Article
Chemistry, Multidisciplinary
Lorenz M. Urner, Ga Young Lee, Joseph W. Treacy, Aneta Turlik, Saeed Khan, K. N. Houk, Michael E. Jung
Summary: The 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline scaffold is proposed as a novel model system for studying weak NH...F hydrogen bonding interactions, with experimental and theoretical methods used to characterize this interaction. The results demonstrate that fluorine can act as a weak hydrogen bond acceptor, and the strength of the hydrogen bond can be modulated through changes in electron distribution and resonance.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Gui-Hua Chen, Yi-Meng Duan, Ying Li, Xiao-Ni Han, Kun-Peng Wang, Zhi-Qiang Hu, Chuan-Feng Chen
Summary: The complexation behaviors of pagoda[n]arenes (n = 4, 5) with ferrocene, ferrocenium, and analogues cobaltocenium have been studied. The inclusion complexes of pagoda[n]arenes can protect ferrocenium from oxidation in organic solvents and improve the stability and oxygen resistance of ferrocenium.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Hiromasa Matsuda, Erina Yoshida, Takaaki Shinoda, Kazuki Sato, Rintaro Iwata Hara, Takeshi Wada
Summary: Recent advances in nucleic acid therapeutics have increased the demand for efficient methods to chemically synthesize oligodeoxyribonucleotides (ODNs). This study introduces a new approach using the H-phosphonate method and N-unprotected 5'-phosphite monomers to achieve the synthesis of ODNs, including TTT and tetramers with four different nucleobases.
Article
Chemistry, Organic
Chaowei Yin, Hanwei Lu, Hebo Ye, Zelin Feng, Hanxun Zou, Meilan Zhang, Lei You
Summary: This study presents double n -> nr* interactions between one common electron donor of the carbonyl oxygen and two individual acceptor aldehyde/imine units. The orientation and energetic dependence of orbital interactions were regulated by the size of cyclic urea scaffolds, the bulkiness of aldehydes/imines, and the flexibility of imine macrocycles, as revealed by experimental and computational evidence.
Article
Chemistry, Multidisciplinary
Pavel A. A. Shelyganov, Mehdi Elsayed Moussa, Michael Seidl, Manfred Scheer
Summary: Synthesis and reactivity of transition metal compounds with naked pnictogen atoms have been actively studied, revealing interesting bonding patterns in the formed compounds. While coordination behavior of complexes with P-n and As-n (2 <= n <= 5) groups has been extensively investigated, studies on heavier analogues have been overlooked due to challenges in yields and air stability. In this work, we report the first comprehensive study on the reactivity of organometallic complexes containing Sb-donor atoms with various Ag-I salts, leading to the formation of unprecedented aggregates including monomers, dimers, and chains of Ag-I ions that were previously considered inaccessible. Computational evidence and interatomic distances suggest the presence of Ag···Ag interactions in complexes with multiple Ag-I ions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Organic
Liulei Ma, Jesus Daniel Loya, Michael Findlater, Kristin M. Hutchins
Summary: A convenient, high-yielding, and scalable synthetic approach to construct 4'-vinylbenzocrown ethers has been developed. The identity of the crown ethers was further confirmed using single-crystal X-ray diffraction studies.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Organic
Ying Li, Yi-Meng Duan, Gui-Hua Chen, Hao-Ran Hu, Xiao-Ni Han, Kun-Peng Wang, Zhi-Qiang Hu, Chuan-Feng Chen
Summary: In this study, the host-guest complexation between pagoda[n]arenes and the tropylium cation was investigated. Both P4 and P5 showed strong binding affinities towards the tropylium cation, with association constants of more than 107 M-1 for the 1:1 host-guest complexes. Theoretical calculations revealed different complexation modes for G@P4 and G@P5, with pi center dot center dot center dot pi and C-H center dot center dot center dot pi interactions playing important roles.
Article
Biochemical Research Methods
Hamid Reza Ghenaatian, Mehdi Shakourian-Fard, Ganesh Kamath
Summary: This study investigated the interaction of noble metal nanoparticles with ChCl:Urea deep eutectic solvent using density functional theory. It was found that the ChCl:Urea interacted with the nanoparticles mainly through anions and nonconventional hydrogen bonds, with larger nanoparticles exhibiting stronger interactions.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Physics, Particles & Fields
Augustus Brown, Congkao Wen, Haitian Xie
Summary: We consider integrated correlators in N = 4 super Yang-Mills theory with SU(N) gauge group, where operators are properly reorganised. We show that these correlators satisfy a universal Laplace-difference equation relating operators with different charges, which can be computed via supersymmetric localisation and are modular functions of the Yang-Mills coupling. This equation, along with initial conditions, completely determines all the integrated correlators.
