Article
Biochemical Research Methods
Pengyu Zhang, Yingfu Wu, Haoru Zhou, Bing Zhou, Hongming Zhang, Hao Wu
Summary: This article proposes a new deep learning model called CLNN-loop, which can predict chromatin loops in different cell lines and CTCF-binding site pair types by fusing multiple sequence-based features. The results of experiments show that CLNN-loop performs well in predicting chromatin loops and outperforms existing methods. Additionally, the study finds that CTCF motif and sequence conservation are important indicators of chromatin loops in different cell lines and CTCF-binding site pair types.
Article
Chemistry, Multidisciplinary
Evgueni Gorobets, James W. Papatzimas, Jorge Dourado, Goonay Yousefalizadeh, JinGyu Lee, Duncan K. Brownsey, Kevin Stamplecoskie, Rebecca Davis, Darren J. Derksen
Summary: The reactions of bicyclic divinyl ketones exhibit wavelength-dependent changes in product formation. UV irradiation leads to the formation of competitive [6,3,5] and [7,3,5] tricyclic unsaturated ketones, which subsequently undergo ring expansion and react with various nucleophiles. DFT calculations and transient absorption experiments support a vinylogous Type II Norrish pathway associated with energy cascade.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Organic
Michael J. Nutt, Jack W. Annear, Kieran D. Jones, Gavin R. Flematti, Stephen A. Moggach, Scott G. Stewart
Summary: The synthesis of a range of C2-substituted 2,3-dehydropiperazines using a dirhodium(II) catalyst and 1-mesyl-1,2,3-triazoles and β-haloalkylcarbamates is reported. The reaction involves an α-iminorhodium carbene 1,3-insertion into N-H followed by a base-mediated cyclization. Additionally, C-substituted dehydropiperazines can be synthesized directly from terminal alkynes in a one-pot operation, forming the triazole in situ. This methodology has also been extended to produce 2,5-disubstituted 2,3-dehydropiperazines and a larger 4,5,6,7-tetrahydro-1H-1,4-diazepine derivative.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Sung Un Cho, Wanki Park, Bum-Kyu Kim, Minky Seo, Dongsung T. Park, Hyungkook Choi, Nam Kim, H. -S. Sim, Myung-Ho Bae
Summary: This article proposes a new type of single-electron source with more functionalities compared to existing sources, and achieves the emission of holes and electrons on demand through RF drive. Triangular islands, consistent with the theoretical model, are obtained through quantized current.
Article
Chemistry, Multidisciplinary
Benedikt Koestler, Michael Bolte, Hans-Wolfram Lerner, Matthias Wagner
Summary: SixGey alloys are emerging materials for modern semiconductor technology, and well-defined model systems aid in understanding their intrinsic characteristics. By synthesizing SixGey heteroadamantanes, the assembly mechanism and structural features can be revealed.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Croix J. Laconsay, Dean J. Tantillo
Summary: Density functional theory calculations were employed to study metal-catalyzed [2,3]-rearrangements, revealing that the dissociation of metal catalyst is primarily influenced by the steric bulkiness of adjacent functional groups.
Article
Chemistry, Multidisciplinary
Tomohiro Hattori, Hisashi Yamamoto
Summary: Efficient and straightforward peptide bond formation of unprotected N- and C- terminal amino acids was achieved using trimethylaluminum. This reaction system allows one-pot tripeptide synthesis without the need for expensive coupling reagents, even for amino acids with bulky substituents. Furthermore, peptide elongation can be achieved by adding amino acids and trimethylaluminum. This cost-effective and efficient protocol holds promise for the synthesis of a wide variety of peptides.
Article
Chemistry, Organic
Xiaoxiang Zhang, Yingying Zhang, Xiaoting Gu, Zhuan Zhang, Wanxing Wei, Taoyuan Liang
Summary: A copper-mediated 2,3-difunctionalization of indoles to afford 3-halogenated 2,3 '-biindoles is described. The protocol uses readily available feedstocks and a naturally abundant copper catalyst system, which allows the regioselective formation of C-C and C-X (X = Cl & Br) bonds in one single operation. Copper metal salt serves not only as a catalyst but also as a reactant to provide the source of halogen, avoiding the use of environmentally unfriendly reagents and displaying good functional group compatibility.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Chemistry, Organic
Julio Cesar Orejarena Pacheco, Stefan Pusch, Leander Geske, Till Opatz
Summary: In this study, a new method for the synthesis of pyrido[2,1-a]isoquinolines via one-pot and metal-free oxidative C-H activation/aza-Prins type cyclization of alkynylamines was reported, showing moderate to high yields (38-92%). Additionally, a mechanistic proposal for the alkyne aza-Prins cyclization was described based on DFT calculations.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Organic
Demin Ren, Oskar Smaga, Xinliang Fu, Xiaofang Li, Milosz Pawlicki, Sebastian Koniarz, Piotr J. Chmielewski
Summary: In this study, aromatic zwitterionic corrole nickel(II) complexes were synthesized via a three-component reaction, while a nonaromatic chiral adduct of zwitterionic phlorine character was obtained under certain conditions. This research provides a new perspective for the synthesis of related complexes.
