jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Misbah Naseem | Saleha Asghar | Umar Farooq | Ahmed Lakhani | Yasir Altaf | Muhammad Alı Hashmı
Source: ACS Omega (article, 2023-01-04)
Field: Chemistry — Spectroscopy

Determination of the Absolute Configuration of Ballonigrin Lactone A Using Density Functional Theory Calculations We report the determination of the absolute configuration of a diterpenoid, namely, ballonigrin lactone A (BLA), by comparison of the computed optical rotations, [α]D, of its two diastereomers using density functional theory (DFT) calculations to the experimental [α]D value of +22.4. One of the diastereomers having configurations 4S, 5R, 6S, 10S, 15S was named “α-BLA,” and the other one with configuration 4S, 5R, 6S, 10S, 15R was called “β-BLA”. Six conformers for each diastereomer (α-BLA and β-BLA) of BLA were identified through their conformational analysis. [α]D values of these six conformations for each diastereomer were calculated using DFT at the mPW1PW91/6-311G(d,p)/SMDChloroform level of theory, leading to the conformationally averaged [α]D values of −96.8 for α-BLA and +65.1 for β-BLA. Thus, it was found that the experimental [α]D value of +22.4 was of 4S, 5R, 6S, 10S, 15R, i.e., β-BLA. Experimental and computed nuclear magnetic resonance (NMR) data were also compared, and this comparison was in accordance with the conclusion drawn from the comparison of [α]D values. Finally, the results were augmented with the calculation of the DP4 analysis, and the probability obtained also endorsed our earlier calculations. Density functional theory ; Absolute configuration ; Absolute (philosophy) ; Computational chemistry ; Chemistry ; Stereochemistry ; Philosophy ; Epistemology Molecular spectroscopy and chirality ; Phytochemistry and Biological Activities ; Natural product bioactivities and synthesis
Authors: Patrick Purder | Christian Meyners | Wisely Sugiarto | Jürgen Kolos | Frank Löhr | Jakob Gebel | Thomas Nehls | Volker Dötsch | Frederik Lermyte | Felix Hausch
Source: ChemRxiv (preprint, 2023-05-12)
Field: Chemistry — Organic Chemistry

Deconstructing Protein Binding of Sulfonamides and Sulfonamide Analogs Sulfonamides are one of the most important pharmacophores in medicinal chemistry and sulfonamide analogs have gained substantial interest in recent years. However, the protein interactions of sulfonamides and especially of their analogs are underexplored. Using FKBP12 as a model system, we describe the synthesis of optically pure sulfenamide, sulfinamide and sulfonimidamide analogs of a well characterized sulfonamide ligand. This allowed us to precisely determine the binding contributions of each sulfonamide oxygen atom and the consequence of nitrogen replacements. We also present high resolu-tion cocrystal structures of sulfonamide analogs buried in the pocket of a protein target. This revealed intimate contacts with the protein, including an unprecedented hydrogen bond acceptor of sulfonimidamides. The use of sulfonamide analogs ena-bled new exit vectors that allowed to remodel a subpocket in FKBP12. Our results illuminate the protein interaction potential of sulfonamides/sulfonamide analogs and will aid in their rational design. Sulfonamide ; Chemistry ; Pharmacophore ; Combinatorial chemistry ; Stereochemistry Synthesis and Catalytic Reactions ; Enzyme function and inhibition ; Receptor Mechanisms and Signaling
Authors: Martti Kaasalainen | Ran Zhang | Priya Vashisth | Anahid A. Birjandi | Mark S’ari | Davide Alessandro Martella | Mark A. Isaacs | Ermei Mäkilä | Cong Wang | Evelin Moldenhauer | Paul B. S. Clarke | Alessandra Pinna | Valeria Caprettini | Alexander Morell | Owen Addison | Xuehui Zhang | Mads S. Bergholt | Khuloud T. Al‐Jamal | Ana Angelova Volponi | Jarno Salonen | Nicole Hondow | Paul T. Sharpe | Ciro Chiappini
Source: Research Square (preprint, 2023-01-04)
Field: Materials Science — Materials Chemistry

