bluuebunny/crossref_metadata_2025 huggingface dataset:
High-throughput Calculation of Atomic Planar Density for Compounds
Authors: Baird Sterling , Sparks Taylor
Published: February 2022

A large collection of element-wise planar densities for compounds obtained from the Materials Project is calculated using brute force computational geometry methods. We demonstrate that the element-wise max lattice plane densities can be useful as machine learning features. The methods described here are implemented in an open-source Mathematica package hosted at https://github.com/sgbaird/LatticePlane.
Diazaborines Resist H2O2-Mediated Oxidation But React Rapidly with Peroxynitrite in Aqueous Buffer
Authors: Haggett Jack G. , Han Gun Su , Moser Angela R. , Domaille Dylan
Published: February 2022

Arylboronic acids oxidize with H2O2 and peroxynitrite (ONOO-) to yield their corresponding phenols. However, simple arylboronic acids struggle to discriminate between these two biological reactive oxygen species (ROS). Here, we show that diazaborines (DABs) react slowly with H2O2 but rapidly with peroxynitrite in aqueous buffer. Moreover, oxidation of DABs with H2O2 and ONOO- first yields a long-lived intermediate that ultimately converts to the phenol. Taken together, our work shows that diazaborines exhibit enhanced kinetic discrimination between H2O2 and ONOO-, opening up new opportunities for diazaborine-based tools in chemical biology.
Geographical Distribution of Amino Acid Mutations in Human SARS-CoV-2 Orf1ab Poly-Proteins Compared to the Equivalent Reference Proteins from China
Authors: Guruprasad Kunchur
Published: February 2022

The amino acid mutations among 28,345 poly-protein sequences corresponding to human SARS-CoV-2 orf1AB gene representing the six geographical locations; Africa, Asia, Europe, North America, Oceania and South America were identified by comparing with the equivalent reference poly-protein sequences derived from the first human SARS-CoV-2 genome sequence, reported from Wuhan-Hu-1, China. The mutations were analysed according to the following three datasets; i) 27,956 poly-proteins comprising 7,096 amino acid residues, ii) 373 poly-proteins comprising between 7,051-7,095 amino acid residues and iii) 16 poly-proteins comprising between 7,097-7,099 amino acid residues. In all, 3,204 distinct mutation sites were observed among the poly-proteins comprising 7,096 amino acid residues contributing to ~45% of the poly-protein sequence in SARS-CoV-2 orf1AB gene that have undergone mutations since the outbreak of COVID-19 pandemic disease in December 2019. Fifteen proteins of the poly-protein sequence were associated with mutations and the mutation propensities for the “leader protein”, nsp2, nsp3, nsp6, nsp7, nsp8, endoRNAse proteins was higher (> 1) compared to nsp4, nsp9, nsp10, 3C-like proteinase, RdRp, helicase, 3’-to-5’ exonuclease and 2’-O-ribose methyltransferase proteins. Relatively higher mutation percentages were observed for the RdRp (35.32%), nsp2 (26.42%), nsp3 (11.73%) and helicase (7.88%) proteins, whereas, mutation percentages for the remaining proteins ranged between 0.16% for nsp10 protein to 4.11% for the 3’ -to-5’ exonuclease proteins. Five mutations; T265I in nsp2 protein, T1246I in nsp3, G3278S in 3C-like proteinase, L3606F in nsp6 and P4715L in RdRp were common across all six geographical locations. The P4715L RdRp mutation was predominant in all geographical locations, except Africa, where G5215S mutation was predominant. The maximum number of distinct mutation sites were observed for the nsp3 protein. In 373 orf1AB poly-protein sequences comprising between 7,051-7,095 amino acid residues, deletion mutations were observed that were associated with “leader protein” between positions; 82-86 (GHVMV) and positions 141-143 (KSF). Among 16 orf1AB poly-proteins comprising between 7,097-7,099 amino acid residues, certain insertion mutations were observed that were associated with the nsp2 (517K), nsp3 (938E, 1901Y), 2’ -O-ribose methyltransferase (7046F) and nsp6 (3610F, 3611L) proteins. In this work, all mutations observed among the 28,345 orf1AB poly-proteins of human SARS CoV-2 relative to the reference sequences are presented.
Photo-induced degradation of PFASs: Excited-state mechanisms from real-time time-dependent density functional theory
Authors: Yamijala Sharma , Shinde Ravindra , Hanasaki Kota , Ali Zulfikhar , Wong Bryan
Published: February 2022

Per- and polyfluoroalkyl substances (PFASs) are hazardous, carcinogenic, and bioaccumulative contaminants found in drinking water sources. To mitigate and remove these persistent pollutants, recent experimental efforts have focused on photo-induced processes to accelerate their degradation; however, the mechanistic details of these promising degradation processes remain unclear. To shed crucial insight on these electronic-excited state processes, we present the first study of photo-induced degradation of explicitly-solvated PFASs using excited-state, real-time time-dependent density functional theory (RT-TDDFT) calculations. Furthermore, our large-scale RT-TDDFT calculations show that these photo-induced excitations can be highly selective by enabling a charge-transfer process that only dissociates the C–F bond while keeping the surrounding water molecules intact. Collectively, the RT-TDDFT techniques used in this work (1) enable a new capability for probing photo-induced mechanisms that cannot be gleaned from conventional ground-state DFT calculations and (2) provide a rationale for understanding ongoing experiments that are actively exploring photo-induced degradation of PFAS and other environmental contaminants.
Divergent effects of laser irradiation on ensembles of nitrogen-vacancy centers in bulk and nano-diamonds: implications for biosensing
Authors: Olivares Postigo Domingo , Gorrini Federico , Bitonto Valeria , Ackermann Johannes , Giri Rakshyakar , Krueger Anke , Bifone Angelo
Published: February 2022

