
of highly reactive reagents in organic synthesis.</b> | Dawid Lichosyt; Yang Zhang; Karolina Hurej; Pawel Dydio | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1b337d6c6980e264b5/original/dual-catalytic-transition-metal-systems-for-functionalization-of-unreactive-sites-of-molecules.pdf |
60c742ac702a9b12ec18a4c5 | 10.26434/chemrxiv.8332490.v1 | Molecular Doping of PCPDT-BT Copolymers: Comparison of Molecular Complexes with and Without Integer Charge Transfer | <div>
<div>
<div>
<p>Molecular doping in conjugated polymers is a crucial process for their application in organic
photovoltaics and optoelectronics. In the present work we theoretically investigate p-type molecu-
lar doping in a series of (poly[2,6-(4,4-bis(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b”]dithiophene)-alt-
4,7-(2,1,3-benzothiadiazole)] (PCPDT-BT) conjugated oligomers with different lengths and three
widely-used dopants with different electron affinities, namely F4TCNQ, F6TCNNQ, and CN6-CP.
We study in detail the molecular geometry of possible oligomer-dopant complexes and its influence
on the doping mechanisms and electronic system properties. We find that the mechanisms of dop-
ing and charge transfer observed sensitively depend on the specific geometry of the oligomer-dopant
complexes. For a given complex different geometries may exist, some of which show transfer of
an entire electron from the oligomer chain onto the dopant molecule resulting in an integer-charge
transfer complex, leaving the system in a ground state with broken spin symmetry. In other ge-
ometries merely hybridization of oligomer and dopant frontier orbitals occurs with partial charge
transfer but spin-symmetric ground state. Considering the resulting electronic density of states both
cases may well contribute to an increased electrical conductivity of corresponding film samples while
the underlying physical mechanisms are entirely different.
</p>
</div>
</div>
</div> | Chuanding Dong; Stefan Schumacher | Oligomers; Computational Chemistry and Modeling; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ac702a9b12ec18a4c5/original/molecular-doping-of-pcpdt-bt-copolymers-comparison-of-molecular-complexes-with-and-without-integer-charge-transfer.pdf |
60c7404aee301c0ebec78a54 | 10.26434/chemrxiv.7688396.v1 | [Co(TPP)]-Catalyzed Formation of Substituted Piperidines | Radical cyclization via cobalt(III)–carbene radical intermediates is a powerful method for the synthesis of (hetero)cycles. Building on the recently reported synthesis of N-heterocyclic pyrrolidines catalyzed by Co(II) porphyrins, we herein report the [Co(TPP)]-catalyzed formation of desirable six membered N heterocyclic piperidines, directly from linear aldehydes. Piperidines were obtained in overall high yields, with linear alkenes being formed as side products in small amounts. A DFT study was performed to gain a deeper mechanistic understanding of the cobalt(II)-porphyrin-catalyzed formation of pyrrolidines, piperidines and linear alkenes. The calculations show that the alkenes are unlikely to be formed through 1,2-HAT. Instead, the calculations are consistent with a pathway involving benzyl radical formation followed by radical rebound ring-closure to form the piperidines. Competitive 1,5-HAT from the beta-position to the benzyl radical explains the formation of linear alkenes.<br /> | Bas de Bruin; Marianne Lankelma; Astrid M. Olivares | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7404aee301c0ebec78a54/original/co-tpp-catalyzed-formation-of-substituted-piperidines.pdf |
60e971ca551cb01db6ae2d32 | 10.26434/chemrxiv-2021-kfr3s-v2 | Double Excitations in Molecules from Ensemble Density Functionals: Theory and Approximations | Double excitations, which are dominated by a Slater-determinant with both electrons in the highest occupied molecular orbital promoted to the lowest unoccupied orbital(s), pose significant challenges for low-cost electronic structure calculations based on density functional theory (DFT). Here, we demonstrate that recent advances in ensemble DFT [{\it Phys. Rev. Lett.} {\bf 125}, 233001 (2020)], which extend concepts of ground-state DFT to excited states via a rigorous physical framework based on the ensemble fluctuation-dissipation theorem, can be used to shed light on the double excitation problem. We find that the exchange physics of double excitations is reproducible by standard DFT approximations using a linear combination formula, but correlations are more complex. In passing, to analyze correlation, we extend the random-phase approximation to ensembles. We then show, using selected test systems, that standard DFT approximations may be adapted to tackle double excitations based on theoretically motivated simple formulae that employ ensemble extensions of expressions that use the on-top pair density.
| Tim Gould; Leeor Kronik; Stefano Pittalis | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e971ca551cb01db6ae2d32/original/double-excitations-in-molecules-from-ensemble-density-functionals-theory-and-approximations.pdf |
64c30fe5658ec5f7e54af7b3 | 10.26434/chemrxiv-2023-jpwvn | Regularized indirect learning improves phage display ligand discovery | Phage display is commonly employed for the discovery of high affinity ligands to biomolecular targets. However, ranking the discovered ligands for their affinity and specificity to the target is obscured by genetic amplification bias and amplification of target-unrelated phage, resulting in inefficient experimental validation and potentially intractable discovery. Here, we describe the use of indirect machine learning (ML) to improve the efficient discovery of target-specific peptide ligands from next-generation sequencing (NGS) data. We combine peptide sequence information (input) with experimental fitness scores (output) of the individual peptide performance across the rounds of bio-panning in a bidirectional long short-term memory (BiLSTM) architecture. Because the fitness scores contain bias, we use regularization to facilitate limited indirect learning and effectively process the peptide sequence information, while still using the predicted fitness scores to rank the peptides. Peptides containing high-affinity binding motifs to our target were ranked by the regularized model more than threefold higher, compared to any combination of experimental fitness scores. Baseline models of random forest (RF) and -nearest neighbor (KNN) demonstrated slightly lower performance but also demonstrated the importance of regularization. However, the BiLSTM model emerged as the most robust, as it was less sensitive to the peptide representation and the specific fitness score used. Shapley residue analysis generated interpretable structure-activity-relationship (SAR) by providing insight into predicted affinity-driving residues and physicochemical properties across the entire peptide and as well as at motif-specific positions. We expect that this approach will elucidate high-affinity ligands against a multitude of targets, vastly improving the discovery capability of phage display. | Joseph S. Brown; Yitong Tseo; Michael A. Lee; Jeffrey Y.-K. Wong; Soojung Yang; Yehlin Cho; Chae Rin Kim; Andrei Loas; Ratmir Derda; Rafael Gomez-Bombarelli; Bradley L. Pentelute | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c30fe5658ec5f7e54af7b3/original/regularized-indirect-learning-improves-phage-display-ligand-discovery.pdf |
64ac469c6e1c4c986b2865e5 | 10.26434/chemrxiv-2023-gbb9x | Reversible Hydration Enabling High-Rate Aqueous Li-ion Batteries | Two-dimensional TiS2 has been proposed as a versatile host material for various battery chemistries. Nevertheless, its compatibility with aqueous electrolytes has not been thoroughly understood. Herein, we report on a reversible hydration process to account for the electrochemical activity and structural evolution of TiS2 in a dilute electrolyte for sustainable aqueous Li-ion batteries. Solvated water molecules intercalate into TiS2 layers together with Li+ cations, forming a hydrated phase with a nominal formula unit of Li0.38(H2O)2 δTiS2 as the end product. We unambiguously confirm the presence of two layers of intercalated water by complementary electrochemical cycling, operando structural characterization, and computational simulation. Such a process is fast and reversible, delivering 60 mAh g-1 discharge capacity at a current density of 1250 mA g-1. Our work provides further design principles for high-rate aqueous Li-ion batteries based on reversible water co-intercalation. | Leiting Zhang; Franziska Kühling; Agnes-Matilda Mattsson; Xu Hou; Gustav Ek; Thomas Dufils; Chao Zhang; William R. Brant; Kristina Edström; Erik J. Berg | Inorganic Chemistry; Energy; Electrochemistry; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ac469c6e1c4c986b2865e5/original/reversible-hydration-enabling-high-rate-aqueous-li-ion-batteries.pdf |
67587df4085116a133f95d0c | 10.26434/chemrxiv-2024-55jgh | Separation of Tetrahydrocannabinol Fraction from Cannabis indica Extracts by Chromatographic Method | Tetrahydrocannabinol (∆9-THC) from Cannabis indica leaves was extracted by using solvent extraction method applying condenser apparatus. The molecular and physical attributes of ∆9-THC, or tetrahydrocannabinol, were identified. The collected oil’s content and a number of additional variables were studied. The optimum oil yield was predicted. Two samples were produced with multiple parameters. Sample (B) was made by soaking the leaves for seven days, whilst sample; (A) was made by using a condenser the instrument. The derived oil’s content and multiple kinds of other factors were studied. For characterization of both samples TLC, GC-MS, IR and HPLC techniques were applied. Various physical and chemical characteristics for Tetrahydrocannabinol (∆9- THC) oil was analyzed as different values such as acid value, specific gravity, saponification value, refractive Index by titration. Some physical tests were also performed for the detection of proteins, carbohydrates, Steroids, tennins, gums and mucilage. Both samples’ results proved wide differences. Due to elevate oxidative stability and psychoactive nature Tetrahydrocannabinol (∆9-THC) oil has many medicinal applications. | Ubaid Ullah Khan; Shafqat Munir; Shamsher Khan; Nishat noorani sha | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Separation Science; Bioengineering and Biotechnology; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67587df4085116a133f95d0c/original/separation-of-tetrahydrocannabinol-fraction-from-cannabis-indica-extracts-by-chromatographic-method.pdf |
