NMR 1H-Shielding Constants of Hydrogen-Bond Donor Reflect Manifestation of the Pauli Principle.
Ontology highlight
ABSTRACT:
SUBMITTER: Zarycz MNC
PROVIDER: S-EPMC6038099 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The liquid state NMR chemical shift of protons is a parameter frequently used to characterize host-guest complexes. Its theoretical counterpart, that is, the 1H NMR chemical shielding affected by the solvent (1H CS), may provide important insights into spatial arrangements of supramolecular systems, and it can also be reliably obtained for challenging cases of an aggregation of aromatic and antiaromatic molecules in solution. This computational analysis is performed for the complex of coronene and an antiaromatic model compound in acetonitrile by employing the GIAO-B3LYP-PCM approach combined with a saturated basis set. Predicted 1H CS values are used to generate volumetric data, whose properties are thoroughly investigated. The 1H CS isosurface, corresponding to a value of the proton chemical shift taken from a previous experimental study, is described. The presence of the 1H CS isosurface should be taken into account in deriving structural information about supramolecular hosts and their encapsulation of small molecules.
| S-EPMC8036968 | biostudies-literature
Project description:In this work, we explore the accuracy of post-Hartree-Fock (HF) methods and double-hybrid density functional theory (DFT) for the computation of solid-state NMR chemical shifts. We apply an embedded cluster approach and investigate the convergence with cluster size and embedding for a series of inorganic solids with long-range electrostatic interactions. In a systematic study, we discuss the cluster design, the embedding procedure, and basis set convergence using gauge-including atomic orbital (GIAO) NMR calculations at the DFT and MP2 levels of theory. We demonstrate that the accuracy obtained for the prediction of NMR chemical shifts, which can be achieved for molecular systems, can be carried over to solid systems. An appropriate embedded cluster approach allows one to apply methods beyond standard DFT even for systems for which long-range electrostatic effects are important. We find that an embedded cluster should include at least one sphere of explicit neighbors around the nuclei of interest, given that a sufficiently large point charge and boundary effective potential embedding is applied. Using the pcSseg-3 basis set and GIAOs for the computation of nuclear shielding constants, accuracies of 1.6 ppm for 7Li, 1.5 ppm for 23Na, and 5.1 ppm for 39K as well as 9.3 ppm for 19F, 6.5 ppm for 35Cl, 7.4 ppm for 79Br, and 7.5 ppm for 25Mg as well as 3.8 ppm for 67Zn can be achieved with MP2. Comparing various DFT functionals with HF and MP2, we report the superior quality of results for methods that include post-HF correlation like MP2 and double-hybrid DFT.
| S-EPMC7659039 | biostudies-literature
Project description:The 1H chemical shielding anisotropy (CSA) is an NMR parameter that is exquisitely sensitive to the local environment of protons in crystalline systems, but it is difficult to obtain it experimentally due to the need to concomitantly suppress other anisotropic interactions in the solid-state NMR (SSNMR) pulse sequences. The SSNMR measurements of the 1H CSA are particularly challenging if the fast magic-angle-spinning (MAS) is applied. It is thus important to confront the results of both the single-crystal (SC) and fast-MAS experiments with their theoretical counterparts. Here the plane-waves (PW) DFT calculations have been carried out using two functionals in order to precisely characterize the structures and the 1H NMR chemical shielding tensors (CSTs) of the solid forms of maleic, malonic, and citric acids, and of L-histidine hydrochloride monohydrate. The level of agreement between the PW DFT and either SC or fast-MAS SSNMR 1H CSA data has been critically compared. It has been found that for the eigenvalues of the 1H CSTs provided by the fast-MAS measurements, an accuracy limit of current PW DFT predictions is about two ppm in terms of the standard deviation of the linear regression model, and sources of this error have been thoroughly discussed.
| S-EPMC6539467 | biostudies-literature
Project description:A dual photochemical/nickel-mediated decarboxylative strategy for the assembly of C(sp3)-C(sp2) linkages is disclosed. Under light irradiation at 390 nm, commercially available and inexpensive Hantzsch ester (HE) functions as a potent organic photoreductant to deliver catalytically active Ni(0) species through single-electron transfer (SET) manifolds. As part of its dual role, the Hantzsch ester effects a decarboxylative-based radical generation through electron donor-acceptor (EDA) complex activation. This homogeneous, net-reductive platform bypasses the need for exogenous photocatalysts, stoichiometric metal reductants, and additives. Under this cross-electrophile paradigm, the coupling of diverse C(sp3)-centered radical architectures (including primary, secondary, stabilized benzylic, α-oxy, and α-amino systems) with (hetero)aryl bromides has been accomplished. The protocol proceeds under mild reaction conditions in the presence of sensitive functional groups and pharmaceutically relevant cores.
