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65f24b85e9ebbb4db9a7b432 | 10.26434/chemrxiv-2024-bcg2r | Combined Machine Learning and Molecular Dynamics Reveal Two States of Hydration of a Single Functional Group of Cationic Polymeric Brushes | The state of hydration of a macromolecular system regulates a plethora of different properties of such a system. In this article, we develop a novel machine learning (ML) approach, based on the unsupervised clustering algorithm, for probing the hydration behavior of the {N(CH3)3}+ functional group of the PMETAC [Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride] polyelectrolyte (PE) brush system. The PE brushes and the brush-supported water molecules and counterions (chloride ions) are first described using all-atom molecular dynamics (MD) simulations. The simulation data is subsequently used in our ML framework to identify that (1) the {N(CH3)3}+ functional groups of the PMETAC brushes have two distinct hydration states with one state (state 1) being characterized by less structured water molecules and the other state (state 2) being characterized by more structured water molecules and (2) an enhancement in the brush grafting density leads to the progressive dissapparenace of state 2. An increase in the grafting density increases the number of chloride counterions in a given volume around the {N(CH3)3}+ functional group and increases the number of shared water molecules between the {N(CH3)3}+ and Cl-. The chloride counterions are associated with a hydration layer with much less structured water molecules. Therefore, with an increase in the grafting density, an increase in the percentage of shared water molecules leads to the prevalence of the hydration state [of the {N(CH3)3}+ moiety] with less structured water molecules. Finally, we explain how the present findings are commensurate with two key previous related results, namely a significantly large chloride ion mobility inside the PMETAC brush layer and the {N(CH3)3}+-Cl- average distance remaining independent of the PMETAC brush grafting density. We anticipate that the combined ML-MD-simulation approach proposed in this study can be adapted to probe other soft matter systems to reveal new insights of the underlying mechanisms of emergent phenomenon. | Raashiq Ishraaq; Tanmay Sarkar Akash; Siddhartha Das | Materials Science; Polyelectrolytes - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f24b85e9ebbb4db9a7b432/original/combined-machine-learning-and-molecular-dynamics-reveal-two-states-of-hydration-of-a-single-functional-group-of-cationic-polymeric-brushes.pdf |
63317c0efee74e6c544af272 | 10.26434/chemrxiv-2022-8mc2h-v2 | A multiconfigurational approach to the electronic structure of electro-generated species of the Re2(μ- Ph2PCH2PPh2)(S2CNEt2)4 complex | The nature of Re-Re bonding in Re2(µ-Ph2PCH2PPh2)(S2CNEt2)4 complex, including its neutral (10) and two oxidized (1+ and 12+) species, was explored utilizing state-of-the-art quantum chemical methodologies within density functional theory (DFT) and complete active space self-consistent field (CASSCF). Our results show that the ground state electron configuration of the 10 is σ^2 π^4 δ^2 δ^(*2) with an effective bond order (EBO) of 2.73 computed with CASSCF. The oxidation discloses an electron removal from a metal-based orbital, giving 1+ and 12+ with an EBO of 2.71 and 2.64, respectively. The relative similarity in EBO values among neutral and oxidized species suggests that the oxidation processes have almost no effect on the Re-Re bond strength even though electrons removal from metal-based orbitals because the electrons that occupied the δ components of Re-Re bonds in 1+ and 12+ localized on the two Re ions, thus, they were excluded from EBO estimation. | Mohammed Obies | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bonding; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63317c0efee74e6c544af272/original/a-multiconfigurational-approach-to-the-electronic-structure-of-electro-generated-species-of-the-re2-ph2pch2p-ph2-s2cn-et2-4-complex.pdf |
60c7569b0f50db3a793980ee | 10.26434/chemrxiv.14270012.v1 | Generalizing the Chiral Self-Assembly of Spheres and Tetrahedra to Non-Spherical and Polydisperse Molecules in (C70)x(C60)(1-x)(SnI4)2 | We describe the spontaneous chiral self-assembly of C<sub>70</sub> with SnI<sub>4</sub> as well as a mixture of C<sub>60</sub> and C<sub>70</sub> with SnI<sub>4</sub>. Macroscopic single crystals with the formula (C<sub>70</sub>)<sub>x</sub>(C<sub>60</sub>)<sub>1-x</sub>(SnI<sub>4</sub>)<sub>2</sub> (x = 0-1) are reported. C<sub>60</sub>, which is spherical, and C<sub>70</sub>, which is ellipsoidal, form a solid solution in these crystals, and the cubic lattice parameter of the chiral phase linearly increases as x grows from 0 to 1 in accordance with Vegard’s law. Our results demonstrate that nonspherical particles and polydispersity are not an impediment to the growth of chiral crystals from high-symmetry achiral precursors, providing a route to assemble achiral particles including colloidal nanocrystals and engineered nanostructures into chiral materials without the need to use external templates.<br /> | Daniel B. Straus; Robert J. Cava | Stereochemistry; Carbon-based Materials; Nanostructured Materials - Nanoscience; Self-Assembly; Structure; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7569b0f50db3a793980ee/original/generalizing-the-chiral-self-assembly-of-spheres-and-tetrahedra-to-non-spherical-and-polydisperse-molecules-in-c70-x-c60-1-x-sn-i4-2.pdf |
6630fda4418a5379b01a17bd | 10.26434/chemrxiv-2024-jqz3r | An atomistic picture on build-up and degradation reactions in area-selective atomic layer deposition with a small molecule inhibitor | We investigate the blocking layer formation of the trimethoxypropylsilane small molecule inhibi-tor (SMI), its blocking mechanisms, and all relevant blocking layer disintegration reactions on SiO2 in the area-selective atomic layer deposition of Al2O3 with density functional theory-based methods. The choice of amorphous silica (a-SiO2) surface models proves essential to obtain the correct SMI chemistry. We demonstrate that complete blocking of reactive sites is possible here and deduce an upper SMI density limit of the resulting blocking layer which is limited by Pauli repulsion. The SMI adsorption process can nevertheless leave unreacted silanol groups, which could be remedied by using a second monodentate SMI. The SMI layer is neither inert against common aluminum precursors nor the co-reactant water as our comprehensive analysis of the var-ious blocking layer disintegration reactions for different SMI layer densities shows. We report a new blocking mechanism of the SMI layer and propose to differentiate what is discussed as the ‘steric blocking’ effect into the known ‘adsorption prevention’ and the newly found ‘reactivity reduction’ effects. For trimethylaluminum (TMA) an additional favorable SMI layer decomposi-tion mechanism is found compared to the bulkier triethylaluminum (TEA) which could explain the lower selectivity of TMA found experimentally. Our computational work offers some princi-ples and ideas for future experiments to improve selectivity in AS-ALD processes. | Paul Philipp Wellmann; Fabian Pieck; Ralf Tonner-Zech | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630fda4418a5379b01a17bd/original/an-atomistic-picture-on-build-up-and-degradation-reactions-in-area-selective-atomic-layer-deposition-with-a-small-molecule-inhibitor.pdf |
6609326c9138d23161ceac90 | 10.26434/chemrxiv-2024-67z5l | A Bioinspired Non-heme FeIII−(O22−)−CuII Complex with a St = 1 Ground State | Cytochrome c oxidase (CcO) is a heme−copper oxidase (HCO) that catalyzes the natural reduction of oxygen to water. A pro-found understanding of some of the elementary steps leading to the intricate 4e−/4H+ reduction of O2 is presently lacking. A St = 1 FeIII−(O22−)−CuII (IP) intermediate is proposed to reduce the overpotentials associated with the reductive O−O bond rupture by allowing electron transfer from a tyrosine moiety without the necessity of any spin-surface crossing. Direct evidence of the in-volvement of IP in the HCO catalytic cycle is, however, missing. A number of heme-copper peroxido complexes have been pre-pared as synthetic models of IP; but all of them possess the catalytically non-relevant St = 0 ground state resulting from antiferro-magnetic coupling between the S = 1/2 FeIII and CuII centers. In a complete non-heme approach, we now report the spectroscopic characterization and reactivity of the FeIII−(O22−)−CuII intermediates 1 and 2, which differ only by a single −CH3 versus −H sub-stituent on the central amine of the tridentate ligands binding to copper. Complex 1 with an end-on peroxido core, and ferromag-netically (St=1) coupled FeIII and CuII centers performs H-bonding mediated O−O bond cleavage in presence of phenol to generate oxoiron(IV), copper(II) and PhO•. In contrast, the side-on peroxide complex 2, with a St = 0 ground-state is unreactive towards phenol. Thus, the implications for spin topology contributions to O−O bond cleavage, as proposed for the heme FeIII−(O22−)−CuII intermediate in CcO, can be extended to non-heme chemistry. | Dustin Kass; Thomas Lohmiller; Sagi Katz; Stefan Mebs; Michael Haumann; Ricardo Garcia-Serres; Holger Dau; Peter Hildebrandt; Kallol Ray | Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Small Molecule Activation (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2024-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6609326c9138d23161ceac90/original/a-bioinspired-non-heme-fe-iii-o22-cu-ii-complex-with-a-st-1-ground-state.pdf |
6763965381d2151a022c8998 | 10.26434/chemrxiv-2024-xq474 | Machine-learning-guided design of electroanalytical pulse waveforms | Voltammetry is widely used to detect and quantify oxidizable or reducible species in complex environments. The neurotransmitter serotonin epitomizes an analyte that is challenging to detect in situ due to low concentrations and co-existing similarly structured analytes and interferents. We developed rapid-pulse voltammetry for brain neurotransmitter monitoring due to the high information content elicited from voltage pulses. Generally, the design of voltammetry waveforms remains challenging due to prohibitively large combinatorial search spaces and a lack of design principles. Here, we illustrate how Bayesian optimization can be used to hone searches for optimized rapid pulse waveforms. Our machine-learning-guided workflow (SeroOpt) outperformed random and human-guided waveform designs and is tunable a priori to enable selective analyte detection. We interpreted the black box optimizer and found that the logic of machine-learning-guided waveform design reflected domain knowledge. Our approach is straightforward and generalizable for all single and multi-analyte problems requiring optimized electrochemical waveform solutions. Overall, SeroOpt enables data-driven exploration of the waveform design space and a new paradigm in electroanalytical method development. | Cameron Movassaghi; Katie Perrotta; Maya Curry; Audrey Nashner; Katherine Nguyen; Mila Wesely; Miguel Alcañiz; Chong Liu; Aaron Meyer; Anne Andrews | Theoretical and Computational Chemistry; Analytical Chemistry; Chemoinformatics; Electrochemical Analysis; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6763965381d2151a022c8998/original/machine-learning-guided-design-of-electroanalytical-pulse-waveforms.pdf |
6113b404711750ab21e7115d | 10.26434/chemrxiv-2021-97fr1 | The Spectral Fingerprint of Excited-State Energy Transfer in Dendrimers through Polarization-Sensitive Transient-Absorption Pump-Probe Signals: On-the-Fly Nonadiabatic Dynamics Simulations | The time-resolved polarization-sensitive transient-absorption (TA) pump-probe (PP) spectra are simulated using on-the-fly surface-hopping nonadiabatic dynamics and the doorway-window (DW) representation of nonlinear spectroscopy. A typical dendrimer model system composed of two linear phenylene ethynylene units (2-ring, 3-ring) is taken as an example. The fewest switches trajectory surface hopping algorithm along with the TDDFT method is adopted in the nonadiabatic dynamics simulations. The ground-state bleach (GSB), stimulated emission (SE), excited-state absorption (ESA) contributions as well as the total TA PP signals are obtained and carefully analyzed. The correlations between these signals and the coupled nuclear-electronic dynamics are established. It is shown that intramolecular excited-state energy transfer from the 2-ring unit to the 3-ring unit can be conveniently monitored and accurately identified by employing pump and probe pulses with different polarizations. Our on-the-fly nonadiabatic simulation results demonstrate that time-resolved polarization-sensitive TA PP signals provide a powerful tool for the elucidation of excited-state energy transfer pathways, notably in molecular systems possessing several optically-bright nonadiabatically-coupled electronic states with different orientations of transition dipole moments. | Deping Hu; Jiawei Peng; Lipeng Chen; Maxim Gelin; Zhenggang Lan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6113b404711750ab21e7115d/original/the-spectral-fingerprint-of-excited-state-energy-transfer-in-dendrimers-through-polarization-sensitive-transient-absorption-pump-probe-signals-on-the-fly-nonadiabatic-dynamics-simulations.pdf |
643f9bcf83fa35f8f6e44137 | 10.26434/chemrxiv-2023-d1s8w | Lowering the energetic landscape for negative thermal expansion in 3DL-MOFs | Tuning the coefficient of thermal expansion (CTE) of functional materials is paramount for their practical implementation. The multicomponent nature of metal-organic frameworks (MOFs) offers an opportunity to finely adjust negative thermal ex-pansion (NTE) properties by varying the metal ions and linkers used. We describe a new strategy to adjust NTE by using organic linkers that include additional rotational degrees of freedom. Specifically, we employ cubane-1,4-dicarboxylate and bicyclo[1.1.1]pentate-1,3-dicarboxylate to form the MOFs CUB-5 and 3DL-MOF-1, respectively, where each linker has low torsional energy barriers. The core of these non-conjugated linkers is decou-pled from the carboxylate functionalities, which frees the relative movement of these components. This results in enhanced NTE compared to the analogous, conjugated system; VT-PXRD results were used to calculate the CTE for 3DL-MOF-1 (αL = −13.9(2) × 10−6 K−1), and CUB-5 (αL = −14.7(3) × 10−6 K−1), which is greater than the NTE of MOF-5 (αL = −13.1(1) × 10−6 K−1). These results identify a new route to enhanced NTE behaviors in IRMOF materials, influenced by low energy molecular torsion of the linker. | Lauren Macreadie; Jack Evans; Cameron Kepert; Celia Chen; Helen Maynard-Casely; Samuel Duyker; Ravichandar Babarao | Inorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643f9bcf83fa35f8f6e44137/original/lowering-the-energetic-landscape-for-negative-thermal-expansion-in-3dl-mo-fs.pdf |
66aef7afc9c6a5c07af5787f | 10.26434/chemrxiv-2024-gfqt2 | A kinetic trapping approach for facile access to 3FaxNeu5Ac and a photo-crosslinkable sialyltransferase probe | Sialic acid (Neu5Ac) is installed onto glycoconjugates by sialyltransferases (STs) using cytidine monophosphate-Neu5Ac (CMP-B-D-Neu5Ac) as their donor. The only class of cell-active ST inhibitors are those based on a 3FaxNeu5Ac scaffold, which is metabolically converted into CMP-3FaxNeu5Ac within cells. It is essential for the fluorine to be axial, yet stereoselective installation of fluorine in this specific orientation is challenging. Sialic acid aldolase can convert 3-fluoropyruvate and 2-acetamido-2-deoxy-D-mannopyranose (ManNAc) to 3FNeu5Ac but stereocontrol of the fluorine in the product has not been possible. We hypothesized that the 3Fax kinetic product of a sialic acid aldolase reaction could be trapped by coupling with CMP-sialic acid synthetase, to yield CMP-3FaxNeu5Ac. Here, we report that highly active CMP-sialic acid synthetase and short reaction times produces exclusively CMP-3FaxNeu5Ac. Removal of CMP from CMP-3FaxNeu5Ac, under acidic conditions unexpectedly led to 3-fluoro-B-D-Neu5Ac 2-phosphate (3FaxNeu5Ac-2P). Alkaline phosphatase enabled the successful conversion of 3FaxNeu5Ac-2P to 3FaxNeu5Ac, enabling the stereochemically-controlled access to 3FaxNeu5Ac, which is effective in lowering the sialoglycan ligands for Siglecs on cells. Moreover, our kinetic trapping approach could be used to access CMP-3FaxNeu5Ac with modifications at the C5, C9, or both positions, which enabled the chemoenzymatic synthesis of a photo-crosslinkable version of CMP-3FaxNeu5Ac that selectively photo-crosslinked to ST6Gal1 over two other sialyltransferases. | Dhanraj Kumawat; Taylor E. Gray; Cole R. Garnier; Duong T. Bui; Zhixiong Li; Zeinab Jame-Chenarboo; Jeremy Jerasi; Warren O. Wong; John S. Klassen; Chantelle J. Capicciotti; Matthew S. Macauley | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aef7afc9c6a5c07af5787f/original/a-kinetic-trapping-approach-for-facile-access-to-3fax-neu5ac-and-a-photo-crosslinkable-sialyltransferase-probe.pdf |
60c73f9dbb8c1a9b7d3d9bbd | 10.26434/chemrxiv.7433969.v1 | Highly Adjustable 3D Nano-Architectures and Chemistries via Assembled 1D Biological Templates | Porous
metal nanofoams have made significant contributions to a diverse set of
technologies from separation and filtration to aerospace. Nonetheless, finer control over nano and
microscale features must be gained to reach the full potential of these
materials in energy storage, catalytic, and sensing applications. As biologics naturally occur and assemble
into nano and micro architectures, templating on assembled biological materials
enables nanoscale architectural control without the limited chemical scope or
specialized equipment inherent to alternative synthetic techniques. Here, we rationally assemble 1D biological
templates into scalable, 3D structures to fabricate metal nanofoams with a
variety of genetically programmable architectures and material
chemistries. We demonstrate that
nanofoam architecture can be modulated by manipulating viral assembly,
specifically by editing the viral surface coat protein, as well as altering
templating density. These architectures
were retained over a broad range of compositions including monometallic and
bi-metallic combinations of noble and transition metals of copper, nickel,
cobalt, and gold. Phosphorous and boron
incorporation was also explored. In addition to increasing the surface area
over a factor of 50, as compared to the nanofoam’s geometric footprint, this
process also resulted in a decreased average crystal size and altered phase
composition as compared to non-templated controls. Finally, templated hydrogels
were deposited on the centimeter scale into an array of substrates as well as
free standing foams, demonstrating the scalability and flexibility of this
synthetic method towards device integration.