648f2984e64f843f41f8ae2c | 10.26434/chemrxiv-2023-3vcmx-v2 | Time-dependent density functional theory for x-ray absorption spectra: Comparing the real-time approach to linear response | We examine the simulation of x-ray absorption spectra at elemental K-edges using time-dependent density functional theory, in both its conventional linear-response implementation and also its "real-time" formulation. Real-time simulations enable broadband x-ray spectra calculations without the need to invoke frozen occupied orbitals or "core/valence separation", but we find that the spectra are frequently contaminated by transitions to the continuum originating from lower-energy core and semi-core orbitals. This problem becomes acute in triple-zeta basis sets although it is sometimes bypassed serendipitously in lower-quality basis sets. Transitions to the continuum acquire surprisingly large dipole oscillator strengths, leading to spectra that are difficult or impossible to interpret. Meaningful spectra can be recovered by means of a filtering technique that decomposes the spectrum into contributions from individual occupied orbitals, and the same procedure can be used to separate L- and K-edge spectra. Nevertheless, the conventional linear-response approach is significantly more efficient even when hundreds of individual states are needed to reproduce near-edge absorption features, and even when Pade approximants are used to reduce the real-time simulations to less than 2 fs of time propagation. The real-time approach may be useful for examining the validity of core/valence separation, however. | John Herbert; Ying Zhu; Bushra Alam; Avik Ojha | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648f2984e64f843f41f8ae2c/original/time-dependent-density-functional-theory-for-x-ray-absorption-spectra-comparing-the-real-time-approach-to-linear-response.pdf |
6759d9aff9980725cfc15ee3 | 10.26434/chemrxiv-2024-kxf6j-v2 | Realization of a photoelectrochemical cascade for the generation of methanol, a liquid solar fuel | Biochemical networks use reaction cascades to selectively reduce CO2 using energy from sunlight, but can similar selectivity be achieved by applying a cascade approach to an engineered system? Here, we report the design and implementation of a two-step photoelectrochemical (PEC) cascade to a liquid solar fuel: reduction of CO2 to CO and subsequent reduction of CO to methanol. The potentials required to perform the reductions were generated using custom-made III-V-based three-terminal tandem (3TT) solar cells. Cobalt phthalocyanine immobilized on multi-walled carbon nanotubes (CoPc/MWCNT) catalyzed both reactions. Multiphysics simulations of electrolyte flow and non-illuminated electrochemical measurements were used to narrow the operating parameters for the CoPc/MWCNT 3TT photocathodes. The champion integrated photocathode produced methanol with 3.8 ± 0.4% Faradaic efficiency (FE), with tested photocathodes having 0.7-3.8% methanol FE. Products were quantified by nuclear magnetic resonance spectroscopy and gas chromatography. The current output of the tested photocathodes was highly stable, and methanol production continued over multiple experiments. The low methanol yield is attributed to insufficient CO flux to, and CO2 depletion at, the methanol-producing subcell when both contacts are active, which is supported by the observation that a control photoelectrode slightly outperformed the methanol production of the 3TT device. Methanol production ceased when the 3TT subcell driving CO reduction was deactivated, supporting the assignment of a cascade mechanism. The major factors resulting in low methanol FE by the CoPc/MWCNT 3TT photocathodes are insufficient CO2 depletion at the methanol-producing contact and uncertainty in operating potential selection using the 3TT design. Although the CoPc/MWCNT 3TT photocathode is not yet highly selective, this work develops the basic science principles underlying the PEC cascade, demonstrates the co-design of a 3TT-based photoelectrode to produce carbon-based fuels, and finally discusses routes for improving product yields with this concept, including CO2 supply optimization and alternative photoelectrode and catalyst materials. | Thomas Chan; Calton J. Kong; Grace A. Rome; Darci Collins; Alex J. King; Rajiv Ramanujam Prabhakar; Sarah A. Collins; Michelle S. Young; Mickey J. Wilson; Myles A. Steiner; Adele C. Tamboli; Emily L. Warren; Clifford P. Kubiak; Joel W. Ager; Ann L. Greenaway | Materials Science; Catalysis; Energy; Electrocatalysis; Fuels - Energy Science; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6759d9aff9980725cfc15ee3/original/realization-of-a-photoelectrochemical-cascade-for-the-generation-of-methanol-a-liquid-solar-fuel.pdf |
67c96c1981d2151a024cf390 | 10.26434/chemrxiv-2025-0rplb | Machine Learning-Based Retention Time Prediction Tool for Routine LC-MS Data Analysis | The continuous evolution of machine learning (ML) methodologies and the aggregation of data have culminated in the development of highly accurate qualitative structure – property relationship (QSPR) models. For instance, liquid chromatography–mass spectrometry (LC-MS) data analysis widely used during chemical synthesis can be considerably improved by predicting retention time (RT). With hundreds of thousands of syntheses per year at Enamine Ltd., a large amount of high quality data has been produced from this analysis. In this paper we report on the development of an RT prediction model based on the GATv2Conv+DL graph neural network (NN) using internal data and evaluation of the selected NN architecture with METLIN SMRT dataset. The final model shows a mean absolute error (MAE) value of 2.83 s for the 120-s LC-MS method. It was integrated into the existing in-house LC-MS viewing tool. We also performed a thorough analysis of RT prediction errors and suggested the range between RT – 11.34 s and RT + 10.68 s, as this interval contained over 95% of the data. | Sofiia A. Dymura; Oleksandr O. Viniichuk; Kostiantyn P. Melnykov; Dmytro S. Radchenko; Oleksandr O. Grygorenko | Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Combinatorial Chemistry; Chemoinformatics; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c96c1981d2151a024cf390/original/machine-learning-based-retention-time-prediction-tool-for-routine-lc-ms-data-analysis.pdf |
639b529d16e9a86d7129682a | 10.26434/chemrxiv-2022-xmjqd-v2 | Ingenious Dual Pulse Photoacoustic Tomography in Drug-Responsive Clinical Imaging Perspectives | Detection of the real-time growth rate of cancer and visualization of the effectiveness of chemotherapy using live cell imaging techniques are yet to be invented. However, these could be conducive to monitoring the cancer treatment more precisely. In the present article, a new technique is proposed that will be able to accomplish the necessity mentioned earlier. The recent development and success of organometallic carbonyl clusters as photoacoustic contrast agents and cancer drugs have fetched a few freedom for the fate of new technologies towards the invention of time-dependent photoacoustic tomography (TD-PAT) that could ease the detection and treatment of cancer using advanced clinical chemotherapy. | Diyasha Sen; Arijit Bag | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b529d16e9a86d7129682a/original/ingenious-dual-pulse-photoacoustic-tomography-in-drug-responsive-clinical-imaging-perspectives.pdf |
60c7551a702a9b8c4618c61c | 10.26434/chemrxiv.12764726.v3 | Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference-Potential. 4. Adaptive QM/MM | Although Quantum Mechanical/Molecular Mechanics (QM/MM) methods are now routinely applied to the studies of chemical reactions in condensed phases and enzymatic reactions, they may experience technical difficulties when the reactive region is varying over time. For instance, when the solvent molecules are directly participating in the reaction, the exchange of water molecules between the QM and MM regions may occur on a time scale comparable to the reaction time. To cope with this situation, several adaptive QM/MM schemes have been proposed. However, these methods either add significantly to the computational cost or introduce artificial restraints to the system. In this work, we developed a novel adaptive QM/MM scheme and applied it to a study of a nucleophilic addition reaction. In this scheme, the configuration sampling was performed with a small QM region (without solvent molecules), and the thermodynamic properties under another potential energy function with a larger QM region (with a certain number of solvent molecules and/or different levels of QM theory) are computed via extrapolation using the reference-potential method. Our simulation results show that this adaptive QM/MM scheme is numerically stable, at least for the case studied in this work. Furthermore, this method also offers an inexpensive way to examine the convergence of the QM/MM calculation with respect to the size of the QM region.<br /> | Jia-Ning Wang; Wei Liu; Pengfei Li; Yan Mo; Wenxin Hu; Jun Zheng; Xiaoliang Pan; Yihan Shao; Ye Mei | Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7551a702a9b8c4618c61c/original/accelerated-computation-of-free-energy-profile-at-ab-initio-quantum-mechanical-molecular-mechanics-accuracy-via-a-semiempirical-reference-potential-4-adaptive-qm-mm.pdf |
65b9504b9138d23161116300 | 10.26434/chemrxiv-2024-rsh7w-v2 | Remote Fluorination of α,β-Unsaturated Carbonyls via Silyl Dienol Ethers | We report a general, regioselective, and metal free γ-fluorination of α,β-unsaturated carbonyls via silyl dienol ethers that are readily prepared from simple ketones and aldehydes. The transformation displays broad scope including 27 cyclic and acyclic siloxydienes providing γ-fluoro compounds in 28–91% yield. Notably, the reported conditions are also suitable for the synthesis of challenging tertiary fluorides. The regioselectivity of the reaction was studied on a series of acyclic siloxydienes and was observed to be sensitive to the conformational flexibility of the substrate. Diversification of the γ-fluorocarbonyls demonstrates the promise of fluorine as a stereocontrol element. | Daria Galaktionova; Sara Siddiqui; Justin Mohr | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b9504b9138d23161116300/original/remote-fluorination-of-unsaturated-carbonyls-via-silyl-dienol-ethers.pdf |