Ensembles of negatively charged nitrogen vacancy centers (NV-) in diamond have been proposed for sensing of magnetic fields and paramagnetic agents, and as a source of spin-order for the hyperpolarization of nuclei in magnetic resonance applications. To this end, strongly fluorescent nanodiamonds represent promising materials, with large surface areas and dense ensembles of NV-. However, surface effects tend to favor the less useful neutral form, the NV0 centers. Here, we study the fluorescence properties and optically detected magnetic resonance (ODMR) of NV- centers as a function of laser power in strongly fluorescent bulk diamond and in nanodiamonds obtained by nanomilling the native material. In bulk diamond, we find that increasing laser power increases ODMR contrast, consistent with a power-dependent increase in spin-polarization. Surprisingly, in nanodiamonds we observe a non-monotonic behavior, with a decrease in ODMR contrast at higher laser power that can be ascribed to more efficient NV-→NV0 photoconversion in nanodiamonds compared to bulk diamond, resulting in depletion of the NV- pool. We also studied this phenomenon in cell cultures following internalization of NDs in macrophages. Our findings show that surface effects in nanodiamonds substantially affect the NV properties and provide indications for the adjustment of experimental parameters.
Behavior of Linear and Nonlinear Dimensionality Reduction for Collective Variable Identi�cation of Small Molecule Solution-Phase Reactions
Authors: Le Hung , Kumar Sushant , May Nathan , Martinez-Baez Ernesto , Sundararaman Ravishankar , Krishnamoorthy Bala , Clark Aurora
Published: February 2022

Identifying collective variables for chemical reactions is essential to reduce the 3$N$ dimensional energy landscape into lower dimensional basins and barriers of interest. However in condensed phase processes, the non-meaningful motions of bulk solvent often overpower the ability of dimensionality reduction methods to identify correlated motions that underpin collective variables. Yet solvent can play important indirect or direct roles in reactivity and much can be lost through treatments that remove or dampen solvent motion. This has been amply demonstrated within principal component analysis, although less is known about the behavior of nonlinear dimensionality reduction methods, e.g., UMAP, that have become more popular recently. The latter presents an interesting alternative to linear methods though often at the expense of interpretability. This work presents distance attenuated projection methods of atomic coordinates that facilitate the application of both PCA and UMAP to identify collective variables in solution, and further the specific identity of solvent molecules that participate in chemical reactions. The performance of both methods is examined in detail for two reactions where the explicit solvent plays very different roles within the collective variables. The first reaction consists of the dynamic exchange of a cation about a polyhydroxy anion that is facilitated by waters of solvation, while the second reaction consists of a nucleophilic attack of water upon ethylene to initiate cis/trans isomerization. When applied to raw data, both PCA and UMAP representations are dominated by bulk solvent motions. On the other hand, when applied to data preprocessed by our attenuated projection methods, both PCA and UMAP identify the appropriate collective variables in solution.
Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path
Authors: Qin Zhi-Xin , Tremblay Matthew , Hong Xin , Yang Zhongyue
Published: February 2022

Fleeting intermediates constitute dynamically-stepwise mechanisms. They have been characterized in molecular dynamics trajectories, but whether these intermediates form a free energy minimum to become entropic intermediate remains elusively defined. We developed a computational protocol known as entropic path sampling to evaluate the entropic variation of reacting species along a reaction path based on an ensemble of trajectories. Using cyclopentadiene dimerization as a model reaction, we observed a shallow entropic trap (–T∆S = –0.8 kcal/mol) along the reaction path which originates from an enhanced conformational flexibility as the reacting species enter into a flat energy region. As the reacting species further approach product formation, unfavorable entropic restriction fails to offset the potential energy drop, resulting in no free energy minimum along the post-TS pathway. Our results show that cyclopentadiene dimerization involves an entropic trap that leads to dynamic intermediates with elongated lifetime, but the reaction does not involve entropic intermediates.
Capillaric - Field Effect Transistors
Authors: Meffan Robert Claude , Menges Julian , Dolamore Fabian , Mak Daniel , Fee Conan , Dobson Renwick , Nock Volker
Published: February 2022

Controling fluid flow in capillaric circuits is a key requirement to increase their uptake for assay applications. Capillary action off-valves provide such functionality by pushing an occluding bubble into the channel using a difference in capillary pressure. Previously, we utilised the binary switching mode of this structure to develop a powerful set of fundamental fluidic valving operations. In this work we provide evidence that these structures are in fact functionally complementary to electronic Junction Field Effect Transistors and thus warrant the use of the new term of capillaric- Field Effect Transistor to describe these types of valves. To support this conclusion, we present a theoretical description, experimental characterisation, and practical application of analog flow resistance control. In addition, we demonstrate that the valves can also be re-opened. These are two key capabilities previously missing for a full analogy to electronic transistors. We show modulation of the flow resistance from fully open to pinch-off, determine the flow rate – trigger channel volume relationship and demonstrate that the latter can be modelled using Shockley’s equation for electronic transistors. Finally, we provide a first example of how the valves can be opened and closed repeatedly.
Theoretical evaluation of equilibrium constant for boron isotopes exchange between boric acid and borate in pure and saline water
Authors: Alibakhshi Amin , Hartke Bernd , Steffen Julien , Pinilla Carlos
Published: February 2022