As such, we anticipate that this method will provide a platform to
better study the synergistic and de-coupled effects between nano-structure and
composition for a variety of applications including energy storage, catalysis,
and sensing. | Jacqueline F. Ohmura; F. John Burpo; Chamille Lescott; Alan Ransil; Youngmin Yoon; William Records; Angela Belcher | Alloys; Catalysts; Core-Shell Materials; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Nanofabrication; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9dbb8c1a9b7d3d9bbd/original/highly-adjustable-3d-nano-architectures-and-chemistries-via-assembled-1d-biological-templates.pdf |
6701f37151558a15ef381662 | 10.26434/chemrxiv-2024-qrwxd | Superacid-Promoted Synthesis of Imidazole-Containing Spirocycles | A series of imidazole-containing fluorenyl spirocycles have been prepared from 9-fluorenol derivatives. Highly acidic media and superacid media are shown to promote spirocyclization to this new class of spirocycles. A mechanism is proposed involving fluorenyl cationic species, including dicationic ions. Electrochemical and optical experiments were conducted for the calculation of frontier molecular orbital energy levels. Fluorescence spectroscopy showed that select conjugated fluorophores were intensely emissive in the near-UV visible (blue-purple) spectrum range. | Jeffrey Ferreira; Douglas Klumpp | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6701f37151558a15ef381662/original/superacid-promoted-synthesis-of-imidazole-containing-spirocycles.pdf |
667a3ef401103d79c50f7061 | 10.26434/chemrxiv-2024-b6j96 | THREE COMPOSITIONS OF HIGH-ENTROPY MELTS OF LITHIUM, SODIUM AND POTASSIUM FLUORIDES AND CHLORIDES AS PROMISING COOLANTS FOR MOLTEN SALT REACTORS | Suggestions are made for potentially promising solvent melts for molten salt reactors from a mixture of six lithium, sodium, and potassium fluoride and chloride salts having high mixing entropy. These compositions, containing less lithium salts, should have higher thermodynamic stability than FLiNaK or FLiBe because of their high entropy. Chemical formula of maximum high-entropy solution may result from mixing the variety of alkali halides like MX (M=Li, Na, K and X=F, Cl) taken in an equimolar ratio. The configurational part of the mixing entropy of such a mixture equal to 1/2Rln24 (1.59R), which is very close to Rln5. At the same time, this is much larger than for standard compositions like FLiNaK-eutectic (0.83R). On the basis of the experimental phase diagram for the quasi-ternary salt mixture (LiF)1/2(LiCl)1/2 - (NaF)1/2(NaCl)1/2 - (KF)1/2(KCl)1/2 two more high-entropy compositions with reduced lithium content can be considered, namely, Li(0.1)Na(0.2)K(0.2)F(0.25)Cl(0.25) and Li(0.08)Na(0.1625)K(0.2575)F(0.25)Cl(0.25) , having a liquidus temperature of 606 and 630 Celsius. Their configurational entropy is equal to 1.57R and 1.54R, correspondingly. | Nikolay Tkachev | Physical Chemistry; Energy; Power; Solution Chemistry; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667a3ef401103d79c50f7061/original/three-compositions-of-high-entropy-melts-of-lithium-sodium-and-potassium-fluorides-and-chlorides-as-promising-coolants-for-molten-salt-reactors.pdf |
61bbd1e9d6dcc27fcb3b5326 | 10.26434/chemrxiv-2021-v2x7j | Analysis of Preferred Mechanisms of CO Oxidation with Atomically Dispersed Pt1/TiO2 Using the Energetic Span Model | This work examines the mechanisms of low-temperature CO oxidation with atomically dispersed Pt on rutile TiO2 (110) using density functional theory and the energetic span model (ESM). Of the 13 distinct pathways spanning Eley-Rideal (ER), termolecular ER (TER), Langmuir-Hinshelwood(LH), Mars-Van Krevelen (MvK) mechanisms as well as their combinations, TER with CO-assisted CO2 desorption yields the highest turnover frequency (TOF). However, this pathway is ruled out because Pt is dynamically unstable in an intermediate state in the TER cycle, determined in a prior ab initio molecular dynamics study by our group. We instead find that a previously neglected pathway – the ER mechanism – is the most plausible CO oxidation route based on agreement with experimental TOFs and turnover-determining states. The preferred mechanism is sensitive to temperature, with LH becoming more favorable than ER and TER above 750 K. By comparing TOFs for Pt1/TiO2 with prior mechanistic studies of various oxide-supported atomically dispersed catalysts in the literature, we also attempt to identify the most viable metal and support materials for CO oxidation. | Selin Bac; Shaama Mallikarjun Sharada | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bbd1e9d6dcc27fcb3b5326/original/analysis-of-preferred-mechanisms-of-co-oxidation-with-atomically-dispersed-pt1-ti-o2-using-the-energetic-span-model.pdf |
60c758f9bb8c1a1e293dcb35 | 10.26434/chemrxiv.14616636.v1 | Direction-Dependent Properties in Inverted Carbon Nitride Colloidal Glasses with Gradient Porosity | It is well known that the step from a dense packing of colloidal beads to the inverted systems was important for the optimization of photonic crystal properties. Inverted opals made of high-refractive index semiconductors have attracted great attention due to their supreme optical features such as the occurrence of a photonic band-gap and because of an astonishing behavior in photocatalysis or for photovoltaics caused by so-called slow photons. It is much less known that photonic glasses, despite being disordered, exhibit unique optical properties too like random lasing or high-contrast structural colors. In analogy to opals and inverted opals, one can expect that inverted colloidal glasses may lead to an amplification of photonic properties as well or even to the emergence of unexpected features. An inverted photonic glass is characterized by a dense packing of monodisperse voids with colloidal dimensions without any long-range order. The preparation of inverse photonic glasses has rarely been reported by now and cases for materials composed of a semiconductor as a pore-wall material are unknown. The synthesis of porous carbon nitride (C<sub>3</sub>N<sub>4</sub>) with inverted colloidal glass structure is demonstrated here using a template approach. The formation of the template with glass-like order is achieved by analytical ultracentrifugation (AUZ) of size-selected silica colloids, followed by infiltration of a precursor sol, transformation to carbon nitride and the final removal of the template. The use of AUZ is particularly important because it even allows to use a mixture of differently sized template particles, which are gradually fractionated. Monoliths with optimized morphological features exhibiting a gradient porosity and highly accessible pores are obtained. The result are materials with a graded structure. What makes such functional gradient material interesting is, a dependence of the optical features on the position can be expected. In addition, the method presented here allows to synthesize materials with adjustable composition ranging from carbon over nitrogen-doped carbon to C<sub>3</sub>N<sub>4</sub> with either graphitic or polymeric structure. Therefore, the optical band gap is highly adjustable and tunable with regards to the photonic properties, as confirmed by optical absorption and photoluminescence measurements. | Jochen Bahner; Lukas Dobler; Marvin Frisch; Lars Vogelsang; Helmut Cölfen; Sebastian Polarz | Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758f9bb8c1a1e293dcb35/original/direction-dependent-properties-in-inverted-carbon-nitride-colloidal-glasses-with-gradient-porosity.pdf |
672a6cb97be152b1d0162331 | 10.26434/chemrxiv-2024-mjnc4 | Revealing polymerisation defects and formation mechanisms in aldol condensation for conjugated polymers via high-resolution molecular imaging | Aldol condensation is a crucial synthetic reaction in organic chemistry, particularly valued for fabricating conjugated polymers without the use of metals or toxic organostannanes. However, due to the lack of reliable and precise analytical methods, no direct evidence of the microstructure and sequence of synthesised polymers has been obtained, limiting control over their structure and performance. Here, by combining electrospray deposition and scanning tunnelling microscopy (ESD-STM), we analyse sub-monomer resolution images of four different n-type polymers produced via aldol condensation, revealing unexpected defects in both the sequence of (co)monomers and their coupling. These defects, observed across all polymer samples, indicate alternative side reaction pathways inherent to aldol condensation, affecting both polymerisation and small-molecule reactions. Our findings not only uncover the reaction mechanism responsible for these defects but also bring new insights for the design of more effective synthetic pathways to minimise structural defects in conjugated polymers. | Xiaocui Wu; Stefania Moro; Adam Marks; Maryam Alsufyani; Zidi Yu; Luís Perdigão; Xingxing Chen; Alexander Luci; Callum Crockford; Simon Spencer; David Fox; Jian Pei; Iain McCulloch; Giovanni Costantini | Physical Chemistry; Polymer Science; Nanoscience; Conducting polymers; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a6cb97be152b1d0162331/original/revealing-polymerisation-defects-and-formation-mechanisms-in-aldol-condensation-for-conjugated-polymers-via-high-resolution-molecular-imaging.pdf |
60c742f04c8919ad76ad2578 | 10.26434/chemrxiv.8858549.v1 | Multiple Anti-Kasha Emissions in Transition Metal Complexes | <p>In this manuscript we present a <i>from-first-principles</i>evidence that several higher-lying excited states are responsible for the emission spectrum of [M(CO)<sub>4</sub>(bpy)] (M = Cr, Mo, W and bpy=2,2’-bipyrimidine) complexes. These results highlight the violation of Kasha’s rule, which states that after irradiation molecules emit light with appreciable yield only from its lowest energy excited state. Furthermore, in [W(CO)<sub>4</sub>(bpy)] and [Mo(CO)<sub>4</sub>(bpy)], the breaking of Kasha’s rule is two-fold, because at least two different excited states besides T<sub>1</sub>are involved in emission. To our knowledge, these are the first transition metal complexes unambiguously demonstrated to display simultaneous equilibrated and non-equilibrated anti-Kasha emissions. This work also highlights the complexity of the emissive processes of tetracarbonyl-diimine transition metal complexes, which are controlled<i>via</i>a subtle interplay of electronic and geometrical effects along the excited state deactivation dynamics.</p> | Milena Röhrs; Daniel Escudero | Transition Metal Complexes (Inorg.); Theory - Computational; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f04c8919ad76ad2578/original/multiple-anti-kasha-emissions-in-transition-metal-complexes.pdf |
652cf97945aaa5fdbb1c180b | 10.26434/chemrxiv-2023-t48bf | Cascade exotherms for rapidly producing hybrid non-isocyanate polyurethane foams from room temperature formulations | For decades, self-blown polyurethane foams - found in an impressive range of materials - are produced by the toxic isocyanate chemistry and are difficult to recycle. Producing them in existing production plants by a rapid isocyanate-free self-blowing process from room temperature (RT) formulations is a long-lasting challenge. The recent water-induced self-blowing of non-isocyanate polyurethane (NIPU) formulations composed of a CO2-based tri-cyclic carbonate, diamine, water and a catalyst, successfully addressed the isocyanate issue, however failed to provide foams at RT. Herein, we elaborate a practical solution to empower the NIPU foam formation in record timeframes from RT formulations. We generate cascade exotherms by the addition of a highly reactive triamine and an epoxide to the formulation of the water-induced self-foaming process. These exotherms, combined to a fast crosslinking imparted by the triamine and epoxide, rapidly raise the temperature to the foaming threshold and deliver hybrid NIPU foams in 5 minutes with KOH as catalyst. Careful selection of the monomers enables producing foams with a wide range of properties, as well as with an unprecedented high bio-based content up to 90 wt%. Moreover, foams can be upcycled into polymer films by hot-pressing, offering them a facile reuse scenario. This robust cheap process opens huge perspectives for greener foams of high bio-based contents, expectedly responding to the sustainability demands of the foam sector. It is potentially compatible to the retrofitting of industrial foaming infrastructures, which is of paramount importance to accommodate existing foam production plants and address the huge foam market demands. | Maxime Bourguignon; Bruno Grignard; Christophe Detrembleur | Polymer Science; Organic Polymers; Polymerization (Polymers); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652cf97945aaa5fdbb1c180b/original/cascade-exotherms-for-rapidly-producing-hybrid-non-isocyanate-polyurethane-foams-from-room-temperature-formulations.pdf |
652eb61345aaa5fdbb3573c2 | 10.26434/chemrxiv-2023-66jqr-v2 | Classification of Hemilabile Ligands Using Machine
Learning | Discovery of hemilabile ligands that optimally balance reactivity and stability is
important for identifying novel catalyst structures. We design a workflow for identifying ligands
in the Cambridge Structural Database (CSD) that have been crystalized with distinct denticities
and are thus identifiable as hemilabile ligands. To overcome the difficulty of identifying negative
example, non-hemilabile ligands in our data set, we implement a semi-supervised learning
approach using a label-spreading algorithm together with a set of heuristic rules based on ligand
frequency of appearance. We show that a heuristic based on coordinating atom identity alone is
not sufficient to identify whether a ligand is hemilabile and our trained machine-learning
classification models are instead needed to predict whether a bi-, tri-, or tetradentate ligand is
hemilabile with high accuracy and precision. We gain deeper insight into the factors that govern
ligand hemilability by conducting feature importance analysis on our models, finding that the
second, third, and fourth coordination spheres all play an important role in ligand hemilability. | Ilia Kevlishvili; Chenru Duan; Heather Kulik | Theoretical and Computational Chemistry; Catalysis; Machine Learning; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652eb61345aaa5fdbb3573c2/original/classification-of-hemilabile-ligands-using-machine-learning.pdf |
655b54632c3c11ed71c59df0 | 10.26434/chemrxiv-2023-jx61g | Organocatalyzed Enantio- and Diastereoselective Domino [3+2]-Dipolar Cycloaddition: Synthesis of Chiral Pyrrorlo-thiazine-2-carbaldehydes and Dihydropyrrole-3-carbaldehydes | 1,3-Dipolar cycloaddition of azomethine ylide and dipolarophile is an efficient method to construct N, S heterocycles such as thiazoles, 1,4-thiazines, and their chiral polyhydro derivatives. Herein, we report a proline-derived organocatalytic enantioselective synthesis of pyrrolo[1,2-d][1,4]thiazine-2-carbaldehydes using domino 1,3-dipolar cycloaddition/rearrangement sequence. This domino process yields fluorescent emissive, highly enantioenriched chiral molecules with three contiguous stereogenic centers, having one chiral quaternary center in a single step, with excellent yield, enantio- and diastereoselectivity. This strategy was extended to the stereoselective one-pot synthesis of novel chiral tetrasubstituted dihydropyrrole-3-carbaldehydes via domino 1,3-dipolar cycloaddition/rearrangement, followed by S-alkylation/base promoted ring-opening. A DFT study showed that the formation of hydropyrrolo-thiazole intermediate is the rate-determining step (TS7 E‡ = -28.49 kcal/mol) which is responsible for the formation of pyrrolo[1,2-d][1,4]thiazine-2-carbaldehydes. Due to high energy, the intermediate hydropyrrolo-thiazole’s ring opens to yield thiolate anion, followed by C-N-bond rotation, intramolecular 1,2-addition of ketone and spontaneous protonation provides pyrrolo[1,2-d][1,4]thiazine-2-carbaldehydes. An in-silico study showed that the pyrrolo-thiazine-2-carbaldehyde scaffolds have substantial anticancer activity with respect to B-Raf kinase, a non-small cell line lung cancer. | Solai Pandidurai; Venkata Surya Kumar Choutipalli; Venkatesan Subramanian; Govindasamy Sekar | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655b54632c3c11ed71c59df0/original/organocatalyzed-enantio-and-diastereoselective-domino-3-2-dipolar-cycloaddition-synthesis-of-chiral-pyrrorlo-thiazine-2-carbaldehydes-and-dihydropyrrole-3-carbaldehydes.pdf |
678ea0f9fa469535b9da6ed3 | 10.26434/chemrxiv-2025-5jkhj | Unlocking A New Biological Interface of Chiral Supramolecular Helical Polymers | Supramolecular helical polymers and helicates are two well-known and structurally different families of materials that share the same chiral axial motif, the helix. In this work, we describe how it is possible to design a molecule capable of folding in water into either of these two supramolecular entities. To do that we prepared a C3 symmetric benzene-1,3,5-triyltrimethanamine (BTMA) core conjugated to three peptide sequences, i.e. H-Arg-βAla-Bpy-βAla-Bpy-NH2 (BTMA-1). This molecule comprises all the structural requirements to self-assembly in water either into a chiral supramolecular helical polymer or into a chiral discrete helicate in the absence/presence of CoII ions in the aqueous media. We demonstrated that the discrete CoII peptide helicate folded can recognize DNA three-way junctions with high affinity and selectivity against canonical DNA and, moreover, that this recognition process can be operated from both the preformed discrete chiral peptide helicate and the chiral supramolecular helical polymer. Finally, we also proved that the labile CoII peptide helicate can be oxidized in situ in water to generate the corresponding kinetically inert CoIII derivative, which also possess selective 3WJ recognition capabilities. This study opens a new scenario in the biological applications of chiral supramolecular helical polymers, demonstrating that can be maintained inactively dispersed in water with time and further transformed into discrete bioactive molecules by an external stimulus. | Ana Alcalde Ordóñez; Axel Sarmiento Fuentes; Jacobo Gómez González; Manuel Núñez Martínez; Manuel Fernández Míguez; Rafael Rodríguez Riego; Félix Freire Iribarne ; M. Eugenio Vázquez Sentís; Miguel Vázquez López | Biological and Medicinal Chemistry; Materials Science; Biological Materials; Optical Materials; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ea0f9fa469535b9da6ed3/original/unlocking-a-new-biological-interface-of-chiral-supramolecular-helical-polymers.pdf |
6724fb5b7be152b1d0ae66f8 | 10.26434/chemrxiv-2024-37v2j | Spectro: A multi-modal approach for molecule elucidation using IR and NMR data | Molecular structure elucidation is a crucial but fundamentally challenging step in the characterization of materials given the large number of possible structures. Here, we introduce Spectro, an innovative multi-modal approach for molecular elucidation that combines $\CNMR$ and $\HNMR$ NMR data with IR. Spectro translates the embedded representations of the spectra into molecular structures using the SELFIES notation. We employed a vision model for the embedded representation of the IR data, which was pretrained to detect relevant functional group peaks in the IR spectra achieving an F1 score of 91\%. For NMR data, we utilized LLM2Vec, treating the NMR spectra as text. This integration of multiple spectroscopic techniques allows Spectro to achieve an overall test accuracy of 93\% when trained jointly with the vision model for the IR spectra, and 82\% when trained with fixed embeddings. Our approach demonstrates the potential of multi-modal learning in tackling complex molecular characterization tasks. | Edwin Chacko; Rudra Sondhi; Arnav Praveen; Kylie L. Luska; Rodrigo Alejandro Vargas Hernandez | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6724fb5b7be152b1d0ae66f8/original/spectro-a-multi-modal-approach-for-molecule-elucidation-using-ir-and-nmr-data.pdf |