630c940aeadd9a912b85b2e6 | 10.26434/chemrxiv-2022-5382g | Poly-N-isopropylacrylamide colloidal arrays as templates for droplet-assisted fabrication of plasmonic nanostructure patterns | Poly-N-isopropylacrylamide colloidal arrays are exploited for site-selective self-assembly of gold nanoparticles on large areas. The soft colloids host the drying process of gold nanoparticle dispersion droplets and leave room for capillary convection and Marangoni convection flow paving the road to a simple bottom-up fabrication strategy for nanostructure arrays. | Ruth Fabiola Balderas-Valadez; Alessandro Nagel; Yuya Kanehira; Ilko Bald; Claudia Pacholski | Physical Chemistry; Materials Science; Nanoscience; Nanofabrication; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630c940aeadd9a912b85b2e6/original/poly-n-isopropylacrylamide-colloidal-arrays-as-templates-for-droplet-assisted-fabrication-of-plasmonic-nanostructure-patterns.pdf |
66fb9b4151558a15efac21f6 | 10.26434/chemrxiv-2024-0kkf8 | NONCONDUCTIVE FERROFLUIDS FROM PERMANENTLY MAGNETIC NANOPLATELETS HYBRIDIZED WITH POLAR PHOSPHONIC LIGANDS | Stable ferrofluids of permanently magnetic nanoplatelets of barium hexaferrite (BHF NPLs) in 1-hexanol were obtained using phosphonic acid- and phosphonate ester-based polar ligands. These ligands with the different electron-withdrawing groups and alkyl chain lengths of the terminal chain and linker were synthesized. Their attachment to the surface of the BHF NPLs was studied for various conditions and followed by a combination of spectroscopic techniques, thermogravimetry, and electrokinetic measurements. The results confirmed the theoretically predicted surface condensation of the ligands onto the BHF NPLs surfaces at 120 °C in 1-hexanol, whereas at lower temperatures or in more polar solvents the ligands were mostly physisorbed. The NPL hybrids with chemisorbed ligands having surface densities of at least 0.4 molecules/nm2 formed stable ferrofluids in 1-hexanol. The hybridization of the BHF NPLs via the condensation reaction in 1-hexanol creates sufficient steric-solvation repulsion to overcome the magnetic dipolar attraction between the NPLs and stabilizes the NPLs in 1-hexanol. Due to the relatively low polarity of 1-hexanol, the ligands remain protonated and the ferrofluids have negligible electric conductivity. In addition, an increase in the saturation magnetization of such hybrid BHF NPLs was correlated with their superior sensitivity to a magnetic field compared to the core NPLs. The ferrofluids can be exploited for the development of novel magneto-optic sensors that can operate under an electric field. | Ali Tufani; Nina Popov; Janez Kovač; Stanislav Čampelj; Andraž Mavrič; Tomaš Landovsky; Martin Cigl; Petra Vantakova; Martin Loula; Vladimira Novotna; Matic Poberžnik; Gabriela Herrero-Saboya; Layla Martin-Samos; Alenka Mertelj; Darja Lisjak | Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Magnetic Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fb9b4151558a15efac21f6/original/nonconductive-ferrofluids-from-permanently-magnetic-nanoplatelets-hybridized-with-polar-phosphonic-ligands.pdf |
66b8a3d55101a2ffa8fc1d9a | 10.26434/chemrxiv-2024-k4rsz | Machine learning guided discovery of Non-Linear Optical materials | Nonlinear optical(NLO) materials are crucial in achieving desired frequencies in solid-state lasers. So far, new NLO materials have been discovered using high-throughput calculations or chemical intuition. This study demonstrates the effectiveness of utiliz- ing a high refractive index as a proxy for a high second harmonic generation(SHG) coefficient. We also emphasize the importance of hardness in screening balanced NLO materials. We develop two machine learning models to predict refractive indices and Vickers hardness. By applying these models to the OQMD database, we identify po- tential NLO candidates based on non-centrosymmetricity, refractive index, hardness value, and bandgap properties. Our findings are validated using density functional theory(DFT) calculations. Notably, our approach successfully identifies several already established NLO materials, reinforcing the validity of our methodology. | Sownyak Mondal; Raheel Hammad | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b8a3d55101a2ffa8fc1d9a/original/machine-learning-guided-discovery-of-non-linear-optical-materials.pdf |
66b219ca01103d79c5e4e7be | 10.26434/chemrxiv-2024-jx2h1 | Role of Hartree-Fock Exchange in Spontaneous Proton Transfer Reactions | The electric field experienced by a protic group depends primarily on the solvent configuration and those configurations in which the electric field along the protic group exceeds a critical value results in spontaneous proton transfer. Electronic structure calculations using DFT result in artifacts in estimating the critical electric fields for the spontaneous proton transfer process, often leading to bistable behaviour, in contrast to MP2 level calculations. The discrepancies in assessing the critical electric fields using the DFT method can be attributed to the under-representation of Hartree-Fock exchange in many commonly used functionals such as B3LYP and M06-2X, whose effect is precipitative in the proton transferred structures. Using the (critical) electric field values obtained by the MP2 level of theory as a benchmark, it is shown that the B3LYP functional altered to include 40% Hartree-Fock exchange omits the bistable behaviour and calculates reasonably accurate critical electric fields. | Arzoo Arzoo; G Naresh Patwari | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b219ca01103d79c5e4e7be/original/role-of-hartree-fock-exchange-in-spontaneous-proton-transfer-reactions.pdf |
60c7468a469df48662f4369c | 10.26434/chemrxiv.11349713.v1 | Internal Atomic-Scale Structure Determination and Band Alignment of II-VI Quantum Dot Heterostructures | <p>This
work shows that ZnTe/CdSe core/shell quantum dots synthesized by standard
literature procedures in actuality have an alloyed Cd<sup></sup><sub>x</sub>Zn<sub>1-x</sub>Te
core. We employ X-ray absorption spectroscopy (XAS) at all four <i>K</i>-shell
ionization edges (Zn, Te, Cd, Se) and perform a global fitting analysis in
order to extract the first-shell bond distances. We combine our XAS results
with transmission electron microscopy (TEM) sizing and elemental analyses,
which allows us to propose models of the internal particle structure. Our
multimodal characterization approach confirms <b>(1) </b>the presence of Cd-Te bonds, <b>(2) </b>cation<b> </b>alloying in the particle core (and the
absence of anion alloying), and <b>(3) </b>a
patchy pure-phase CdSe shell. We synthesize particles of different shell
thicknesses and performed synthetic control studies that allowed us to discard a
ZnTe/CdTe/CdSe core/shell/shell structure and confirm the alloyed core/shell
structure. Our structural analysis is
extended with electronic band structure calculations and UV/vis absorption spectroscopy,
demonstrating that the alloyed Cd<sup></sup><sub>x</sub>Zn<sub>1-x</sub>Te/CdSe
core/shell quantum dots exhibit a direct band gap, different from the predicted
type-II band alignment of the intended ZnTe/CdSe core/shell quantum dots. This study highlights the challenges with
synthesizing II-VI quantum dot heterostructures and the power of XAS for
understanding the internal structure of heterogenous nanoparticles.</p> | Cecilia Gentle; Yuanheng Wang; Tyler N. Haddock; Conner P. Dykstra; Renske M. van der Veen | Nanostructured Materials - Nanoscience; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7468a469df48662f4369c/original/internal-atomic-scale-structure-determination-and-band-alignment-of-ii-vi-quantum-dot-heterostructures.pdf |
67d489176dde43c908ceaa6c | 10.26434/chemrxiv-2025-bzjl4 | Synthesis of 1,3-bis-trifluoromethylated-(hetero)cyclohexane-2-carboxylates | Reported herein is a method for syn-selective 1,3-bis-trifluoromethylation of (hetero)cycloalkylidene-malononitriles. The malononitrile-containing intermediate can be readily converted into carboxylates (and derivatives thereof) by oxidative decyanation. The products of this two-step sequence are 1,3-bis-trifluoromethylated, and thus physico-chemically-altered, analogs of common (hetero)cyclohexane carboxylate. This study includes optimization of the bis-trifluoromethylation reaction, scope studies, synthesis of various new bis-trifluoromethylated (hetero)cycloalkane carboxylates, representative transformations relevant to pharmaceutical synthesis, mechanistic studies, and some computational analyses of the newly accessible scaffolds. | Morgane Mando; Dylan Smith; Jan-Niklas Boyn; Alexander Grenning | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d489176dde43c908ceaa6c/original/synthesis-of-1-3-bis-trifluoromethylated-hetero-cyclohexane-2-carboxylates.pdf |
668d837dc9c6a5c07ac8aba3 | 10.26434/chemrxiv-2024-qz0gw | Trigonal planar heteroleptic lanthanide(III) bis(silyl)amide complexes containing aminoxyl radicals and anions | Modulation of the crystal field (CF) in lanthanide (Ln) complexes can enhance optical and magnetic properties, and large CF-splitting can be achieved with low coordination numbers in specific geometries. We previously reported that the homoleptic near-linear Sm2+ complex [Sm{N(SiiPr3)2}2] (1-Sm) is oxidized by 2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO•) radical to give the heteroleptic, approximately trigonal planar Sm3+ complex, [Sm{N(SiiPr3)2}2(TEMPO)] (2-Sm). Here we report the synthesis of homologous [Ln{N(SiiPr3)2}2(TEMPO)] (2-Ln; Ln = Tm, Yb) complexes by the oxidation of the parent [Ln{N(SiiPr3)2}2] (1-Ln; Ln = Tm, Yb) with TEMPO•; complexes 2-Ln all contain TEMPO– anions. The homoleptic bent Ln3+ complexes [Ln{N(SiiPr3)2}2][B(C6F5)4] (3-Ln; Ln = Sm, Tm, Yb) were also treated with TEMPO• to yield the heteroleptic, approximately trigonal planar Ln3+ complexes [Ln{N(SiiPr3)2}2(TEMPO)][B(C6F5)4] (4-Ln; Ln = Sm, Tm, Yb); the cations of 4-Ln all contain TEMPO• radicals. We have used a combination of UV-vis-NIR and EPR spectroscopy, magnetic measurements and ab initio calculations to compare the electronic structures of geometrically similar 2-Ln and 4-Ln cations. These studies revealed no single-molecule magnet behavior for 2-Yb despite evidence for sizable CF-splitting and high degree of purity of the ground stabilized mJ = |±├ 7/2⟩┤ state, while the radical TEMPO• in 4-Yb did not significantly improve performance. | Gemma Gransbury; Hannah Nicholas; Siobhan Murphy; Jack Emerson-King; Michele Vonci; Conrad Goodwin; Richard Winpenny; Nicholas Chilton; Marcus Giansiracusa; David Mills | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism | CC BY 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668d837dc9c6a5c07ac8aba3/original/trigonal-planar-heteroleptic-lanthanide-iii-bis-silyl-amide-complexes-containing-aminoxyl-radicals-and-anions.pdf |