Article
Physics, Multidisciplinary
Uri Vool, Assaf Hamo, Georgios Varnavides, Yaxian Wang, Tony X. Zhou, Nitesh Kumar, Yuliya Dovzhenko, Ziwei Qiu, Christina A. C. Garcia, Andrew T. Pierce, Johannes Gooth, Polina Anikeeva, Claudia Felser, Prineha Narang, Amir Yacoby
Summary: In this study, current flow in the layered semimetal tungsten ditelluride was investigated by imaging the local magnetic field, revealing non-uniform current density indicative of hydrodynamic flow, with the strongest effects observed around 20 K. Ab initio calculations suggest that electron-electron interactions are predominantly mediated by phonons rather than solely the Coulomb interaction, offering a promising avenue for the search for hydrodynamic flow and prominent electron interactions in high-carrier-density materials.
Article
Crystallography
Nabyl Merbouh, Simon Cassegrain, Wen Zhou
Summary: The crystal structures of two unsubstituted arylnaphthalene lactones and one non-aromatic dihydro arylnaphthene lactone were reported in the study, showing only minor differences in geometrical parameters and the presence of both isomers in the same asymmetric unit cell in certain cases.
Article
Chemistry, Multidisciplinary
Pradipta Das, Michael D. Delost, Munaum H. Qureshi, Jianhua Bao, Jason S. Fell, Kendall N. Houk, Jon T. Njardarson
Summary: This study reveals the significant impact of different gamma-dienolate heteroatom substituents on the product outcomes of lithium ion enabled amino-Cope-like anionic asymmetric cascade reactions. Depending on the substituents, the reaction pathways vary, leading to different relationships between stereocenters in the resulting products. The presence of a lithium counterion is found to be essential in these reactions, which are solvent- and counterion-dependent.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Petra Stanic, Dario Barisic, Damir Pajic, Ana Santic, Kresimir Molcanov
Summary: This study investigates a series of six novel salts formed by aromatic cations and 5,6-dichloro-2,3-dicyanosemiquinone (DDQ) radical anions through structural characterization, magnetization, and conductivity measurements. Different stacking modes of DDQ radicals and the general features of pancake bonding are observed.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Chemistry, Organic
Eric M. Miller, Maciej A. Walczak
Summary: This study presents stereoselective C-arylation and etherification reactions of anomeric trifluoroborates derived from BMIDA esters, exhibiting high anomeric selectivities for 2-deoxysugars and showing a broad substrate scope, including disaccharides and trifluoroborates with free hydroxyl groups. This new class of carbohydrate reagents adds to the palette of anomeric nucleophile reagents suitable for efficient installation of C-C bonds.