62183b885f1d9ad5fea6cc72 | 10.26434/chemrxiv-2022-zrnh5 | Proton Hyperpolarization Relay from Nanocrystals to Liquid Water | Dynamic nuclear polarization (DNP) using transient electron spin polarization generated by photoexcitation can improve nuclear magnetic resonance (NMR) sensitivity far beyond the thermal equilibrium limit for analysis in life science and drug discovery. However, DNP of liquid water at room temperature remains an important challenge. In previous studies, polarization has been transferred directly from the electron spins in the solid to the nuclear spins of the target, and this has been limited to near-surface solid or highly-viscous targets. Here, we propose a new method called hyperpolarization relay, in which the polarization of electron spins is transferred to proton spins in the nanocrystals and then to proton spins in bulk water by the nuclear Overhauser effect (NOE). Molecular nanocrystals doped with a polarizing agent that generates a highly-polarized photoexcited triplet were synthesized by a reprecipitation method while controlling the size of the nanocrystals. As the size of the nanocrystals decreases, the efficiency of polarization transfer from nanocrystals to water was improved due to the increase in the surface area. | Naoto Matsumoto; Koki Nishimura; Nobuo Kimizuka; Yusuke Nishiyama; Kenichiro Tateishi; Tomohiro Uesaka; Nobuhiro Yanai | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Photochemistry (Physical Chem.); Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62183b885f1d9ad5fea6cc72/original/proton-hyperpolarization-relay-from-nanocrystals-to-liquid-water.pdf |
677cd39e6dde43c908956bb4 | 10.26434/chemrxiv-2025-lkgpg | Substituted Fullerenes for Enhanced Optical Nuclear Hyperpolarization in Random Orientations | Polarized electron spins in photoexcited triplet states enable dynamic nuclear polarization (DNP) at high temperatures, leading to increased sensitivity in magnetic resonance imaging (MRI). For a practical nuclear polarization of 10%, single crystals must be precisely oriented in a magnetic field to generate electron spin resonances in a narrow field range that satisfies resonance conditions for polarization transfer. However, this is not realistic for medical applications. Substituted fullerenes as triplet polarizing agents have enabled 1H polarizations above 10%, even for random molecular orientations. They have not been used as polarizing agents for triplet-DNP because of electron spin relaxation via pseudo-rotation. Here, the spin-lattice relaxation time was significantly increased by chemical modification of two sites on C60 fullerenes. Symmetry considerations revealed fullerenes that avoided pseudo-rotations. Di-substituted fullerenes were ideal polarizing agents with sharp linewidths and long relaxation times that enabled 14.2% 1H polarization in randomly oriented orientations. Optimized polarizing agents would enable ultra-sensitive MRI medical diagnostics under mild preparation conditions. | Keita Sakamoto; Katsuki Miyokawa; Tomoyuki Hamachi; Haoxuan Zhang; Jiarui Song; Kenichiro Tateishi; Tomohiro Uesaka; Hiroshi Imahori; Yuki Kurashige; Nobuhiro Yanai | Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677cd39e6dde43c908956bb4/original/substituted-fullerenes-for-enhanced-optical-nuclear-hyperpolarization-in-random-orientations.pdf |
6411d6ebdab08ad68f2898f5 | 10.26434/chemrxiv-2023-gtvm1-v2 | Boronyl borinic esters: preparation as B2pin2/secBuLi/TFAA adducts, structural insights and reactivity in Pd-catalyzed allylic borylation | Novel class of diboron reagent boronyl borinic ester was developed that were generated as B2pin2/secBuLi/TFAA adducts. Detailed NMR with solid-state 2D NMR techniques and ESI-MS investigations were used to get structural insights of these new reagent. The new boronyl borinic esters were proved to be promising for allylic borylations of base-sensitive substrates. | Maxim Novikov; Roman Novikov; Yury Tomilov | Organometallic Chemistry; Spectroscopy (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6411d6ebdab08ad68f2898f5/original/boronyl-borinic-esters-preparation-as-b2pin2-sec-bu-li-tfaa-adducts-structural-insights-and-reactivity-in-pd-catalyzed-allylic-borylation.pdf |
66e5f22f12ff75c3a1561c3e | 10.26434/chemrxiv-2024-bhlvj | An Experimental and Modeling Study of CaCO3 Nucleation and Inhibition Under a Dynamic Oversaturation Regime with Implications for Energy Production from Subsurface Reservoirs | Energy production from subsurface reservoirs perturbs the equilibrium between fluids and the surrounding rocks. As the saturation increases, nucleation begins, forming a scale that is detrimental to production. Inhibitor addition for scale prevention is a common practice with significant economic and environmental costs. Traditional experiments to determine induction times (tind) and evaluate inhibitor efficiency are performed under constant oversaturation. Similarly, constant oversaturation is used in both the empirical and the classical nucleation theory modeling schemes used for scale prediction. Subsequently, experiments and models do not address the dynamic nature of oversaturation increase during energy production. We developed an experimental system for quantitative investigation of nucleation kinetics under a regime of dynamic oversaturation and a simple algorithm for determining tind from laser measurements. Using our system, we studied the precipitation kinetics of CaCO3 minerals at a pH of ~6.76, ionic strength of I = 1m, temperature range of 50-90 oC, and varying rates of oversaturation increase. We quantified the effect of a potent inhibitor (Polyamino Polyether Methylene Phosphonate; PAPEMP) on the tind and the forming solid phase. Finally, we developed a numerical model that explicitly accounts for the dynamic nature of oversaturation. Here, we present our experimental system, results, and modeling scheme. We show that for a given set of conditions, calcite induction occurs at a similar oversaturation, regardless of the rate at which oversaturation increases. Moreover, we show that PAPEMP retards CaCO3 nucleation at below ppm levels and that it has a temperature-dependent effect on polymorphism. Lastly, we suggest that expanding existing models such that: t_ind=f(∆SI)*f(static) Where f(ΔSI) is a function of oversaturation with time and f(static) are existing modeling schemes, adequately describe the dynamic nature of oversaturation and show a form of f(ΔSI) that provides an excellent fit with measured tind. | Amit Gilad Reiss; Xin Wang; Yuqing Ye; Amy Kan; Mason Tomson | Inorganic Chemistry; Energy; Earth, Space, and Environmental Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e5f22f12ff75c3a1561c3e/original/an-experimental-and-modeling-study-of-ca-co3-nucleation-and-inhibition-under-a-dynamic-oversaturation-regime-with-implications-for-energy-production-from-subsurface-reservoirs.pdf |
61ef17f5360c847ab9a9d075 | 10.26434/chemrxiv-2022-kmh23 | Polymorphism of boron phosphide: Theoretical and experimental assessments | Stable crystal structures of wurtzite (w-BP) and recently discovered rhombohedral (rh-BP) polymorphic modifications of boron phosphide were obtained based on crystal chemistry rationale and unconstrained geometry optimization calculations within the density functional theory (DFT), and compared with known cubic polymorph (c-BP). Both w-BP and rh-BP are mechanically (elastic constants) and dynamically (phonons) stable and exhibit thermodynamic and mechanical properties very close to those of c-BP. The electronic band structures depict semi-conducting behavior with band gap magnitudes close to 0.5 eV for cubic and rhombohedral polymorphs and 1 eV for w-BP. | Vladimir L. Solozhenko; Samir F. Matar | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ef17f5360c847ab9a9d075/original/polymorphism-of-boron-phosphide-theoretical-and-experimental-assessments.pdf |
66e40397cec5d6c142f09308 | 10.26434/chemrxiv-2024-wcxr0 | Bridged Bicyclic gamma-Sultams by Intramolecular Flow Photochemical [2+2] Cycloaddition | An elegant synthetic approach to the construction of a novel saturated heterocycle – 2-thia-3-azabicyclo[2.1.1]hexane 2,2-dioxide – was designed. The key step included intramolecular flow photochemical [2 + 2] cycloaddition of appropriately substituted dienes, in turn obtained from readily available starting materials on a multigram scale. Further synthetic transformations of the resulting bicyclic compounds enabled the preparation of numerous functionalized derivatives useful for early drug discovery programs as promising isosteres of pyrrolidine, pyrrolidone, and gamma-sultams, and also demonstrated tolerance of the title bicyclic system towards typical organic chemistry reaction conditions. | Yevhen Zaika; Illia Borodin; Heorhii Olekh; Maksym Kovalov; Oleksandr Diachenko; Volodymyr Brovarets; Bohdan Vashchenko; Oleksandr Grygorenko | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e40397cec5d6c142f09308/original/bridged-bicyclic-gamma-sultams-by-intramolecular-flow-photochemical-2-2-cycloaddition.pdf |
62e15c0acc34e5284e67e59b | 10.26434/chemrxiv-2022-8rhkf-v2 | The annual-hydrogen-yield-climatic-response ratio: evaluating the real-life performance of integrated solar water splitting devices | Integrated solar water splitting devices that produce hydrogen without the use of power inverters operate outdoors and are hence exposed to varying weather conditions. As a result, they might sometimes work at non-optimal operation points below or above the maximum power point of the photovoltaic component, which would directly translate into efficiency losses. Up until now, however, no common parameter describing and quantifying this and other real-life operating related losses (e.g. spectral mismatch) exists in the community. Therefore, the annual-hydrogen-yield-climatic-response (AHYCR) ratio is introduced as a figure of merit to evaluate the outdoor performance of integrated solar water splitting devices. This value is defined as the ratio between the real annual hydrogen yield and the theoretical yield assuming the solar-to-hydrogen device efficiency at standard conditions. This parameter is derived for an exemplary system based on state-of-the-art AlGaAs//Si dual-junction solar cells and an anion exchange membrane electrolyzer using hourly resolved climate data from a location in southern California and from reanalysis data of Antarctica. Moreover, the advantage of devices operating at low current densities over completely decoupled PV-electrolysis is discussed. This work will help to evaluate, compare and optimize the climatic response of solar water splitting devices in different climate zones. | Moritz Kölbach; Oliver Höhn; Kira Rehfeld; Manuel Finkbeiner; James Barry; Matthias M. May | Physical Chemistry; Energy; Energy Storage; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e15c0acc34e5284e67e59b/original/the-annual-hydrogen-yield-climatic-response-ratio-evaluating-the-real-life-performance-of-integrated-solar-water-splitting-devices.pdf |
617106c94c04e814a189578e | 10.26434/chemrxiv-2021-2fwxt | Atomistic simulations of dopamine diffusion dynamics on a pristine graphene surface | Carbon microelectrodes enable in vivo detection of neurotransmitters, and new electrodes are being developed to optimize the carbon surface. However, the work is mainly empirical and there have not been corresponding theoretical studies using molecular-level simulations of the diffusion and orientation of neurotransmitters near these surfaces. Here, we employ molecular dynamics simulations to investigate in atomistic detail the surface diffusion of dopamine (DA), its oxidation product dopamine-o-quinone (DOQ), and their protonated forms on the pristine basal plane of flat graphene. All DA species rapidly adsorb to the surface and remain adsorbed for the full length of the equilibrium simulations, even without a holding potential or graphene surface defects. The diffusivities of the adsorbed and the fully solvated DA are similar, and all molecular diffusion on the surface is slower than that of an adatom of comparable molecular weight. The protonated species diffuse more slowly than their corresponding neutral forms, and the oxidized species diffuse more rapidly. The underlying hexagonal graphene structure has little influence over the molecular adsorbate's lateral position. The vertical placement of the amine group on dopamine is highly dependent upon its charge, and the protonated amine prefers to be above the surface near the solvating waters. Solvation has a large effect on surface diffusivities when diffusion is compared to that in a vacuum. These are the first results of molecular dynamics simulations of dopamine diffusion at the aqueous-graphene interface, and they show that dopamine diffuses quickly on graphene surfaces, even without an applied potential. These calculations provide a basis for future simulations to predict the behavior of neurotransmitter diffusion on advanced carbon materials electrodes. | Qizhang Jia; Cheng Yang; B. Jill Venton; Kateri H. DuBay | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617106c94c04e814a189578e/original/atomistic-simulations-of-dopamine-diffusion-dynamics-on-a-pristine-graphene-surface.pdf |
60c74218bb8c1a05103da065 | 10.26434/chemrxiv.8088482.v2 | Deep Learning Model for Predicting Solvation Free Energies in Generic Organic Solvents | Prediction of aqueous solubilities or hydration free energies is an extensively studied area in machine learning applications on chemistry since water is the sole solvent in the living system. However, for non-aqueous solutions, few machine learning studies have been undertaken so far despite the fact that the solvation mechanism plays an important role in various chemical reactions. Here, we introduce a novel, machine-learning based quantitative structure-property prediction method which predicts solvation free energies for various organic solute and solvent systems. A novelty of our method involves two separate solvent and solute encoder networks that can quantify structural features of given compounds via word embedding and recurrent layers, with the attention mechanism which extracts important substructures from outputs of recurrent neural networks. As a result, the predictor network calculates solvation free energy of a given mixture using features from encoders. With results obtained from extensive calculations on 2495 solute-solvent mixtures, we demonstrate that our methodology outperforms both <i>ab initio</i> and MD solvation model in terms of estimation error for solvation energy. | Hyuntae Lim; Younjoon Jung | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Solution Chemistry | CC BY NC 4.0 | CHEMRXIV | 2019-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74218bb8c1a05103da065/original/deep-learning-model-for-predicting-solvation-free-energies-in-generic-organic-solvents.pdf |
60c74691567dfe9659ec4655 | 10.26434/chemrxiv.10282346.v2 | Chemically Interpretable Graph Interaction Network for Prediction of Pharmacokinetic Properties of Drug-like Molecules | <div>Solubility of drug molecules is related to pharmacokinetic properties such as absorption and distribution, which affects the amount of drug that is available in the body for its action. Computational or experimental evaluation of solvation free energies of drug-like molecules/solute that quantify solubilities is an arduous task and hence development of reliable computationally tractable models is sought after in drug discovery tasks in pharmaceutical industry. Here, we report a novel method based on graph neural network to predict solvation free energies. Previous studies considered only the solute for solvation free energy prediction and ignored the nature of the solvent, limiting their practical applicability. The proposed model is an end-to-end framework comprising three phases namely, message passing, interaction and prediction phases. In the first phase, message passing neural network was used to compute inter-atomic interaction within both solute and solvent molecules represented as molecular graphs. In the interaction phase, features from the preceding step is used to calculate a solute-solvent interaction map, since the solvation free energy depends on how (un)favorable the solute and solvent molecules interact with each other. The calculated interaction map that captures the solute-solvent interactions along with the features from the message passing phase is used to predict the solvation free energies in the final phase. The model predicts solvation free energies involving a large number of solvents within the limits of chemical accuracy. We also show that the interaction map captures the electronic and steric factors that govern the solubility of drug-like molecules and hence is chemically interpretable.</div> | Yashaswi Pathak; Siddhartha Laghuvarapu; Sarvesh Mehta; U. Deva Priyakumar | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74691567dfe9659ec4655/original/chemically-interpretable-graph-interaction-network-for-prediction-of-pharmacokinetic-properties-of-drug-like-molecules.pdf |
664d278e418a5379b0e8cd6f | 10.26434/chemrxiv-2024-1s25h | Enhancing High-Fidelity Neural Network Potentials through Low-Fidelity Sampling | The efficacy of neural network potentials (NNPs) critically depends on the quality of the configurational datasets used for training. Prior research using empirical potentials has shown that well-selected liquid-solid transitional configurations of a metallic system can be translated to other metallic systems. This study demonstrates that such validated configurations can be relabeled using density functional theory (DFT) calculations, thereby enhancing the development of high-fidelity NNPs. Training strategies and sampling approaches are efficiently assessed using empirical potentials and subsequently relabeled via DFT in a highly parallelized fashion for high-fidelity NNP training. Our results reveal that relying solely on energy and force for NNP training is inadequate to prevent overfitting, highlighting the necessity of incorporating stress terms into the loss functions. To optimize training involving force and stress terms, we propose employing transfer learning to fine-tune the weights, ensuring the potential surface is smooth for these quantities composed of energy derivatives. This approach markedly improves the accuracy of elastic constants derived from simulations in both empirical potential-based NNP and relabeled DFT-based NNP. Overall, this study offers significant insights into leveraging empirical potentials to expedite the development of reliable and robust NNPs at the DFT level. | Gang Seob Jung | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664d278e418a5379b0e8cd6f/original/enhancing-high-fidelity-neural-network-potentials-through-low-fidelity-sampling.pdf |
60c75208337d6ca3b1e28651 | 10.26434/chemrxiv.13242188.v1 | Theoretical Study of a Derivative of Chlorophosphine with Aliphatic and Aromatic Grignard Reagents: SN2@P or the Novel SN2@Cl Followed by SN2@C? | <p>The proposed S<sub>N</sub>2
reactions of a hindered organophosphorus reactant with aliphatic and aromatic nucleophiles
[Ye <i>et al.</i>, Org. Lett. <b>19</b>, 5384–5387 (2017)] were studied
theoretically in order to explain the observed stereochemistry of the products.