673da9a47be152b1d0d0d388 | 10.26434/chemrxiv-2024-jgprs | Pareto-based Optimization of Sparse Dynamical Systems | Sparse data-driven approaches enable the approximation of governing laws of physical processes with parsimonious equations. While a great effort over the last decade has been made in this field, data-driven approaches generally rely on the paradigm of imposing a fixed base of library functions. In order to promote sparsity, finding the optimal set of basis functions is a necessary condition but a challenging task to guess in advance.Here, we propose an alternative approach which consists of optimizing the very library of functions while imposing sparsity. The robustness of our results is not only evaluated by the quality of the fit of the discovered model, but also by the statistical distribution of the residuals with respect to the original noise in the data. In order to avoid to choose one metric over the other, we rather rely on a multi-objective genetic algorithm (NSGA-II) for systematically generating a subset of optimal models sorted in a Pareto front. We illustrate how this method can be used as a tool to derive microkinetic equations from experimental data, and as a kernel approach for design of experiments. | Gianmarco Ducci; Maryke Kouyate; Karsten Reuter; Christoph Scheurer | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673da9a47be152b1d0d0d388/original/pareto-based-optimization-of-sparse-dynamical-systems.pdf |
60c753480f50db4947397b3f | 10.26434/chemrxiv.13472373.v1 | Evolving to an Ideal Synthesis of Molnupiravir, an Investigational Treatment for COVID-19 | <p>Molnupiravir (MK-4482) is an investigational
direct-acting antiviral agent that is under development for the
treatment of COVID-19. Given the potential high demand for this
compound, it was critical to develop a sustainable and efficient
synthesis from commodity raw materials. The three-step route that
we report here embodies the shortest possible synthesis to
molnupiravir, and was enabled through the invention of a novel
biocatalytic cascade and final condensation step. Each step occurs
in over 95% yield and only utilizes widely available commodity
reagents and simple operations. Compared to the initial route, the
new route is 70% shorter, and approximately seven-fold higher in
overall yield. <br /></p> | Tamas Benkovics; John McIntosh; Steven Silverman; Jongrock Kong; Peter Maligres; Tetsuji Itoh; Hao Yang; Mark Huffman; Deeptak Verma; Weilan Pan; Hsing-I Ho; Jonathan Vroom; Anders Knight; Jessica Hurtak; William Morris; Neil Strotman; Grant Murphy; Kevin Maloney; Patrick Fier | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753480f50db4947397b3f/original/evolving-to-an-ideal-synthesis-of-molnupiravir-an-investigational-treatment-for-covid-19.pdf |
60c744b2567dfe97b2ec430a | 10.26434/chemrxiv.9878729.v1 | Controlling Through-Space and Through-Bond Exchange Pathways in Bis-Cobaltocenes for Molecular Spintronics | Pinching molecules via chemical strain suggests intuitive consequences, such as compression at the pinched site, and clothespin-like opening of other parts of the structure. If this opening affects two spin centers, it should result in reduced communication between them. We show that for a naphthalene-bridged biscobaltocenes with competing through-space and through-bond pathways, the consequences of pinching are far less intuitive: despite the known dominance of through-space interactions, the bridge plays a much larger role for exchange spin coupling than previously assumed. Based on a combination of chemical synthesis, structural, magnetic and redox characterization, and a newly developed first-principles theoretical pathways analysis, we can suggest a comprehensive explanation for this nonintuitive behavior. These results are of interest for molecular spintronics, as naphthalene-linked cobaltocenes can form wires on surfaces for potential spin-only information transfer. | Sarah Puhl; Torben Steenbock; Carmen Herrmann; Jürgen Heck | Magnetism; Organometallic Compounds; Theory - Inorganic; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b2567dfe97b2ec430a/original/controlling-through-space-and-through-bond-exchange-pathways-in-bis-cobaltocenes-for-molecular-spintronics.pdf |
61b73f78d10aa55ce40f7bb7 | 10.26434/chemrxiv-2021-9jdkr | Reactivity-Selectivity Principle: Phenyl Group in Indazole Makes It More Lucid | Linear free energy relationship (LFER) plots are constructed for the deprotonation equilibriums (pKaH+) of pyrazolium and indazolium (benzopyrazolium) cations. The reaction constants Taft * and Hammett are found to be 2.75 and 1.32 for deprotonation (pKaH+) of pyrazolium and indazolium cations respectively. Higher value of Taft * than the Hammett is explained in terms of extra stability of the indazolium cation due to its greater number of resonance structures. This article is an exercise to undergraduate students for writing different resonance structures of indazolium cation. | Sanjeev Rachuru; Jagannadham Vandanapu | Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2021-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b73f78d10aa55ce40f7bb7/original/reactivity-selectivity-principle-phenyl-group-in-indazole-makes-it-more-lucid.pdf |
62278dd5daa4fb8b26843d0a | 10.26434/chemrxiv-2022-xcqq5 | Spontaneous Ammonia Oxidation Through Coordination Induced Bond Weakening in Molybdenum Complexes of a Dianionic Pentadentate Ligand Platform | Ammonia oxidation catalyzed by molecular compounds is of current interest as a carbon free source of dihydrogen. Activation of N-H bonds through coordination to transition metal centers is a key reaction in this process. We report the substantial activation of ammonia through via reaction with low valent Mo complexes of a diborate pentadentate ligand system. Spontaneous loss of hydrogen atoms from (B2Pz4Py)Mo(II)-NH3 at room temperature to produce H2 and the dinuclear -nitrido compound (B2Pz4Py)Mo-N-Mo(B2Pz4Py) is observed due to substantial N-H bond weakening upon coordination to Mo. Mechanistic details are supported through the experimental observation characterization of terminal amido, imido and nitrido complexes and density functional theory computations. The generally under-appreciated role of bridging nitrido intermediates is revealed and discussed, providing guidance for further catalyst development for this process. | C. Christopher Almquist; Nicole Removski; Thayalan Rajeshkumar; Benjamin Gelfand; Warren Piers; Laurent Maron | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Coordination Chemistry (Inorg.); Small Molecule Activation (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62278dd5daa4fb8b26843d0a/original/spontaneous-ammonia-oxidation-through-coordination-induced-bond-weakening-in-molybdenum-complexes-of-a-dianionic-pentadentate-ligand-platform.pdf |
647896fee64f843f41246f8b | 10.26434/chemrxiv-2023-jsrz0 | Targeting G-quadruplex in SARS-CoV-2 RNA Genome with Tetraphenylethene Derivatives for Antiviral Therapy | Targeting genomic RNA conformations that are crucial for SARS-CoV-2 replication is a promising antiviral strategy. Herein we have developed tetraphenylethene (TPE) derivatives to target RNA G-quadruplexes (RGQs) present in the SARS-CoV-2 nucleocapsid gene ORF. Our EMSA, fluorescence and CD data suggests the binding of two TPE derivatives i.e., TPE−MePy and TPE-AllylPy, with RGQ derived from SARS-CoV-2 nucleocapsid gene. In addition, in vitro luciferase assay demonstrated suppression in translation efficiency by 3.86-fold and 2.89-fold in presence of TPE-MePy and TPE-AllylPy, respectively. Subsequently, the cytotoxicity and immunofluorescence-based antiviral assay in VeroE6 cells indicated 82% inhibition in SARS-CoV-2 nucleocapsid gene expression without any effect on cell viability. These results highlight the promising use of TPE derivatives as an antiviral drug to alter the crucial genes expression in SARS-CoV-2 as well as other viruses. | Payal Gupta; Rushikesh Khadake; Harshad Mirgane; Sheshnath Bhosale; Dharmender Gupta; Sudhanshu Vrati; Ambadas Rode | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647896fee64f843f41246f8b/original/targeting-g-quadruplex-in-sars-co-v-2-rna-genome-with-tetraphenylethene-derivatives-for-antiviral-therapy.pdf |
670a43adcec5d6c142ed957a | 10.26434/chemrxiv-2024-mdl4q | Integration of Transferable Prediction of Retention Index and Universal Library Search Enhances Exposome Identification Probability in RPLC/HRMS-Based Non-Targeted Analysis | In non-targeted analysis, spectral matching is one of the most commonly used approaches for annotation or identification of the chemicals of emerging concern in complex samples via high-resolution mass spectrometry (HRMS). Conventional confidence assessment systems struggle to resolve multiple hits during library searches, resulting in ambiguities in identification. In this study, a combination of information extracted from the MS/MS spectra and calibrate-free predicted retention indices (RIs) yielded the probability of true positive (TP) for each hit by machine learning (ML), including a pre-trained molecular fingerprint (MF)-to-retention index (RI) model, a cumulative neutral loss (CNL)-to-RI model trained by 693,681 spectra, and a binary classification model that incorporated 5 significant features from the universal library search algorithm and the difference between the predicted RIs from both RI models. Our results demonstrated a high correlation (R2 = 0.96 and 0.88) between MF-derived and CNL-derived RI values for the model training and testing datasets, respectively, suggesting reduced RI error for TP annotations. When applied to pesticides-spiked samples, the k-nearest neighbors algorithm achieved a weighted F1 score of 0.65 and a Matthews correlation coefficient of 0.30. Integrating ML with reference spectral match enhanced the identification probability of exposome by half in a proof-of-concept study in pesticide contaminants in black tea. This study highlights the potential of integrating ML with reference library matching to enhance the identification probability of contaminants. | Hiu Lok NGAN; Viktoriia Turkina; Denice van Herwerden; Hong Yan; Zongwei Cai; Saer Samanipour | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Analysis; Mass Spectrometry; High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670a43adcec5d6c142ed957a/original/integration-of-transferable-prediction-of-retention-index-and-universal-library-search-enhances-exposome-identification-probability-in-rplc-hrms-based-non-targeted-analysis.pdf |
60c73d3a9abda2508bf8b690 | 10.26434/chemrxiv.5514871.v1 | Understanding Energy Conversion and Loss Mechanisms in Ternary Metal Oxide Photoelectrodes: The Case of Copper Vanadate | Essential
photoelectrochemical (PEC) functionalities are systematically analyzed on a
series of copper vanadate photoanodes with different Cu:V elemental ratios.