Evaluation of the equilibrium constant of boron isotope fractionation between boric acid and borate (k3−4) in water is of high geochemical importance, due to its contribution in reconstruction of ancient seawater pH and atmospheric CO2. As a result, precise evaluation of k3−4 has been the subject of numerous studies, yielding diverse and controversial results. In the present study, employing three different rigorous and high-precision theoretical approaches, we provide a reliable estimation of k3−4 which is a value between 1.028 to 1.030 for both pure and saline water. Within the context of present study, we also propose partial normal mode analysis, Boltzmann weighted averaging and a revision on the Bigeleisen and Mayer method which allow a more rigorous evaluation of isotope fraction in solution and can be used for studying other isotopic systems as well.
Homogeneous Electrocatalytic Reduction of CO2 by a CrN3O Complex: Electronic Coupling with Redox-Active Terpyridine Fragment Favors Selectivity for CO
Authors: Hooe Shelby , Moreno Juan , Dickie Diane , Machan Charles
Published: February 2022

Electrocatalyst design and optimization strategies continue to be an active area of research interest for the applied use of renewable energy resources and the development of associated technologies. The electrocatalytic conversion of CO2 is an attractive approach in this context, because of the added potential benefit of addressing its rising atmospheric concentrations. In previous experimental and computational studies we have described the mechanism of the first molecular Cr complex capable of electrocatalytically reducing CO2 to CO in the presence of an added proton donor, which contained a redox-active 2,2'-bipyridine (bpy) fragment, CrN2O2. The high selectivity for CO in the bpy-based system was dependent on a delocalized Cr(II)(bpy•–) active state. Subsequently, we became interested in exploring how expanding the polypyridyl ligand core would impact selectivity and activity during electrocatalytic CO2 reduction. Here, we report a new CrN3O catalyst, Cr(tpytbupho)Cl2 1, where 2-([2,2':6',2''-terpyridin]-6-yl)-4,6-di-tert-butylphenolate = [tpytbupho]–, which reduces CO2 to CO with quantitative selectivity via a different mechanism than our previously reported Cr(tbudhbpy)Cl(H2O) catalyst. Computational analyses indicate that changes in the overall reaction are the combined result of a decrease in intrinsic ligand charge (L3X vs L2X2) and an increase in ligand redox activity, which result in increased electronic coupling between the doubly reduced tpy fragment of the ligand and a Cr(II) center. The strong electronic coupling enhances the rate of protonation and subsequent C–OH bond cleavage, resulting in CO2 binding becoming the rate-determining step, which is an uncommon mechanism during protic CO2 reduction.
Colloidal SERS sensors for inflammatory biomarker detection in urine for patient risk stratification
Authors: Kidd Rachel , Anderson William , Prince Josh , Agyemang-Prempeh Akosua , Roach Peter , Newman Tracey , Mahajan Sumeet
Published: February 2022

Consistently raised levels of inflammatory marker - Neopterin, in urine is linked to increased risk of progression of age-related disease and poorer prognosis. We have developed colloidal SERS sensors and demonstrate their ability, and ease of use, for quantification of neopterin in human urine samples. Results with the sensors are comparable and in agreement with those obtained by HPLC and allow individuals to be stratified into ‘risk’ categories based on their results. With an average 17.85% difference in results between the two analytical approaches, SERS with colloidal sensors, demonstrates an alternative method that is rapid, inexpensive, requires minimal sample treatment, can be performed on a portable instrument with little need for complex data analysis, whilst having the analytical strength to reliably demonstrate an individual’s risk category based on inflammatory load.
Exploiting redox activity of MIL-100(Fe) carrier enables carvacrol prolonged antimicrobial activity
Authors: Caamaño Katia , Calbo Jaquín , Heras-Mozos Raquel , Vieira Bruno J. C , Waerenborgh Joao C. , Hernández-Muñoz Pilar M. , Gavara Rafael , Giménez-Marqués Mónica
Published: February 2022

The design of efficient food contact materials that maintain optimal levels of food safety is of paramount relevance to reduce the increasing foodborne illnesses. In this work, we develop a smart composite MOF-based material that fosters a unique prolonged antibacterial activity. The composite is obtained by entrapping a natural preserving food molecule, carvacrol, into the mesoporous MIL-100(Fe) material following a direct and biocompatible impregnation method and obtaining particularly high payloads. By exploiting the intrinsic redox nature of MIL-100(Fe) material it is possible to achieve a prolonged activity against E. coli bacteria due to a triggered two-step carvacrol release of films containing the carvacrol@MOF composite. Essentially, it was discovered that based on the underlying chemical interaction among MIL-100(Fe) and carvacrol, it is possible to undergo a reversible charge transfer process between the metallic MOF counterpart and the carvacrol upon certain physical stimuli. During this process, the preferred carvacrol binding site has been monitored by IR, Mössbauer and EPR spectroscopies and is supported by theoretical calculations.
Modification of the Basic Dilution Equation for the Programming of Serial Dilutions
Authors: Bassa Babu , Uppu Rao
Published: February 2022

