Automated structure elucidation of organic molecules from (13)c NMR spectra using genetic algorithms and neural networks.

The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using (13)C NMR spectrum as readily obtainable information. (13)C NMR chemical shift, intensity, and multiplicity information is available from (13)C NMR DEPT spectra. By means of artificial neural networks a fast and accurate method for calculating the (13)C NMR spectrum of the generated structures exists. The approach is limited by the size of the constitutional space that has to be searched and by the accuracy of the shift prediction for the unknown substance. The method is implemented and tested successfully for organic molecules with up to 20 non-hydrogen atoms.     

Fluorine-19 NMR chemical shift probes molecular binding to lipid membranes

The binding of amphiphilic molecules to lipid bilayers is followed by 19F NMR using chemical shift and line shape differences between the solution and membrane-tethered states of -CF 3 and -CHF 2 groups. A chemical shift separation of 1.6 ppm combined with a high natural abundance and high sensitivity of 19F nuclei offers an advantage of using 19F NMR spectroscopy as an efficient tool for rapid time-resolved screening of pharmaceuticals for membrane binding. We illustrate the approach with molecules containing both fluorinated tails and an acrylate moiety, resolving the signals of molecules in solution from those bound to synthetic dimyristoylphosphatidylcholine bilayers both with and without magic angle sample spinning. The potential in vitro and in vivo biomedical applications are outlined. The presented method is applicable with the conventional NMR equipment, magnetic fields of several Tesla, stationary samples, and natural abundance isotopes.     

The role of water molecules in a resorcinarene capsule as probed by NMR diffusion measurements

[structure: see text] NMR diffusion measurements were used to probe the role of water molecules in a resorcinarene capsule in a CDCl(3) solution. It was found that the water/resorcinarene ratio affects both the chemical shift and the diffusion coefficient of the water molecules. From the NMR diffusion measurements we could conclude that the major species in the chloroform solution is the hexamer having eight water molecules that are in fast exchange, on the NMR time scale, with the bulk water.     

Predicting chemical shifts with graph neural networks

Inferring molecular structure from Nuclear Magnetic Resonance (NMR) measurements requires an accurate forward model that can predict chemical shifts from 3D structure. Current forward models are limited to specific molecules like proteins and state-of-the-art models are not differentiable. Thus they cannot be used with gradient methods like biased molecular dynamics. Here we use graph neural networks (GNNs) for NMR chemical shift prediction. Our GNN can model chemical shifts accurately and capture important phenomena like hydrogen bonding induced downfield shift between multiple proteins, secondary structure effects, and predict shifts of organic molecules. Previous empirical NMR models of protein NMR have relied on careful feature engineering with domain expertise. These GNNs are trained from data alone with no feature engineering yet are as accurate and can work on arbitrary molecular structures. The models are also efficient, able to compute one million chemical shifts in about 5 seconds. This work enables a new category of NMR models that have multiple interacting types of macromolecules.

This model can predict chemical shifts on proteins and small molecules purely from atom elements and coordinates. It can capture important phenomena like hydrogen bonding induced downfield shift, thus can be used to infer intermolecular interactions.     

Novel methods of automated structure elucidation based on 13C NMR spectroscopy

Three new approaches for automated structure elucidations of organic molecules using NMR spectroscopic data were introduced recently. These approaches apply a neural network 13C NMR chemical shift prediction method to rank the results of structure generators by their agreement of the predicted and experimental chemical shifts. These three existing implementations are compared using realistic example molecules. The applicability and reliability of such approaches is addressed.     

Deep Learning-Based Method for Compound Identification in NMR Spectra of Mixtures

Nuclear magnetic resonance (NMR) spectroscopy is highly unbiased and reproducible, which provides us a powerful tool to analyze mixtures consisting of small molecules. However, the compound identification in NMR spectra of mixtures is highly challenging because of chemical shift variations of the same compound in different mixtures and peak overlapping among molecules. Here, we present a pseudo-Siamese convolutional neural network method (pSCNN) to identify compounds in mixtures for NMR spectroscopy. A data augmentation method was implemented for the superposition of several NMR spectra sampled from a spectral database with random noises. The augmented dataset was split and used to train, validate and test the pSCNN model. Two experimental NMR datasets (flavor mixtures and additional flavor mixture) were acquired to benchmark its performance in real applications. The results show that the proposed method can achieve good performances in the augmented test set (ACC = 99.80%, TPR = 99.70% and FPR = 0.10%), the flavor mixtures dataset (ACC = 97.62%, TPR = 96.44% and FPR = 2.29%) and the additional flavor mixture dataset (ACC = 91.67%, TPR = 100.00% and FPR = 10.53%). We have demonstrated that the translational invariance of convolutional neural networks can solve the chemical shift variation problem in NMR spectra. In summary, pSCNN is an off-the-shelf method to identify compounds in mixtures for NMR spectroscopy because of its accuracy in compound identification and robustness to chemical shift variation.     