Homogeneous, highly continuous, and phase-pure thin films of <i>β</i>-Cu<sub>2</sub>V<sub>2</sub>O<sub>7</sub>,
<i>γ</i>-Cu<sub>3</sub>V<sub>2</sub>O<sub>8</sub>,
Cu<sub>11</sub>V<sub>6</sub>O<sub>26</sub> and Cu<sub>5</sub>V<sub>2</sub>O<sub>10</sub>
are grown via reactive co-sputtering deposition and then evaluated for their
performances in light-driven oxygen evolution reaction (OER). Despite all four
compounds have similar 1.8 – 2.0 eV bandgaps, Cu-rich phases are found to
exhibit shorted absorption length in addition to higher charge separation
efficiencies at the semiconductor/electrolyte junction. In the presence of
sacrificial hole acceptor, the superior bulk properties of Cu<sub>5</sub>V<sub>2</sub>O<sub>10</sub>
photoanode translate to the most cathodic (0.67 V vs. RHE) onset potential and
a 206 μA/cm<sup>2</sup> photocurrent density that is four times higher than <i>β</i>-Cu<sub>2</sub>V<sub>2</sub>O<sub>7</sub>
at 1.23 V. vs. RHE. Nevertheless, the sluggish OER kinetics competes with
carrier recombination through Cu-associated surface states, and transient photocurrent
spectroscopy quantitatively reveals the deterioration of surface catalytic
activity with increasing Cu:V elemental ratio. This comprehensive analysis of
PEC characteristics – light absorption, carrier separation, and heterogeneous
charge transfer – not only gives insights into functional roles of individual
elements in ternary metal oxide photoanodes, but also provides strategies for
rational discovery, design, and engineering of new photoelectrode materials for
solar fuel production. | Chang-Ming Jiang; Gideon Segev; Lucas H. Hess; Guiji Liu; Gregory Zaborski; Francesca M. Toma; Jason K. Cooper; Ian D. Sharp | Catalysts; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d3a9abda2508bf8b690/original/understanding-energy-conversion-and-loss-mechanisms-in-ternary-metal-oxide-photoelectrodes-the-case-of-copper-vanadate.pdf |
60c74e2c469df421e3f443f7 | 10.26434/chemrxiv.12720644.v1 | Conformational Preferences of Triantennary and Tetraantennary Hybrid N-Glycans in Solution: Insights from 20 μS Long Atomistic Molecular Dynamic Simulations | In the current study, we have investigated the conformational dynamics of a triantennary and a tetraantennary hybrid N-glycan associated with HIV glycoprotein using 20 micro-second long all-atom molecular dynamics simulations. <br /> | Rajarshi Roy; Sayan Poddar; Parimal Kar | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e2c469df421e3f443f7/original/conformational-preferences-of-triantennary-and-tetraantennary-hybrid-n-glycans-in-solution-insights-from-20-s-long-atomistic-molecular-dynamic-simulations.pdf |
67c994a86dde43c908bbecbf | 10.26434/chemrxiv-2025-x8tzc | Reversible Electron-responsive Self-Assembly of a Supramolecular Gel Network | Redox-active supramolecular gels involving highly ordered assemblies of small organic molecules are very promising soft materials for many applications ranging from catalysis to electronics. These materials however mostly rely on the use of chemical fuels, making their reversibility intrinsically limited. Even though the use of electrochemical stimulation could greatly improve the reversibility of redox-responsive systems it still remains mostly unexplored due to major scientific and technical bottlenecks. We now report the electron-responsiveness of a supramolecular gel obtained through the chiral self-assembly of a low molecular weight gelator derived from 4,4-bipyridinium salts (viologens). The reduction of the viologen-based gels was achieved using photochemical and electrochemical stimulation. The link between the sample composition and microstructure upon reduction of viologen moieties have been thoroughly investigated using both in operando bright microscopy and absorption spectroscopy measurements. We showed that the system electron-responsiveness is based on the association/dissociation of charge transfer complexes. We also showed that different strategies can be used to efficiently stimulate the viologen moieties which are entrapped in the gel 2 supramolecular network. Both the dissolution and reformation of the viologen-based supramolecular network could be achieved through electrochemical stimulation. We consequently report here one of the very first systems able to undergo a reversible electrochemically induced supramolecular polymerization. | Vivien Andrieux; Rémi Savin; Julien Bauland; Floris Chevallier; Thomas Gibaud; Denis Frath; Christophe Bucher | Physical Chemistry; Organic Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c994a86dde43c908bbecbf/original/reversible-electron-responsive-self-assembly-of-a-supramolecular-gel-network.pdf |
60c75764337d6c2544e29011 | 10.26434/chemrxiv.14292476.v2 | Microwave-assisted Automated Glycan Assembly | Automated synthesis of DNA, RNA, and peptides provides quickly and reliably important tools for biomedical research. Automated glycan assembly (AGA) is significantly more challenging as highly branched carbohydrates require strict regio- and stereocontrol during synthesis. A new AGA synthesizer enables rapid temperature adjustment from -40 °C to +100 °C to control glycosylations at low temperature and accelerates capping, protecting group removal, and glycan modifications by using elevated temperatures. Thereby, the temporary protecting group portfolio is extended from two to four orthogonal groups that give rise to oligosaccharides with up to four branches. In addition, sulfated glycans and unprotected glycans can be prepared. The new design reduces the typical coupling cycles from 100 min to 60 min while expanding the range of accessible glycans. The instrument drastically shorten and generalizes the synthesis of carbohydrates for use in biomedical and material science.<br /> | José Danglad Flores; Sabrina Leichnitz; Eric T. Sletten; A. Abragam Joseph; Klaus Bienert; Kim Le Mai Hoang; Peter H. Seeberger | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75764337d6c2544e29011/original/microwave-assisted-automated-glycan-assembly.pdf |
67bca5126dde43c908495c3e | 10.26434/chemrxiv-2025-6vbn2 | Bicyclic selenenyl sulfides tune stepwise rates of thiol/selenol addition, resolution, and cyclisation, to reveal cellular constraints for bioreductive probes targeting mammalian thioredoxin reductase | The bioreductive activation of dichalcogenide probes by mammalian thiol-type oxidoreductases proceeds via a cascade of consecutive, partly-reversible steps. Stereocontrol elements can exert control over these steps' reaction rates, which was recently exploited in bicyclic reduction substrates that fuse a reducible disulfide ring to a templating nitrogenous ring to reach powerful substrate-controlled kinetic selectivities for, e.g., vicinal dithiol vs monothiol reductants in live cells. We now deploy regio-, diastereo-, template-, and pH-control elements to shape the reactivity of unprecedented bicyclic selenenyl sulfides (SeSP), arriving at probes that selectively address the mammalian selenoenzyme thioredoxin reductase TrxR1. We accessed these densely-functionalised cis- or trans-fused-1,2-thiaselenanes on gram scale over 5 steps, via a regioselective key step that elaborates an unusual, differentially protected 2,2’-biaziridine intermediate through sequential one-pot chalcogen introduction and selenenyl sulfide formation. By profiling all regio- and diastereo-isomeric bicycles for their partly- or fully-reversible reactivity, we showed how effects that slow their reduction steps (addition then resolution) can compensate by vastly accelerating subsequent cyclisation speeds, such that cellular redox processing is effective and TrxR-selective. More broadly, this study shows how multistep cascade probes can leverage conformational effects and internal non-covalent interactions to differentiate step kinetics along their on-target vs off-target reaction pathways, thus achieving reaction-based target selectivity in complex biological settings. | Lukas Zeisel; Lucas Dessen-Weissenhorn; Karoline C. Scholzen; Andrea Madabeni; Laura Orian; Elias S. J. Arnér; Oliver Thorn-Seshold | Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bca5126dde43c908495c3e/original/bicyclic-selenenyl-sulfides-tune-stepwise-rates-of-thiol-selenol-addition-resolution-and-cyclisation-to-reveal-cellular-constraints-for-bioreductive-probes-targeting-mammalian-thioredoxin-reductase.pdf |
66db73a512ff75c3a19f4370 | 10.26434/chemrxiv-2024-5xv8x | Development of receptor desolvation scoring and covalent sampling in DOCK 6: methods evaluated on a RAS test set | Molecular docking methods are widely used in drug discovery efforts. RAS proteins are important cancer drug targets, and are useful systems for evaluating docking methods, including accounting for solvation effects and covalent small molecule binding. Water often plays a key role in small molecule binding to RAS proteins, and many inhibitors, including approved drugs, covalently bind to oncogenic RAS proteins. We assembled a RAS test set, consisting of 138 RAS protein structures and 2 structures of KRAS DNA in complex with ligands. In DOCK 6, we have implemented a receptor desolvation scoring function and a covalent docking algorithm. These new features were evaluated using the test set, with pose reproduction, cross-docking, and enrichment calculations. We tested two solvation methods for generating receptor desolvation scoring grids: GIST, and 3D-RISM. Using grids from GIST or 3D-RISM, water displacements are precomputed with Gaussian-weighting, and trilinear interpolation is used to speed up this scoring calculation. To test receptor desolvation scoring, we prepared GIST and 3D-RISM grids for all KRAS systems in the test set, and we compare enrichment performance with and without receptor desolvation. Accounting for receptor desolvation using GIST improves enrichment for 51% of systems, while using 3D-RISM improves enrichment for 44% of systems. To more rigorously test accounting for receptor desolvation using 3D-RISM, we compare pose reproduction with and without 3D-RISM receptor desolvation. Pose reproduction docking with 3D-RISM yields a 5.5% increase in success rate compared to docking without 3D-RISM. Accounting for receptor desolvation provides a small, but significant, improvement in both enrichment and pose reproduction for this set. We tested the covalent attach-and-grow algorithm on 70 KRAS systems containing covalent ligands, obtaining similar pose reproduction success rates between covalent and noncovalent docking. Comparing covalent docking to noncovalent docking, there is a 7.2% increase and a 2.9% decline in success rate when docking with experimental and SMILES-generated ligand conformations, respectively. As a proof-of-concept, we performed covalent virtual screens with and without receptor desolvation scoring, targeting the switch II pocket of KRAS, using 3.4 million make-on-demand acrylamide compounds from the Enamine REAL database. On average, the attach-and-grow algorithm spends approximately 17.61 seconds per molecule across the screen. The test set is available at https://github.com/tbalius/teb_docking_test_sets. | Y. Stanley Tan; Mayukh Chakrabarti; Reed M Stein; Lauren E Prentis; Robert C Rizzo; Tom Kurtzman; Marcus Fischer; Trent E Balius | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66db73a512ff75c3a19f4370/original/development-of-receptor-desolvation-scoring-and-covalent-sampling-in-dock-6-methods-evaluated-on-a-ras-test-set.pdf |
60c74581702a9b131c18aa14 | 10.26434/chemrxiv.10050128.v1 | A Bis-Monophospholyl Dysprosium Cation Showing Magnetic Hysteresis at 48 Kelvin | Single-molecule magnets (SMMs) have potential applications in high-density
data storage, but magnetic relaxation times at elevated temperatures must be
increased to make them practically useful. <i>Bis</i>-cyclopentadienyl
lanthanide sandwich complexes have emerged as the leading candidates for SMMs
that show magnetic memory at liquid nitrogen temperatures, but the relaxation
mechanisms mediated by aromatic C<sub>5</sub> rings have not been fully
established. Here we synthesise a <i>bis</i>-monophospholyl
dysprosium SMM [Dy(Dtp)<sub>2</sub>][Al{OC(CF<sub>3</sub>)<sub>3</sub>}<sub>4</sub>]
(<b>1</b>, Dtp = {P(C<sup>t</sup>BuCMe)<sub>2</sub>})
by the treatment of <i>in situ</i>-prepared
“[Dy(Dtp)<sub>2</sub>(C<sub>3</sub>H<sub>5</sub>)]” with [HNEt<sub>3</sub>][Al{OC(CF<sub>3</sub>)<sub>3</sub>}<sub>4</sub>].