| S-EPMC8179655 | biostudies-literature
Project description:Methionine residues fulfill a broad range of roles in protein function related to conformational plasticity, ligand binding, and sensing/mediating the effects of oxidative stress. A high degree of internal mobility, intrinsic detection sensitivity of the methyl group, and low copy number have made methionine labeling a popular approach for NMR investigation of selectively labeled protein macromolecules. However, selective labeling approaches are subject to more limited information content. In order to optimize the information available from such studies, we have performed DFT calculations on model systems to evaluate the conformational dependence of (3)J (CSCC), (3)J (CSCH), and the isotropic shielding, sigma(iso). Results have been compared with experimental data reported in the literature, as well as data obtained on [methyl-(13)C]methionine and on model compounds. These studies indicate that relative to oxygen, the presence of the sulfur atom in the coupling pathway results in a significantly smaller coupling constant, (3)J (CSCC)/(3)J (COCC) approximately 0.7. It is further demonstrated that the (3)J (CSCH) coupling constant depends primarily on the subtended CSCH dihedral angle, and secondarily on the CSCC dihedral angle. Comparison of theoretical shielding calculations with the experimental shift range of the methyl group for methionine residues in proteins supports the conclusion that the intra-residue conformationally-dependent shift perturbation is the dominant determinant of delta(13)Cepsilon. Analysis of calmodulin data based on these calculations indicates that several residues adopt non-standard rotamers characterized by very large approximately 100 degrees chi(3) values. The utility of the delta(13)Cepsilon as a basis for estimating the gauche/trans ratio for chi(3) is evaluated, and physical and technical factors that limit the accuracy of both the NMR and crystallographic analyses are discussed.
| S-EPMC5598763 | biostudies-literature
Project description:Fermions need to satisfy the Pauli exclusion principle: no two can be in the same state. This restriction is most compactly expressed in a second quantization formalism by the requirement that the creation and annihilation operators of the electrons satisfy anticommutation relations. The usual classical limit of quantum mechanics corresponds to creation and annihilation operators that satisfy commutation relations, as for a harmonic oscillator. We discuss a simple classical limit for Fermions. This limit is shown to correspond to an anharmonic oscillator, with just one bound excited state. The vibrational quantum number of this anharmonic oscillator, which is therefore limited to the range 0 to 1, is the classical analog of the quantum mechanical occupancy. This interpretation is also true for Bosons, except that they correspond to a harmonic oscillator so that the occupancy is from 0 up. The formalism is intended to be useful for simulating the behavior of highly correlated Fermionic systems, so the extension to many electron states is also discussed.
| S-EPMC15737 | biostudies-other
Project description:NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation.
| S-EPMC4218771 | biostudies-literature
Project description:The importance of relativity and dispersion in metallophilicity has been discussed in numerous studies. The existence of hybridization in the bonding between closed shell d10-d10 metal atoms has also been speculated, but the presence of attractive MO interaction in the metal-metal bond is still a matter of an ongoing debate. In this comparative study, a quantitative molecular orbital analysis and energy decomposition is carried out on the metallophilic interaction in atomic dimers (M+···M+) and molecular perpendicular [H3P-M-X]2 (where M = Cu, Ag, and Au; X = F, Cl, Br, and I). Our computational studies prove that besides the commonly accepted dispersive interactions, orbital interactions and Pauli repulsion also play a crucial role in the strength and length of the metal-metal bond. Although for M+···M+ the orbital interaction is larger than the Pauli repulsion, leading to a net attractive MO interaction, the bonding mechanism in perpendicular [H3P-M-X] dimers is different due to the larger separation between the donor and acceptor orbitals. Thus, Pauli repulsion is much larger, and two-orbital, four-electron repulsion is dominant.
| S-EPMC5842375 | biostudies-literature
Project description:Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatic calculations are essential for this purpose, but their use has been limited by a long-standing discussion on which value to use for the dielectric constants (?(eff) and ?(p)) required in Coulombic and Poisson-Boltzmann models. The currently used values for ?(eff) and ?(p) are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for ?(eff) and ?(p) by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in 14 proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (?(eff)) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (?(p)) ranged from 2 to 5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders and how different it is from the ?(p) of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of ?(p) = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pK(a) values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable ?(p) common to most folded proteins.
| S-EPMC4480918 | biostudies-literature
Project description:UV/Vis absorption and NMR spectroscopy titrations have been used to investigate the formation of complexes between cations and neutral H-bond acceptors in organic solvents. Complexes formed by two different H-bond acceptors with fifteen different cations were studied in acetone and in acetonitrile. The effects of water and ion pairing with the counter-anion were found to be negligible in the two polar solvents employed for this study. The data were used to determine self-consistent H-bond donor parameters (α) for a series of organic and inorganic cations; guanidinium, primary, tertiary and quaternary ammonium, imidazolium, methylpyridinium, lithium, sodium, potassium, rubidium and caesium. The results demonstrate the transferability of α parameters for cations between different solvents and different H-bond acceptor partners, allowing reliable prediction of cation recognition properties in different environments. Lithium and protonated nitrogen cations form the most stable complexes, but the α parameter is only 5.0, which is similar to the neutral H-bond donor 3-trifluoromethyl,4-nitrophenol (α = 5.1). Quaternary ammonium is the weakest H-bond donor investigated with an α value of 2.7, which is comparable to an alcohol. The α parameters for alkali metal cations decrease down the group from 5.0 (Li+) to 3.5 (Cs+).
| S-EPMC6566073 | biostudies-literature