Structural and dynamic aspects of hydrogen-bonded complexes and inclusion compounds containing alpha,omega-dicyanoalkanes and urea, investigated by solid-state 13C and 2H NMR techniques

Solid-state 13C NMR and 2H NMR techniques have been used to investigate structural and dynamic properties of the 1,4-dicyanobutane/urea and 1,5-dicyanopentane/urea 1:1 hydrogen-bonded complexes and the 1,6-dicyanohexane/urea inclusion compound. The pure crystalline phase of urea has also been investigated. The 13C NMR studies have focused on 13C chemical shift anisotropy and second-order quadrupolar effects (arising from 13C-14N interaction) for the urea molecules and the cyano groups of the alpha,omega-dicyanoalkanes. Parameters describing these interactions are derived and are discussed in relation to the known structural properties of these materials. Comparison of 13C chemical shift anisotropies of the cyano carbons and rates of 13C dipolar dephasing suggest that 1,4-dicyanobutane and 1,5-dicyanopentane are effectively static, whereas 1,6-dicyanohexane has greater mobility. 2H NMR line shape analysis for the 1,4-dicyanobutane/urea-d4 and 1,5-dicyanopentane/urea-d4 complexes indicates that the only motion of the urea molecules that is effective on the 2H NMR time scale is a rapid libration about the C=O bond over an angular range of about 26 degrees . For the 1,6-dicyanohexane/urea-d4 inclusion compound, the 2H NMR line shape is consistent with a motion comprising 180 degrees jumps about the C=O bond at rates that are intermediate on the 2H NMR time scale. In addition, rapid libration about the C=O bond also occurs over an angular range of about 20 degrees . The dynamic properties of the urea molecules in these materials are compared with those of urea molecules in other crystalline environments.     

1H NMR chemical shift calculations as a probe of supramolecular host-guest geometry

The self-assembled supramolecular host [Ga(4)L(6)](12-) (1; L = 1,5-bis[2,3-dihydroxybenzamido]naphthalene) can encapsulate cationic guest molecules within its hydrophobic cavity and catalyze the chemical transformations of bound guests. The cavity of host 1 is lined with aromatic naphthalene groups, which create a magnetically shielded interior environment, resulting in upfield shifted (1-3 ppm) NMR resonances for encapsulated guest molecules. Using gauge independent atomic orbital (GIAO) DFT computations, we show that (1)H NMR chemical shifts for guests encapsulated in 1 can be efficiently and accurately calculated and that valuable structural information is obtained by comparing calculated and experimental chemical shifts. The (1)H NMR chemical shift calculations are used to map the magnetic environment of the interior of 1, discriminate between different host-guest geometries, and explain the unexpected downfield chemical shift observed for a particular guest molecule interacting with host 1.     

95Mo nuclear magnetic resonance parameters of molybdenum hexacarbonyl from density functional theory: appraisal of computational and geometrical parameters

Solid-state (95)Mo nuclear magnetic resonance (NMR) properties of molybdenum hexacarbonyl have been computed using density functional theory (DFT) based methods. Both quadrupolar coupling and chemical shift parameters were evaluated and compared with parameters of high precision determined using single-crystal (95)Mo NMR experiments. Within a molecular approach, the effects of major computational parameters, i.e. basis set, exchange-correlation functional, treatment of relativity, have been evaluated. Except for the isotropic parameter of both chemical shift and chemical shielding, computed NMR parameters are more sensitive to geometrical variations than computational details. Relativistic effects do not play a crucial part in the calculations of such parameters for the 4d transition metal, in particular isotropic chemical shift. Periodic DFT calculations were tackled to measure the influence of neighbouring molecules on the crystal structure. These effects have to be taken into account to compute accurate solid-state (95)Mo NMR parameters even for such an inorganic molecular compound.     