Article
Chemistry, Multidisciplinary
Robert Izsak, Christoph Riplinger, Nick S. Blunt, Bernardo de Souza, Nicole Holzmann, Ophelia Crawford, Joan Camps, Frank Neese, Patrick Schopf
Summary: Quantum computers are expected to be useful in simulating strongly correlated chemical systems, but careful selection of orbital spaces is crucial. This study presents a scheme for automatically selecting an active space and combines quantum phase estimation and variational quantum eigensolver algorithms to accurately describe the environment. The protocol outlined here can be applied to chemical systems of any size, including those beyond the capabilities of classical computation.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Pragyansh Singh, Soeren Schlittenhardt, Dewendra Thakre, Saroj Kumar Kushvaha, Sunil Kumar, Harsha S. Karnamkkott, Mario Ruben, Masooma Ibrahim, Abhishek Banerjee, Kartik Chandra Mondal
Summary: Due to their potential future applications in high-density data storage devices, single-ion magnets (SIMs) have become one of the most exciting classes of materials for research at present. In this study, two mixed-valent organo-polyoxovanadyl complexes were investigated for their SIM properties using a combination of experimental techniques and computational methods. The complexes exhibited SIM behaviors characterized by maxima in the plots of out-of-phase magnetic susceptibility against AC frequency at different temperatures. The spin relaxation time was determined and different models were used to understand the slow relaxation process in the system under an applied DC magnetic field.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Chemistry, Multidisciplinary
Sai Manoj N. V. T. Gorantla, Harsha S. Karnamkkott, Selvakumar Arumugam, Sangita Mondal, Kartik Chandra Mondal
Summary: The factors influencing the binding, activation, and reduction of N-2 by FeMoco of nitrogenase are not completely understood. Model complexes have been synthesized and studied, but they differ from the real Fe-sites of FeMoco. This study focuses on a series of complexes containing a weak field ligand and investigates their effect on Fe-centers and N-2 binding.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Akshay Chauhan, Harsha S. Karnamkkott, Sai Manoj N. V. T. Gorantla, Kartik Chandra Mondal
Summary: This article introduces the role of vanadium cofactor in providing nitrogen source in soil and its differences from iron cofactor, and reports the relevant research of vanadium-nitrogen complexes. The results show that vanadium-nitrogen complexes have higher interaction energy and more covalent properties.
Article
Chemistry, Multidisciplinary
Selvakumar Arumugam, Madhuri Bhattacharya, Sai Manoj N. V. T. Gorantla, Kartik Chandra Mondal
Summary: Two new series of air stable compounds containing cAAC(X)= fluorene/indene groups were isolated and characterized. These compounds showed green light emission and solvatochromism in solution, and exhibited a quasi-reversible electron transfer process as confirmed by cyclic voltammogram and electron paramagnetic resonance studies. DFT/TDDFT calculations and energy decomposition analysis were performed to study their bonding and electronic transitions. These redox active and thermally stable organic molecules may have potential applications in molecule based spin memory devices.
CHEMISTRY-AN ASIAN JOURNAL
(2023)
Article
Chemistry, Physical
Nick S. Blunt, Joan Camps, Ophelia Crawford, Robert Izsak, Sebastian Leontica, Arjun Mirani, Alexandra E. Moylett, Sam A. Scivier, Christoph Sunderhauf, Patrick Schopf, Jacob M. Taylor, Nicole Holzmann
Summary: Computational chemistry is crucial for the pharmaceutical industry, and quantum computing is a rapidly advancing technology that promises to revolutionize computational capabilities in chemical research. This article explores the potential applications of quantum computation in pharmaceutical problems, specifically in simulating molecules. The authors provide estimates of the quantum computational cost for simulating a protein-drug complex and highlight recent advancements in quantum algorithms that significantly reduce the required resources.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Medicinal
Markus R. Hermann, Christofer S. Tautermann, Peter Sieger, Marc A. Grundl, Alexander Weber
Summary: We conducted a comprehensive study on predicting the reactivity of propynamides. Covalent inhibitors like propynamides have improved potency, selectivity, and unique pharmacologic properties compared to non-covalent counterparts. By using three different in silico methods, we were able to predict the in vitro properties of propynamides, a covalent warhead class found in approved drugs. While the electrophilicity index only applies to specific subclasses, adduct formation and transition state energies are good predictors of in vitro reactivity with glutathione (GSH). Overall, these methods are suitable for estimating the reactivity of propynamides, allowing for the fine tuning of reactivity and speeding up the design process of covalent drugs.
Article
Chemistry, Inorganic & Nuclear
Sunil Kumar, Selvakumar Arumugam, Bjoern Schwarz, Helmut Ehrenberg, Kartik Chandra Mondal
Summary: A representative Co(II) based single ion magnet (SIM) with N2O2 donor set and distorted pseudo-tetrahedral geometry has been synthesized and characterized. The atomic and electronic structure have been studied through DC magnetometry, ab-initio multi-reference CASSCF calculations, and qualitative ligand field theory. AC magnetometry has been used for the investigation of spin-lattice relaxation with temperature and magnetic field variations.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Physical
Robert Izsak, Aleksei V. Ivanov, Nick S. Blunt, Nicole Holzmann, Frank Neese
Summary: In this article, the different measures of electron correlation in wave function theory, density functional theory, and quantum information theory are briefly reviewed. The focus is then placed on a more traditional metric based on dominant weights in the full configuration solution and its behavior regarding the choice of N-electron and one-electron basis. The impact of symmetry is discussed, and the usefulness of distinguishing between determinants, configuration state functions, and configurations as reference functions is emphasized.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Inorganic & Nuclear
Maxim V. Andreev, Iuliia A. Akishkina, Vyacheslav S. Bogdanov, Rinat R. Aysin, Fedor M. Dolgushin, Vladimir V. Burlakov
Summary: Heating five-membered zircona- and hafnacyclocumulene complexes with an excess of acetonitrile results in the formation of dimeric metallaazacyclopentadiene complexes, bicyclic amidine complexes, and tricyclic metallacycles. These products are kinetically (dimeric complexes) and thermodynamically (complexes 2 and 5) favorable, and their yield depends on the reaction conditions and the structure of the initial complexes. Based on experimental and theoretical data, the reaction proceeds through the formation of competitive monomeric metallaazacyclopentadienes.