Stock solutions made with accurately weighable quantities of biologically active compounds often do not result in physically measurable delivery volumes, delivered to cell cultures, assay buffers etc., consequently requiring delineation of the serial dilution steps of the stock solution in a case by case manner. The basic dilution equation (C1V1 = C2V2) alone is not amenable for the programming and computerization of the serial dilutions. The best solution to this dilemma is to develop an equation with the delivery volume as one of the variables. We present here a modified dilution equation (MDA) that has the delivered volume as one of the variables. We demonstrate with examples how the equation can be used in delineating serial dilution steps either manually or through programming. The equation is D = C1p/C2V2, where D is the fold dilution required of a stock solution of C1 concentration which is diluted and delivered (pipetted) at a volume p to cell culture media, assay mixture etc., of volume (V2 – p), to achieve a final concentration of C2. The equation is useful when the volume of the stock solution made up to the final volume as calculated with basic dilution equation is not measurable physically.
Precise Molecular Engineering of Type I Photosensitizers with Near-Infrared Aggregation-Induced Emission for Image-Guided Photodynamic Killing of Multidrug-Resistant Bacteria
Authors: Xiao Peihong , Shen Zipeng , Wang Deliang , Pan Yinzhen , Li Ying , Gong Junyi , Wang Lei , Wang Dong , Tang Ben Zhong
Published: February 2022

Multidrug resistance (MDR) bacteria pose a serious threat to human health. The development of alternative treatment modalities and therapeutic agents for treating MDR bacteria-caused infections remains a global challenge. Herein, we rationally designed and successfully developed a series of near-infrared (NIR) anion-π+ photosensitizers featuring aggregation-induced emission (AIE-PSs) for broad-spectrum MDR bacteria eradication. Due to the strong intramolecular charge transfer (ICT) and enhanced highly efficient intersystem crossing (ISC), these electron-rich anion-π+ AIE-PSs showed boosted type I reactive oxygen species (ROS) generation capability involving hydroxyl radicals and superoxide anion radicals, and up to 99% photodynamic killing efficacy was achieved for both Methicillin-resistant Staphylococcus aureus (MRSA) and multi-drug resistant Escherichia coli (MDR E.coli) under a low dose white light irradiation (16 mW cm-2). In vivo experiments confirmed that one of these AIE-PSs exhibited excellent therapeutic performance in curing MRSA or MDR E.coli-infected wounds with negligible side-effects. The study would thus provide useful guidance for the rational design of high-performance type I AIE-PSs to overcome antibiotic resistance.
FRET Pumping of Rhodamine-Based Probe in Light-Harvesting Nanoparticles for Highly Sensitive Detection of Cu2+
Authors: Mironenko Aleksandr , Tutov Mikhail , Chepak Aleksandr , Bratskaya Svetlana
Published: February 2022

In this work we presented novel strategy for increasing the performance of popular fluorescent probes on the basis of rhodamine-lactam platform. This strategy is based on the incorporation of probe molecules into the light-harvesting nanoparticles to pump modulated optical signal by Förster resonant energy transfer. Using the commercially available Cu2+ probe as a reference chemical, we have developed an efficient approach to significantly improve its sensing performance. Within obtained nanoparticles coumarin-30 nanoantenna absorbs excitation light and pumps incorporated sensing molecules providing bright fluorescence to a small number of emitters, while changing the probe-analyte equilibrium from liquid-liquid to solid-liquid significantly increased the apparent association constant, which together provided a ~100-fold decrease in the detection limit. The developed nanoprobe allows highly sensitive detection of Cu2+ ions in aqueous media without organic co-solvents usually required for dissolution of the probe, and demonstrate compatibility with inexpensive fluorometers and the ability to detect low concentrations with the naked eye.
All-Red-Light Photoswitching of Indirubin Controlled by Supramolecular Interactions
Authors: Thumser Stefan , Köttner Laura , Hoffmann Nadine , Mayer Peter , Dube Henry
Published: February 2022

Red light responsiveness of photoswitches is a highly desired property for many important application areas such as biology or material sciences. The main approach to elicit this property uses strategic substitution of long known photoswitch motives such as azobenzenes or diarylethenes. Only very few photoswitches possess inherent red-light absorption of their core chromophore structures. Here we present a strategy to convert the long known purple indirubin dye into a prolific red light responsive photoswitch. In a supramolecular approach its photochromism can be changed from a negative to a positive one while at the same time significantly higher yields of the metastable E isomer are obtained. E to Z photoisomerization can then also be induced by red light of longer wavelengths. Indirubin therefore represents a unique example of reversible photoswitching using entirely red light for both switching directions.
Determination of Kinetic Properties in Unimolecular Dissociation of Complex Systems from Graph-Theory Based Analysis of an Ensemble of Reactive Trajectories.
Authors: Perez-Mellor Ariel F. , Spezia Riccardo
Published: February 2022

We describe and apply a general approach based on graph-theory to obtain kinetic and structural properties from direct dynamics simulations. In particular, we focus on the unimolecular fragmentation of complex systems in which, prior to dissociation, different events can take place, and notably isomerizations and formation of ion-molecule complex.3-state and 4-state kinetic models are thus obtained and rate constants for global or specific pathways are obtained from direct counting and flux calculation, both being in agreement.