Our computations indicate that the reaction with the aliphatic nucleophile
occurs through a backside S<sub>N</sub>2@P pathway while the reaction with the
aromatic nucleophile proceeds through a novel S<sub>N</sub>2@Cl mechanism,
followed by a frontside S<sub>N</sub>2@C mechanism. To the best of our
knowledge, this is the first time that a S<sub>N</sub>2@Cl mechanism is
reported. We also found that on reducing the bulkiness of substituents around
the phosphorus atom, the backside S<sub>N</sub>2@P mechanism is preferred. The
conclusions made from investigating the steric effect should help
experimentalists to decide for the organophosphorus reactant to achieve the
products of desired stereochemistry.</p> | Nandini Savoo; Lydia Rhyman; Ponnadurai Ramasami | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75208337d6ca3b1e28651/original/theoretical-study-of-a-derivative-of-chlorophosphine-with-aliphatic-and-aromatic-grignard-reagents-sn2-p-or-the-novel-sn2-cl-followed-by-sn2-c.pdf |
664315dc91aefa6ce1ed0b76 | 10.26434/chemrxiv-2024-w4vth | Imaging-based profiling for elucidation of antibacterial mechanisms of action | In this review, we aim to summarize experimental data and approaches to identifying cellular targets or mechanisms of action of antibacterials based on imaging techniques. Imaging-based profiling methods such as bacterial cytological profiling, dynamic bacterial morphology imaging and others have become a useful research tool for mechanistic studies of new antibiotics as well as combinations with conventional ones and other therapeutic options. The main methodological, experimental details and obtained results are summarized and discussed. The review covers the literature up to Feb 2024. | Anna A. Baranova; Vera A. Alferova; Vladimir A. Korshun; Anton P. Tyurin | Biological and Medicinal Chemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664315dc91aefa6ce1ed0b76/original/imaging-based-profiling-for-elucidation-of-antibacterial-mechanisms-of-action.pdf |
6488823fe64f843f41bae3a1 | 10.26434/chemrxiv-2023-74p0j | Reaction dynamics as the missing puzzle piece: the origin of selectivity in oxazaborolidinium ion-catalysed reactions | The selectivity in a group of oxazaborolidinium ion-catalysed reactions between aldehyde and diazo compounds cannot be explained using transition state theory. VRAI-selectivity, developed to predict the outcome of dynamically controlled reactions, can account for both the chemo- and the stereo-selectivity in these reactions, which are controlled by reaction dynamics. Subtle modifications to the substrate or catalyst substituents alter the potential energy surface, leading to changes in predominant reaction pathways and altering the barriers to the major product when reaction dynamics are considered. In addition, this study suggests an explanation for the mysterious inversion of enantioselectivity resulting from the inclusion of an ortho iPrO group in the catalyst. | Ching Ching Lam; Jonathan M. Goodman | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Physical Organic Chemistry; Computational Chemistry and Modeling; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6488823fe64f843f41bae3a1/original/reaction-dynamics-as-the-missing-puzzle-piece-the-origin-of-selectivity-in-oxazaborolidinium-ion-catalysed-reactions.pdf |
6568dfa65bc9fcb5c9c0eb14 | 10.26434/chemrxiv-2023-sw9kv | Informative Training Data for Efficient Property Prediction in Metal-Organic Frameworks by Active Learning | In recent data-driven approaches to materials discov- ery, scenarios where target quantities are expensive to compute or measure are often overlooked. In such cases, it becomes imperative to construct a training set that includes the most diverse, representative, and informative samples. Here, a novel regression tree-based active learning algorithm is employed for such a purpose. It is applied to predict band gap and adsorption properties of metal-organic frameworks (MOFs), a novel class of materials that results from the virtually infinite combinations of their building units. Simpler and low dimensional descrip- tors, such as the Stoichiometric-120 and geometric properties, found here to better represent MOFs in the low data regime, are used to compute the feature space for this model. The partition given by a regression tree constructed on the labeled part of the dataset is used to select new samples to be added to the training set, thereby limiting its size while maximizing the prediction quality. Through tests on the QMOF, hMOF, and dMOF data sets, we show that our method is effective in constructing small training data sets to learn regression models that predict well the target properties, thus reducing the label- ing cost. Specifically, our active learning approach is highly beneficial when labels are unevenly distributed in the descriptor space and when the label distribution is imbalanced, which is often the case for real world data. This offers a unique tool to efficiently analyze complex structure-property relationships in materials and accelerate materials discovery. | Ashna Jose; Emilie Devijver; Noel Jakse; Roberta Poloni | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6568dfa65bc9fcb5c9c0eb14/original/informative-training-data-for-efficient-property-prediction-in-metal-organic-frameworks-by-active-learning.pdf |
6508935bb6ab98a41caeed8e | 10.26434/chemrxiv-2023-bhsjh | Implementation of SPME and Rapid GC-MS as a Screening Approach for Forensic Fire Debris Applications | Analysis of ignitable liquids in fire debris samples can be a time-consuming process, from extraction of volatile compounds to instrumental analysis. Rapid gas chromatography-mass spectrometry (GC-MS) is a screening technique that can be utilized prior to confirmatory GC-MS analysis to provide an informative screening approach and reduce the need to further analyze negative samples. Though rapid GC-MS is fast (less than two minutes), extraction techniques such as passive headspace extraction remain a bottleneck for decreasing overall workflow times. In this work, solid phase microextraction (SPME) was implemented with rapid GC-MS for ignitable liquid analysis for a faster, more sensitive screening approach compared to extraction with passive headspace. Using optimized inlet conditions, limits of detection as low as 27 ng/mL per compound were achieved. Gasoline and diesel fuel were extracted and analyzed, and major compounds in each liquid were identified in the resulting chromatograms. Extracted ion profiles (EIPs) and deconvolution methods were useful for additional compound identifications. Lastly, the SPME-rapid GC-MS workflow was extended to the analysis of gasoline and diesel fuel in mock burn samples using carpet and wood substrates. From SPME sample extraction to rapid GC-MS instrumental analysis and data processing, the total workflow for a single sample was reduced to under 20 min. These results indicate that SPME is a suitable injection technique for rapid GC-MS to provide a fast and sensitive screening approach for fire debris applications. | Briana Capistran | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6508935bb6ab98a41caeed8e/original/implementation-of-spme-and-rapid-gc-ms-as-a-screening-approach-for-forensic-fire-debris-applications.pdf |
669158665101a2ffa8351d0c | 10.26434/chemrxiv-2024-d8jvk | In situ observation of topotactic linker reorganisation in the aperiodic metal–organic framework TRUMOF-1 | We use in situ synchrotron X-ray diffraction measurements to monitor the solvothermal crystallisation mechanism of the aperiodic metal–organic framework TRUMOF-1. Following an initial incubation period, TRUMOF-1 forms as a metastable intermediate that subsequently transforms into an ordered product with triclinic crystal symmetry. We determine the structure of this ordered phase, which we call P1-TRUMOF-1, and show that it is related to TRUMOF-1 through topotactic reorganisation of linker occupancies. Our results imply that the degree and nature of correlated disorder in TRUMOF-1 is not fixed, and might be synthetically tuned as required for data storage and manipulation applications. | Guy Greenbaum; Patrick Doheny; Robert Paraoan; Yevheniia Kholina; Stefan Michalik; Simon Cassidy; Hamish Yeung; Andrew Goodwin | Inorganic Chemistry; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669158665101a2ffa8351d0c/original/in-situ-observation-of-topotactic-linker-reorganisation-in-the-aperiodic-metal-organic-framework-trumof-1.pdf |
60c7587f469df4a523f45693 | 10.26434/chemrxiv.12345434.v2 | Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen. | The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19, however<br />efforts to model ebselen in silico have been hampered by the lack of a efficient and accurate method to assess<br />its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which<br />incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to<br />simulate the sigma?-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach<br />is justified using an energy decomposition analysis of a number DFT optimised structures, which shows that the<br />?sigma-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting MD simulations<br />on a number of simple complexes, as well the clinically relevant SOD1, which is known to bind to ebselen. | Thomas Fellowes; JONATHAN WHITE | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7587f469df4a523f45693/original/simulating-chalcogen-bonding-using-molecular-mechanics-a-pseudoatom-approach-to-model-ebselen.pdf |
60c743f09abda25554f8c275 | 10.26434/chemrxiv.9696512.v1 | Access to Highly Functionalized Cyclopentenones via Diastereoselective Pauson Khand Reaction of Siloxy-Tethered 1,7-Enynes | A diastereoselective Co<sub>2</sub>(CO)<sub>8</sub>-mediated
Pauson-Khand reaction (PKR) of siloxy-tethered 1,7-enynes for the synthesis of
cyclopentaoxasilinones has been developed. This transformation can be performed
on a multi-gram scale and is characterized by broad substrate scope, functional
group compatibility, and high chemo- and diastereoselectivity. Oxidation of the
resulting cyclopentaoxasilinones delivers stereoenriched β-alkylated
cyclopentenones, which are inaccessible by intermolecular PKRs. This research
provides a practical solution to the challenges associated with the classical
intermolecular PKR. | Austin Gallagher; Huan Tian; Osmar A. Torres-Herrera; Shuai Yin; Anxin Xie; Daniel M. Lange; Jerica K. Wilson; Louis G. Mueller; Michael R. Gau; Patrick J. Carroll; Dionicio Martinez Solorio | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f09abda25554f8c275/original/access-to-highly-functionalized-cyclopentenones-via-diastereoselective-pauson-khand-reaction-of-siloxy-tethered-1-7-enynes.pdf |
62501d4285d81403a701c38b | 10.26434/chemrxiv-2022-cx468-v2 | Discovery, Isolation, Heterologous Expression and Mode of Action Studies of the Antibiotic Polyketide Tatiomicin from Amycolatopsis sp. DEM30355 | A genomic and bioactivity informed analysis of the metabolome of the extremophile Amycolatopsis sp. DEM30355 has allowed for the discovery and isolation of the polyketide antibiotic tatiomicin. Identification of the biosynthetic gene cluster was confirmed by heterologous expression in Streptomyces coelicolor M1152. Structural elucidation, including absolute stereochemical assignment, was performed using complementary crystallographic, spectroscopic and computational methods. Tatiomicin shows antibiotic activity against Gram-positive bacteria, including methicillin resistant Staphylococcus aureus (MRSA). Cytological profiling experiments suggest a putative antibiotic mode-of-action, involving membrane depolarisation and chromosomal decondensation of the target bacteria.
| Bernhard Kepplinger; Lina Mardiana; Joseph Cowell; Stephanie Morton-Laing; Corinne Wills; Yousef Dashti; Emma Marrs; John Perry; Joe Grey; Michael Goodfellow; Jeff Errington; Michael Probert; Bill Clegg; Jonathan Bogaerts; Wouter Herrebout; Nick E. E. Allenby; Michael Hall | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Microbiology; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62501d4285d81403a701c38b/original/discovery-isolation-heterologous-expression-and-mode-of-action-studies-of-the-antibiotic-polyketide-tatiomicin-from-amycolatopsis-sp-dem30355.pdf |
6440007f83fa35f8f6e7d622 | 10.26434/chemrxiv-2023-lvv6m | Combined Homogeneous and Heterogeneous Hydrogenation with Parahydrogen to Yield Catalyst-Free Solutions of Hyperpolarized [1-13C]Succinate | We show that catalyst-free aqueous solutions of hyperpolarized [1-13C]succinate can be produced using
parahydrogen-induced polarization (PHIP) and a combination of homogeneous and heterogeneous catalytic hydrogenation reactions. We generate hyperpolarized [1-13C]fumarate at 23% 13C polarization via PHIP with a homogeneous ruthenium catalyst, and subsequently remove the toxic catalyst and reaction side products via a purification procedure. Following this, we perform a second hydrogenation reaction to convert the fumarate into succinate using a solid Pd/Al2O3 catalyst. The catalyst is filtered off to yield a clean aqueous solution containing [1-13C]succinate at 11.9% 13C polarization for the hyperpolarized molecules. In this proof-of-principle demonstration we simplified the purification procedure by adding unpolarized fumarate to the mixtures so the observed succinate polarization was lower, but this step is not necessary for applications. This inexpensive polarization protocol has a turnover time of a few minutes, and represents a major advance for in vivo applications of [1-13C]succinate as a hyperpolarized contrast agent. | James Eills; Román Picazo-Frutos; Dudari Burueva; Larisa Kovtunova; Marc Azagra; Irene Marco Rius; Dmitry Budker; Igor Koptyug | Physical Chemistry; Catalysis; Analytical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6440007f83fa35f8f6e7d622/original/combined-homogeneous-and-heterogeneous-hydrogenation-with-parahydrogen-to-yield-catalyst-free-solutions-of-hyperpolarized-1-13c-succinate.pdf |
60c75608337d6c25b4e28d64 | 10.26434/chemrxiv.14192879.v1 | The Interaction of Chondroitin Sulfate with a Lipid Monolayer Observed by Using Nonlinear Vibrational Spectroscopy | <p>We present the
first vibrational sum-frequency generation spectroscopic study of chondroitin
sulfate (CS) interacting with dipalmitoyl phosphatidylcholine (DPPC) at the air-liquid
interface. In the presence of Ca<sup>2+</sup> and CS, the DPPC headgroups
reoriented, while the tail orientations remained mostly unchanged. The results
further suggest a chiral secondary structure for CS.</p> | Gergo Peter Szekeres; Szilvia Krekic; Rebecca L. Miller; Mark Mero; Kevin Pagel; Zsuzsanna Heiner | Biophysical Chemistry; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75608337d6c25b4e28d64/original/the-interaction-of-chondroitin-sulfate-with-a-lipid-monolayer-observed-by-using-nonlinear-vibrational-spectroscopy.pdf |
60c7463abb8c1a05113da834 | 10.26434/chemrxiv.9860906.v2 | Direct Steering of de novo Molecular Generation using Descriptor Conditional Recurrent Neural Networks (cRNNs) | <p>Deep learning has acquired considerable momentum over
the past couple of years in the domain of <i>de-novo</i> drug design. Particularly,
transfer and reinforcement learning have demonstrated the capability of
steering the generative process towards chemical regions of interest. In this
work, we propose a simple approach to the focused generative task by
constructing a conditional recurrent neural network (cRNN). For this purpose,
we aggregate selected molecular descriptors along with a QSAR-based bioactivity
label and transform them into initial LSTM states before starting the
generation of SMILES strings that are focused towards the aspired properties. We
thus tackle the inverse QSAR problem directly by training on molecular
descriptors, instead of iteratively optimizing around a set of candidate molecules.
The trained cRNNs are able to generate molecules near multiple specified
conditions, while maintaining an output that is more focused than traditional
RNNs yet less focused than autoencoders. The method shows promise for
applications in both scaffold hoping and ligand series generation, depending on
whether the cRNN is trained on calculated scalar molecular properties or
structural fingerprints. This also demonstrates that fingerprint-to-molecule
decoding is feasible, leading to molecules that are similar – if not identical
– to the ones the fingerprints originated from. Additionally, the cRNN is able
to generate a larger fraction of predicted active compounds against the DRD2
receptor when compared to an RNN trained with the transfer learning model. </p> | Panagiotis-Christos Kotsias; Josep Arús-Pous; Hongming Chen; Ola Engkvist; Christian Tyrchan; Esben Jannik Bjerrum | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7463abb8c1a05113da834/original/direct-steering-of-de-novo-molecular-generation-using-descriptor-conditional-recurrent-neural-networks-c-rn-ns.pdf |
6721f611f9980725cf5fb826 | 10.26434/chemrxiv-2024-kj11f | FCIQMC–CASPT2 with Imaginary–Time–Averaged Wave Functions | A new method to perform complete active space second–order perturbation theory on–top of large active spaces optimised with full configuration quantum Monte Carlo is presented. Three– and four–particle density matrices, including contractions with the Fock matrix, are computed from imaginary–time–averaged wave functions, which resolves fermionic positivity violations and ensures numerical stability. The protocol is applied to [NiFe]$^{2-}$ , [Cu(NH$_3$)]$_2$O$_2^{2+}$ and Fe–porphyrin model systems up to 26 electrons in 27 orbitals and benchmarked against DMRG–CASPT2. | Arta Safari; Robert Anderson; Ali Alavi; Giovanni Li Manni | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6721f611f9980725cf5fb826/original/fciqmc-caspt2-with-imaginary-time-averaged-wave-functions.pdf |
65364afb87198ede07155b70 | 10.26434/chemrxiv-2023-z5pnd | Photoresponsive adenosine derivatives for optical control of adenosine A2A receptor in living cells | Subtype-selective ligands with photoswitchable properties are highly desired for photopharmacology of G protein-coupled receptors (GPCRs). We developed photoswitchable ligands targeting adenosine A2A receptor (A2AR), a GPCR subtype. Spatiotemporal activation of A2AR was successfully demonstrated in living cells using the photoswitchable ligand. | Harufumi Suzuki; Tomohiro Doura; Yuya Matsuba; Yuma Matsuoka; Tsuyoshi Araya; Hidetsugu Asada; So Iwata; Shigeki Kiyonaka | Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65364afb87198ede07155b70/original/photoresponsive-adenosine-derivatives-for-optical-control-of-adenosine-a2a-receptor-in-living-cells.pdf |
627bff85809e32045e8c69f5 | 10.26434/chemrxiv-2022-0x7vd-v2 | Surfactin and surfactin-like production, purification, and application at marine environments | Surfactin, a biosurfactant with great activity on interfaces, have been reported as a great substitute to non-renewable sources, non-biologically synthesized surfactants. It is expected to see more studies at the next years evolving its application, including on marine environments, especially ones impacted with petroleum or other contaminants. In this review we address in details the main aspects of surfactin production, including main microorganisms, cultivation modes, pathways and conditions. We address the main aspects of surfactin production by Bacillus subtilis with the different strategies explored to reach this bioprocess up to large scale, as well as the main challenges encountered. As well, is detailed its recovery and purification methods, that generally combine two or more steps as acid precipitation, solvent extraction, liquid membrane extraction, foam fractionation and membrane-based techniques. We also provide a brief summary of its potential application on marine environments, and our prospects from future application, as a brief outlook on physiochemistry characteristics of the main molecules. | Leticia Dobler; Gabriela Coelho Breda; Patricia Maria Rocha; Wilza Kímilly Vital de Paiva; Everaldo Silvino dos Santos; Ricardo Rodrigues de Oliveira | Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Biochemistry; Bioengineering and Biotechnology; Environmental biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627bff85809e32045e8c69f5/original/surfactin-and-surfactin-like-production-purification-and-application-at-marine-environments.pdf |
6516c03ca69febde9eeb5525 | 10.26434/chemrxiv-2023-15tgf | Expanding the palette of SWIR emitting nanoparticles based on Au nanoclusters for single-particle tracking microscopy | Single-molecule localization microscopy has proved very promising to unravel the dynamics and molecular architecture of thin biological samples down to the nanoscale. However, achieving meaningful results in complex, thick biological tissues requires shifting the observation wavelengths to the shortwave-infrared (SWIR) region, where biological tissues are most transparent. In consequence, nanomaterials with optical activity in the SWIR exhibiting brightness and photostability suitable for detection at the single-molecule level are needed. Currently mainly single-walled carbon nanotubes (SWCNTs) satisfy this, but are inherently 1D objects. Here we present 0D ultra-small gold nanoclusters (AuNCs, <3nm) and ~25 nm AuNC-loaded-polymeric particles that can be detected at the single-particle level in the SWIR. Thanks to their high brightness and excellent photostability, we show that the dynamics of the spherical polymeric particles can be followed at the single-particle level in solution at video rates for minutes. Analysis of the mean square displacement confirms the diameter of the particles in aqueous media, and enables us to compare their brightness with that of biocompatible SWCNTs. This extends the library of SWIR emitting nanomaterials to 0D nano-objects of variable size for single-molecule localization microscopy in the second biological window, opening unprecedented possibilities for mapping structure and dynamics of complex biological systems. | Apolline, A. Simon; Lucie Haye; Abdallah Alhalabi; Stéphane Mornet; Andreas Reisch; Xavier Le Guével; Laurent Cognet | Physical Chemistry; Materials Science; Nanoscience; Optical Materials; Nanostructured Materials - Nanoscience; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516c03ca69febde9eeb5525/original/expanding-the-palette-of-swir-emitting-nanoparticles-based-on-au-nanoclusters-for-single-particle-tracking-microscopy.pdf |
670dfad2cec5d6c1422dc912 | 10.26434/chemrxiv-2024-r19z4 | Assembly of the Tricyclic Core of Alopecurone C by Asymmetric Donor/Donor Carbene C–H Insertion | ABSTRACT: Two routes to assemble the complete tricyclic core of alopecurone C are described. In the first-generation route, an efficient synthesis of the “eastern” half of the target, including a decagram-scale rhodium-catalyzed C–H insertion reaction, was developed. When this route proved intractable for assembling the final flavanone ring, a successful second-generation route was developed from a flavanone precursor (naringenin) employing a later stage C–H insertion. Although the second route was ultimately unsuccessful for preparation of the final target, it does provide the basis for the efficient assembly of the complete tricyclic core of alopecurone C and related flavonostilbenoid natural products. | Yuan-Shin Shiue; Matthew Dyer; Noah Burlow; Nutthakarn Soisaeng; Kellan Lamb; Cristian Soldi; James Fettinger; Dean Tantillo; Jared Shaw | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670dfad2cec5d6c1422dc912/original/assembly-of-the-tricyclic-core-of-alopecurone-c-by-asymmetric-donor-donor-carbene-c-h-insertion.pdf |
60c74b90bb8c1a15b23db255 | 10.26434/chemrxiv.12354770.v1 | Ethanol Dehydration over Hybrid Mesoporous Aluminosilicate Catalysts Obtained in One Pot by Non-Hydrolytic Sol-Gel | <p>Ethanol dehydration is
effectively catalyzed by solid acids, such as HZSM-5,
alumina, or silica-alumina. In these catalysts, the amount, nature, and
strength of acid sites is believed to determine catalyst activity and
stability. However, surface hydrophilicity or hydrophobicity can
be suggested as another decisive catalyst property that can directly influence
performance. For example, a more hydrophobic surface might be beneficial in repelling
the co-product of the reaction, water. However, these aspects have been studied
only scarcely in the context of alcohol dehydration. Here, a series of mesoporous hybrid aluminosilicate catalysts containing CH<sub>3</sub>Si
groups was prepared in
one pot by non-hydrolytic sol-gel (NHSG). The presence
of the methyl groups was verified by IR, solid-state NMR, and ToF-SIMS. Aluminum
is mostly incorporated in tetrahedral coordination in the hybrid silica matrix.
