Gauge-including Atomic Orbital Calculations Research Articles

Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks.

Computer prediction of NMR chemical shifts plays an increasingly important role in molecular structure assignment and elucidation for organic molecule studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) have established a framework to predict NMR chemical shifts but often at a significant computational expense with a limited prediction accuracy. Recent advancements in deep learning methods, especially graph neural networks (GNNs), have shown promise in improving the accuracy of predicting experimental chemical shifts, either by using 2D molecular topological features or 3D conformational representation. This study presents a new 3D GNN model to predict 1H and 13C chemical shifts, CSTShift, that combines atomic features with DFT-calculated shielding tensor descriptors, capturing both isotropic and anisotropic shielding effects. Utilizing the NMRShiftDB2 data set and conducting DFT optimization and GIAO calculations at the B3LYP/6-31G(d) level, we prepared the NMRShiftDB2-DFT data set of high-quality 3D structures and shielding tensors with corresponding experimentally measured 1H and 13C chemical shifts. The developed CSTShift models achieve the state-of-the-art prediction performance on both the NMRShiftDB2-DFT test data set and external CHESHIRE data set. Further case studies on identifying correct structures from two groups of constitutional isomers show its capability for structure assignment and elucidation. The source code and data are accessible at https://yzhang.hpc.nyu.edu/IMA.

On the importance of intramolecular hydrogen bond cooperativity in d-glucose - an NMR and QTAIM approach.

The idea that hydrogen bond cooperativity is responsible for the structure and reactivity of carbohydrates is examined. Density functional theory and gauge-including atomic orbital calculations on the known conformers of the α and β anomers of d-glucopyranose in the gas phase are used to compute proton NMR chemical shifts and interatomic distances, which are taken as criteria for probing intramolecular interactions. Atom-atom interaction energies are calculated by the interacting quantum atoms approach in the framework of the quantum theory of atoms in molecules. Association of OH1 in the counterclockwise conformers with a strong acceptor, pyridine, is accompanied by cooperative participation from OH2, but there is no significant change in the bonding of the two following 1,2-diol motifs. The OH6... O5 (G-g+/cc/t and G+g-/cc/t conformers) or OH6... O4 (Tg+/cc/t conformer) distance is reduced, and the OH6 proton is slightly deshielded. In the latter case, this shortening and the associated increase in the OH6-O4 interaction energy may be interpreted as a small cooperative effect, but intermolecular interaction energies are practically the same for all three conformers. In most of the pyridine complexes, one ortho proton interacts with the endocyclic oxygen O5. Analogous results are obtained when the clockwise conformer, G-g+/cl/g-, detected for the α anomer, and a hypothetical conformer, Tt/cl/g-, are complexed with pyridine through OH6. Generally, the cooperative effect does not go beyond the first two OH groups of a chain. Copyright © 2017 John Wiley & Sons, Ltd.

GIAO Calculations of Chemical Shifts of NMR Spectra of 1H and 13C of the Hexahydroindoles Products

Isotropic 1 H and 13 C nuclear magnetic shielding constants of hexahydroindoles products of intramolecular Diels-Alder of the triene-amide reaction have been calculated by employing the gauge-including-atomic-orbital (GIAO), Continuous Set of Gauge Transformations (CSGT) and a slight variation on the CSGT (IGAIM) methods at the B3LYP/6-311(d,p) density functional level of theory. Geometry of each compound has been optimized employing 6-31G(d,p) basis sets. The comparison of the theoretical results to the experimental results of the Ha compound shows that the GIAO method is the most reliable. On the other hand we calculate the chemicals shifts of the carbon ( 13 C) and hydrogen ( 1 H) of the Hb and Hc compounds. This calculation was performed using the B3LYP functional, using the GIAO method at the level of the following bases: 6-31G, 6-31 G(d), 6-31G(d,p), 6-311G, 6-311G(d). The theoretical trends are compared with experimental data taken from the literature. The least squares regression analyses of the results indicate R-square values greater than 0.90 in the range for total data set.

Theoretical investigation to characterize the inclusion complex of α-lipoic acid and β-cyclodextrin

Abstract We simulated the docking of α-lipoic acid (α-LA) in β-cyclodextrin (β-CD) using two models. We considered in this study complexes formed by 1:1 host–guest stoichiometry in vacuo and in aqueous phase, using PM6, DFT and ONIOM2 hybrid calculations. The results obtained with PM6 method clearly indicate that the complexes formed are energetically favored with or without solvent, model 2 (α-LA entering the cavity of β-CD from its wide side by COOH group) is found more favored than model 1 (α-LA entering into the cavity of β-CD from its wide side by cyclic group), the preference being greater in the case of ONIOM2 calculations. In addition, NBO analysis gives that mutual interactions between the donor and acceptor orbitals of α-lipoic acid and β-CD plays an important role to the stabilization of such a complex. Finally, 1 H nuclear magnetic resonance (NMR) chemical shifts of free and complexed α-LA were calculated by the Gauge-Including Atomic Orbital (GIAO) method and compared with available experimental data. The results of GIAO calculations were analyzed and discussed.