Finally, we show how a theoretical mass spectrum can also be obtained automatically.
A Programmable Synthesis of Diverse Terpene Architectures from Phenols
Authors: Salahi Farbod , Yao Chengbo , Norton Jack , Snyder Scott
Published: February 2022

Over millennia, Nature has evolved exquisite synthetic pathways that combine isoprenes into chains, folds them into carbocycles, and then oxidizes/rearranges them into vast complexity (>50,000 members). While laboratory chemical synthesis can sometimes emulate this process, room exists for additional approaches that can also programmably lead to molecular diversity. Here we show that from simple phenols using 1) prenylation, 2) dearomatization/prenyl migration, and 3) epoxidation/radical cyclization, we can predictably, reliably, and expeditiously make polycyclic terpene frameworks; critically, step three uses the first cooperative bimetallic catalyst to effect cyclization of epoxy enones under H2. Indeed, our approach has led to the stereocontrolled formation of bicyclic, linear, angular, clovane, and propellane-based architectures with functional groups that allow further manipulation; for example, these motifs can be repurposed for ring contractions. Of note, several formal total syntheses have been achieved in routes that are as concise as, and often shorter than, previous efforts.
Featurization Strategies for Polymer Sequence or Composition Design by Machine Learning
Authors: Patel Roshan , Borca Carlos , Webb Michael
Published: February 2022

The emergence of data-intensive scientific discovery and machine learning has dramatically changed the way in which scientists and engineers approach materials design. Nevertheless, for designing macromolecules or polymers, one limitation is the lack of appropriate methods or standards for converting systems into chemically informed, machine-readable representations. This featurization process is critical to building predictive models that can guide polymer discovery. Although standard molecular featurization techniques have been deployed on homopolymers, such approaches capture neither the multiscale nature nor topological complexity of copolymers, and they have limited application to systems that cannot be characterized by a single repeat unit. Herein, we present, evaluate, and analyze a series of featurization strategies suitable for copolymer systems. These strategies are systematically examined in diverse prediction tasks sourced from four distinct datasets that enable understanding of how featurization can impact copolymer property prediction. Based on this comparative analysis, we suggest directly encoding polymer size in polymer representations when possible, adopting topological descriptors or convolutional neural networks when the precise polymer sequence is known, and using simplified constitutional unit representations depending on the noise-level of underlying data. These results provide guidance and future directions regarding polymer featurization for copolymer design by machine learning.
Halide-selective, proton-coupled anion transport by phenylthiosemicarbazones
Authors: Howe Ethan N.W. , Chang Vai-Vai Tiffany , Wu Xin , Fares Mohamed , Lewis William , Macreadie Lauren K. , Gale Philip Alan
Published: February 2022

Phenylthiosemicarbazones (PTSCs) are proton-coupled anion transporters with pH-switchable behaviour known to be regulated by an imine protonation equilibrium. Previously, chloride/nitrate exchange by PTSCs was found to be inactive at pH 7.2 due to locking of the thiourea anion binding site by an intramolecular hydrogen bond, and switched ON upon imine protonation at pH 4.5. The rate-determining process of the pH switch, however, was not examined. We here develop a new series of PTSCs and demonstrate their conformational behaviour by X-ray crystallographic analysis and pH-switchable anion transport properties by liposomal assays. We report the surprising finding that the protonated PTSCs are extremely selective for halides over oxyanions in membrane transport. Owing to the high chloride over nitrate selectivity, the pH-dependent chloride/nitrate exchange of PTSCs originates from the rate-limiting nitrate transport process being inhibited at neutral pH.
Optical Properties of Zinc Selenide Quantum Dots
Authors: Toufanian Reyhaneh , Zhong Xingjian , Kays Joshua , Saeboe Alexander , Dennis Allison
Published: February 2022

The focus on heavy metal-free semiconductor nanocrystals has increased interest in ZnSe semiconductor quantum dots (QDs) over the past decade. Reliable and consistent incorporation of ZnSe cores into core/shell heterostructures or devices requires empirical fit equations correlating the lowest energy electron transition (1S peak) to their size and molar extinction coefficients (ε). While these equations are known and heavily used for CdSe, CdTe, CdS, PbS, etc., they are not well established for ZnSe and are non-existent for ZnSe QDs with diameters < 3.5 nm. In this study, a series of ZnSe QDs with diameters ranging from 2 to 6 nm were characterized with small angle X-ray scattering (SAXS), transmission electron microscopy (TEM), UV-Vis spectroscopy, and microwave plasma atomic emission spectroscopy (MP-AES). SAXS-based size analysis enabled practical inclusion of small particles in the evaluation, and elemental analysis with MP-AES elucidates a non-stoichiometric Zn:Se ratio consistent with zinc-terminated spherical ZnSe QDs. Using these combined results, empirical fit equations correlating QD size with its lowest energy electron transition (i.e., 1S peak position), Zn:Se ratio, and molar extinction coefficients for 1S peak, 1S integral, and high energy wavelengths are reported. Finally, the equations are used to track the evolution of a ZnSe core reaction. These results will enable the consistent and reliable use of ZnSe core particles in complex heterostructures and devices.
Molecular Z-Scheme for H2 Production via Dual Photocatalytic Cycles
Authors: Ayare Pooja J. , Watson Noelle , Helton Maizie R. , Warner Matthew J. , Dilbeck Tristan , Hanson Kenneth , Vannucci Aaron K.
Published: February 2022