Two parameters were varied: (i) the Si:Al ratio and (ii) the Si:MeSi ratio. On
the one hand, changing the Si:Al ratio had a marked impact on hydrophilicity,
as attested by water sorption measurements. On the other hand, unexpectedly,
the introduction of methyl groups had no clear influence on sample
hydrophilicity. Nevertheless, some of the methylated aluminosilicate catalysts
markedly outperformed the purely inorganic catalysts and a commercial
silica-alumina benchmark. While a direct influence of surface hydrophilicity or
hydrophobicity could be excluded, characterization of acidity (IR-pyridine) revealed that these improved
performances are correlated with a modification of the acidic properties in the hybrid catalysts caused by the presence of methyl groups. A decisive role of acidity in ethanol dehydration was confirmed by an
experiment with delayed addition of the Al precursor in the NHSG synthesis.
This led to a higher Al surface concentration, marked acid sites number increase,
and better catalytic performance, even competing with HZSM-5 in terms of
activity.</p> | Ales Styskalik; Imène Kordoghli; Claude Poleunis; Arnaud Delcorte; Zdenek Moravec; Lucie Simonikova; Viktor Kanický; Carmela Aprile; Luca Fusaro; Damien Debecker | Catalysts; Hybrid Organic-Inorganic Materials; Acid Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b90bb8c1a15b23db255/original/ethanol-dehydration-over-hybrid-mesoporous-aluminosilicate-catalysts-obtained-in-one-pot-by-non-hydrolytic-sol-gel.pdf |
67bd910a81d2151a02f90fb0 | 10.26434/chemrxiv-2025-gzq66 | Removal of Phenol derivatives from water systems with the use of silver nanoparticles | Phenolic compounds and their derivatives represent a significant concern within the realm of water pollution, due to their pronounced toxicity, environmental persistence, and extensive utilization across industrial sectors. These pollutants emanate from a multitude of sources, including petrochemical industries, pharmaceutical production, and the manufacture of pesticides, thereby posing considerable threats to both aquatic ecosystems and human health. Conventional water treatment methodologies, encompassing biological degradation, adsorption, and chemical oxidation, frequently fall short in achieving complete elimination of these contaminants or may inadvertently generate secondary pollutants, thereby underscoring the need for the formulation of alternative treatments that are more effective and sustainable. Silver nanoparticles (AgNPs) have been recognized as an innovative material for the remediation of phenol and its derivatives, because of their high surface area, remarkable catalytic efficacy, and pronounced adsorption properties. The distinctive characteristics of AgNPs facilitate the efficient degradation and transformation of phenolic compounds through mechanisms such as adsorption, photocatalysis, and catalytic degradation redox reactions. Furthermore, the functionalization of AgNPs with stabilizing agents enhances their stability, selectivity, and reusability, thereby rendering them as a viable option for water purification. This article critically reviews recent progress in AgNP-based purification of waterbodies by removing phenols. Notable findings indicate that AgNPs substantially augment the rates of phenol degradation, with variables such as nanoparticle size, surface modifications, and prevailing environmental conditions playing pivotal roles in their operational efficiency. Nevertheless, challenges pertaining to nanoparticle aggregation, potential environmental toxicity, and the feasibility of large-scale application require further exploration. Future research should prioritize eco-friendly synthesis or green synthesis methodologies, enhanced recovery techniques, and the mitigation of potential risks linked to nanoparticle discharge. | VARUN MALI | Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Geochemistry; Biochemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bd910a81d2151a02f90fb0/original/removal-of-phenol-derivatives-from-water-systems-with-the-use-of-silver-nanoparticles.pdf |
60c750e1702a9b3c6718be80 | 10.26434/chemrxiv.13090559.v1 | Synthesis, Characterization and Stress-Testing of a Novel Quillaja Saponin Stabilized Oil-in-Water Phytocannabinoid Nanoemulsion | <div>This study describes the design, optimization, and stress-testing of a novel phytocannabinoid nanoemulsion generated using high-pressure homogenization. QNaturale®, a plant-derived commercial emulsifier containing quillaja saponin, was used to stabilize the lipid phase droplets in water. Optimization studies revealed that after 10 homogenization cycles at a pressure of 30,000 psi in the presence of 10 wt% QNaturale® (1.5 wt% quillaja saponin), average nanoemulsion droplet diameters were ca.</div><div>120 nm and average droplet surface zeta-potentials were ca. -30 mV for a lipid phase comprising 16.6 wt% CBD-enriched cannabis extract and 83.4 wt% carrier (soybean) oil. The optimized nanoemulsion proved to be stable to droplet agglomeration and phase separation upon storage under ambient conditions for 6 weeks, as well as under a variety of physical stressors such as heat, cold, dilution, and</div><div>carbonation. pH values under 2 and moderately high salt concentrations (> 100 mM), however, destabilized 0the CD<sub>CBD</sub> nanoemulsion, eventually leading to phase separation. Cannabis potency, determined by HPLC, was detrimentally affected by any changes in the nanoemulsion phase stability. Quillaja saponin stabilized cannabidiol (CBD)-enriched nanoemulsions are stable, robust systems even at low emulsifier concentrations, and are therefore significant from both a scientific as well as a commercial perspective.</div> | Abhinandan Banerjee; Justin Binder; Ryan Salama; John F. Trant | Food | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750e1702a9b3c6718be80/original/synthesis-characterization-and-stress-testing-of-a-novel-quillaja-saponin-stabilized-oil-in-water-phytocannabinoid-nanoemulsion.pdf |
62fbea4bd0c5cb41f3669804 | 10.26434/chemrxiv-2022-fwh4p | Synthesis of Fluorescent Carbon Nanoparticles by Dispersion Polymerization
of Acetylene | Carbon nanoparticles (CNPs) have emerged as one of the most promising nanomaterials
due to their distinct optoelectronic properties for a diverse range of applications in the area of
electronics, energy conversion and storage, and bio-imaging. Their functions and properties can
be changed by varying their shape, size and dimensionality. The synthetic methods reported until
now involve high-temperature (>100 °C) processes, which often result in uncontrolled shape, size
and polydispersity. In this work, we focus on the development of a low-temperature synthetic
method for the preparation of fluorescent carbon nanoparticles and modulation of properties. Our
method, based on the dispersion Glaser-Hay polymerization of acetylene followed by
decomposition into a carbonaceous material, yields CNPs with sizes varying from 30 nm to 60
nm. The shape and size of the resulting carbon nanoparticles are influenced by changing different
reaction parameters such as temperature, reaction time and pressure. The control over the different
reaction parameters allows us to obtain monodisperse CNPs in spherical shapes. After isolation, CNPs were characterized by microscopy and spectroscopy techniques. The residual alkynes in the
CNPs’ structure were exploited for further post-functionalization/ graphitization to yield
multifunctional CNPs, which were fluorescent in the blue region. | Vijay K. Jayswal; Anna M. Ritcey; Jean-Francois Morin | Physical Chemistry; Materials Science; Polymer Science; Carbon-based Materials; Polymerization (Polymers); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fbea4bd0c5cb41f3669804/original/synthesis-of-fluorescent-carbon-nanoparticles-by-dispersion-polymerization-of-acetylene.pdf |
60c7457bbb8c1a59e93da6c8 | 10.26434/chemrxiv.10031888.v1 | Visualizing 3D Molecular Structures Using an Augmented Reality App | <p>We present a
simple procedure to make an augmented reality app to visualize any 3D chemical
model. The molecular structure may be based on data from crystallographic data
or from computer modelling. This guide is made in such a way, that no programming
skills are needed and the procedure uses free software and is a way to
visualize 3D structures that are normally difficult to comprehend in the 2D
space of paper. The process can be applied to make 3D representation of any 2D
object, and we envisage the app to be useful when visualizing simple
stereochemical problems, when presenting a complex 3D structure on a poster
presentation or even in audio-visual presentations. The method works for all
molecules including small molecules, supramolecular structures, MOFs and
biomacromolecules.</p> | Kristina Eriksen; Bjarne Nielsen; Michael Pittelkow | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457bbb8c1a59e93da6c8/original/visualizing-3d-molecular-structures-using-an-augmented-reality-app.pdf |
61b8907902c2142e5224a9f2 | 10.26434/chemrxiv-2021-qlsgm | Fast and automated identification of reactions with low barriers using meta-MD simulations |
We test our meta-molecular dynamics (MD) based approach for finding low-barrier (<30 kcal/mol) reactions (SciPost Chem. 2021, 1, 003) on uni- and bimolecular reactions extracted from the barrier dataset developed by Grambow et al. (Scientific Data 2020, 7, 137). For unimolecular reactions the meta-MD simulations identify 25 of the 26 products found by Grambow et al., while the subsequent semiempirical screening eliminates an additional four reactions due to at an overestimation of the reaction energies or estimated barrier heights relative to DFT. In addition, our approach identifies an additional 36 reactions not found by Grambow et al., 10 of which are <30 kcal/mol. For bimolecular reactions the meta-MD simulations identify 19 of the 20 reactions found by Grambow et al., while the subsequent semiempirical screening eliminates an additional reaction. In addition, we find 34 new low-barrier reactions. For bimolecular reactions we found that it is necessary to ”encourage” the reactants to go to previously undiscovered products, by including products found by other MD simulations when computing the biasing potential as well as decreasing the size of the molecular cavity in which the MD occurs, until a reaction is observed. We also show that our methodology can find the correct products for two reactions that are more representative of those encountered in synthetic organic chemistry. The meta-MD hyperparameters used in this study thus appears to be generally applicable to finding low-barrier reactions. | Maria H. Rasmussen; Jan H. Jensen | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b8907902c2142e5224a9f2/original/fast-and-automated-identification-of-reactions-with-low-barriers-using-meta-md-simulations.pdf |
60c74a9f702a9be2e218b2b8 | 10.26434/chemrxiv.11861817.v2 | Designing Singlet Fission Candidates from Donor-Acceptor Copolymers | <p>Singlet Fission (SF) has demonstrated significant
promise for boosting the power conversion efficiency (PCE) of solar cells.
Traditionally, SF is targeted as an intermolecular process, however its
dependence on crystal packing makes molecular design difficult. In contrast,
intramolecular SF (iSF) enables the exploration of tunable bi-chromophoric
systems following well-defined structure-property relationships. In this work,
we propose a set of parameters to screen conjugated donor-acceptor copolymer
candidates with potential iSF behaviour. We focus our analysis on the E(S<sub>1</sub>)>2E(T<sub>1</sub>)
thermodynamic condition and on the appropriate charge transfer (CT) character
of S<sub>1</sub>. We map the CT character with respect to the frontier
molecular orbital (FMO) energies of the constituent monomers, providing a
cost-effective protocol for an accelerated screening of promising iSF
donor-acceptor pairs, while minimizing the number of computations. These
parameters are applied to a chemically diverse, curated library of 81 truncated
dimers of synthetically feasible donor-acceptor copolymers. From our dataset,
four candidates are flagged for iSF, two of which were previously
experimentally reported. This protocol is envisioned to be scaled up for the high-throughput
screening of large databases of donor-acceptor dimers for the design and
identification of conjugated polymers capable of iSF. </p> | Jacob Terence Blaskovits; Maria Fumanal; Sergi Vela; Clemence Corminboeuf | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a9f702a9be2e218b2b8/original/designing-singlet-fission-candidates-from-donor-acceptor-copolymers.pdf |
60c74ad6f96a002e762874d8 | 10.26434/chemrxiv.11299121.v2 | Fast Predictions of Liquid-Phase Acid-Catalyzed Reaction Rates Using Molecular Dynamics Simulations and Convolutional Neural Networks | The rates of liquid-phase, acid-catalyzed reactions
relevant to the upgrading of biomass into high-value chemicals are highly sensitive
to solvent composition and identifying suitable solvent mixtures is theoretically
and experimentally challenging. We show that the atomistic configurations of reactant-solvent
environments generated by classical molecular dynamics simulations can be exploited
by 3D convolutional neural networks to enable fast predictions of Brønsted acid-catalyzed
reaction rates for model biomass compounds. We develop a computational implementation,
which we call SolventNet, and train it using experimental reaction data for seven
biomass-derived oxygenates in water-cosolvent mixtures. We show that SolventNet
can predict reaction rates for additional reactants and solvent systems an
order of magnitude faster than prior simulation methods. This combination of
machine learning with molecular dynamics enables the rapid screening of solvent
systems and identification of improved biomass conversion conditions. | Alex Chew; Shengli Jiang; Weiqi Zhang; Victor Zavala; Reid Van Lehn | Computational Chemistry and Modeling; Machine Learning; Acid Catalysis; Homogeneous Catalysis; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ad6f96a002e762874d8/original/fast-predictions-of-liquid-phase-acid-catalyzed-reaction-rates-using-molecular-dynamics-simulations-and-convolutional-neural-networks.pdf |
6656457321291e5d1d7f1c0a | 10.26434/chemrxiv-2024-dsp32 | Improved Mechanistic Degradation Modes Modeling of Lithium and Sodium Plating | Lithium and Sodium plating are inevitable when using negative electrodes with an electrochemical potential close to the one of the charge carrier. Typical testing and modeling usually assumed that plating occurs at 0V when measured against the charge carrier. While this might be true under thermodynamic equilibrium, this is not true outside of steady state. This has significant implications as, by taking this into account, the testing voltage window of negative electrodes could be extended to allow gathering data for more complete discharges at higher rates. Moreover, from a modeling standpoint, it could also allow to more accurately predict plating initiation potentials dynamically. This work presents preliminary results on the investigation of what parameters are influencing the plating potential and how to take them into account in testing and modeling. | David Beck; Agata Greszta; Alexander Roberts; Matthieu Dubarry | Materials Science; Carbon-based Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6656457321291e5d1d7f1c0a/original/improved-mechanistic-degradation-modes-modeling-of-lithium-and-sodium-plating.pdf |
65944c7e66c13817299059cd | 10.26434/chemrxiv-2024-xg3j1 | Multicomponent delivery system based on biologically produced gold nanoparticles for targeted therapy of breast cancer in vivo | This study recognized biologically produced gold nanoparticles (AuNP) as multiple cargo carriers with a perspective of drugs delivery into specialized tumor cells in vivo. Paclitaxel (PTX), transferrin, and antimiR-135b were conjugated with AuNPs and their uptake by mouse tumor cells in an induced breast cancer model was investigated. Each of the above-mentioned molecules was conjugated to the AuNPs separately as well as simultaneously, loading efficiency of each cargo was assessed, and performance of the final product (FP) was assessed. After tumor induction in BALB/c mice, sub-IC50 doses of FP as well as control AuNPs, PTX, and PBS were administered in vivo. Round AuNPs were prepared using Fusarium oxysporum and exhibited size of 13 ± 1.3 nm and zeta potential of -35.8 ± 1.3 mV. The cytotoxicity of individual conjugates and FP were tested by MTT assay in breast tumor cells 4T1 and non-tumor fibroblasts NIH/3T3 cells. The conjugation of the individual molecules with AuNPs was confirmed and FP (size of 54 ± 14 nm and zeta potential of -31.9 ± 2.08 mV) showed higher 4T1-specific toxicity in vitro when compared to control conjugates. After in vivo application of the FP, TEM analyses proved presence of AuNPs in the tumor cells. Hematoxylin and eosin staining of the tumor tissue revealed that the FP group exhibited the highest amounts of inflammatory, necrotic, and apoptotic cells in contrast to control groups. Finally, qPCR results showed that FP could transfect and suppress miR-135b expression in vivo, confirming the tumor-targeting properties of FP. The capacity of biologically produced gold nanoparticles to conjugate with multiple decorative molecules while remaining their stability and effective intracellular uptake makes them promising alternative strategy superior to current drug carriers. | Parastoo Pourali; Eva Neuhoferova; Volha Dzmitruk; Milan Svoboda; Eva Stodulkova; Miroslav Flieger; Behrooz Yahyaei ; Veronika Benson | Biological and Medicinal Chemistry; Nanoscience; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65944c7e66c13817299059cd/original/multicomponent-delivery-system-based-on-biologically-produced-gold-nanoparticles-for-targeted-therapy-of-breast-cancer-in-vivo.pdf |
647f6a5ae64f843f416c5432 | 10.26434/chemrxiv-2023-sv0cd | Detecting Reactive Products in Carbon Capture Polymers with Chemical Shift Anisotropy and Machine Learning | Aminopolymers are attractive sorbents for CO2 direct air capture applications as their amines readily react with atmospheric levels of CO2 to form chemisorbed species. The identity of the chemisorbed species varies upon experimental conditions like amine chemistry, support material, CO2 loading, and humidity, forming a variety of carbonyl-type sites. 13C solid-state nuclear magnetic resonance (NMR) is often used to help elucidate the identity of the chemisorbed species however the chemical shift range for carbonyl sites is small and comparable to observed chemisorbed 13C peak widths. Herein, application of a 2D chemical shift anisotropy (CSA) recoupling pulse sequence (ROCSA) is used to obtain CSA tensor values at each isotropic chemical shift, overcoming the isotropic peak resolution limitation. CSA tensor values describe the local chemical environment and can readily differentiate between chemisorbed products. To aid this experimental technique, we also developed a k-nearest-neighbor (KNN) classification model to distinguish chemisorbed compounds via their CSA tensor parameters. The combination of 2D CSA measurements coupled with a KNN classification model enhances the ability to accurately identify chemisorbed products especially in the case of mixtures. This methodology is demonstrated on poly(ethylenimine) in a solid-support γ-Al2O3 exposed to CO2 followed by incomplete regeneration at 100 °C and shows a mixture of strongly bound chemisorbed products, ammonium carbamate and urea. | Maxwell Marple; Sichi Li; Elwin Hunter-Sellars; Simon Pang | Physical Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647f6a5ae64f843f416c5432/original/detecting-reactive-products-in-carbon-capture-polymers-with-chemical-shift-anisotropy-and-machine-learning.pdf |