SQUID magnetometry reveals that <b>1</b> has
an effective barrier to magnetisation reversal of 1,760 K (1,223 cm<sup>–1</sup>)
and magnetic hysteresis up to 48 K. <i>Ab
initio</i> calculation of the spin dynamics reveal that transitions out of the
ground state are slower in <b>1</b> than in the first reported dysprosocenium SMM,
[Dy(Cp<sup>ttt</sup>)<sub>2</sub>][B(C<sub>6</sub>F<sub>5</sub>)<sub>4</sub>]
(Cp<sup>ttt</sup> = C<sub>5</sub>H<sub>2</sub><sup>t</sup>Bu<sub>3</sub>-1,2,4),
however relaxation is faster in <b>1</b> overall due to the compression of
electronic energies and to vibrational modes being brought on-resonance by the
chemical and structural changes introduced by the <i>bis</i>-Dtp framework. With the preparation and analysis of <b>1</b> we are thus able to further refine
our understanding of relaxation processes operating in <i>bis</i>-C<sub>5</sub>/C<sub>4</sub>P sandwich lanthanide SMMs, which is the
necessary first step towards rationally achieving higher magnetic blocking
temperatures in these systems in future. | Peter Evans; Daniel Reta; George F. S. Whitehead; Nicholas Chilton; David Mills | Coordination Chemistry (Organomet.); Ligand Design; Ligands (Organomet.); Theory - Organometallic; Transition Metal Complexes (Organomet.); Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74581702a9b131c18aa14/original/a-bis-monophospholyl-dysprosium-cation-showing-magnetic-hysteresis-at-48-kelvin.pdf |
65af10a89138d2316183aa5b | 10.26434/chemrxiv-2023-0mdlq-v2 | Intramolecular London Dispersion Interactions in Single-Molecule Junctions | This manuscript shows the first example of using intramolecular London dispersion interactions to control molecular geometry and quantum transport in single-molecule junctions. Flexible σ-bonded molecular junctions typically occupy straight-chain geometries due to steric effects. Here we synthesize a series of thiomethyl-terminated oligo(dimethylsilmethylene)s that bear [CH2-Si(CH3)2]n repeat units, where all backbone dihedral states are sterically equivalent. Scanning tunneling microscopy break-junction (STM-BJ) measurements and theoretical calculations indicate that in the absence of a strong steric bias, concerted intramolecular London dispersion interactions staple the carbosilane backbone into coiled conformations that remain intact even as the junction is stretched to its breakpoint. As these kinked conformations are highly resistive to electronic transport, we observe record-high conductance decay values on an experimental junction length basis (β = 1.86 ± 0.12 Å-1). These studies reveal the potential in using intramolecular London dispersion interactions to design single-molecule electronics. | Matthew O. Hight; Joshua Y. Wong; Ashley E. Pimentel; Timothy A. Su | Organic Chemistry; Inorganic Chemistry; Nanoscience; Physical Organic Chemistry; Nanodevices; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65af10a89138d2316183aa5b/original/intramolecular-london-dispersion-interactions-in-single-molecule-junctions.pdf |
61c32db37f367e4f9f5c24e7 | 10.26434/chemrxiv-2021-cvcgw | Photochemical α-Aminonitrile Synthesis using Zn Phthalocyanines as Near Infrared Photocatalysts | While photochemical transformations with sunlight almost exclusively utilize the UV-Vis part of the solar spectrum, the majority of the photons emitted by the sun have frequencies in the near-infrared region. Phthalocyanines show high structural similarity to the naturally occurring light harvesting porphyrins, chlorins and mainly bacteriochlorins, and are also known for being efficient and affordable near-infrared light absorbers as well as triplet sensitizers for the production of singlet oxygen. Although having been neglected for a long time in synthetic organic chemistry due to their low solubility and high tendency towards aggregation, their unique photophysical properties and chemical robustness make phthalocyanines attractive photocatalysts for the application in near-infrared light-driven synthesis strategies. Herein, we report a cheap, simple and efficient photocatalytic protocol, which is easily scalable under continuous flow conditions. Various phthalocyanines were studied as near-infrared photosensitizers in oxidative cyanations of tertiary amines to generate α-aminonitriles, a synthetically versatile compound class. | Caroline Grundke; Rodrigo Silva; Winald Kitzmann; Katja Heinze; Kleber de Oliveira; Till Opatz | Organic Chemistry; Catalysis; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c32db37f367e4f9f5c24e7/original/photochemical-aminonitrile-synthesis-using-zn-phthalocyanines-as-near-infrared-photocatalysts.pdf |
66c32c4a20ac769e5f1150a3 | 10.26434/chemrxiv-2024-dz2dv | The evolving roles of data and citations in journal articles | Since 2000, most published journal articles are assigned a persistent identifier known as a DOI issued by the Crossref registration agency. This identifier is associated with a metadata record describing key aspects of the article. It has become more common recently to include article citations in this record and most recently to also include reference to published datasets, themselves also assigned a DOI. Until very recently, the Crossref schema describing the properties of the metadata record did not allow the type of the citation to be declared, but a proposal has now been made to augment the schema to allow citations to be identified as relating to datasets. The implications of these evolving changes to scholarly journal articles are here discussed both in the context of the increasing importance of artificial intelligence and machine learning (AI/ML) and of the increasing need for declaring not only how data can be made available for AI/ML but also to be discovered in the first place. | Henry Rzepa | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c32c4a20ac769e5f1150a3/original/the-evolving-roles-of-data-and-citations-in-journal-articles.pdf |
66d30855a4e53c48763dc2a0 | 10.26434/chemrxiv-2024-ztldb-v2 | Beyond Natural Dyes: Embracing Sustainable Innovations in Industrial Textile Dyeing | The textile dyeing industry is a major contributor to environmental pollution, necessitating the development of more sustainable dyeing processes. This review examines recent advancements in eco-friendly dyeing technologies, including improvements in natural dye extraction, the develop-ment of synthetic dyeing methods, and emerging innovations such as plasma technology, digital textile printing with biodegradable inks, and microbial dyeing. While natural dyes face challenges like variability and high production costs, new technologies which use synthetic dyes yet eco-friendly offer more consistent and scalable solutions. This paper highlights the limitations and potential of these methods, emphasizing the need for further research to address cost, scalability, and environmental impact. By reviewing these advancements, this paper aims to provide a com-prehensive understanding of the current state of eco-friendly dyeing technologies and suggest di-rections for future research to achieve broader industrial adoption and sustainability in textile dyeing. | Diane Da-in Kim | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Wastes | CC BY 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d30855a4e53c48763dc2a0/original/beyond-natural-dyes-embracing-sustainable-innovations-in-industrial-textile-dyeing.pdf |
65fcb1359138d23161f9af08 | 10.26434/chemrxiv-2024-fbpss | Non-Ionic Fluorosurfactants for Droplet-Based in vivo Applications | Fluorocarbon oils are uniquely suited for many biomedical applications due to their inert, bioorthogonal properties. In order to interface fluorocarbon oils with biological systems, non-ionic fluorosurfactants are necessary. However, there is a paucity of non-ionic fluorosurfactants with low interfacial tension to stabilize fluorocarbon phases in aqueous environments (such as oil-in-water emulsions). We developed non-ionic fluorosurfactants composed of a polyethylene glycol (PEG) segment covalently bonded to a flexible perfluoropolyether (PFPE) segment that confer lower interfacial tensions (IFTs) between a fluorocarbon oil, HFE-7700, and water. Synthesis of a panel of surfactants spanning a molecular weight range of 0.64–66 kDa with various hydrophilic-lipophilic balances allowed for identification of minimal IFTs, ranging from 1.4 to 17.8 mN m-1. The majority of these custom fluorosurfactants display poor solubility in water, allowing their co-introduction with fluorocarbon oils and minimal leaching. We applied the PEG5PFPE1 surfactant for mechanical force measurements in zebrafish, enabling exceptional sensitivity. | Heidi van de Wouw; Shuo-Ting Yen; Manon Valet; Joseph Garcia; Antoine Vian; Yucen Liu; Jennifer Pollock; Otger Campàs; Ellen Sletten | Materials Science; Polymer Science; Surfactants; Fluoropolymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fcb1359138d23161f9af08/original/non-ionic-fluorosurfactants-for-droplet-based-in-vivo-applications.pdf |
60c7449af96a00c3a3286a66 | 10.26434/chemrxiv.9162299.v2 | Polymer Metal-Organic Cage Gels Based on Cu24L24 Cuboctahedra: Design, Synthesis, and Additive Manufacturing Enabled by Three-State Photoswitching | We present a polymer network that can reversibly switch between three distinct states of mechanical and chemical properties, significantly extending the boundaries of state-switching materials. This switching behavior is enabled by a photoreduction mechanism that leverages coumarin-functionalized cuboctahedral Cu<sub>24</sub>L<sub>24</sub> metal-organic cages (MOCs) linked by polymers in a "polyMOC" gel. The properties of each material state can be used in a cooperative fashion to achieve advanced functions such as network toughening, metallic patterning, and additive manufacturing<br /> | Nathan J. Oldenhuis; Peter Qin; Shu Wang; Hong-Zhou Ye; Eric Alt; Adam Willard; Troy Van Voorhis; Stephen Craig; Jeremiah Johnson | Coordination polymers; Hydrogels; Inorganic Polymers; Organic Polymers; Polymerization catalysts; Polymer scaffolds | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7449af96a00c3a3286a66/original/polymer-metal-organic-cage-gels-based-on-cu24l24-cuboctahedra-design-synthesis-and-additive-manufacturing-enabled-by-three-state-photoswitching.pdf |
6386ee9a1234cb1d69285c81 | 10.26434/chemrxiv-2022-t2c5c | 1,3-diketone analogs as selective lysyl hydroxylase 2 (LH2) antagonists
| Lysyl hydroxylase 2 (LH2), an Fe(II) and α-ketoglutarate (αKG, also called 2-oxoglutarate, or 2OG)-dependent oxygenase, is an endoplasmic reticulum-resident enzyme that hydroxylates telopeptidyl lysine residues on fibrillar collagen molecules. It leads to the formation of hydroxylysine aldehyde-derived collagen cross-links (HLCCs), which are more stable than lysine aldehyde-derived collagen cross-links (LCCs) generated devoid of LH2. It has been reported that LH2 enhances lung cancer metastatic and invasive proclivity and modulates the types of collagen cross-links (HLCC-to-LCC) in the tumor stroma. Herein, we prepared a series of 1,3-diketone analogs 1–18 and identified 12 and 13 that inhibit the LH2-driven hydroxylation of a collagen peptide substrate with IC50 approximately 300 nM and 500 nM, respectively. 12 and 13 demonstrate a 9-fold selectivity for LH2 over LH1 and LH3. Quantum Mechanics/Molecular Mechanics (QM/MM) modeling indicates that in addition to the relatively stronger interactions between compounds 12 and 13 with the active site, the selectivity stems from non-covalent interactions like hydrogen bonding between the morpholine/piperazine rings with LH2-specific Arg661, where the corresponding residue in LH1 and LH3 is Pro. Migration assays in the 344SQ lung adenocarcinoma cell line reveal that 13 shows anti-migration activity. | Juhoon Lee; Hou-fu Guo; Yazdan Maghsoud; Erik Antonio Vázquez-Montelongo; Zhifeng Jing; Shike Wang; Rachel M. Sammons; Eun Jeong Cho; Pengyu Ren; G. Andrés Cisneros; Jonathan M. Kurie; Kevin N. Dalby | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6386ee9a1234cb1d69285c81/original/1-3-diketone-analogs-as-selective-lysyl-hydroxylase-2-lh2-antagonists.pdf |