Natural photosynthesis uses an elaborate array of molecular structures in a multi-photon Z-scheme for the conversion of light energy into chemical bonds (i.e. solar fuels). Extensive research effort has been dedicated to achieving artificial photosynthesis but a fully molecular artificial Z-scheme for solar fuels production has yet to be realized. Here we show that upon excitation of both a molecular photocatalyst (PC) and an aryl alcohol (ROH) in the presence of a sacrificial electron donor and proton source, we achieve artificial photosynthesis of H2. Chemical, electrochemical, and spectroscopic data support a mechanism consisting of: 1) photoexcitation of PC, 2) reduction of excited state PC, 3) electron transfer from PC- to photoexcited ROH, and 4) generation of H2 from reduced ROH. The system is catalytic with respect to both PC and ROH and operates at a reaction overpotential of ~40 meV. This molecular Z-scheme circumvents the thermodynamic and overpotential constraints associated with reduction of weak acids in their ground-state and offers a new paradigm for the conversion of light energy into H2 bond energy.
Reaction Classification and Yield Prediction using the Differential Reaction Fingerprint DRFP
Authors: Probst Daniel , Schwaller Philippe , Reymond Jean-Louis
Published: February 2022

Predicting the nature and outcome of reactions using computational methods is a crucial tool to accelerate chemical research. The recent application of deep learning-based learned fingerprints to reaction classification and reaction yield prediction has shown an impressive increase in performance compared to previous methods such as DFT- and structure-based fingerprints. However, learned fingerprints require large training data sets, are inherently biased, and are based on complex deep learning architectures. Here we present the differential reaction fingerprint \textit{DRFP}. The \textit{DRFP} algorithm takes a reaction SMILES as an input and creates a binary fingerprint based on the symmetric difference of two sets containing the circular molecular n-grams generated from the molecules listed left and right from the reaction arrow, respectively, without the need for distinguishing between reactants and reagents. We show that \textit{DRFP} outperforms DFT-based fingerprints in reaction yield prediction and other structure-based fingerprints in reaction classification, reaching the performance of state-of-the-art learned fingerprints in both tasks while being data-independent.
Taming Unhindered Alkyl Azides by Intramolecular Hydrogen-Azide Interaction for Discriminative Conjugation onto Alkyl Diazides
Authors: Maegawa Koshiro , Tanimoto Hiroki , Onishi Seiji , Tomohiro Takenori , Morimoto Tsumoru , Kakiuchi Kiyomi
Published: February 2022

We report herein the unique reactivities of α-azido secondary acetamides (α-AzSAs) as minimal and unhindered azide structures. The NH–azide interaction in the α-AzSAs, supposed by DFT calculation, allowed selective conjugation in the presence of other azido moieties. With Staudinger-Bertozzi ligation, α-AzSAs proceeded the conjugation prior to the other primary alkyl azides. On the other hand, in propargyl cation-mediated triazole synthesis, other alkyl azides, including tertiary alkyl azides, underwent the conjugation faster than α-AzSAs. We also demonstrated discriminative integration of the functional components onto the diazide modular hubs.
Nickel-Catalyzed Reductive Alkylation of Heteroaryl Imines
Authors: Brandstätter Marco , Turro Raymond F. , Reisman Sarah
Published: February 2022

A Ni-catalyzed reductive cross-coupling of heteroaryl imines with C(sp3) electrophiles for the preparation of heterobenzylic amines is reported. This umpolung-type alkylation proceeds under mild conditions, avoids the pre-generation of organometallic reagents, and ex-hibits good functional group tolerance. Mechanistic studies are consistent with the imine substrate acting as a redox-active ligand upon coordination to a low-valent nickel center. The resulting Ni-bis(2-imino)heterocycle complexes can engage in alkylation reactions with a variety of C(sp3) electrophiles, giving the heterobenzylic amine products in good yields.
BH9, a New Comprehensive Benchmark Dataset for Barrier Heights and Reaction Energies: Assessment of Density Functional Approximations and Basis Set Incompleteness Potentials
Authors: Prasad Viki Kumar , Pei Zhipeng , Edelmann Simon , Otero-de-la-Roza Alberto , DiLabio Gino
Published: February 2022