Lithiated porous silicon nanowires stimulate periodontal regeneration Abstract Periodontal disease is a significant burden for oral health, causing progressive and irreversible damage to the support structure of the tooth. This complex structure, the periodontium, is composed of interconnected soft and mineralised tissues, posing a challenge for regenerative approaches. Materials combining silicon and lithium are widely studied in periodontal regeneration, as they stimulate bone repair via silicic acid release while providing regenerative stimuli through lithium activation of the Wnt/β-catenin pathway. Yet, existing materials for combined lithium and silicon release have limited control over ion release amounts and kinetics. Porous silicon can provide controlled silicic acid release, inducing osteogenesis to support bone regeneration. Prelithiation, a strategy developed for battery technology, can introduce large, controllable amounts of lithium within porous silicon, but yields a highly reactive material, unsuitable for biomedicine. This work debuts a strategy to lithiate porous silicon nanowires (LipSiNs) which generates a biocompatible and bioresorbable material. LipSiNs incorporate lithium to between 1% and 40% of silicon content, releasing lithium and silicic acid in a tailorable fashion from days to weeks. LipSiNs combine osteogenic, cementogenic and Wnt/β-catenin stimuli to regenerate bone, cementum and periodontal ligament fibres in a murine periodontal defect. Nanowire ; Regeneration (biology) ; Materials science ; Porous silicon ; Silicon ; Silicon nanowires ; Porosity ; Business ; Nanotechnology ; Chemical engineering ; Composite material ; Metallurgy ; Cell biology ; Engineering Silicon Nanostructures and Photoluminescence ; Nanowire Synthesis and Applications ; Dielectric properties of ceramics
Authors: Elin Dypvik Sødahl | Seyedmojtaba Seyedraoufi | Carl Henrik Görbitz | Kristian Berland
Source: arXiv (Cornell University) (preprint, 2023-06-12)
Field: Materials Science — Materials Chemistry

Discovering Ferroelectric Plastic (Ionic) Crystals in the Cambridge Structural Database: Database Mining and Computational Assessment Hybrid or organic plastic crystals have the potential as lead-free alternatives to conventional inorganic ferroelectrics. These materials are gaining attention for their multiaxial ferroelectricity, above-room-temperature Curie temperatures, and low-temperature synthesis. Here, we report a screening study of the Cambridge Structural Database (CSD) resulting in 55 new candidate plastic and plastic ionic ferroelectric molecular crystals, along with 16 previously reported ferroelectrics. With over 1.2 million entries in the CSD, the screening procedure involved many steps, including considerations of molecular geometry and size, space group, and hydrogen bonding pattern. The spontaneous polarization and electronic band gaps were predicted using density functional theory. 21 of the candidate ferroelectrics have a polarization greater than $10 \mathrm{μC/cm^2}$, out of which nine are reported at room temperature. Ferroelectricity ; Plastic crystal ; Ionic bonding ; Curie temperature ; Materials science ; Polarization (electrochemistry) ; Density functional theory ; Curie ; Database ; Condensed matter physics ; Ion ; Optoelectronics ; Chemistry ; Computational chemistry ; Physical chemistry ; Computer science ; Dielectric ; Physics Machine Learning in Materials Science ; Inorganic Fluorides and Related Compounds ; Data Quality and Management
Authors: John M. Herbert
Source: ChemRxiv (preprint, 2023-12-12)
Field: Chemistry — Electrochemistry

Visualizing and Characterizing Excited States from Time-Dependent Density Functional Theory Time-dependent density functional theory (TD-DFT) is the most widely-used electronic structure method for excited states, due to a favorable combination of low cost and (in many contexts) semi-quantitative accuracy. This Perspective describes various ways in which excited states from TD-DFT calculations can be visualized and analyzed, both qualitatively and quantitatively. This includes not just orbitals and densities but also well-defined statistical measures of electron-hole separation and of Frenkel-type exciton delocalization. Emphasis is placed on mathematical connections between methods that have often been discussed separately. Particular attention is paid to charge-transfer diagnostics, which provide indicators to diagnose when TD-DFT may not be trustworthy due to its categorical failure to describe long-range electron transfer. Measures of exciton size and charge separation that are directly connected to the underlying transition density are recommended over more ad hoc metrics for quantifying charge-transfer character. Excited state ; Delocalized electron ; Exciton ; Density functional theory ; Atomic orbital ; Categorical variable ; Charge (physics) ; Statistical physics ; Electron ; Physics ; Atomic physics ; Computer science ; Quantum mechanics ; Machine learning Electrochemical Analysis and Applications ; Molecular Junctions and Nanostructures ; Photochemistry and Electron Transfer Studies
Authors: Di Song | Tianrui ZHENG | Zhuoran Kuang | Andong Xia
Source: Chinese Journal of Luminescence (article, 2023-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