60c74f40702a9b518318bb42 | 10.26434/chemrxiv.12867350.v1 | Molecular Docking of Secondary Metabolites from Psidium guajava L. and Piper nigrum L. to COVID-19 Associated Receptors ACE2, Spike Protein RBD, and TMPRSS2 | The SARS-CoV-2 virus has spread worldwide, affecting millions, and showing no signs of slowing down or stopping. Secondary metabolites have been important sources of medicine for millennia. In this study, the secondary metabolites of Psidium guajava L. and Piper nigrum L. were screened for binding to three key coronavirus disease (COVID-19) associated proteins, namely, the viral spike protein, its target ACE2, and its primer TMPRSS2. Through molecular docking, the compounds isoquercetin, terpinyl acetate, morin-3-O-lyxoside, guineensine and brachyamide A were found to have considerable binding to these three receptors. With almost benign ADME-Tox profiles and energetically favorable binding, the secondary metabolite compounds caryophyllene, terpinyl acetate, morin and morin glycosides may be considered for assays, further development, and clinical investigations. | Maurice De Jesus; Jokent Gaza; Hiyas A. Junio; Ricky Nellas | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f40702a9b518318bb42/original/molecular-docking-of-secondary-metabolites-from-psidium-guajava-l-and-piper-nigrum-l-to-covid-19-associated-receptors-ace2-spike-protein-rbd-and-tmprss2.pdf |
66fd45da51558a15efd29b91 | 10.26434/chemrxiv-2024-5cc4t | Decoding Aromaticity in the [24]paracyclophanetetraene Anions | Paracyclophanetetraene (PCT) anions are known for their extraordinary stability that determines cycling performance under fast-charge/fast-discharge conditions, making PCT a suitable material for energy storage in batteries. In previous studies, it was suggested that the unique energy-harnessing capabilities of PCT are associated with the redox-based aromaticity switching from local 24𝜋-aromaticity (PCT) through global 26𝜋-aromaticity (PCT2-) to 28𝜋-antiaromaticity (PCT4-), in accordance with the famous 𝜋-electron bookkeeping rules by Hückel ("4n+2" / "4n"). In this work, however, we call into question this interpretation by showing that the ability of PCT to accumulate up to four electrons is associated with the superposition of the ionic forms that represent the migration of multiple 𝜋-sextets in accordance with Clar's rule. Our findings challenge existing paradigms and offer insight into the resonance-electronic structure of the conjugated macrocycles to better understand the origins of their exceptional electron-transport capabilities and thermodynamic stability. | Dariusz Szczepanik; Ouissam El Bakouri; Paweł Wieczorkiewicz | Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Materials Chemistry; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fd45da51558a15efd29b91/original/decoding-aromaticity-in-the-24-paracyclophanetetraene-anions.pdf |
60c745719abda29be5f8c561 | 10.26434/chemrxiv.10012937.v1 | Nitroreductase-Mediated Release of Inhibitors of Lysine-Specific Demethylase 1 (LSD1) from Prodrugs in Transfected Acute Myeloid Leukaemia Cells | Lysine-specific demethylase 1 (LSD1) has evolved as a promising therapeutic target for cancer treatment, especially in acute myeloid leukaemia (AML). To approach the challenge of site-specific LSD1 inhibition, we developed an enzyme-prodrug system with the bacterial nitroreductase NfsB (NTR) that was expressed in the virally transfected AML cell line THP1-NTR+. The cellular activity of the NTR was proven with a new luminescent NTR probe. We synthesised a diverse set of nitroaromatic prodrugs that by design do not affect LSD1 and are reduced by the NTR to release an active LSD1 inhibitor. The 2-nitroimidazolyl prodrug (1f) of a potent LSD1 inhibitor emerged as one of the best prodrug candidates with a pronounced selectivity window between wild-type and transfected NTR+ cells. Our prodrugs are selectively activated and release the LSD1 inhibitor locally in turn blocking colony formation. This system may be applied in future targeting approaches to reach tissue- or organ-type-specific inhibition of LSD1.<br /> | Manfred Jung; Eva-Maria Herrlinger; Mirjam Hau; Desiree M. Redhaber; Gabriele Greve; Dominica Willmann; Simon Steimle; Michael Müller; Michael Lübbert; Cornelius Miething; Roland Schüle | Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745719abda29be5f8c561/original/nitroreductase-mediated-release-of-inhibitors-of-lysine-specific-demethylase-1-lsd1-from-prodrugs-in-transfected-acute-myeloid-leukaemia-cells.pdf |
6765505e81d2151a025c0a0b | 10.26434/chemrxiv-2024-gn2rv-v2 | A Universal Foundation Model for Transfer Learning in Molecular Crystals | The physical and chemical properties of molecular crystals are a combined function of molecular structure and the molecular crystal packing. Specific crystal packings can enable applications such as pharmaceuticals, organic electronics, and porous materials for gas storage. However, to design such materials, we need to predict both crystal structure and the resulting physical properties, and this is expensive using traditional computational methods. Machine-learned interatomic potential methods offer major accelerations here, but molecular crystal structure prediction remains challenging due to the weak intermolecular interactions that dictate crystal packing. Moreover, machine-learned interatomic potentials do not accelerate the prediction of all physical properties for molecular crystals. Here we present Molecular Crystal Representation from Transformers (MCRT), a transformer-based model for molecular crystal property prediction that is pre-trained on more than 700,000 experimental structures extracted from the Cambridge Structural Database (CSD). MCRT employs four different pre-training tasks to extract both local and global representations from the crystals using multimodal features to encode crystal structure and geometry. MCRT has the potential to serve as a universal foundation model for predicting a range of properties for molecular crystals, achieving state-of-the-art results even when fine-tuned on small-scale datasets. We demonstrate MCRT’s practical utility in both crystal property prediction and crystal structure prediction. We also show that model predictions can be interpreted by using attention scores. | Minggao Feng; Chengxi Zhao; Graeme M. Day; Xenophon Evangelopoulos; Andrew I. Cooper | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6765505e81d2151a025c0a0b/original/a-universal-foundation-model-for-transfer-learning-in-molecular-crystals.pdf |
626bf144ed4d88a0301cf4a4 | 10.26434/chemrxiv-2022-hthz6 | Selective reductions of ketones in the presence of aldehydes with Chiralidon a superabsorbed alcohol dehydrogenase - a "green" metal free alternative to the Luche-reduction | The selective reduction of a keto group in the presence of an aldehyde group with a superabsorbed alcohol dehydrogenase in an organic solvent is described. Remarkably a high preference for the reduction of the keto group was found. For example the 4-acetylbenzaldehyde was reduced with Chiralidon-R to the chiral alcohol (R)-1-(4-formylphenyl)ethanol with 96.5% yield. | Guenter Jeromin; Eugen Huber | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626bf144ed4d88a0301cf4a4/original/selective-reductions-of-ketones-in-the-presence-of-aldehydes-with-chiralidon-a-superabsorbed-alcohol-dehydrogenase-a-green-metal-free-alternative-to-the-luche-reduction.pdf |
67c231e181d2151a0280d2bf | 10.26434/chemrxiv-2025-6hh3g | Exact Møller-Plesset Adiabatic Connection Correlation Energy Densities | The Møller–Plesset adiabatic connection (MPAC) provides a powerful tool for developing density functional theory (DFT)-like approximations that map Hartree–Fock densities to the wavefunction-based correlation energy, thereby leveraging both wavefunction and DFT concepts for electronic structure approximations. A key object in this context is the correlation energy density, which represents the local (pointwise) contribution to the total correlation energy. While well-studied in DFT, it remains largely unexplored in the wavefunction framework. Here, we introduce a rigorous formulation of the wavefunction-based correlation energy density within MPAC, implement it via full configuration interaction calculations, and analyze its behavior and physically meaningful contributions for representative small (di)atomic systems. We define this quantity by employing a general gauge strategy, from which the conventional DFT correlation energy density gauge also arises. We then discuss the resulting commonalities and differences between correlation energy densities in the DFT and wavefunction frameworks and derive the small-interaction (MP2) limit of the latter in terms of Hartree–Fock orbitals. Finally, we show how these newly introduced energy densities can serve as new approximation targets in both machine-learning-assisted and traditional electronic structure methods for mapping HF-density-based features to correlation energy within the wavefunction framework. | Kimberly Jennifer Daas; Heng Zhao; Elias Polak; Stefan Vuckovic | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c231e181d2151a0280d2bf/original/exact-m-ller-plesset-adiabatic-connection-correlation-energy-densities.pdf |
641e7d1d62fecd2a8365138a | 10.26434/chemrxiv-2023-q88sc | Advancements in the synthesis of diaryliodonium salts: Updated protocols | Our group has reported several one-pot protocols for the synthesis of diaryliodonium salts, which have been recognized as attractive multi-purpose reagents in areas ranging from organic synthesis to materials chemistry. Over the years, we have identified limitations in the published protocols concerning synthesis of mixed electron-rich and electron-poor, as well as highly electron-poor diaryliodonium salts, as the corresponding starting materials are either too reactive or too unreactive. In this update, we discuss the underlying limitations concerning the stability and reactivity of the involved reagents and provide strategies to overcome these challenges through updated synthetic protocols. | Erika Linde; Shobhan Mondal; Berit Olofsson | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641e7d1d62fecd2a8365138a/original/advancements-in-the-synthesis-of-diaryliodonium-salts-updated-protocols.pdf |
669e1239c9c6a5c07a5f8c0b | 10.26434/chemrxiv-2024-5w7nc | Activation and Fixation of Atmospheric CO2 Through a 1,2,3-Triazole-based Mesoionic Carbene-Boron Adduct | Capturing atmospheric CO2 and converting it to valuable chemicals are important goals in contemporary science. We present here a simple, transition metal-free triazolylidene-borane adduct that can capture atmospheric CO2 and convert it to formate. Several key intermediates were isolated and characterized by a combination of multinuclear NMR spectroscopy, IR spectroscopy and single crystal X-ray diffraction. A first closed cycle for the conversion of CO2 to formic acid by using the aforementioned triazolylidene-borane compound is presented as well. | Maren Neubrand; Jessica Stubbe; Richard Rudolf; Robert Walter; Maite Nößler; Biprajit Sarkar | Inorganic Chemistry; Organometallic Chemistry; Energy; Bond Activation; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e1239c9c6a5c07a5f8c0b/original/activation-and-fixation-of-atmospheric-co2-through-a-1-2-3-triazole-based-mesoionic-carbene-boron-adduct.pdf |