The calculation of accurate reaction energies and barrier heights is essential in computational studies of reaction mechanisms and thermochemistry. In order to assess methods regarding their ability to predict these two properties, high-quality benchmark sets are required that comprise a reasonably large and diverse set of organic reactions. Due to the time-consuming nature of both locating transition states and computing accurate reference energies for reactions involving large molecules, previous benchmark sets have been limited in scope, the number of reactions considered, and the size of the reactant and product molecules. Recent advances in coupled-cluster theory, in particular local correlation methods like DLPNO-CCSD(T), now allow the calculation of reaction energies and barrier heights for relatively large systems. In this work, we present a comprehensive, and diverse benchmark set of barrier heights and reaction energies based on DLPNO-CCSD(T)/CBS, called BH9. BH9 comprises 449 chemical reactions belonging to nine types common in organic chemistry and biochemistry. We examine the accuracy of DLPNO-CCSD(T) vis-a-vis canonical CCSD(T) for a subset of BH9 and conclude that, although there is a penalty in using the DLPNO approximation, the reference data are accurate enough to serve as benchmark for density-functional theory (DFT) methods. We then present two applications of the BH9 set. First, we examine the performance of several density functional approximations commonly used in thermochemical and mechanistic studies. Second, we assess our basis set incompleteness potentials regarding their ability to mitigate basis set incompleteness error. The number of data points, the diversity of the reactions considered, and the relatively large size of the reactant molecules make BH9 the most comprehensive thermochemical benchmark set to date, and a useful tool for the development and assessment of computational methods.
Omniligase-1-mediated ligation for insulin analog synthesis in solu-tion and on phage surface
Authors: Lin Nai-Pin , Zhang Yi , Szabo-Fresnais Nicolas , Chou Danny Hung-Chieh
Published: February 2022

The B-chain C-terminal region of insulin has been mutated or modified to achieve improved therapeutic efficacies. For ex-ample, all FDA-approved insulin analogs have altered C-terminal segments, which leads to improved pharmacokinetic prop-erties and provide significant clinical benefits on blood sugar regulation. Nonetheless, there is still no efficient method to synthesize insulin analogs with the altered C-terminal region. Herein, we report a facile synthesis using omniligase-1 to li-gate an insulin core with a peptide segment in high conversion. We further apply this ligation to M13 phage surface modifi-cations and demonstrate that the phage displayed insulin molecules can bind to insulin receptor ectodomain in an insulin-dependent manner. These results pave the way for building phage display insulin library for therapeutic selections and demonstrate the feasibility of using omniligase-1 to display other disulfide-rich peptides and proteins on phage.
Unravelling a novel mechanism in polymer self-assemblies: An order-order transition based on molecular interactions between hydrophilic and hydrophobic polymer blocks
Authors: Hahn Lukas , Zorn Theresa , Kehrein Josef , Kielholz Tobias , Ziegler Anna-Lena , Forster Stefan , Sochor Benedikt , Lisitsyna Ekaterina S. , Durandin Nikita , Laaksonen Timo , Aseyev Vladimir , Sotriffer Christoph , Windbergs Maike , Pöppler Ann-Christin , Luxenhofer Robert
Published: February 2022

Thermoresponsive hydrogel formation upon cooling in aqueous media is rarely described for synthetic polymers in the literature. However, if the sol-gel transition occurs in the physiologically relevant range (0-40 °C), there are many possible applications in areas such as drug delivery and biofabrication. Here, we describe a new mechanism of a thermally induced order-order transition in polymer self-assembly of an ABA triblock consisting of hydrophilic A blocks and a hydrophobic aromatic B block. Small-angle X-ray scattering confirmed worm-to-sphere transition upon heating on the nanoscale level while wide-angle X-ray scattering indicated a more uniform ordering of the macromolecular chains on the scale of 4-7 Å. NMR spectroscopy showed reduced mobility of various polymer segments in the hydrogel state, especially in the hydrophobic aromatic region. More importantly however, solution and solid-state NMR investigations also revealed close proximity of hydrophobic and hydrophilic repeat units in the gel state, which is less pronounced in the sol state. This interaction between the hydrophilic and hydrophobic block is responsible for the order-order transition and –ipso facto– inverse thermogelation. This unusual interaction is supported in silico by molecular dynamics modeling. Changes in the structure of the hydrophilic A blocks can be used to tune the gel strength, persistence, and gelation kinetics. This order-order transition based on unexpected and previously not described interactions between the hydrophilic and the hydrophobic repeat units opens new avenues to control and design macromolecular self-assembly.
Two-dimensional Graphitic Metal Carbides: A New Class of Atomically Thin Carbon-based Crystals
Authors: Yam Kah-Meng , Zhang Yongjie , Guo Na , Deng Hui , Zhang Chun
Published: February 2022

The recent prediction of several single-atom thin two-dimensional (2D) graphitic metal carbides (g-MCs) with honeycomb-in-honeycomb (HIH) structures is the first instance of designing 2D metal-carbon-only crystals from porous carbon allotropes via lattice reconstruction and these 2D g-MCs represent a new class of 2D carbon-based crystals. Here by extensive first-principles calculations, we show that this class of carbon-based crystals can be expanded to include 33 different members in total. These materials exhibit a myriad of properties, which can be useful in many different applications such as catalysis, spintronics, thermoelectrics, optoelectronics, etc. We reveal the chemical bonding in 2D g-MCs in terms of natural bonding orbitals to shed light on the origin of their unique electronic properties. In addition, these crystals show interesting but puzzling magnetic properties. A unified model to understand the origin of the magnetic properties of 2D g-MCs is hence proposed.
The effect of orientated electric fields on biologically relevant iron-sulfur clusters: Tuning redox reactivity for catalysis
Authors: Gaughan Samuel , Hirst Jonathan , Croft Anna , Jaeger Christof
Published: February 2022

Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases and radical S-adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyond simple electron transfer, relying primarily on the redox activity of the clusters, with a remarkable diversity for different enzymes. The active site structure and the electrostatic environment in which the cluster resides direct this redox reactivity. Orientated electric fields in enzymatic active sites can be significantly strong and to understand the extent of their effect on iron-sulfur cluster reactivity can inform first steps towards rationally engineering their reactivity. An extensive systematic density functional theory based screening approach using OPBE/TZP has afforded a simple electric field effect representation. The results demonstrate that the orientation of an external electric field of strength 0.288 MV cm-1 at the centre of the cluster can have a significant effect on its relative stability in the order of 35 kJ mol˗1. This shows clear implications for the reactivity of iron-sulfur clusters in enzymes. The results also demonstrate that the orientation of the electric field can alter the most stable broken symmetry state, which further has implications on the directionality of initiated electron transfer reactions. These insights open the path for manipulating enzymatic redox reactivity of iron-sulfur cluster containing enzymes by rationally engineering orientated electric fields within the enzymes.
Electronic structure of NdO via slow photoelectron velocity-map imaging spectroscopy of NdO¯
Authors: Babin Mark , DeWitt Martin , DeVine Jessalyn , McDonald II David , Ard Shuan , Shuman Nicholas , Viggiano Albert , Cheng Lan , Neumark Daniel
Published: February 2022

Electronically excited NdO is a possible product of the chemistry associated with the release of Nd into the ionosphere, and emission from these states may contribute to the observations following such experiments. To better characterize the energetics and spectroscopy of NdO, we report a combined experimental and theoretical study using slow photoelectron velocity-map imaging spectroscopy of cryogenically cooled NdO¯ anions (cryo-SEVI) supplemented by wavefunction-based quantum-chemical calculations. Using cryo-SEVI, we measure the electron affinity of NdO to be 1.0091(7) eV and resolve numerous transitions to low-lying electronic and vibrational states of NdO that are assigned with the aid of the electronic structure calculations. Additionally, temperature-dependent data suggests contributions from the (2)4.5 state of NdO¯ residing 2350 cm-1 above the ground anion state. Photodetachment to higher-lying excited states of NdO is also reported, which may help clarify observations from prior release experiments.
JigCell: A New Environment to Simulate the Dynamics of Memory Formation
Authors: Alpturk Onur
Published: February 2022

Since their initial discovery, long-term potentiation (LTP), and long-term depression (LTD) are accepted as the main biomolecular mechanism that controls memory acquisition. In doing this, both mechanisms are fairly complex and involve specific triggers and many cascades reactions that cross-talk and communicate with others. Thus, they are very complex. To reveal how these mechanisms operate and instruct the brain to remember and forget, one judicious approach is developing the mathematical models of processes. However, this notion requires some basic knowledge regarding ordinary differential equations and writing codes. To this respect, it can be postulated that tools, which can be utilized rather by everyone, would certainly expedite and facilitate the formulation of such models. With this rationale in mind, we demonstrate that JigCell offers the perfect platform to develop such models of LTP. Our choice for this tool stems from the fact that it is designed to simulate complex biological systems in a modular way. Thus, this manuscript is crafted to illustrate how this model was constructed in the JigCell environment and to give an idea of how this tool works.
Sulfur and azobenzenes, a profitable liaison: straightforward synthesis of photoswitchable thioglycosides with tunable properties
Authors: Berry Jonathan , Lindhorst Thisbe , Despras Guillaume
Published: February 2022

Azobenzene photoswitches are valuable tools for controlling properties of molecular systems with light. In particular, we have been investigating azobenzene glycoconjugates to probe carbohydrate-protein interactions and also to design photoresponsive glycomacrocycles with modulable chiroptical and physicochemical properties. To date, direct conjugation of glycosides to azobenzenes was performed by reactions providing target compounds in limited yields. We therefore sought for a more effective and reliable coupling method. In this paper, we report on a straightforward thioarylation of azobenzene derivatives with glycosyl thiols as well as other thiol substrates, increasing the scope of azobenzene conjugation. Importantly, red-shifted azoswitches that can be addressed with visible light were easily functionalized and challenging unsymmetrical conjugates were prepared in good yields via sequential or one pot procedures. In addition, we took advantage of the presence of the sulfide bridge to tune both photochromic and thermal relaxation properties of the core azobenzene via sulfur oxidation. Based on our photochemical investigations, we finally demonstrated orthogonal three-state photoswitching in mixtures containing two distinct azobenzene thioglycosides.
Organocatalytic synthesis of vinylene carbonates
Authors: Onida Killian , Haddleton Alice J. , Norsic Sébastien , Boisson Christophe , D'Agosto Franck , Duguet Nicolas
Published: February 2022

The organocatalytic synthesis of vinylene carbonates from benzoins and acyloins was studied using diphenyl carbonate as a carbonyl source. A range of N-Heterocyclic Carbene (NHC) precursors were screened and it was found that imidazolium salts were the most active for this transformation. The reaction occurs at 90°C under solvent-free conditions. A wide range of vinylene carbonates (symmetrical and unsymmetrical, aromatic or aliphatic), including some derived from natural products, were prepared with 20-99% isolated yields (24 examples). The reaction was also developed using thermomorphic polyethylene-supported organocatalysts as recoverable and recyclable species. The use of such species facilitates the workup and allows the synthesis of vinylene carbonates on the preparative scale (> 30 g after 5 runs).