Effect of Solvation on Thermally Activated Delayed Fluorescence Within Electron Donor/Acceptor Chromophores å ·æç­æ¿æ´»å»¶è¿è§å ï¼Thermally activated delayed fluorescenceï¼TADFï¼ç¹æ§çææºç»ãåä½ï¼Donorâacceptorï¼DâAï¼åå­ä½ç³»éè¿ååç³»é´çªè¶æè·ä¸éææ¿å­ï¼å¯ä»¥å°å éå­æçççè®ºä¸éæé«å°100%ï¼å èåå°æå¤§å ³æ³¨ãéå¸¸ï¼å ·æåå­å çµè·è½¬ç§»ç¹æ§çDâAä½ç³»å¯ä»¥éè¿æå»ºæ­æ²çåå­æè±¡æ¥åå°åãä¸éæä¹é´çè½å·®Î<italic>E</italic><sub>SâT</sub>ï¼ä»¥ç¡®ä¿ååç³»é´çªè¶å¿«éåçãå½åå­è¢«æ¿ååï¼è¥æ¿åææè±¡ä¸­DâAçäºé¢è§æ´æ¥è¿90Ëæ¶ï¼Î<italic>E</italic><sub>SâT</sub>ä¼æ´å°ï¼å»¶è¿è§å ä¹ä¼å¢å¼ºãç¶èï¼å¿«éçæº¶ååè¿ç¨å¸¸å¸¸ä¼å½±åæ¿åææè±¡ãåå­å çµè·è½¬ç§»è¿ç¨ãå»¶è¿è§å åå°ï¼è¿ä½¿å¾ç ç©¶TADFåå­åå è¿ç¨æ´å¯æææãæ¬æç»¼è¿°äºæ¬è¯¾é¢ç»è¿æå¨æº¶ååå¯¹DâAä½ç³»å»¶è¿è§å çå½±ååè°æ§æ¹é¢æåå¾çåæ­¥è¿å±ãç»ææ¾ç¤ºï¼å¼ºææ§æº¶åä¼å¯¼è´éè¾å°å¼è±«å¢å ï¼ä¸å©äºTADFåå°ï¼æ¹åæº¶åç²åº¦ä¼å½±åæ¿åææè±¡å¼è±«ï¼ä»èå¯ä»¥å®ç°å¯¹TADFçå¢å¼ºæåå¼±çè°æ§ãè¿äºç»ææå©äºçè§£æº¶ååæåºä¸æè±¡å¼è±«ãTADFä¹é´çå ³ç³»ï¼ä¸ºTADFåå­çè®¾è®¡ä¸åææä¾æå¯¼ã Materials science ; Fluorescence ; Acceptor ; Electron donor ; Chromophore ; Photochemistry ; Chemistry ; Optics ; Catalysis ; Organic chemistry ; Physics ; Condensed matter physics Photochemistry and Electron Transfer Studies ; Electrochemical Analysis and Applications ; Photonic and Optical Devices
Authors: Hengyue Wang | Zhiyong Zhang
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-09-05)
Field: Materials Science — Materials Chemistry

Supporting CIF Format of Biomolecular Structures in GROMACS Abstract In the Protein Data Bank (PDB), the PDB format stands as the major file format for protein structures. However, there are certain intrinsic limitations in the PDB format, such as the storage of structural information in a fixed-width format that would be an issue for very large protein complexes. Therefore, the CIF (crystallographic information framework) format has been proposed, which is characterized by superior expansibility. GROMACS, a widely used software suite for molecular dynamics simulations, currently supports only the PDB format. In this study, we modified the source code of GROMACS, which enables it to support the CIF format structure files as input and subsequently generate molecular topology files. This work simplifies the preprocessing of large protein complexes for MD simulations. Program summary Program title: GROMACS-CIF GitHub link to program files: https://github.com/zyzhangGroup/Gromacs-CIF Licensing provisions: GPL-3.0 license Programming language: C++ Nature of problem: GROMACS currently supports only the PDB format but does not support the CIF format of protein structures. For a very large protein complex, the PDB format is not suitable, and only a CIF file is available in the protein data bank. However, the latter cannot be used as a direct input of GROMACS. Solution method: Source codes of the program “pdb2gmx” in GROMACS have been modified by adding several CIF analysis functions parallel to the PDB analysis functions. Protein Data Bank (RCSB PDB) ; Computer science ; Protein Data Bank ; Software ; MIT License ; Computational science ; Preprocessor ; File format ; Programming language ; Protein structure ; Chemistry Enzyme Structure and Function ; Protein Structure and Dynamics ; Microbial Metabolic Engineering and Bioproduction
Authors: Lei Wang | Clodette Punzalan | Bekim Bajrami | Louis Riel | Bin Deng | Amy R. Howell | Xudong Yao
Source: ChemRxiv (preprint, 2023-03-16)
Field: Chemistry — Spectroscopy