6687f54b5101a2ffa87b5f4d | 10.26434/chemrxiv-2024-2xk5n-v2 | FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses | The fragment molecular orbital (FMO) method is an efficient quantum chemical calculation technique for large biomolecules, dividing each into smaller fragments and providing inter-fragment interaction energies (IFIEs) that support our understanding of molecular recognition. The ab initio fragment MO method program (ABINIT-MP), an FMO processing software, can automatically divide typical proteins and nucleic acids. In contrast, small molecules such as ligands and hetero systems must be manually divided. Thus, we developed a graphical user interface to easily handle such manual fragmentation as a library for Molecular Operating Environment (MOE) that preprocesses and visualizes FMO calculations. We demonstrated fragmentation with IFIE analyses for the two following cases: 1) covalent cysteine–ligand bonding inside the SARS-CoV-2 main protease (Mpro) and nirmatrelvir (Paxlovid) complex, and 2) the metal coordination inside a zinc-bound cyclic peptide. IFIE analysis successfully identified the key amino acid residues for the molecular recognition of nirmatrelrvir with Mpro and the details of their interactions (e.g., hydrogen bonds and CH/π interactions) via ligand fragmentation of functional group units. In metalloproteins, we found an efficient and accurate scheme for the fragmentation of Zn2+ ions with four histidines coordinated to the ion. FMOe simplifies manual fragmentation, allowing users to experiment with various fragmentation patterns and perform in-depth IFIE analysis with high accuracy. In the future, our findings will provide valuable insight into complicated cases, such as ligand fragmentation in modality drug discovery, especially for medium-sized molecules and metalloprotein fragmentation around metals. | Hirotomo Moriwaki; Yusuke Kawashima; Chiduru Watanabe; Kikuko Kamisaka; Yoshio Okiyama; Kaori Fukuzawa; Teruki Honma | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687f54b5101a2ffa87b5f4d/original/fm-oe-preprocessing-and-visualizing-package-of-the-fragment-molecular-orbital-method-for-molecular-operating-environment-and-its-applications-in-covalent-ligand-and-metalloprotein-analyses.pdf |
6464e6a5fb40f6b3eebcc8de | 10.26434/chemrxiv-2023-xgq7f | DFT studies of binding of fluoride anions with silyl-fluorescein derivatives | Fluoride is abundantly used in dental healthcare and pharmaceutical industry, it is harmful if it is found over certain concentration in drinking water and in soil. It is therefore essential to develop portable tools to detect fluoride. Fluorescence sensing can be used as a simple and sensitive tool to detect fluoride anions. Fluorescent detection of anions is less widely studied compared to metal cation and neutral organic small molecules. As such, the interactions between F- anion and two silyl-fluorescein based sensors were studied here using density functional theory (DFT). Chemical shifts and electronic properties of the free sensor and the sensors in the presence of different number of fluoride anions were obtained and compared. The DFT results show that strong binding responses can be found as a function of fluoride concentration. The change in UV-Vis spectra due to the presence of fluoride indicates they are promising sensor candidates for fluoride detection and further studies on fluorescence response of these sensors are worthwhile. | Krishanthi Weerasinghe; Lichang Wang | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6464e6a5fb40f6b3eebcc8de/original/dft-studies-of-binding-of-fluoride-anions-with-silyl-fluorescein-derivatives.pdf |
60c75085337d6cd73ae2833e | 10.26434/chemrxiv.13050329.v1 | Rapid Survey of Nuclear Quadrupole Resonance by Broadband Excitation with Comb Modulation and Dual-Mode Acquisition | Nuclear Quadrupole Resonance (NQR) provides spectra carrying information
as to the electric-field gradient around nuclei with a spin quantum number I > 1/2
and offers helpful clues toward characterizing the electronic structure of materials
of chemical interest. A major challenge in NQR is finding hitherto unknown resonance frequencies, which can scatter over a wide range, requiring time consuming
repetitive measurements with stepwise frequency increments. Here, we report on
an efficient, two-step NQR protocol by bringing rapid-scan and frequency-comb together. In the first step, wideband excitation and simultaneous signal acquisition,
both realized by a non-adiabatic, frequency-swept hyperbolic secant (HS) pulse
with comb modulation, offers a clue for the existence/absence of the resonance
within the frequency region under investigation. When and only when the sign of
the resonance has been detected, the second step is implemented to compensate
the limited detection bandwidth of the first and to unambiguously determine the
NQR frequency. We also study the spin dynamics under the comb-modulated HS
pulse by numerical simulations, and experimentally demonstrate the feasibility of
the proposed scheme, which is referred to as RApid-Scan with GApped excitation
with Dual-mode Operation (RASGADO) NQR<br /> | Yuta Hibe; Yasuto Noda; K. Takegoshi; Kazuyuki Takeda | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75085337d6cd73ae2833e/original/rapid-survey-of-nuclear-quadrupole-resonance-by-broadband-excitation-with-comb-modulation-and-dual-mode-acquisition.pdf |
60c74db89abda229e1f8d4f6 | 10.26434/chemrxiv.12652934.v1 | Finding the Next Superhard Material through Ensemble Learning | We report an ensemble machine-learning method capable of finding new superhard materials by directly predicting the load-dependent Vickers hardness
based only on the chemical composition. A total of 1062 experimentally measured load-dependent Vickers hardness data were extracted from the literature and used to train a supervised machine-learning algorithm utilizing boosting, achieving excellent accuracy (R2 = 0.97). This new model was then tested
by synthesizing and measuring the load-dependent hardness of several unreported disilicides as well as analyzing the predicted hardness of several classic superhard materials. The trained ensemble method was then employed to
screen for superhard materials by examining more than 66,000 compounds in
crystal structure databases, which showed that only 68 known materials surpass the superhard threshold. The hardness model was then combined with
our data-driven phase diagram generation tool to expand the limited num1
ber of reported compounds. Eleven ternary borocarbide phase spaces were
studied, and more than ten thermodynamically favorable compositions with
superhard potential were identified, proving this ensemble model’s ability to
find previously unknown superhard materials | Ziyan Zhang; Aria Mansouri Tehrani; Anton Oliynyk; Blake Day; Jakoah Brgoch | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db89abda229e1f8d4f6/original/finding-the-next-superhard-material-through-ensemble-learning.pdf |
63205d9ffaf4a43c78105370 | 10.26434/chemrxiv-2022-8ldw9-v2 | Active Learning Assisted MCCI to Target Spin States | Strongly correlated systems and their accurate solutions have been challenging to quantum chemistry. Several methods have been developed over the years for the accurate understanding of such systems, and selected configuration interaction and Monte Carlo configuration interaction (MCCI) form important classes of systems in this category. However, MCCI is plagued by slow convergence. This is further exacerbated by the fact that most of the current MCCI implementations do not target specific spin states. In our work, we use active learning assisted MCCI to speed up the convergence manyfold and also develop a method for spin targeting. This method has been tested with several model Hamiltonian systems akin to molecular systems and has shown improved convergence and accuracy. | Koushik Seth; Debashree Ghosh | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63205d9ffaf4a43c78105370/original/active-learning-assisted-mcci-to-target-spin-states.pdf |
60c752d1bb8c1a151d3dbf2d | 10.26434/chemrxiv.13353257.v1 | Endohedral Hydrogen Bonding Templates the Formation of a Highly Strained Covalent Organic Cage Compound | A highly strained covalent organic cage compound was synthesized from hexahydroxy tribenzotriquinacene (TBTQ) and a meta-terphenyl-based diboronic acid with an additional benzoic acid substituent in 2’-position. Usually, a 120° bite angle in the unsubstituted ditopic linker favors the formation of a [4+6] cage assembly. Here we show that introduction of the benzoic acid group leads to a perfectly preorganized circular hydrogen-bonding array in the cavity of a trigonal-bipyramidal [2+3] cage, which energetically overcompensates the additional strain energy caused by the larger mismatch in bite angles for the smaller assembly. The strained cage compound was analyzed by mass spectrometry and <sup>1</sup>H, <sup>13</sup>C and DOSY NMR spectroscopy. DFT calculations revealed the energetic contribution of the hydrogen-bonding template to the cage stability. Furthermore, molecular dynamics simulations on early intermediates indicate an additional kinetic effect, as hydrogen-bonding also preorganizes and rigidifies small oligomers to facilitate the exclusive formation of smaller and more strained macrocycles and cages. | Natalie Schäfer; Michael Bühler; Lisa Heyer; Merle Röhr; Florian Beuerle | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752d1bb8c1a151d3dbf2d/original/endohedral-hydrogen-bonding-templates-the-formation-of-a-highly-strained-covalent-organic-cage-compound.pdf |
60c758c6469df4169bf45744 | 10.26434/chemrxiv.14602716.v1 | Image2SMILES: Transformer-based Molecular Optical Recognition Engine | The rise of deep learning in various scientific and technology areas promotes the development of AI-based tools for information retrieval. Optical recognition of organic structures is a key part of the automated extraction of chemical information. However, this is a challenging task because there is a large variety of representation styles. In this research, we present a Transformer-based artificial neural network to convert images of organic structures to molecular structures. To train the model, we created a comprehensive data generator that stochastically simulates various drawing styles, functional groups, functional group placeholders (R-groups), and visual contamination. We demonstrate that the Transformer-based architecture can gather chemical insights from our generator with almost absolute confidence. That means that, with Transformer, one can fully concentrate on data simulation to build a good recognition model. A web demo of our optical recognition engine is available online at <i>Syntelly</i> platform. | Ivan Khokhlov; Lev Krasnov; Maxim Fedorov; Sergey Sosnin | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758c6469df4169bf45744/original/image2smiles-transformer-based-molecular-optical-recognition-engine.pdf |
627b51123f1e7c2a1eb9f362 | 10.26434/chemrxiv-2022-zdrw5-v2 | Advanced Database Mining of Efficient Biocatalysts by Sequence and Structure Bioinformatics and Microfluidics | Next-generation sequencing doubles genomic databases every 2.5 years. The accumulation of sequence data provides a unique opportunity to identify interesting biocatalysts directly in the databases without tedious and time-consuming engineering. Herein, we present a pipeline integrating sequence and structural bioinformatics with microfluidic enzymology for bioprospecting of efficient and robust haloalkane dehalogenases. The bioinformatic part identified 2,905 putative dehalogenases and prioritized a “small-but-smart” set of 45 genes, yielding 40 active enzymes, 24 of which were biochemically characterized by microfluidic enzymology techniques. Combining microfluidics with modern global data analysis provided precious mechanistic insights related to the high catalytic efficiency of selected enzymes. Overall, we have doubled the dehalogenation “toolbox” characterized over three decades, yielding biocatalysts that surpass the efficiency of currently available wild-type and engineered enzymes. This pipeline is generally applicable to other enzyme families and can accelerate the identification of efficient biocatalysts for industrial use. | Michal Vasina; Pavel Vanacek; Jiri Hon; David Kovar; Hana Faldynova; Antonin Kunka; Tomas Buryska; Christoffel P.
S. Badenhorst; Stanislav Mazurenko; David Bednar; Stavros Stavrakis; Uwe T. Bornscheuer; Andrew de Mello; Jiri Damborsky; Zbynek Prokop | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627b51123f1e7c2a1eb9f362/original/advanced-database-mining-of-efficient-biocatalysts-by-sequence-and-structure-bioinformatics-and-microfluidics.pdf |
60c73d50702a9bf1b1189b44 | 10.26434/chemrxiv.5662372.v1 | Robust operation of mesoporous antireflective coatings under variable ambient conditions | Antireflective coatings (ARCs) are important components in optical applications due to their ability to reduce reflection and maximize transmission of light across interfaces. Generating mesoporous films with adequate film thickness and refractive index is a common method to achieve amplitude and phase matching in low-cost single- layer interference-based ARCs. For high surface energy materials, pores on the 2 - 50 nm, i.e. the sub-wavelength scale, are subject to capillary condensation, and pore filling by surrounding gas phase water molecules at size-characteristic humidity values hampers their functioning. In this work, we examine the effect of relative humidity on mesoporous ARCs and present a simple method for the preparation of ARCs with robust operation under variable conditions. The materials route is based on the generation of well-defined porous aluminosilicate networks by block copolymer co- assembly with poly(isobutylene)block-poly(ethylene oxide) and post-synthesis grafting of trichloro(octyl)silane molecules to the pore walls. The functionalized films exhibited a maximum transmittance value of 99.8% with an average transmittance of 99.1% in the visible wavelength range from 400 nm to 700 nm. Crucially, the AR performance was maintained at high humidity values with an average transmittance decrease of only 0.2% and maximum values maintained at 99.7 %, which compared to maximum and average losses of 3.6% and 2.7 %, respectively, for non-functionalized reference samples. The ARCs were shown to withstand at least 50 humidity cycles, indicating long-term stability against fluctuating environmental conditions. | Barry Reid; Yinong Chen; Benjamin Schmidt-Hansberg; Stefan Guldin | Coating Materials | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d50702a9bf1b1189b44/original/robust-operation-of-mesoporous-antireflective-coatings-under-variable-ambient-conditions.pdf |
60c75988337d6c25cfe29406 | 10.26434/chemrxiv.14650131.v2 | Practical and Regioselective Synthesis of C4-Alkylated Pyridines | The direct position-selective C–4 alkylation of pyridines has been a longstanding challenge in heterocyclic chemistry, particularly from pyridine itself. Historically this has been addressed using pre-functionalized materials to avoid overalkylation and mixtures of regioisomers. This study reports the invention of a simple maleate-derived blocking group for pyridines that enables exquisite control for Minisci-type decarboxylative alkylation at C–4 that allows for inexpensive access to these valuable building blocks. The method is employed on a variety of different pyridines and carboxylic acid alkyl donors, is operationally simple, scalable, and is applied to access known structures in a rapid and inexpensive fashion. Finally, this work points to an interesting strategic departure for the use of Minisci chemistry at the earliest possible stage (native pyridine) rather than current dogma that almost exclusively employs Minisci as a late-stage functionalization technique. | jin choi; Gabriele Laudadio; Edouard Godineau; Phil Baran | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75988337d6c25cfe29406/original/practical-and-regioselective-synthesis-of-c4-alkylated-pyridines.pdf |
62c944c7332f027651e2d23f | 10.26434/chemrxiv-2022-97b0f | Electronic substitution effect on the ground and
excited state properties of indole chromophore:
A computational study | Indole, being the main chromophore of amino acid tryptophan and several other biologically relevant molecules like serotonin, melatonin, has prompted considerable theoretical and experimental interest. The current work focuses on the investigation of photophysical and photochemical properties of indole and indole derivatives e.g. tryptophan, serotonin and melatonin using theoretical and computational methodologies. Having three close-lying excited electronic states, the vibronic coupling effect becomes extremely important yet challenging for the photophysics and photochemistry of indole. Here, we have used density functional theory (DFT) extensively and evaluated the performance of DFT in compared to available experimental and ab initio results from literature. The benchmarking of the method is followed by investigation of the chemical and geometrical effects of ring substitution in indole. A bathochromic shift has been observed in the HOMO-LUMO gap as well as vertical excitation energy from indole to melatonin. While the contribution of the in-plane small adjacent groups increases the electron density of the indole ring, the out-of-plane long substituent groups have minor effect. The comparison of singlet-triplet gaps suggests highest probability of inter-system crossing for tryptophan which is in line with previous experiment. The absorption spectra calculated including the vibronic coupling are in good agreement with experiment. These results can be used to estimate the error in photophysical observables of indole derivatives calculated considering indole as prototypical system. This study also demonstrates the merits and demerits of using DFT functionals to compute the photophysical properties of indole derivatives. | Soumyadip Ray; Padmabati Mondal | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c944c7332f027651e2d23f/original/electronic-substitution-effect-on-the-ground-and-excited-state-properties-of-indole-chromophore-a-computational-study.pdf |
6542473bc573f893f1937773 | 10.26434/chemrxiv-2023-72r06-v2 | IR of Vanillin: A classic study with a twist | In this research, we delve into the vibrational spectroscopy of vanillin, a widely used aromatic and flavouring agent, through a comprehensive computational analysis. We employ a variety of common computational chemistry functionals and basis sets to calculate the infrared (IR) and Raman spectra of vanillin, aiming to shed light on its structural and spectroscopic properties. Our investigation entails benchmarking these theoretical results against one another to identify the most accurate computational approach. Furthermore, we compared our theoretical findings with experimental IR and Raman spectra to evaluate the degree of agreement between theory and experiment. This comparative analysis provides insights into the reliability of the chosen computational methods in capturing the vibrational behaviour of vanillin, a crucial aspect for applications in the food and pharmaceutical industries. In future work we plan to expand this study to other compounds aiming to bridge the gap between theory and experiment, this study contributes to a deeper understanding of vanillin's molecular behaviour, ultimately enhancing our knowledge of its sensory and chemical attributes. | Michael Nicolaou ; Hans Senn; Emma Gibson; Laia Vilà-Nadal | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6542473bc573f893f1937773/original/ir-of-vanillin-a-classic-study-with-a-twist.pdf |
626c34bfebac3a70dde7b068 | 10.26434/chemrxiv-2022-w83bw | Molecular Signatures of the Glass Transition in Polymers | The glass transition temperature (Tg) is one of the most fundamental properties of polymers.
