We present the implementation of the solid state (SoS)NMR module for the simulation of several 1D and 2D NMR spectra of all the elements in the periodic table in the virtual multifrequency spectrometer (VMS). This module is fully integrated with the graphical user interface of VMS (VMS-Draw) [Licari et al., J. Comput. Chem. 36, 2015, 321-334], a freeware tool which allows a user-friendly handling of structures and analyses of advanced spectroscopical properties of chemical compounds-from model systems to real-world applications. Besides the numerous modules already available in VMS for the study of electronic, optical, vibrational, vibronic, and EPR properties, here the simulation of NMR spectra is presented with a particular emphasis on those techniques usually employed to investigate solid state systems. The SoSNMR module benefits from its ability to work under both periodic and nonperiodic conditions, such that small molecules/molecular clusters can be treated, as well as extended three-dimensional systems enforcing (or not) translational periodicity. These features allow VMS to simulate spectra resulting from NMR calculations by some popular quantum chemistry codes, namely Gaussian09/16, Castep, and Quantum Espresso. The effectiveness of the SoSNMR module of VMS is examined throughout the manuscript, and applied to simulate 1D static, MAS, and VAS NMR spectra as well as 2D correlation (90°, MAS) and MQMAS spectra of active NMR nuclei embedded in different amorphous and crystalline systems of actual interest in chemistry and material science. Finally, the program is able to simulate the spectra of both the total ensemble of spin-active nuclei present in the system and of subensembles differentiated depending on the chemical environment of the first and second coordination sphere in a very general way applicable to any kind of systems.
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http://dx.doi.org/10.1021/acs.jctc.7b00154 | DOI Listing |
Protein Sci
February 2025
Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.
Loz1 is a zinc-responsive transcription factor in fission yeast that maintains cellular zinc homeostasis by repressing the expression of genes required for zinc uptake in high zinc conditions. Previous deletion analysis of Loz1 found a region containing two tandem CH zinc-fingers and an upstream "accessory domain" rich in histidine, lysine, and arginine residues to be sufficient for zinc-dependent DNA binding and gene repression. Here we report unexpected biophysical properties of this pair of seemingly classical CH zinc fingers.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
Core Facility Center "Arktika", Northern (Arctic) Federal University named after M.V. Lomonosov, Northern Dvina Emb., 17, Arkhangelsk 163002, Russian Federation. Electronic address:
Dioxane lignin (DL) is isolated from plant material under mild acidolysis conditions and is widely used in many studies as a representative sample of protolignin, an alternative to milled wood lignin (MWL). However, the structural changes caused by hydrolytic degradation reactions during DL extraction are still poorly understood. In this work, an integrated approach based on 2D NMR and high-resolution mass spectrometry was used to establish the features of the lignin structure on the example of pine lignin isolated using dioxane under various conditions: MWL, DL and "formaldehyde stabilized" lignin (LSF).
View Article and Find Full Text PDFBioinformatics
January 2025
Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom.
Unlabelled: Metabolomics extensively utilizes Nuclear Magnetic Resonance (NMR) spectroscopy due to its excellent reproducibility and high throughput. Both one-dimensional (1D) and two-dimensional (2D) NMR spectra provide crucial information for metabolite annotation and quantification, yet present complex overlapping patterns which may require sophisticated machine learning algorithms to decipher. Unfortunately, the limited availability of labeled spectra can hamper application of machine learning, especially deep learning algorithms which require large amounts of labelled data.
View Article and Find Full Text PDFMolecules
January 2025
Instituto Andaluz de Ciencias de la Tierra (IACT-CSIC), Consejo Superior de Investigaciones Científicas, Av. de las Palmeras 4, 18100 Armilla, Granada, Spain.
Many properties of 2,4-dichlorophenoxyacetic acid (2,4-D) depend on its molecular environment, such as whether it is an isolated molecule, a dimer, or in a crystalline state. The molecular geometry, conformational analysis, and vibrational spectrum of 2,4-D were theoretically calculated using Density Functional Theory (DFT) methods. A new slightly more stable conformer was found, which is different to those previously reported.
View Article and Find Full Text PDFMolecules
January 2025
Department of Chemistry, Texas A&M University, College Station, TX 77842-3012, USA.
Five representatives of a novel type of di(hydroperoxy)alkane adducts of phosphine oxides have been synthesized and fully characterized, including their solubility in organic solvents. The phosphine oxide CyPO () has been used in combination with the corresponding aldehydes to create the adducts CyPO·(HOO)CHCH (), CyPO·(HOO)CHCHCH (), CyPO·(HOO)CH(CH)CH (), CyPO·(HOO)CH(CH)CH (), and CyPO·(HOO)CH(CH)CH (). All adducts crystallize easily and contain the peroxide and phosphine oxide hydrogen-bonded in 1:1 ratios.
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