Single-Sequence Identification of Modified Peptides: A One-Pot Method Using Homologous Biotinyl Azides Identifying probe-modified peptides in chemical proteomics experiments is challenging due to the production of only one modified peptide per probe reaction at a specific site on a protein and the possibility of inconclusive proteomic identification. To address these issues, we propose a principle of Single-Sequence Identification (SSI) and a method for identifying probe-modified peptides in chemical proteomics experiments. The new approach creates multiple versions of the modified peptide in the proteomic identification space to increase identification probability and confidence. The SSI method, tagging-triplication, is implemented using a one-pot triplex tagging approach, attaching three homologous biotinyl azides with different PEG linker lengths to clickable proteins. The identification of modified peptides carrying two forms of tags was assigned as confident, with tag diagnostic ions and elution time dependent on the linker length further enhancing confidence. Variability in CuAAC-tagged proteins was also identified, and a split-and-pool strategy was recommended to minimize the variability. The tagging-triplication method can be easily integrated into existing chemical proteomics workflows to identify peptides modified by alkynyl covalent probes confidently. Our findings demonstrate the potential of the SSI principle to significantly enhance modified peptide identification for proteomes with post-translational and chemical modifications. Data are available through ProteomeXchange: identifier PXD037770. Proteomics ; Linker ; Proteome ; Identification (biology) ; Computational biology ; Peptide ; Combinatorial chemistry ; Chemistry ; Sequence (biology) ; Peptide sequence ; Computer science ; Biochemistry ; Biology ; Gene Advanced Proteomics Techniques and Applications ; Advanced biosensing and bioanalysis techniques ; Advanced Biosensing Techniques and Applications
Authors: Narsingh Verma | Ravindra Singh | Dushyant Singh Raghuvanshi
Source: ChemistrySelect (article, 2023-06-13)
Field: Chemistry — Organic Chemistry

A New Avenue to Diversity‐Oriented Synthesis of Diaryl Sulfones Abstract We describe a highly efficient route for the sulfonylation (C‐SO 2 ) of various halo arenes, boronic acids, and aromatic diazonium salt through a cross‐coupling reaction. The protocol incorporates the efficient use of Cu(OAc) 2 /K 2 CO 3 and N‐Hydoxy aryl sulfonamide as an aryl sulfone surrogate. Various substrates and functional groups were well tolerated in this reaction system. Aryl ; Sulfone ; Sulfonamide ; Chemistry ; Combinatorial chemistry ; Functional diversity ; Reaction conditions ; Coupling reaction ; Organic chemistry ; Catalysis ; Biology Sulfur-Based Synthesis Techniques ; Catalytic C–H Functionalization Methods ; Radical Photochemical Reactions
Authors: Angus C. Grey | Qingsong Lin | Teck Yew Low | Wei Wu | Paul A. Haynes | M.C.M. Chung | Yu‐Ju Chen | Stuart J. Cordwell | Yasushi Ishihama | Ping Xu | Peter Hoffmann | Ho Jeong Kwon | Terence Chuen Wai Poon
Source: Molecular & Cellular Proteomics (article, 2023-07-31)
Field: Chemistry — Spectroscopy

11th Asia Oceania Human Proteome Organization Congress Report As the first in-person Asia Oceania Human Proteomics Organization (AOHUPO) congress since 2018, the 11th AOHUPO congress was an opportune time for the research community to reconnect and to renew friendships after the long period of restricted travel due to the global pandemic. Moreover, this congress was a great opportunity for the many AO regional proteomics and mass spectrometry scientists to meet in Singapore to exchange ideas and to present their latest findings. Cohosted by the Singapore Society for Mass Spectrometry and the Malaysian Proteomics Society and held in conjunction with the seventh Asia Oceania Agricultural Proteomics Organization Congress and Singapore Society for Mass Spectrometry 2023, the meeting featured both human and agricultural proteomics. Over five hundred scientists from the AO region converged on the MAX Atria @ Singapore EXPO, Changi, Singapore from May 8 to 10 for the main congress. The diverse program was made up of 64 invited speakers and panellists for seven plenary lectures, 27 concurrent symposia, precongress and postcongress workshops, and 174 poster presentations. The AOHUPO society were able to celebrate not only their 20th anniversary but also the outstanding academic research from biological and agricultural proteomics and related 'omics fields being conducted across the Asia-Oceania region. Library science ; Political science ; Proteomics ; Human proteome project ; China ; Agriculture ; Chinese academy of sciences ; Data science ; Geography ; Biology ; Law ; Computer science ; Archaeology Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Metabolomics and Mass Spectrometry Studies
Authors: Suresh Mani | R. Ramesh Raju | Natarajan Arumugam | Abdulrahman I. Almansour | Raju Suresh Kumar | Karthikeyan Perumal
Source: Green Processing and Synthesis (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