Tg is predicted as a sudden change in a “macroscopic” quantity (e.g. compressibility). However,
for systems with “soft” glass transitions where the change is gradual it becomes hard to pinpoint
precisely the transition temperature as well as the set of molecular changes occurring during this
transition. Here, we introduce two new molecular signatures for the glass transition of polymers
that exhibit clear changes as one approaches Tg: i) differential change of the probability distribution
of dihedral angles as a function of temperature, and ii) the distribution of fractional of time spent
in the different torsional states. These new signatures provide insights into the glass transition
in polymers by directly exhibiting the concept of spatial heterogeneity and dynamical ergodicity
breaking in such systems, as well as provide a key step to quantitatively obtain the transition
temperature from molecular characteristics of the polymeric systems. | Tianyi Jin; Connor Coley; Alfredo Alexander-Katz | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626c34bfebac3a70dde7b068/original/molecular-signatures-of-the-glass-transition-in-polymers.pdf |
67959d016dde43c9086a1f4b | 10.26434/chemrxiv-2025-b6n4m | OCNet: A Domain Knowledge-Enhanced General Moleculer Representation Framework for Optoelectronic and Charge-transport Materials | The characterization of material properties plays a crucial role in revealing the structure-property relationship and optimizing device performance. Organic optoelectronic and transporting materials, widely used in various fields, face challenges in experimental property characterization not only due to their high cost but also the requirement of multidisciplinary knowledge. To address this problem, we introduce OCNet, a domain knowledge-enhanced representation learning framework, with which the efficient and accurate virtual characterization is made possible. Based on the SE(3) transformer architecture and a self-constructed large-scale conjugated molecular database with millions of structures and properties, OCNet realizes general molecular and bimolecular representation and supports the integration of domain knowledge features. In multiple optoelectronic property prediction tasks, OCNet shows a significant improvement in accuracy compared to previously reported models. It also constructs a DFT accuracy database for the transfer integrals of thin-film materials and renders the general prediction of such properties possible. With its user-friendly interface, OCNet can serve as an effective virtual characterization tool, facilitating the development of optoelectronic devices and other functional material research. | Guojiang Zhao ; Qi Ou; Zifeng Zhao ; Shangqian Chen ; Haitao Lin ; Xiaohong Ji; Zhen Wang ; Hongshuai Wang ; Hengxing Cai ; Lirong Wu ; Shuqi Lu; FengTianCi Yang; Zhifeng Gao ; Zheng Cheng | Energy; Energy Storage; Photovoltaics; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67959d016dde43c9086a1f4b/original/oc-net-a-domain-knowledge-enhanced-general-moleculer-representation-framework-for-optoelectronic-and-charge-transport-materials.pdf |
60c755c10f50db2e70397f92 | 10.26434/chemrxiv.14159159.v1 | Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees | <div>We present open-source implementations of the linear-scaling Fast Multipole Method (FMM) within the Polarizable Embedding (PE) model for efficient treatment of large polarizable environments in computational spectroscopy simulations. The implementations are tested for accuracy, efficiency, and usability on model systems as well as more realistic biomolecular systems. We explain how FMM parameters affect the calculation of molecular properties and show that PE calculations employing FMM can be carried out in a black-box manner. The efficiency of the linear-scaling approach is demonstrated by simulating the UV/Vis spectrum of a chromophore in an environment of more than one million polarizable sites. Our implementations are interfaced to several open-source quantum chemistry programs, making computational spectroscopy</div><div>simulations within the PE model and FMM available to a large variety of methods and a broad user base.</div> | Maximilian Scheurer; Peter Reinholdt; Jógvan Magnus Haugaard Olsen; Andreas Dreuw; Jacob Kongsted | Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c10f50db2e70397f92/original/efficient-open-source-implementations-of-linear-scaling-polarizable-embedding-use-octrees-to-save-the-trees.pdf |
644f35226ee8e6b5ed625bb0 | 10.26434/chemrxiv-2023-p3188-v3 | Limitations of atomistic molecular dynamics to reveal ejection of proteins from charged nanodroplets | Atomistic molecular dynamics (MD) is frequently used to unravel the mechanisms of macroion release from electrosprayed droplets. However, atomistic MD is currently feasible for only the smallest window of droplet sizes appearing at the end steps of a droplet's lifetime. The relevance of the observations made to the actual droplet evolution, which is much longer that the simulated sizes, has not been addressed yet in the literature. Here, we perform a systematic study of desolvation mechanisms of poly(ethylene glycol) (PEG), protonated peptides of different compositions and proteins in order to (a) obtain insight into the charging mechanism of macromolecules in larger droplets than those that are currently amenable to atomistic MD, and (b) examine whether currently used atomistic modeling can establish the extrusion mechanism of proteins from droplets. To mimic larger droplets that are not amenable to MD modeling, we scale down the systems, by simulating a large droplet size relative to the macromolecule. MD of PEG charging reveals that above a critical droplet size, ions are available near the backbone of the macromolecule, but charging occurs only transiently by transfer of ions from the solvent to the macroion, while below the critical size, the capture of the ion from PEG has a lifetime sufficiently long for extrusion of a charged PEG from the aqueous droplet. This is the first report of the role of droplet curvature in the relation between macroion conformation and charging. Simulations of peptides with high degree of hydrophobicity show that partial extrusion of a peptide from the droplet surface is rare relative to desolvation by drying-out. Differently from what has been presented in the literature we argue that atomistic MD simulations have not sufficiently established extrusion mechanism of proteins from droplets and their charging mechanism. We also argue that release of highly charged proteins can occur at an earlier stage of a droplet's lifetime than predicted by atomistic MD. In this earlier stage, we emphasize the key role of jets emanating from a droplet at the point of charge-induced instability in the release of proteins. | Victor Kwan; Pranav Ballaney; Titiksha Titiksha; Styliani Consta | Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644f35226ee8e6b5ed625bb0/original/limitations-of-atomistic-molecular-dynamics-to-reveal-ejection-of-proteins-from-charged-nanodroplets.pdf |
625af88fed4d8884bd0d221e | 10.26434/chemrxiv-2022-0g577 | Solution Processable Polytriazoles from Spirocyclic Monomers for Membrane-based Hydrocarbon Separations | The thermal distillation of crude oil mixtures is an energy intensive process conducted on massive scale worldwide. Membrane-based separations are, in principle, much more efficient in energetic terms, if useful fractions can be obtained. We describe here a family of spirocyclic polytriazoles for membrane applications prepared by a convenient step-growth method using copper-catalyzed azide-alkyne cycloaddition, providing very fast reaction rates, high molecular weights and solubilities in common organic solvents, and non-interconnected microporosity. Fractionation of whole Arabian light crude oil and atmospheric tower bottoms feeds using these materials significantly enriched the low-boiling components and removed trace heteroatom and metal impurities, demonstrating opportunities to reduce the energy cost of crude oil distillation with tandem membrane processes. Membrane-based molecular separation under these demanding conditions is made possible by high thermal stability and a moderate level of dynamic chain mobility leading to transient interconnections between micropores, as revealed by calculations of static and swollen pore structures. | Nicholas Bruno; Ronita Mathias; Guanghui Zhu; Yun-Ho Ahn; Neel Rangnekar; J.R. Johnson; Scott Hoy; Irene Bechis; Andrew Tarzia; Kim Jelfs; Benjamin McCool; Ryan Lively; MG Finn | Organic Chemistry; Polymer Science; Organic Polymers; Polymer morphology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625af88fed4d8884bd0d221e/original/solution-processable-polytriazoles-from-spirocyclic-monomers-for-membrane-based-hydrocarbon-separations.pdf |
60c74d6f469df47db7f4429a | 10.26434/chemrxiv.12618998.v1 | Layer-by-Layer Structural Identification of 2D Ruddlesden-Popper Hybrid Lead Iodide Perovskites by Solid-State NMR Spectroscopy | Application
of two-dimensional (2D) organic-inorganic hybrid halide perovskites for
optoelectronic devices requires detailed understanding of the local
structural features including the Pb-I bonding in the 2D layers and the capping
ligand-perovskite interaction. In this study, we show that <sup>1</sup>H and <sup>207</sup>Pb
solid-state Nuclear Magnetic Resonance (NMR) spectroscopy can serve as a
non-invasive and complementary technique to quantify the composition and to
probe the local structural features of 2D Ruddlesden-Popper phase BA<sub>2</sub>MA<i><sub>n</sub></i><sub>-1</sub>Pb<i><sub>n</sub></i>I<sub>3<i>n</i>+1</sub> (<i>n</i>=1-4) with butylammonium (BA) spacers. <sup>207</sup>Pb
echo and <sup>1</sup>H-detected <sup>207</sup>Pb→<sup>1</sup>H heteronuclear
correlation (HETCOR) experiments enables layer-by-layer structural detection of
2D halide perovskites. We show that the observed correlation between <sup>207</sup>Pb
NMR shifts and mean Pb-I bond lengths around each Pb site allows us to probe
the local bonding environment of Pb via its <sup>207</sup>Pb NMR shift. We
envisage that this technique will be vital for better understanding the
materials properties as determined by the local atomistic environments in
multi-dimensional halide perovskites. | Jeongjae Lee; Woocheol Lee; Keehoon Kang; Takhee Lee; Sung Keun Lee | Hybrid Organic-Inorganic Materials; Spectroscopy (Anal. Chem.); Spectroscopy (Inorg.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d6f469df47db7f4429a/original/layer-by-layer-structural-identification-of-2d-ruddlesden-popper-hybrid-lead-iodide-perovskites-by-solid-state-nmr-spectroscopy.pdf |
670e647acec5d6c142390042 | 10.26434/chemrxiv-2024-53lds | Metabolic Profiling of the EmDia Cohort by a Scalable DIA-LC-MS Workflow | The sodium glucose cotransporter-2 (SGLT2) inhibitor empagliflozin improves glycemic control in type 2 diabetes mellitus (T2DM) and has been suggested to additionally reduce CVD comorbidities. Clinical studies, such as the EmDia trial, investigate the short-term effects of empagliflozin on left ventricular diastolic function. Over the course of the trial, the metabolic effects of empagliflozin has been monitored by a limited set of clinical assays. To expand on this data, we here established a LC-MS workflow for comprehensive metabolic profiling of EmDIA. The workflow established enables profiling of >170 metabolites in plasma covering a broad range of compound classes such as carboxylic acids, amino acids, sugars, nucleotides, steroids and drugs at a rate of >100 samples per day. The method is based on optimized metabolite separation by pentafluorophenyl chromatography and high-confidence metabolite annotation based on a well curated in-house spectral library of more than 480 reference standards. Applied to EmDIA, our methodology is characterized by high predictive power of several clinical parameters, especially fasting blood glucose (R2 = 0.97) and estimated glomerular filtration rate (R2 = 0.63) as determined by elastic net-regularized linear and logistic regression. Our data further shows that administration of empagliflozin in addition to standard T2DM medication results in reduced plasma levels of urate, which has been previously linked to improved cardiovascular disease outcome, and reduced plasma levels of deoxyhexoses such as 1,5-anhydroglucitol, a short-term biomarker for glycemic control. | Fabian Constantin Schmitt; Vincent ten Cate; Zlatka Fischer; Mathias Hagen; Barbara A. Steigenberger; Stefan Tenzer; Philipp S. Wild; Thierry Schmidlin | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670e647acec5d6c142390042/original/metabolic-profiling-of-the-em-dia-cohort-by-a-scalable-dia-lc-ms-workflow.pdf |
60c73e14337d6ca46ae26282 | 10.26434/chemrxiv.6342881.v1 | Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation | <div>
<div>
<div>
<p>The most recent version of the Cahn-Ingold-Prelog rules for the determination of stereodescriptors
as described in Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred
Names 2013 (the “Blue Book”) were analyzed by an international team of cheminformatics software
developers. Algorithms for machine implementation were designed, tested, and cross-validated.
Deficiencies in Sequence Rules 1b and 2 were found, and proposed language for their modification
is presented. A concise definition of an additional rule (“Rule 6,” below) is proposed, which
succinctly covers several cases only tangentially mentioned in the 2013 recommendations. Each
rule is discussed from the perspective of machine implementation. The four resultant
implementations are supported by validation suites in 2D and 3D SDF format as well as SMILES.
The validation suites include all significant examples in Chapter 9 of the Blue Book, as well as
several additional structures that highlight more complex aspects of the rules not addressed or not
clearly analyzed in that work. These additional structures support a case for the need for
modifications of the Sequence Rules.
</p>
</div>
</div>
</div> | Robert M. Hanson; John Mayfield; Mikko J. Vainio; Andrey Yerin; Dmitry Redkin; Sophia Musacchio | Theory - Computational | CC BY 4.0 | CHEMRXIV | 2018-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e14337d6ca46ae26282/original/algorithmic-analysis-of-cahn-ingold-prelog-rules-of-stereochemistry-proposals-for-revised-rules-and-a-guide-for-machine-implementation.pdf |
60c755729abda2577ff8e345 | 10.26434/chemrxiv.14102312.v1 | A Comparative Life Cycle Assessment of Different Production Processes for Waterborne Polyurethane Dispersions | This study provides a comparative life cycle assessment (LCA) of four different polyurethane dispersion production processes from cradle-to-gate. The environmental performances of the NMP process, the acetone process, the melt process, and a conceptualized continuous flow process were evaluated and compared following the CML 2001 methodology. The LCA revealed that the conceptualized flow process exhibits the lowest environmental impact in all investigated impact categories. Depending on the impact category, the melt process or the acetone process rank second. The NMP process was observed to have the highest impact in all categories. Consequently, the flow process has the lowest carbon footprint (1.13 kg CO2-eq), according to the global warming potential (100 years), followed by the melt (1.45 kg CO2-eq), the acetone (1.95 kg CO2-eq) and the NMP process (3.11 kg CO2-eq). | Valentin Klug; Josef-Peter Schöggl; Doris Dallinger; Clemens Stueckler; Andreas Steiner; Anton Arzt; C. Oliver Kappe; Rupert J. Baumgartner | Coating Materials; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755729abda2577ff8e345/original/a-comparative-life-cycle-assessment-of-different-production-processes-for-waterborne-polyurethane-dispersions.pdf |
65045721b6ab98a41c7d42b9 | 10.26434/chemrxiv-2022-6k01r-v2 | Synthesis and Base Pairing Properties of Platinum(II) Nucleosides Based on Uracil | The synthesis and base pairing properties of platinum complexes based on uridine and deoxyuridine nucleosides are described. The synthesis was performed by C–I oxidative addition with protected and unprotected nucleosides. The metallated compounds feature an agostic interaction at H6. Uridine complexes undergo self-base pairing and also establish base pairs with adenosine. The formation of an intermolecular N-H-Pt bond is also observed | Maria Inês Leitão; Giulia Orsini; Fernanda Murtinheira; Clara Gomes; Federico Herrera; Ana Petronilho | Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Bond Activation; Bioorganometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65045721b6ab98a41c7d42b9/original/synthesis-and-base-pairing-properties-of-platinum-ii-nucleosides-based-on-uracil.pdf |
60c73f1b0f50db0438395735 | 10.26434/chemrxiv.7235393.v1 | Quadrupole Interaction of the SrTiO3:V4+ System | <div>Analysis were made to calculate the quadrupole interaction of the Jahn-Teller SrTiO3 system from enhanced EPR spectra due to an applied static electric field. The calculations gave a value for the quadrupole constant |P| = (-2.142 0.005)×10-4 cm-1</div> | Thomas (Tom) Kool | Optical Materials; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1b0f50db0438395735/original/quadrupole-interaction-of-the-sr-ti-o3-v4-system.pdf |
60c75061702a9b694d18bd5d | 10.26434/chemrxiv.13033217.v1 | A Data-Driven Perspective on the Colours of Metal-Organic Frameworks | <div>
<div>
<div>
<p>Colour is at the core of chemistry and has been fascinating humans since ancient
times. It is also a key descriptor of optoelectronic properties of materials and is used to
assess the success of a synthesis. However, predicting the colour of a material based on
its structure is challenging. In this work, we leverage subjective and categorical human
assignments of colours to build a model that can predict the colour of compounds
on a continuous scale, using chemically meaningful reasoning. In the process of
developing the model, we also uncover inadequacies in current reporting mechanisms.