Comparative analysis of 13C shielding constants stereospecificity in the silicon and germanium derivatives of acetylenic aldehyde and ketone oximes based on the 13C NMR spectroscopy and GIAO calculations

In the acetylenic aldehyde oximes with substituents containing silicon and germanium, the (13)C NMR signal of the C-2 carbon of triple bond is shifted by 3.5 ppm to lower frequency and that of the C-3 carbon is moved by 7 ppm to higher frequency on going from E to Z isomer. A greater low-frequency effect of 5.5 ppm on the C-2 carbon signal and a greater high-frequency effect of 11 ppm on the C-3 carbon signal are observed in the analogous acetylenic ketone oximes. The carbon chemical shift of the C=N bond is larger by 4 ppm in E isomer relative to Z isomer for the aldehyde and ketone oximes. The (29)Si chemical shifts in the silicon containing acetylenic aldehyde and ketone oximes are almost the same for the diverse isomers. The trends in changes of the measured chemical shifts are well reproduced by the gauge-including atomic orbital (GIAO) calculations of the (13)C and (29)Si shielding constants.

Determination of Enantiomeric Excess of Leucine by 13C CP-MAS Solid-State NMR

The enantiomeric excess can be determined by many methods. One of them is nuclear magnetic resonance in solid state (SS-NMR). In this study we used the SS-NMR experiment of one-dimensional exchange spectroscopy by sideband alteration for determination of the enantiomeric excess of leucine. The density functional theory gauge-including atomic orbital calculations were used to assign all signals in 13C cross polarization magic-angle spinning spectra for two different molecules in the crystal lattice of L-leucine.

Ab initio studies of possible fluorine-bearing four- and fivefold coordinated Al species in aluminosilicate glasses

Ab initio NMR gauge-including atomic orbital (GIAO) calculations were used to constrain assignments of resonances in 27 Al NMR spectra of F-bearing alkali aluminosilicate glasses. The effect of bond angles within the range 126-150° on the chemical shift was investigated using cluster models of next-nearest atoms that are charge balanced by hydrogen atoms. GIAO calculations used geometries obtained through optimization at fixed Al-O-Si bond angles. The calculated peak positions for all of the 4-fold coordinated Al species yielded calculated 27 Al NMR peak positions in good agreement with the experimental data, suggesting that any or all of the species AlF 4 - , AlF 3 O(SiH 3 ) - , AlF 2 O 2 (SiH 3 ) 2 - , and AlFO 3 (SiH 3 ) 3 - may be present. Three of the investigated 5-fold coordinated species AlF 5 2- , AlF 3 O 2 (SiH 3 ) 2 2- , and AlF 2 O 3 (SiH 3 ) 3 2- fit the experimental requirements well, whereas the remaining 5-fold coordinated species that were tested [AlF 4 O(SiH 3 ) 2- , and AlFO 4 (SiH 3 ) 4 2- ] did not.

Natural chemical shielding analysis of nuclear magnetic resonance shielding tensors from gauge-including atomic orbital calculations

Nuclear magnetic shielding tensors computed by the gauge including atomic orbital (GIAO) method in the Hartree–Fock self-consistent-field (HF-SCF) framework are partitioned into magnetic contributions from chemical bonds and lone pairs by means of natural chemical shielding (NCS) analysis, an extension of natural bond orbital (NBO) analysis. NCS analysis complements the description provided by alternative localized orbital methods by directly calculating chemical shieldings due to delocalized features in the electronic structure, such as bond conjugation and hyperconjugation. Examples of NCS tensor decomposition are reported for CH4, CO, and H2CO, for which a graphical mnemonic due to Cornwell is used to illustrate the effect of hyperconjugative delocalization on the carbon shielding.

13C MAS NMR Spectra ofcis,cis-Mucononitrile in Liquid-Crystalline Media and in the Solid State. Orientation of the Carbon Chemical-Shift Tensors

The spinning sidebands observed in the $^{13}C$ MAS NMR spectra ofcis,cis-mucononitrile oriented in liquid-crystalline media and of the neat sample in the solid state are studied. There are differences in the sideband intensity patterns in the two cases. These differences arise because the order parameters which characterize the orientation of the solute in the liquid-crystalline media differ for different axes. It is shown that, in general, the relative intensities of the sidebands contain information on the sign and magnitude of an effective chemical-shift parameter which is a function of the sum of the products of the principal components of the chemical-shift tensor and the corresponding order parameters with respect to the director. A method for obtaining the orientation of the carbon chemical-shift tensor is proposed. The carbon chemical-shift tensors obtained from gauge-including atomic orbital calculations are also presented for comparison.