A one-pot, multicomponent tandem synthesis of fused polycyclic pyrrolo[3,2- <i>c</i> ]quinolinone/pyrrolizino[2,3- <i>c</i> ]quinolinone hybrid heterocycles via environmentally benign solid state melt reaction Abstract Structurally diverse fused polycyclic pyrrolo[3,2- c ]quinolinone/pyrrolizino[2,3- c ]quinolinone hybrids were synthesized to get excellent yields via a tandem multi-component reaction sequence employing an environmentally benign solid state melt reaction involving [3+2]-cycloaddition process followed by two consecutive annulation steps. Baylis–Hillman products, used as dipolarophiles, were synthesized from various substituted aryl/heteroaryl aldehydes in the presence of DABCO and methyl acrylate, while the 1,3-dipole component was derived in situ from indoline-2,3-dione and acyclic/cyclic amino acid viz N -methylgylcine/ l -proline. The structure of the unusual tandem products was unambiguously assigned by spectroscopic and XRD analysis. The products arose through the formation of three new rings, five new bonds, and three adjoining stereocenters with complete diastereomeric control. Chemistry ; Tandem ; Stereocenter ; DABCO ; Diastereomer ; Annulation ; Cycloaddition ; Cascade reaction ; Isatin ; Stereochemistry ; Indoline ; Organic chemistry ; Enantioselective synthesis ; Octane ; Catalysis Multicomponent Synthesis of Heterocycles ; Synthesis and bioactivity of alkaloids ; Synthesis and Characterization of Pyrroles
Authors: T. M. Remya | T. M. Asha | Ayswaria Deepti | Prabha Prakash | Baby Chakrapani P.S | Unnikrishnan P.A.
Source: Research Square (preprint, 2023-01-04)
Field: Chemistry — Organic Chemistry

Biological and Sensing Applications of a Few 1,3,4-Oxadiazole Based Donor-Acceptor Systems Abstract 1,3,4-Oxadiazole pharmacophore is still considered a viable biologically active scaffold for the synthesis of more effectual and broad-spectrum antimicrobial agents. Therefore, the present study is based on five 1,3,4-oxadiazole target structures, viz, CAROT, CAROP, CARON (D-A-D-A systems) and NOPON and BOPOB (D-A-D-A-D systems) bearing various bioactive heterocyclic moieties relevant to potential biological activities. Three of the compounds, CARON, NOPON and BOPOB were assessed in-vitro for their efficacy as antimicrobial agents against gram positive (Staphylococcus aureus and Bacillus cereus) and gram negative (Escherichia coli and Klebsiella pneumonia) bacteria; and two fungi, Aspergillus niger and Candida albicans; also, as an anti-tuberculosis agent against Mycobacterium tuberculosis. Most of the tested compounds displayed promising antimicrobial activity, especially CARON which was then analyzed for the minimum inhibitory concentration (MIC) studies. Similarly, NOPON portrayed the highest anti-TB activity among the studied compounds. Consequently, to justify the detected anti-TB activity of these compounds and to recognize the binding mode and important interactions between the compounds and the ligand binding site of the potential target, these compounds were docked into the active binding site of cytochrome P450 CYP121 enzyme of Mycobacterium tuberculosis, 3G5H. The docking results were in good agreement with the result of in-vitro studies. In addition, all the five compounds were tested for their cell viability and have been investigated for cell labeling applications. To conclude, one of the target compounds, CAROT was used for the selective recognition of cyanide ion by ‘turn-off’ fluorescent sensing technique. The entire sensing activity was examined by spectrofluorometric method and MALDI spectral studies. The limit of detection obtained was 0.14 μM. Pharmacophore ; Antimicrobial ; Oxadiazole ; Bacillus cereus ; Chemistry ; Mycobacterium tuberculosis ; Docking (animal) ; Aspergillus fumigatus ; Candida albicans ; Active site ; Staphylococcus aureus ; Escherichia coli ; Klebsiella pneumoniae ; Combinatorial chemistry ; Klebsiella pneumonia ; Aspergillus niger ; Biological activity ; Stereochemistry ; Biochemistry ; Microbiology ; Bacteria ; Enzyme ; In vitro ; Biology ; Tuberculosis ; Organic chemistry ; Medicine Synthesis and biological activity ; Click Chemistry and Applications ; Synthesis and Biological Evaluation