For example, we show that the majority of colour assignments are subject to perceptive spread that would not comply with common printing standards. To remedy this, we
suggest and implement an alternative way of reporting colour—and chemical data
in general—that is more suitable for a data-driven approach to chemistry. All data is
captured in an electronic lab notebook and subsequently exported to a repository. </p>
</div>
</div>
</div> | Kevin Maik Jablonka; Seyed Mohamad Moosavi; Mehrdad Asgari; Christopher Ireland; Luc Patiny; Berend Smit | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75061702a9b694d18bd5d/original/a-data-driven-perspective-on-the-colours-of-metal-organic-frameworks.pdf |
60c74ad64c89194e8cad32fd | 10.26434/chemrxiv.12213275.v1 | Ligand Engineering in Cu(II) Paddle Wheel Metal-Organic Frameworks for Enhanced Electrical Conductivity | We report the electronic structure of two metal-organic frameworks (MOFs) with copper paddle wheel nodes connected by a N<sub>2</sub>(C<sub>2</sub>H<sub>4</sub>)<sub>3</sub> (DABCO) ligand with accessible nitrogen lone pairs. The coordination is predicted, from first-principles density functional theory, to enable electronic pathways that could facilitate charge carrier mobility. Calculated frontier crystal orbitals indicate extended electronic communication in DMOF-1, but not in MOF-649. This feature is confirmed by bandstructure calculations and effective masses of the valence band egde. We explain the origin of the frontier orbitals of both MOFs based on the energy and symmetry alignment of the underlying building blocks. The effects of doping on the bandstructure of MOF-649 are considered. Our findings highlight DMOF-1 as a potential semiconductor with 1D charge carrier mobility along the framework | Matthias Golomb; Joaquín Calbo; Jessica
K. Bristow; Aron Walsh | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ad64c89194e8cad32fd/original/ligand-engineering-in-cu-ii-paddle-wheel-metal-organic-frameworks-for-enhanced-electrical-conductivity.pdf |
6414f70caad2a62ca1ef2846 | 10.26434/chemrxiv-2023-4dqkx | Facile hyperpolarization chemistry for molecular imaging and metabolic tracking of [1-13C]pyruvate in vivo | Hyperpolarization chemistry based on reversible exchange of parahydrogen, also known as Signal Amplification By Reversible Exchange (SABRE), is a particularly simple approach to attain high levels of nuclear spin hyperpolarization, which can enhance NMR and MRI signals by many orders of magnitude. SABRE has received significant attention in the scientific community since its inception because of its relative experimental simplicity and its broad applicability to a wide range of molecules, however in vivo detection of molecular probes hyperpolarized by SABRE has remained elusive. Here we describe the first demonstration of SABRE-hyperpolarized contrast detected in vivo, specifically using hyperpolarized [1-13C]pyruvate. A biocompatible formulation of hyperpolarized [1-13C]pyruvate was injected into healthy Sprague Dawley and Wistar rats, and metabolic conversion of pyruvate to lactate, alanine, pyruvate-hydrate, and bicarbonate was detected. Measurements were performed on the liver and kidney at 4.7 T via time-resolved spectroscopy and chemical-shift-resolved MRI. In addition, whole-body metabolic measurements were obtained using a cryogen-free 1.5 T MRI system, illustrating the utility of combining lower-cost MRI systems with simple, low-cost hyperpolarization chemistry to develop scalable, next-generation molecular imaging. | Austin Browning; Keilian MacCulloch; David Guarin Bedoya; Carlos Dedesma; Boyd M Goodson; Matthew S Rosen; Eduard Y Chekmenev; Yi-Fen Yen; Patrick TomHon; Thomas Theis | Physical Chemistry; Biological and Medicinal Chemistry; Catalysis; Bioengineering and Biotechnology; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6414f70caad2a62ca1ef2846/original/facile-hyperpolarization-chemistry-for-molecular-imaging-and-metabolic-tracking-of-1-13c-pyruvate-in-vivo.pdf |
6728e27cf9980725cf118177 | 10.26434/chemrxiv-2024-rw8p5 | Exploration of crystal chemical space using text-guided generative artificial intelligence
| The vastness of chemical space presents a long-standing challenge for the exploration of new compounds with pre-determined properties. In materials science, crystal structure prediction has become a mature tool for mapping from composition to structure based on global optimisation techniques. Generative artificial intelligence (AI) now offers the means to efficiently navigate larger regions of crystal chemical space informed by structure-property datasets of materials. We introduce a model, named Chemeleon, designed to generate chemical compositions and crystal structures by learning from both textual descriptions and three-dimensional structural data. The model employs denoising diffusion techniques for compound generation using textual inputs aligned with structural data via cross-modal contrastive learning. The potential of this approach is demonstrated for multi-component compound generation, including the prediction of stable phases in the Li-P-S-Cl quaternary space of relevance to solid-state batteries. Our work highlights the potential of bridging geometric and linguistic data to unlock approaches to materials design. | Hyunsoo Park; Anthony Onwuli; Aron Walsh | Theoretical and Computational Chemistry; Materials Science; Theory - Computational; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6728e27cf9980725cf118177/original/exploration-of-crystal-chemical-space-using-text-guided-generative-artificial-intelligence.pdf |
6648b8e791aefa6ce15aa7b4 | 10.26434/chemrxiv-2024-z1jpj | Confinement Induced Alteration in Interfacial Energy | Hypothesis: When a liquid is confined between two parallel plates, the pressure field at its bulk alters, because of the concave meniscus at the air-water interface. For an aqueous surfactant solution in contact with an oil, like an oil-in-water emulsion, this effect can alter the surfactant concentration at the interface of the two phases thereby changing the interfacial energy. Alteration of interfacial energy is expected to affect morphology of a complex system consisting of three immiscible phases. Experiments: A drop of crosslinkable silicone liquid was placed on a glass slide and was immobilized by partial crosslinking. An aqueous solution of surfactant, with SiO2 microspheres dispersed in it, was dispensed on this drop to create a liquid pool. It was then confined between two parallel plates to create a meniscus. Finding: Consequently, the particles got embedded at the oil-water interface to different extent, depending on the degree of confinement. Force balance along tangents to different interfaces showed that the interfacial energy of silicone-water (aqCTAB 0.3 mM) interface increases from 33.3 ± 0.5 mJ/m2 for an unconfined system to 45.4 ± 2.2 mJ/m2 for the confined one. This effect then elucidates how confinement alters complex emulsion morphologies in multiphase systems. | Nitish Singh; Arka Roy; Animangsu Ghatak | Chemical Engineering and Industrial Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6648b8e791aefa6ce15aa7b4/original/confinement-induced-alteration-in-interfacial-energy.pdf |
60c74cf7bdbb8999cfa398ec | 10.26434/chemrxiv.12575954.v1 | Deciphering the Allosteric Process of Phaeodactylum tricornutum Aureochrome 1a LOV Domain | The conformational-driven allosteric protein diatom Phaeodactylum tricornutum aureochrome 1a (PtAu1a) di ers from other light-oxygen-voltage (LOV) proteins for its uncommon structural topology. The mechanism of signaling transduction in PtAu1a LOV domain (AuLOV) including flanking helices remains unclear because of this dissimilarity, which hinders the study of PtAu1a as an optogenetic tool. To clarify this mechanism, we employed a combination of tree-based machine learning models, Markov state models, machine learning based community analysis and transition path theory to quantitatively analyze the allosteric process. Our results are in good agreement with reported experimental findings and revealed a previously overlooked C-alpha helix and linkers as important in promoting the protein conformational change. This integrated approach can be considered as a general workflow and applied on other allosteric proteins to provide detailed information about their allosteric mechanisms. | Hao Tian; Francesco Trozzi; Brian Zoltowski; Peng Tao | Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cf7bdbb8999cfa398ec/original/deciphering-the-allosteric-process-of-phaeodactylum-tricornutum-aureochrome-1a-lov-domain.pdf |
60c75659bb8c1a7b8c3dc5f8 | 10.26434/chemrxiv.14230043.v1 | Temperature-Dependent Solid-State NMR Proton Chemical-Shift Values and Hydrogen Bonding | Temperature-dependent NMR experiments are often complicated by rather long magnetic-field equilibration times, for example occurring upon a change of sample temperature. We demonstrate that the fast temporal stabilization of the magnetic field can be achieved by actively stabilizing the temperature which allows to quantify the weak temperature dependence of the proton chemical shift which can be diagnostic for the presence of hydrogen bonds. Hydrogen bonding plays a central role in molecular recognition events from both fields, chemistry and biology. Their direct detection by standard structure determination techniques, such as X-ray crystallography or cryo-electron microscopy, remains challenging due to the difficulties of approaching the required resolution, on the order of 1 Å. We herein explore a spectroscopic approach using solid-state NMR to identify protons engaged in hydrogen bonds and explore the measurement of proton chemical-shift temperature coefficients. Using the examples of a phosphorylated amino acid and the protein ubiquitin, we show that fast Magic-Angle Spinning (MAS) experiments at 100 kHz yield sufficient resolution in proton-detected spectra to quantify the rather small chemical-shift changes upon temperature variations.<br /> | Alexander A. Malär; Laura A. Völker; Riccardo Cadalbert; Lauriane Lecoq; Matthias Ernst; Anja Böckmann; Beat H. Meier; Thomas Wiegand | Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75659bb8c1a7b8c3dc5f8/original/temperature-dependent-solid-state-nmr-proton-chemical-shift-values-and-hydrogen-bonding.pdf |
60e71816551cb0d1e6ad9db5 | 10.26434/chemrxiv-2021-fpfkt-v2 | Materials Precursor Score: Modelling Chemists' Intuition for the Synthetic Accessibility of Porous Organic Cage Precursors | <div>Computation is increasingly being used to try to accelerate the discovery of new materials. One specific example of this is porous molecular materials, specifically porous organic cages, where the porosity of the materials predominantly comes from the internal cavities of the molecules themselves. The computational discovery of novel structures with useful properties is currently hindered by the difficulty in transitioning from a computational prediction to synthetic realisation. Attempts at experimental validation are often time-consuming, expensive and, frequently, the key bottleneck of material discovery. In this work, we developed a computational screening workflow for porous molecules that includes consideration of the synthetic difficulty of material precursors, aimed at easing the transition between computational prediction and experimental realisation. We trained a machine learning model by first collecting data on 12,553 molecules categorised either as `easy-to-synthesise' or `difficult-to-synthesise' by expert chemists with years of experience in organic synthesis. We used an approach to address the class imbalance present in our dataset, producing a binary classifier able to categorise easy-to-synthesise molecules with few false positives. We then used our model during computational screening for porous organic molecules to bias towards precursors whose easier synthesis requirements would make them promising candidates for experimental realisation and material development. We found that even by limiting precursors to those that are easier-to-synthesise, we are still able to identify cages with favourable, and even some rare, properties. </div> | Steven Bennett; Filip Szczypiński; Lukas Turcani; Michael Briggs; Rebecca L. Greenaway; Kim Jelfs | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e71816551cb0d1e6ad9db5/original/materials-precursor-score-modelling-chemists-intuition-for-the-synthetic-accessibility-of-porous-organic-cage-precursors.pdf |
60c7582c0f50db30e23983e2 | 10.26434/chemrxiv.14518860.v1 | Quantum Interference and Spin Filtering Effects in Photo-responsive Endoperoxide Based Single Molecular Device | <div>The development of stimuli responsive systems that can switch between two distinct spin states under the application of an external stimuli has always remained an illusory challenge. Here, we report a stimuli-based spin filter by utilizing photo-responsive endoperoxide (EPO) based single molecule device. The photo-irradiation on EPO triggers the homolytic cleavage of the peroxide O-O bond generating diradical intermediate centered on two O-atoms which facilitates high spin filtering efficiency when placed between gold electrodes. The broken conjugated scenario due to peroxide bridge of EPO hinders the propagation of de-Broglie waves across the molecular skeleton. While the diradical intermediate of EPO yields high conductance for one of the spin configuration. The transmission characteristics of various photoproducts along the photochemical reaction pathway of EPO are also investigated using density functional theory in combination with non-equilibrium Green’s function (NEGF-DFT) technique. We demonstrate the key role played by Quantum Interference (QI) effects in dramatic modulation of conductance arising due to different degree of conjugation along the reaction pathway of EPO.</div><div><br /></div> | Ashima Bajaj; Rishu Khurana; Md. Ehesan Ali | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7582c0f50db30e23983e2/original/quantum-interference-and-spin-filtering-effects-in-photo-responsive-endoperoxide-based-single-molecular-device.pdf |
666a402512188379d8f9682c | 10.26434/chemrxiv-2024-vpddp | Enantioselective Decarboxylative C(sp3)-C(sp3) Cross-Coupling of Aliphatic Acids with gem-Borazirconocene Alkanes | Asymmetric decarboxylative cross-couplings of carboxylic acids represent a powerful tool to synthesize chiral building blocks for medicinal chemistry and material science. However, synthesis of versatile chiral alkylboron derivatives via asymmetric decarboxylative C(sp3)-C(sp3) cross-coupling from readily available primary aliphatic acids and mild organometallic reagents is still challenging. In this study, we report a visible-light-induced, Ni-catalyzed enantioconvergent C(sp3)-C(sp3) cross-coupling of unactivated primary aliphatic acids with gem-borazirconocene alkanes, furnishing a diverse array of valuable chiral alkylboron building blocks. The broad substrate scope, high functional group tolerance, and the late-stage modification of complex drug molecules and natural products with high enantioselectivity demonstrate the synthetic potential of the method. Mechanistic investigations suggest an enantioconvergent radical-radical cross-coupling pathway, wherein the primary radical from carboxylic acids is generated through single-electron reduction with ZrIII species, representing an unprecedented example of enantioselective radical C(sp3)-C(sp3) cross coupling in the absence of photocatalysts. | Jing Wang; Songlin Bai; Chao Yang; Xiangbing Qi | Organic Chemistry; Organometallic Chemistry; Photochemistry (Org.); Stereochemistry; Ligand Design | CC BY 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666a402512188379d8f9682c/original/enantioselective-decarboxylative-c-sp3-c-sp3-cross-coupling-of-aliphatic-acids-with-gem-borazirconocene-alkanes.pdf |
6389d19e92f0841e3223efcf | 10.26434/chemrxiv-2022-2nc4q | Quest for a Rational Molecular Design of Alkyl–Distyrylbenzene Liquid by Substitution Pattern Modulation | Alkyl-π functional molecular liquids (FMLs) are of interest for fabricating soft electronic devices due to their fluidic nature and innate optoelectronic functions from the π-conjugated moiety. However, predictable development of alkyl-π FMLs with the desired liquid and optoelectronic properties is challenging. A series of alkyl–distyrylbenzene (DSB) liquids was studied in terms of the substituent position effect by attaching 2-octyldodecyl chains at (2,4-), (2,5-), (2,6-), and (3,5-). The effect of the alkyl chain length was investigated by attaching 2-hexyldecyl, 2-decyltetradecyl (C10C14), and 2-dodecylhexadecyl at the (2,5-) substituent position. The 2,5-C10C14 substituent pattern constructed a superior alkyl–DSB liquid with a lower viscosity, intrinsic optical properties, and high thermal- and photo-stabilities. The discovered 2,5-C10C14 was applied to dicyanostyrylbenzene and comparable liquid physical and optical superiorities were confirmed. This molecular design is useful for creating alkyl-π FMLs with the aforementioned advantages, which are applicable for deformable and flowable optoelectronic devices. | Xiao Zheng; Kazuhiko Nagura; Tomohisa Takaya; Kenjiro Hashi; Takashi Nakanishi | Physical Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.); Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6389d19e92f0841e3223efcf/original/quest-for-a-rational-molecular-design-of-alkyl-distyrylbenzene-liquid-by-substitution-pattern-modulation.pdf |
60c747afee301c7d24c7973e | 10.26434/chemrxiv.11763846.v1 | Evolutionary Chemical Space Exploration for Functional Materials: Computational Organic Semiconductor Discovery | Computational methods, including crystal structure and property prediction, have the potential to accelerate the materials discovery process by enabling structure prediction and screening of possible molecular building blocks prior to their synthesis. However, the discovery of new functional molecular materials is still limited by the need to identify promising molecules from a vast chemical space. We describe an evolutionary method which explores a user specified region of chemical space to identify promising molecules, which are subsequently evaluated using crystal structure prediction. We demonstrate the methods for the exploration of aza-substituted pentacenes with the aim of finding small molecule organic semiconductors with high charge carrier mobility, where the space of possible substitution patterns is too large to exhaustively search using a high throughput approach. The method efficiently explores this large space, typically requiring calculations on only ca.1% of molecules during a search. The results reveal two promising structural motifs: aza-substituted naphtho[1,2-a]anthracenes with reorganisation energies as low as pentacene and a series of pyridazine-based molecules having both low reorganisation energies and high electron affinities. | Chi Y. Cheng; Josh E. Campbell; Graeme Day | Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Machine Learning; Self-Assembly; Structure; Crystallography; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747afee301c7d24c7973e/original/evolutionary-chemical-space-exploration-for-functional-materials-computational-organic-semiconductor-discovery.pdf |
62344b55658bc0eb7eaf26b0 | 10.26434/chemrxiv-2022-3sqwp | Chemical Reaction Network Knowledge Graphs: the OntoRXN Ontology | The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities on a certain field and how these entities are interrelated. In this work, we introduce OntoRXN, a novel ontology describing the reaction networks constructed from computational chemistry calculations. Under our paradigm, these networks are handled as undirected graphs, without assuming any traversal direction. From there, we propose a core class structure including reaction steps, network stages, chemical species, and the lower-level entities for the individual computational calculations. These individual calculations are founded on the OntoCompChem ontology and on the ioChem-BD database, where information is parsed and stored in CML format. OntoRXN is introduced through several examples in which knowledge graphs based on the ontology are generated for different chemical systems available on ioChem-BD. Finally, the resulting knowledge graphs are explored through SPARQL queries, illustrating the power of the semantic approach to standardize the analysis of intricate datasets and to simplify the development of complex workflows.
| Diego Garay-Ruiz; Carles Bo | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62344b55658bc0eb7eaf26b0/original/chemical-reaction-network-knowledge-graphs-the-onto-rxn-ontology.pdf |
60c74909337d6c3658e2764e | 10.26434/chemrxiv.12014925.v1 | Assembly of a Patchy Protein into Variable 2D Lattices via Tunable, Multiscale Interactions | Self-assembly of molecular building blocks into higher-order structures is exploited in living systems to create functional complexity and represents a powerful synthetic strategy for constructing new materials. As nanoscale building blocks, proteins offer unique advantages, including monodispersity and atomically tunable interactions. Yet, control of protein self-assembly has been limited compared to that of inorganic or polymeric nanoparticles, which lack such attributes. We report modular self-assembly of an engineered protein into four physicochemically distinct, precisely patterned 2D crystals via control of four classes of interactions acting locally, regionally and globally. We relate the resulting structures to the underlying free-energy landscape by combining in-situ atomic force microscopy observations of assembly with thermodynamic analyses of protein-protein and -surface interactions. Our results demonstrate rich phase behavior obtainable from a single, highly-patchy protein when interactions acting over multiple length scales are exploited and predict new bulk-scale properties for protein based materials that ensue from such control.<div>
</div> | Shuai Zhang; Robert Alberstein; James De Yoreo; F. Akif Tezcan | Biological Materials; Nanostructured Materials - Materials; Biochemistry; Biophysics; Biophysical Chemistry; Interfaces; Self-Assembly; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74909337d6c3658e2764e/original/assembly-of-a-patchy-protein-into-variable-2d-lattices-via-tunable-multiscale-interactions.pdf |
60c7453dee301cc8b5c79299 | 10.26434/chemrxiv.9994940.v1 | Real-Time in situ Observations Reveal a Double Role for Ascorbic Acid in the Anisotropic Growth of Silver on Gold | Rational nanoparticle design is one of the main goals of materials science, but it can only be achieved via a thorough understanding of the growth process and of the respective roles of the molecular species involved. We demonstrate that a combination of complementary techniques can yield novel information with respect to their individual contributions. We monitored the growth of long aspect ratio silver rods from gold pentatwinned seeds by three in situ techniques (small-angle x-ray scattering, optical absorbance spectroscopy and liquid-cell transmission electron microscopy). Exploiting the difference in reaction speed between the bulk synthesis and the nanoparticle formation in the TEM cell, we show that the anisotropic growth is thermodynamically controlled (rather than kinetically) and that ascorbic acid, widely used for its mild reductive properties plays a shape-directing role, by stabilizing the {100} facets of the silver cubic lattice, in synergy with the halide ions. This approach can easily be applied to a wide variety of synthesis strategies.<br /> | Kinanti Aliyah; Jieli Lyu; Claire Goldmann; Thomas Bizien; Cyrille Hamon; Damien Alloyeau; Doru Constantin | Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453dee301cc8b5c79299/original/real-time-in-situ-observations-reveal-a-double-role-for-ascorbic-acid-in-the-anisotropic-growth-of-silver-on-gold.pdf |
65440b4648dad23120f43add | 10.26434/chemrxiv-2023-r72sm-v2 | Elucidating the effects of temperature on nonaqueous redox flow cell cycling performance | The impact of cell temperature is a relatively underexplored area within the burgeoning field of nonaqueous redox flow batteries (NAqRFBs). Here, we investigate the effect of elevated temperature on the performance of nonaqueous redox electrolytes and associated flow cells. Using a model compound, N-(2-(2-methoxyethoxy)-ethyl)phenothiazine (MEEPT), in a propylene-carbonate-based electrolyte, we experimentally measure the temperature dependence of relevant physicochemical properties (i.e., electrolyte conductivity, viscosity, diffusivity) and electrochemical characteristics (i.e., chemical and electrochemical reversibility) across a temperature range of 30 to 70 °C. We then perform flow cell studies, finding that while ohmic and mass transport resistances decrease significantly with increases in temperature for the MEEPT/MEEPT+● redox couple, accessible electrolyte capacity gradually reduces at temperatures >50 °C. Ex-situ, post-test characterization using microelectrode voltammetry suggests that this capacity fade is due to instability of the MEEPT radical cation. Finally, using MEEPT as a posolyte and a model viologen negolyte (bis(2-(2-methoxyethoxy)ethyl)viologen), we assemble a full cell and perform polarization analysis, observing a 2× increase in the peak power density when the operating temperature is increased from 30 to 70 °C. Broadly, this work highlights opportunities for systematic engineering of nonaqueous electrolytes and flow cells for higher power operation at elevated temperatures. | Alexander Quinn; Katelyn Ripley; Nicholas Matteucci; Bertrand Neyhouse; Chloe Brown; William Woltmann; Fikile Brushett | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65440b4648dad23120f43add/original/elucidating-the-effects-of-temperature-on-nonaqueous-redox-flow-cell-cycling-performance.pdf |
67d8777d6dde43c9082697c9 | 10.26434/chemrxiv-2025-d51r9-v2 | Rapid Acquisition of 103Rh Solid-State NMR Spectra by 31P Detection and Sideband Selective Methods | 103Rh solid-state nuclear magnetic resonance (SSNMR) spectroscopy is potentially a powerful method for investigating the molecular and electronic structure of rhodium compounds. However, 103Rh is a difficult nucleus to study by NMR spectroscopy because of its small gyromagnetic ratio, broad chemical shift range, and long spin-lattice relaxation times (T1). While there are many prior reports demonstrating acquisition of 103Rh solution NMR spectra, there are few examples of 103Rh SSNMR spectra in the literature. Here, we utilize the large 31P-103Rh scalar couplings (J-couplings) to efficiently acquire 31P-detected high-resolution 103Rh SSNMR spectra. 31P{103Rh} J-resolved NMR experiments were used to measure 31P-103Rh J-couplings. Sideband selective SSNMR techniques originally developed for wideline 195Pt SSNMR experiments were then used to rapidly acquire 103Rh SSNMR spectra. Notably, we were able to acquire MAS 103Rh SSNMR spectra in experiment times on the order of 30 minutes to a few hours and from only a few mg of materials. The sideband selective experiments offer significant time savings as compared to existing direct detection methods, which require days of acquisition to obtain a directly detected MAS spectrum, or yield low-resolution static powder patterns. Numerical fits of the spectra provide chemical shift tensor parameters, with the experimental spectra agreeing well with the DFT-calculated spectra. | Benjamin Atterberry; Piotr Paluch; Andrew Lamkins; Wenyu Huang; Aaron Rossini | Physical Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d8777d6dde43c9082697c9/original/rapid-acquisition-of-103rh-solid-state-nmr-spectra-by-31p-detection-and-sideband-selective-methods.pdf |
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