The development of an NMR chemical shift prediction application with the accuracy necessary to grade proton NMR spectra for identity

We have developed an NMR chemical shift prediction system that enables high throughput automatic grading of NMR spectra. In support of high throughput synthetic efforts for our drug discovery program, a rapid and accurate analysis for identity was needed. The system was designed and implemented to take advantage of the NMR assignments that had been tabulated on internally generated research compounds. The system has been operational for four years and has been used in conjunction with an internally written grading program to successfully analyze several hundred thousand samples based only on their 1D ¹H spectrum. A focused test of the system's accuracy on 1006 molecules demonstrated the ability to estimate the proton chemical shift with an average error of +/?0.16 ppm. This level of chemical shift accuracy allows for reliable structure confirmation by automated analysis using only proton NMR. Copyright © 2009 John Wiley & Sons, Ltd.     

DFT‐GIAO1H NMR chemical shifts prediction for the spectral assignment and conformational analysis of the anticholinergic drugs (−)‐scopolamine and (−)‐hyoscyamine

The relatively large chemical shift differences observed in the ¹H NMR spectra of the anticholinergic drugs (?)‐scopolamine 1 and (?)‐hyoscyamine 2 measured in CDCl₃ are explained using a combination of systematic/molecular mechanics force field (MMFF) conformational searches and gas‐phase density functional theory (DFT) single point calculations, geometry optimizations and chemical shift calculations within the gauge including/invariant atomic orbital (GIAO) approximation. These calculations show that both molecules prefer a compact conformation in which the phenyl ring of the tropic ester is positioned under the tropane bicycle, clearly suggesting that the chemical shift differences are produced by the anisotropic effect of the aromatic ring. As the calculations fairly well predict these experimental differences, diastereotopic NMR signal assignments for the two studied molecules are proposed. In addition, a cursory inspection of the published ¹H and ¹³C NMR spectra of different forms of 1 and 2 in solution reveals that most of them show these diastereotopic chemical shift differences, strongly suggesting a preference for the compact conformation quite independent of the organic or aqueous nature of the solvent. Copyright © 2010 John Wiley & Sons, Ltd.     

Selectivity of guest-host interactions in self-assembled hydrogen-bonded nanostructures observed by NMR

We studied the incorporation of various small guest molecules into calix[4]hydroquinone nanotubes and nanoclusters using solid-state proton NMR spectroscopy in combination with quantum chemical calculations. While the molecules exhibit different types of hydrogen bonding and van der Waals interactions, they show different affinities to the nanotube host structures. As the guest molecules are located inside the complexes, they experience a shift in the NMR resonance line caused by screening effects from the aromatic electrons of the host superstructure. The abilities to fill the otherwise empty space within the tubes can hence be measured indirectly by the displacement of the NMR lines relative to the free molecules. In this way, we can probe which guest molecules are recognized by the calix[4]hydroquinones as suitable for filling their nanoporous superstructures. Selective guest-host interactions have been successfully achieved for the three component mixture of water and acetone with either 2-methyl-2-propanol or 2-propanol. In both cases, the alcohols were superior to acetone in filling the CHQ tubes.     

Oxygen-hydrogen stretching frequencies for water and methanol in the primary solvent shells of cations and anions

Since the band for OH stretching of HOD molecules solvating perchlorate ions is clearly resolved, the remaining band can be analysed to give values for the OH absorption for the cation solvation shell: these are closely correlated with NMR shift data.     

Nuclear magnetic resonance spectroscopy : Lanthanide shift reagents. Useful tools for study of conformational equilibria in solution?

Difficulties encountered in the use of lanthanide shift reagents for study of conformational equilibria of simple organic molecules in solution are reviewed. It seems clear that, despite these difficulties, significant conformational information is to be gained from the effect of these reagents on NMR chemical shifts.     

Calculating the response of NMR shielding tensor σ(31P) and 2J(31P,13C) coupling constants in nucleic acid phosphate to coordination of the Mg2+ cation

Dependence of NMR (31)P shielding tensor and (2)J(P,C) coupling constants on solvation of nucleic acid phosphate by Mg(2+) and water was studied using methods of bioinformatic structural analyses of crystallographic data and DFT B3LYP calculations of NMR parameters. The effect of solvent dynamics on NMR parameters was calculated using molecular dynamic. The NMR calculations for representative solvation patterns determined in crystals of B-DNA and A-RNA molecules pointed out the crucial importance of local Mg(2+) coordination geometry, including hydration by explicit water molecules and necessity of dynamical averaging over the solvent reorientation. The dynamically averaged (31)P chemical shift decreased by 2-9.5 ppm upon Mg(2+) coordination, the chemical shielding anisotropy increased by 0-20 ppm, and the (2)J(P,C5') coupling magnitude decreased by 0.2-1.8 Hz upon Mg(2+) coordination. The calculated decrease of the (31)P chemical shift is in excellent agreement with the 1.5-10 ppm decrease of the phosphorothioate (31)P chemical shift upon Cd(2+) coordination probed experimentally in hammerhead ribozyme (Suzumura; et al. J. Am. Chem. Soc. 2002, 124, 8230-8236; Osborne; et al., Biochemistry 2009, 48, 10654-10664). None of the dynamically averaged NMR parameters unequivocally distinguishes the site-specific Mg(2+) coordination to one of the two nonesterified phosphate oxygen atoms of the phosphate determined by bioinformatic analyses. By comparing the limit cases of static and dynamically averaged solvation, we propose that mobility of the solvent has a dramatic impact on NMR parameters of nucleic acid phosphate and must be taken into account for their accurate modeling.     