JOURNAL OF HIGH ENERGY PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Yongquan Ning, Hongwei Wang, Paramasivam Sivaguru, Shuang Li, Giuseppe Zanoni, Steven P. Nolan, Xihe Bi
Summary: A novel method for accessing 5-fluoroalkyl 1,2,3-triazoles from easily prepared PFHZ-Ms has been reported, showing good to excellent yields in the synthesis of 1,2,3-triazoles and applicability to a variety of amines. This method's utility was demonstrated in the late-stage modification of bioactive molecules.
Article
Chemistry, Physical
Haiwei Lei, Liping Chen, Linjun Wang
Summary: This study presents a new global optimization method to obtain the lowest-energy structures of cadmium selenide clusters. The method combines atom-pair hopping, ultrafast shape recognition, and adaptive temperature techniques to enhance search efficiency. The results reveal the systematic structural evolution of cadmium selenide clusters from rings to stacked rings, cages, nanotubes, cage-wurtzite, cage-core, and finally wurtzite structures.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Upendra Chaudhary, Dawa Dawa, Indranil Banerjee, Shivani Sharma, Kuldeep Mahiya, Abdur Rauf, Yuba Raj Pokharel, Paras Nath Yadav
Summary: In this study, four compounds were synthesized and characterized. Molecular docking studies revealed strong interaction between one compound and VEGFR2. In vitro experiments showed significant anticancer activity of these compounds against breast cancer, skin cancer, and lung cancer. One compound exhibited the strongest anticancer activity in A549 cells, while another compound showed high activity in MCF-7 cells.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Applied
Sen Yang, Kuan Li, Yi Tang, Bing Zheng, Wei Wang, Yongjun Wu, Yumei Xiao, Hongchao Guo
Summary: In this paper, we designed and synthesized 4-vinyl-4-butyrolactone as a precursor to generate zwitterionic intermediates, which acted as five-membered all-carbon synthons in palladium-catalyzed (5+3) annulation reactions with azomethine imines, resulting in the formation of eight-membered ring-fused heterocycles.
ADVANCED SYNTHESIS & CATALYSIS
(2022)
Article
Multidisciplinary Sciences
Ilya N. Klyukin, Yulia S. Vlasova, Alexander S. Novikov, Andrey P. Zhdanov, Konstantin Y. Zhizhin, Nikolay T. Kuznetsov
Summary: This study focused on the analysis of structure, bonding, and reactivity of closo-borate anions [BnHn](2-) (n = 5-12). It was found that descriptors like electron density and total energy at bond critical point are useful for investigating B-H interactions. Orbital interactions in [BnHn](2-) were observed to increase with boron cluster size. Atomic charges of the boron atoms were found to vary with their positions, with boron atoms in apical positions having more negative values. Global and local reactivity descriptors were calculated, showing [BnHn](2-) (n = 5-9) to be strong and moderate electrophiles, while [BnHn](2-) (n = 10-12) were marginal electrophiles. Fukui functions for electrophilic attack were also computed, with boron atoms in apical positions having the most positive values.
Article
Energy & Fuels
Haibo Li, Bing Zhu, Xue Wang, Junmin Lv, Subing Fan, Tiansheng Zhao
Summary: A series of [Zn,Ga]/HZ catalysts with modified acid distribution were prepared and studied for their catalytic performance in the coaromatization reaction of n-hexane and methanol. The introduction of Ga greatly increased the content of active centers Zn(OH)+, leading to improved dehydroaromatization ability and higher aromatics yield.
Article
Chemistry, Analytical
Sophie R. Harvey, Carla O'Neale, Kevin L. Schey, Vicki H. Wysocki
Summary: Aquaporin-0 (AQP0) is the most abundant membrane protein in the eye lens, and its post-translational modifications can accumulate with age. Native mass spectrometry and surface-induced dissociation can be used to study these modifications.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sheng Zhang, Stan Yoo, Dalton T. Snyder, Benjamin B. Katz, Amy Henrickson, Borries Demeler, Vicki H. Wysocki, Adam G. Kreutzer, James S. Nowick
Summary: A beta dimers are neurotoxic and pathologically relevant species in Alzheimer's disease. This paper introduces a stable A beta(C18C33) dimer model that forms pure dimers in lipid environments without aggregation into fibrils. This model is important for amyloid and Alzheimer's disease research.
Review
Chemistry, Multidisciplinary
Dalton T. Snyder, Sophie R. Harvey, Vicki H. Wysocki
Summary: Native mass spectrometry (nMS) is an important tool in structural biology, with great potential due to a range of ionization techniques and new hybrid ion mobility and mass spectrometry systems. This review focuses on the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing connectivity in protein and nucleoprotein complexes, demonstrating the importance of SID and nMS in future structural elucidation of biological assemblies.