65c0875566c1381729feb37f | 10.26434/chemrxiv-2023-366tt-v2 | Overpotential-derived thermogenesis in mitochondrial respiratory chain | Thermogenesis, which is associated with intracellular aerobic respiration, is a fundamental function that controls the internal temperatures of living organisms. Proton leakage is considered to be correlated with thermogenesis through aerobic respiration. It is widely known that in electrochemical cells such as fuel cells, overpotentials applied to redox reactions generate heat as energy loss. Even in the electrochemical reaction system of the mitochondrial respiratory chain, a considerable amount of heat is generated by overpotential. However, the physical mechanism of thermogenesis is not yet clear. We propose a thermogenesis model based on the electrochemical overpotential of the mitochondrial respiratory chain. As a result of quantitatively estimating the value of the overpotential applied in each reaction of the mitochondrial respiratory chain, we found that 39-63% of the initial free energy in the respiratory chain was converted into heat, and the rate of thermogenesis changed depending on respiratory activity. Furthermore, that heat was intensively produced in complex IV. The overpotential-derived thermogenesis model is expected to open a research field for electrochemically elucidating mitochondrial functions. | Nuning Namari; Mo Yan; Junji Nakamura; Kotaro Takeyasu | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c0875566c1381729feb37f/original/overpotential-derived-thermogenesis-in-mitochondrial-respiratory-chain.pdf |
60c74dd1842e6514f2db3527 | 10.26434/chemrxiv.12662222.v1 | Characterising the Atomic Structure of Mono-Metallic Nanoparticles from X-Ray Scattering Data Using Conditional Generative Models | The development of new nanomaterials for energy technologies is
dependent on understanding the intricate relation between material
properties and atomic structure. It is, therefore, crucial to be able to
routinely characterise the atomic structure in nanomaterials, and a
promising method for this task is Pair Distribution Function (PDF)
analysis. The PDF can be obtained through Fourier transformation of x-ray total scattering data, and represents a histogram of
all interatomic distances in the sample. Going from the distance
information in the PDF to a chemical structure is an unassigned
distance geometry problem (uDGP), and solving this is often the bottleneck in nanostructure analysis. In this work, we propose to
use a Conditional Variational Autoencoder (CVAE) to automatically
solve the uDGP to obtain valid chemical structures from PDFs. We
use a simple model system of hypothetical mono-metallic nanoparticles containing up to 100 atoms in the face centered cubic (FCC)
structure as a proof of concept. The model is trained to predict the
assigned distance matrix (aDM) from a simulated PDF of the structure as the conditional input. We introduce a novel representation
of structures by projecting them inside a unit sphere and adding
additional anchor points or satellites to help in the reconstruction
of the chemical structure. The performance of the CVAE model is
compared to a Deterministic Autoencoder (DAE) showing that both
models are able to solve the uDGP reasonably well. We further show
that the CVAE learns a structured and meaningful latent embedding
space which can be used to predict new chemical structures. | Andy Sode Anker; Emil T. S. Kjær; Erik B. Dam; Simon J. L. Billinge; Kirsten M. Ø. Jensen; Raghavendra Selvan | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dd1842e6514f2db3527/original/characterising-the-atomic-structure-of-mono-metallic-nanoparticles-from-x-ray-scattering-data-using-conditional-generative-models.pdf |
63b6ee294a7fa1d6af114ffc | 10.26434/chemrxiv-2023-kfwd0 | Linking Experimental and Ab-initio Thermochemistry of Adsorbates with a Generalized Thermochemical Hierarchy | Enthalpies of formation of adsorbates are crucial parameters in the microkinetic modeling of heterogeneously catalyzed reactions, since they quantify the stability of intermediates on the catalyst surface.
This quantity is often computed using density functional theory, as more accurate methods are computationally still too expensive, which means that derived enthalpies have a large uncertainty.
In this study, we propose a new error cancellation method to compute the enthalpies of formation of adsorbates more accurately from DFT through a generalized connectivity-based hierarchy.
The enthalpy of formation is determined through a hypothetical reaction that preserves atomistic and bonding environments.
The method is applied to a dataset of 60 adsorbates on Pt(111) with up to 4 heavy (non-hydrogen) atoms.
Enthalpies of formation of the fragments required for the bond balancing reactions are based on experimental heats of adsorption for Pt(111).
Thus, the proposed methodology creates an interconnected thermochemical network of adsorbates that combines experimental with ab-initio thermochemistry in a single thermophysical database. | Bjarne Kreitz; Kento Abeywardane; C. Franklin Goldsmith | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b6ee294a7fa1d6af114ffc/original/linking-experimental-and-ab-initio-thermochemistry-of-adsorbates-with-a-generalized-thermochemical-hierarchy.pdf |
65e66e0266c138172933f790 | 10.26434/chemrxiv-2024-cq702 | DeltaGzip: Computing Biopolymer-Ligand Binding Affinity via Kolmogorov Complexity and Lossless Compression | The design of bio-sequences for biosensing and therapeutics is a challenging multi-step search and optimization task. In principle, computational modeling may speed up the design process by virtual screening of sequences based on their binding affinities to target molecules. However, in practice, existing machine-learned models trained to predict binding affinities lack the flexibility with respect to reaction conditions, and molecular dynamics simulations that can incorporate reaction conditions suffer from high computational costs. Here, we describe a computational approach called DeltaGzip that evaluates the free energy of binding in biopolymer-ligand complexes from ultra-short equilibrium molecular dynamics simulations. The entropy of binding is evaluated using the Kolmogorov complexity definition of entropy and approximated using a lossless compression algorithm, Gzip. We benchmark the method on a well-studied dataset of protein-ligand complexes comparing the predictions of DeltaGzip to the free energies of binding obtained using the Jarzynski equality and experimental measurements. | Tao Liu; Lena Simine | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e66e0266c138172933f790/original/delta-gzip-computing-biopolymer-ligand-binding-affinity-via-kolmogorov-complexity-and-lossless-compression.pdf |
641d578491074bccd03489f4 | 10.26434/chemrxiv-2023-75pjq | Triazinium Ligation: Bioorthogonal Reaction of N1-alkyl 1,2,4-Triazinium Salts | The development of reagents that can selectively react in complex biological media is an important challenge. Here we show that N1-alkylation of 1,2,4-triazines yields the corresponding triazinium salts, which are three orders of magnitude more reactive in reactions with strained alkynes than the parent 1,2,4-triazines. This powerful bioorthogonal ligation enables efficient modification of peptides and proteins. The positively charged N1-alkyl triazinium salts exhibit favorable cell permeability, which makes them superior for intracellular fluorescent labeling applications when compared to analogous 1,2,4,5-tetrazines. Due to their high reactivity, stability, accessibility and improved water solubility, the new ionic heterodienes represent a valuable addition to the repertoire of existing modern bioorthogonal reagents. | Milan Vrabel; Veronika Šlachtová; Simona Bellová; Agustina La-Venia; Juraj Galeta; Martin Dračínský; Karel Chalupský; Helena Mertlíková-Kaiserová; Peter Rukovanský; Rastislav Dzijak | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641d578491074bccd03489f4/original/triazinium-ligation-bioorthogonal-reaction-of-n1-alkyl-1-2-4-triazinium-salts.pdf |
650b36a460c37f4f76244741 | 10.26434/chemrxiv-2023-77wdm | OptiMS: An Accessible Program for Automating Mass Spectrometry Parameter Optimization and Configuration | Mass spectrometers have an enormous number of user-changeable parameters that drastically affect the observed mass spectrum. Using optimal parameters can significantly improve mass spectrometric data by increasing signal stability and signal to noise ratio, which decreases the limit of detection, thus revealing previously unobservable species. However, ascertaining optimal parameters is time consuming, tedious, and made further challenging by the fact that optimizing one parameter may deoptimize another. Consequently, suboptimal parameters are frequently used during characterization, reducing quality of results. OptiMS, an open-source cross-platform program, was developed to simplify and more accurately determine optimal mass spectrometer parameters for a given system. OptiMS efficacy was demonstrated through its application to multiple systems, quickly and successfully optimizing instrument parameters unassisted, to maximize a user-defined metric, for example, intensity of a particular species. Additionally, amongst other features, OptiMS allows running of a sequence of predefined parameters, reducing workload for users wishing to obtain mass spectra under multiple sets of conditions. | Peter J. H. Williams; Ian C. Chagunda; J. Scott McIndoe | Analytical Chemistry; Analytical Apparatus; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650b36a460c37f4f76244741/original/opti-ms-an-accessible-program-for-automating-mass-spectrometry-parameter-optimization-and-configuration.pdf |
60c73e9a469df4c0d7f428dc | 10.26434/chemrxiv.7064474.v1 | Carbon Chain Growth by Sequential Reactions of CO and CO2 with a Transition Metal Carbonyl Complex | <i>The formation of carbon chains by the coupling of COx (X = 1 or 2) units on transition metals is a fundamental step relevant to Fischer-Tropsch catalysis. Fischer-Tropsch catalysis produces energy dense liquid hydrocarbons from synthesis gas (CO and H2) and has been a mainstay of the energy economy since its discovery nearly a century ago. Despite detailed studies aimed at elucidating the steps of catalysis, experimental evidence for chain growth (Cn to Cn+1 ; n > 2) from the reaction of CO with metal complexes is unprecedented. In this paper, we show that carbon chains can be grown from sequential reactions of CO or CO2 with a transition metal carbonyl complex. By exploiting the cooperative effect of transition and main group metals, we document the first example of chain propagation from sequential coupling of CO units (C1 to C3 to C4), along with the first example of incorporation of CO2 into the growing carbon chain.</i><br /> | Richard Kong; Mark Crimmin | Theory - Computational; Catalysis; Coordination Chemistry (Organomet.); Kinetics and Mechanism - Organometallic Reactions; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e9a469df4c0d7f428dc/original/carbon-chain-growth-by-sequential-reactions-of-co-and-co2-with-a-transition-metal-carbonyl-complex.pdf |
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