Article
Chemistry, Multidisciplinary
Sonam Suthar, Kartik Chandra Mondal
Summary: In this study, energy decomposition analysis and natural orbital for chemical valence (EDA-NOCV) were used to investigate the bonding in cyclopropane rings of 49 different organic compounds. The majority of compounds (37/49) were found to preferentially form two dative covalent C-C bonds, while a smaller portion (7/49) favored two covalent electron sharing bonds. A few compounds (5/49) showed flexibility to adopt either bonding mode. The effects of functional groups on the bonding were also studied. The bonding analyses were supported by QTAIM analyses, which revealed distinct parameters for C-3 rings compared to normal hydrocarbons. The bonding in most cyclopropane rings was found to be similar to metal-olefin systems.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Elena S. Kelbysheva, Mariam G. Ezernitskaya, Rinat R. Aysin, Tatyana V. Strelkova, Alexey N. Rodionov, Lyudmila N. Telegina
Summary: The photochemical properties of a symmetrical pyromellitic diimide containing two cymantrenyl fragments were investigated. Photolysis resulted in the formation of unstable chelates and dissociation of CO ligands from two Mn(CO)3 fragments, leading to significant changes in the electronic and redox properties of the molecule. The color changed from light yellow to green. DFT calculations confirmed the formation of complexes due to the loss of CO ligands. Addition of external ligands altered the color and electrochemical properties, suggesting potential applications as a sensor for small molecules.
Article
Polymer Science
Ulyana S. S. Andropova, Rinat R. R. Aysin, Olga A. A. Serenko, Tatyana O. O. Ershova, Anton A. A. Anisimov, Vladimir N. N. Chernik
Summary: In order to expand the material options for outer space and small spacecraft, researchers studied ladder polyphenylsilsesquioxanes with varying molar weights and Nb-siloxane composites based on them. The polymer films were tested in an oxygen plasma flow and showed extremely low erosion coefficients. The ladder polyphenylsilsesquioxanes demonstrated their suitability for protective and optically transparent coatings for small spacecraft that are resistant to the erosive effects of incoming oxygen plasma.
Article
Chemistry, Inorganic & Nuclear
Selvakumar Arumugam, Bjoern Schwarz, Prathap Ravichandran, Sunil Kumar, Liviu Ungur, Kartik Chandra Mondal
Summary: This work investigates the dynamic magnetic properties of a complex [(Cp-Ar3)(4)(Dy2Cl4K2)-Cl-III]& BULL;3.5(C7H8) synthesized using a tri-aryl-substituted cyclopentadienyl ligand (Cp-Ar3). The Dy(III)-metallocene weakly couples via K2Cl4 and exhibits slow relaxation of magnetization below 14.5 K under zero applied dc field through KD3 energy levels with an energy barrier of 136.9/133.7 cm(-1) at the Dy sites. The coordination of two chloride ions at each Dy centre leads to geometrical distortion and reduction of the single-ion axial anisotropy energy barrier.
DALTON TRANSACTIONS
(2023)
Article
Physics, Multidisciplinary
Aleksei Ivanov, Christoph Sunderhauf, Nicole Holzmann, Tom Ellaby, Rachel N. Kerber, Glenn Jones, Joan Camps
Summary: In this work, a quantum algorithm based on sparse qubitization approach is presented for ground-state energy calculations of periodic solids on error-corrected quantum computers. It is shown that the use of Wannier functions reduces computational resources compared to Bloch functions due to lower Hamiltonian norm and exploitability of translational symmetry. The resource requirements of the algorithm are estimated for industrially relevant transition metal oxides and found to be substantial in terms of gates and qubits.
PHYSICAL REVIEW RESEARCH
(2023)