Article
Biochemistry & Molecular Biology
Kye Stachowski, Andrew S. Norris, Devante Potter, Vicki H. Wysocki, Mark P. Foster
Summary: In this study, the mechanism of Cre recombinase assembly was revealed, which allows for DNA recognition and specific cleavage through a series of intermediates. The results show the importance of protein and DNA flexibility in site selection and recombination efficiency mediated by Cre.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Analytical
Justin T. Seffernick, S. M. Bargeen Ala m Turzo, Sophie R. . Harvey, Yongseok Kim, Arpad Somogyi, Shir Marciano, Vicki H. Wysocki, Steffen Lindert
Summary: Understanding the relationship between protein structure and experimental data is crucial. In this study, a method was developed to predict the full energy-resolved mass spectrometry (ERMS) plot from the structure. The results showed that the accuracy of predictions depended on the quality of the native crystal structures.
ANALYTICAL CHEMISTRY
(2022)
Editorial Material
Biochemical Research Methods
Vicki Wysocki
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Weicheng Li, Andrew S. Norris, Katie Lichtenthal, Skyler Kelly, Elihu C. Ihms, Paul Gollnick, Vicki H. Wysocki, Mark P. Foster
Summary: Homo-oligomeric ligand-activated proteins are widely present in biology and their functions are regulated by allosteric coupling between ligand-binding sites. By combining statistical thermodynamic modeling with native mass spectrometry, the effects of ligand-dependent population shifts and coupling free energy terms can be quantified, providing necessary insights into regulation and enabling a better understanding of cooperativity.
Article
Biochemistry & Molecular Biology
Sherry Bermeo, Andrew Favor, Ya-Ting Chang, Andrew Norris, Scott E. Boyken, Yang Hsia, Hugh K. Haddox, Chunfu Xu, T. J. Brunette, Vicki H. Wysocki, Gira Bhabha, Damian C. Ekiert, David Baker
Summary: The de novo design of protein chains that associate to form a heterotrimer is a challenging task in protein design. In this study, we designed helical heterotrimers with buried hydrogen bond networks and large aromatic residues. We obtained ten designs in which all three chains assembled into heterotrimers. Crystal structures and electron microscopy confirmed the successful assembly of these designed structures, which could be used for constructing larger protein nanostructures and modulating cell signaling.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Vicki H. Wysocki
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Sravya Kovvali, Yuan Gao, Austin Cool, Steffen Lindert, Vicki H. Wysocki, Charles E. Bell, Venkat Gopalan
Summary: Amadori rearrangement products are stable sugar-amino acid conjugates that are formed nonenzymatically during food processing. Understanding bacterial utilization of these fructosamines is crucial due to their impact on the animal gut microbiome. In this study, the catalytic mechanism of the deglycase enzyme FrlB was elucidated through crystallography, computational docking, biochemical assays, and native mass spectrometry. The findings provide insights into the structure-function relationship and mechanisms of enzymes.
Article
Chemistry, Multidisciplinary
Thomas Walker, He Mirabel Sun, Tiffany Gunnels, Vicki Wysocki, Arthur Laganowsky, Hays Rye, David Russell
Summary: Variable-temperature electrospray ionization (vT-ESI) native mass spectrometry (nMS) is used to investigate the thermodynamics of ATP binding to the GroEL tetradecamer chaperonin complex. The study reveals strong enthalpy-entropy compensation (EEC) and variations in stepwise free energy changes, which are consistent with the established nested cooperativity model of GroEL-ATP interactions. The entropy-driven ATP binding is attributed to ligand-induced conformational changes and reorganization of water molecules within the GroEL complex.
ACS CENTRAL SCIENCE
(2023)
Article
Biochemical Research Methods
Mengxuan Jia, Yang Song, Chen Du, Vicki H. Wysocki
Summary: The charge partitioning during the dissociation of protein complexes in the gas phase is influenced by various factors, including interfacial interactions, protein flexibility, protein conformation, and dissociation methods. This study used two cysteine-containing homodimer proteins to investigate the charge partitioning behaviors of collision-induced dissociation (CID) and surface-induced dissociation (SID) processes. Results showed that restructuring dominates with CID, while dissociation with symmetric charge partitioning dominates with SID, regardless of the oxidation state of the intramolecular disulfide bonds. Gas collisions reveal the charge-dependent restructuring/unfolding properties of the protein precursor, while surface collisions predominantly lead to more charge-symmetric monomer separation.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Editorial Material
Biochemical Research Methods
Jenny Brodbelt, Vicki Wysocki
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Editorial Material
Biochemical Research Methods
John C. C. Tran, Iain D. G. Campuzano, Erin S. S. Baker, Vicki H. H. Wysocki
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Multidisciplinary
Shir Marciano, Debabrata Dey, Dina Listov, Sarel J. Fleishman, Adar Sonn-Segev, Haydyn Mertens, Florian Busch, Yongseok Kim, Sophie R. Harvey, Vicki H. Wysocki, Gideon Schreiber
Summary: In this study, the oligomeric state of 17 different bacterial proteins in E. coli was re-evaluated using various methods, and it was found that most proteins exhibit multiple oligomeric states. Some proteins did not show mass-action driven equilibrium between oligomeric states. The predicted oligomeric forms underestimated the complexity of protein quaternary structures in solution, while AlphaFold multimer provided an accurate description.