Review
Chemistry, Multidisciplinary
Alex Elmi, Scott L. Cockroft
Summary: Supramolecular chemistry focuses on interactions between molecules, while molecular chemistry is centered on bonds within molecules. Understanding molecular self-assembly processes remains a challenge, particularly due to computational and practical limitations regarding solvation effects. Tackling these challenges requires a combination of experimental and computational approaches to study the role of solvents in molecular recognition.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Matej Zabka, Lavakumar Naviri, Ruth M. Gschwind
Summary: The study found that breaking the symmetry of one ligand side chain can induce a strong conformational preference and shift the balance between hetero- and homocomplexes. Modulation of aryl substituents and solvent effects can alter enantioselectivity in metal-catalyzed reactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Sinead McCann, William E. Roe, Hannah E. Agnew, Peter C. Knipe
Summary: To imitate the dynamic molecules in biological systems, foldamers need to possess stimulus-responsive behavior. In this study, we present a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is prevented via a copper-catalyzed coupling protocol. The native conformation of the compounds is initially investigated in both solid and solution states. The foldamers can be solubilized in DMSO and pH 9.5 buffer while retaining conformational control. Furthermore, dynamic switching is demonstrated through acid treatment, resulting in stimulus-responsive sidechain reconfiguration.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Applied
O. N. Makshakova, E. R. Safarova, Y. F. Zuev
Summary: This study investigated the molecular interactions between RNase and polysaccharides, revealing the impact of polysaccharide side chains on protein structure in complexes. Computational simulations and spectroscopic analyses confirmed stable interactions, with potential implications for using rhamnogalacturonan I as a matrix material for protein delivery systems.
CARBOHYDRATE POLYMERS
(2021)
Article
Biochemistry & Molecular Biology
Xi Wang, Harry M. Greenblatt, Lavi S. Bigman, Binhan Yu, Channing C. Pletka, Yaakov Levy, Junji Iwahara
Summary: This study investigates how D/E repeats cause autoinhibition of HMGB1 and its specific binding to cisplatin-modified DNA. By varying ionic strength, the conformational equilibrium between autoinhibited and uninhibited states can be shifted, revealing fuzzy interactions of D/E repeats with other intrinsically disordered regions. Mutations mimicking post-translational modifications relevant to nuclear export of HMGB1 can moderately modulate DNA-binding affinity, possibly by impacting the autoinhibition.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Francisco Javier Canada, Angeles Canales, Pablo Valverde, Beatriz Fernandez de Toro, Monica Martinez-Orts, Paola Oquist Phillips, Amaia Pereda
Summary: Carbohydrates, either as free molecules or conjugated with other biomolecules, play important roles in various biological processes. Nuclear Magnetic Resonance spectroscopy (NMR) is a versatile tool for studying the structures and interactions of carbohydrates, providing information about their sequences, structures, and local geometries. Labeling carbohydrates with 13C enhances the resolution and detail of the analyzed structures. Moreover, combining NMR with molecular modeling and theoretical calculations offers insights into the conformational flexibility of carbohydrates. Additionally, the use of partially oriented media or paramagnetic perturbations allows for the study of longer and branched glycan chains. This review presents examples and an overview of recent and relevant NMR applications in the field of glycobiology.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Plant Sciences
Emily B. Crull, Ajay N. Jain, Paul C. D. Hawkins, Ann E. Cleves, Edmund I. Graziani, R. Thomas Williamson
Summary: Rapamycin, a well-known natural product with various biological activities, has been extensively studied since its discovery over fifty years ago. Although it adopts a single conformation in the solid state, it exists as a mixture of two conformations in solution. Previous studies have suggested that the minor conformer is the cis amide based on the analogy to FK-506, but its characterization remained incomplete. By using NMR techniques and computational methods, the solution structure of the minor conformer of rapamycin was revealed to be a trans amide species with rotation around the ester linkage.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Chemistry, Multidisciplinary
Takaya Fujie, Takeshi Yamamoto, Michinori Suginome
Summary: A single-handed poly(quinoxaline-2,3-diyl) (PQX) has been discovered as a new type of chiral shift reagent (CSR) for determining enantiomeric ratio by NMR spectroscopy. Without specific binding site, PQX interacts nonbondingly with chiral analytes, resulting in significant shift of NMR chemical shift and enabling quantification of enantiomeric ratios. This new CSR offers advantages such as wide analyte scope, including ethers, haloalkanes, and alkanes, easy tunability of chemical shifts with temperature, and erasability of proton signals due to short T-2 relaxation of the macromolecular scaffold.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Eloah P. Avila, Larissa A. O. Mendes, Wagner B. De Almeida, Helio F. Dos Santos, Mauro V. De Almeida
Summary: Citrus naringenin is a bioactive flavanone that serves as an important platform for drug development. Inserting lipophilic groups to the flavanone skeleton can enhance biological response, but ring-opening isomerization of the pyranone ring may compromise reaction efficiency. Mechanistic studies and thermodynamic properties of flavanone isomerization have not yet been reported.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Spectroscopy
Yugao Xu, Tingting Yang, Tao Lu, Gang Feng
Summary: The conformational equilibria of cyclohexyl isothiocyanate and its complex with water were investigated by microwave spectroscopy and theoretical calculations. The rotational spectra of the two conformers of the bare cyclohexyl isothiocyanate, a-trans and e-trans, were measured and analyzed, as well as their isotopologues. For the binary complex with water, the rotational spectra of the monohydrates of both a-trans and e-trans were measured, and water isotopologues were also observed. The noncovalent bonding features of the monohydrates were examined using natural bond orbital analysis and symmetry-adapted perturbation theory analysis.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Chemistry, Multidisciplinary
Jan M. Schuemann, J. Philipp Wagner, Andre K. Eckhardt, Henrik Quanz, Peter R. Schreiner
Summary: A comprehensive experimental study was conducted on a molecular balance to measure the effect of different solvents on the equilibrium of folded versus unfolded isomers. The study revealed that London dispersion interactions enthalpically favor the folded state in any measured solvent.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Carlos Romero-Nieto, A. de Cozar, Elzbieta Regulska, John B. Mullenix, Frank Rominger, Philip Hindenberg
Summary: Halogen bonds and pi-stacking interactions lead to the sorting of pi-extended R- and S-isomers, with a positive synergistic effect between the pi-interactions and the halogen bonds being the origin of such phenomena. As a result, enantiomeric building blocks form homoleptically connected quadrangular structures.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Stacey Wardenfelt, Xinyao Xiang, Mouzhe Xie, Lei Yu, Lei Bruschweiler-Li, Rafael Bruschweiler
Summary: This study utilizes a new method to investigate the dynamics of protein interactions with nanoparticles. The results indicate that the interaction between proteins and silica nanoparticles of different sizes is not significant, and the backbone dynamics are confined to sub-nanosecond timescales.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Adrian Gonzalez-Nelson, Srinidhi Mula, Mantas Simenas, Sergejus Balciunas, Adam R. Altenhof, Cameron S. Vojvodin, Stefano Canossa, Juras Banys, Robert W. Schurko, Francois-Xavier Coudert, Monique A. van der Veen
Summary: The organic components in MOFs exhibit unique dynamic behavior, with the rotation of organic linkers playing a crucial role in determining their properties. By modifying the structure and environment of the linkers, the rotation speed and mode can be controlled to achieve function-specific cooperative motion.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Yashu Kharbanda, Mateusz Urbanczyk, Vladimir V. Zhivonitko, Sarah Mailhiot, Mikko Kettunen, Ville-Veikko Telkki
Summary: In this study, a method using low-cost, portable, single-sided NMR instruments for analyzing molecular exchange processes is introduced. By exploiting the inherent magnetic field inhomogeneity of the instruments, diffusion contrast of exchange sites and spatial encoding of 2D data can be achieved. The method, called ultrafast diffusion exchange spectroscopy, significantly shortens the experiment time and improves the sensitivity by several orders of magnitude. The feasibility of the method is demonstrated by quantifying intra- and extracellular exchange of water in a yeast cell suspension.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)