Ultra-high resolution 17O solid-state NMR spectroscopy of biomolecules: a comprehensive spectral analysis of monosodium L-glutamate·monohydrate

Monosodium L-glutamate monohydrate, a multiple oxygen site (eight) compound, is used to demonstrate that a combination of high-resolution solid-state NMR spectroscopic techniques opens up new possibilities for (17)O as a nuclear probe of biomolecules. Eight oxygen sites have been resolved by double rotation (DOR) and multiple quantum (MQ) NMR experiments, despite the (17)O chemical shifts lying within a narrow shift range of <50 ppm. (17)O DOR NMR not only provides high sensitivity and spectral resolution, but also allows a complete set of the NMR parameters (chemical shift anisotropy and electric-field gradient) to be determined from the DOR spinning-sideband manifold. These (17)O NMR parameters provide an important multi-parameter comparison with the results from the quantum chemical NMR calculations, and enable unambiguous oxygen-site assignment and allow the hydrogen positions to be refined in the crystal lattice. The difference in sensitivity between DOR and MQ NMR experiments of oxygen in bio/organic molecules is also discussed. The data presented here clearly illustrates that a high resolution (17)O solid-state NMR methodology is now available for the study of biomolecules, offering new opportunities for resolving structural information and hence new molecular insights.     

Assignments of normally unoccupied orbitals to the temporary negative ion states of several lanthanide NMR shift reagents and comments on resonance involvement in electron circular dichroism

We have measured the total electron scattering cross sections of several NMR shift reagent molecules X(hfc)3, where X = Yb, Er, Eu and Pr, by means of electron transmission spectroscopy (ETS) to determine their vertical attachment energies. A strong low-energy resonance (<1 eV) is observed in all of the compounds except for Yb(hfc)3. We explain this anomaly in terms of the ground-state electron configuration of each molecule. Also, with the aid of restricted open-shell Hartree-Fock (ROHF) calculations on analogous molecules with truncated fluorocarbon chains, we have assigned specific normally unoccupied orbitals to the resonances observed in ETS. To our knowledge, these molecules are the largest for which this procedure has been successfully completed. Nolting et al. (J. Phys. B 1997, 30, 5491) have demonstrated that the above NMR shift reagents exhibit electron circular dichroism (ECD) between 1 and 10 eV. Using our new total cross section data, we comment on the possibility of resonance involvement in the generation of ECD.     

Li＋在PC＋DMF混合溶剂中优先溶剂化的13C NMR研究

利用¹³C NMR光谱技术研究了Li^＋在碳酸丙烯酯(PC)＋N,N-二甲基甲酰胺(DMF)混合溶剂中的优先溶剂化现象. 根据溶剂分子中碳原子的化学位移随锂盐浓度的变化关系, 确定了与Li^＋发生配位的原子. 碳原子的配位位移值随混合溶剂组成的变化关系表明, 在LiClO₄＋PC＋DMF混合物中, DMF分子对Li^＋的溶剂化作用较PC分子强. 定量计算得到, 在n(PC)∶n(DMF)＝1∶1(摩尔比)的混合溶剂中, PC与DMF分子数在Li^＋第一溶剂化层中的比率为0.12, 说明Li^＋优先被DMF分子溶剂化.     

NMR spectra of carotenoporphyrins. Computer-assisted conformational analysis

A computer-assisted method of conformational analysis for porphyrin molecules bearing flexible side-chains has been developed. The method utilizes the ring current-induced chemical shift changes of the side-chain protons which arise from the porphyrin macrocycle and any attached aryl rings. The treatment has been applied to a series of carotenoporphyrin molecules, which are important as models for a variety of photophysical processes in biological systems. Chemical shift data of sufficient accuracy for the conformational analysis were obtained from 500 MHz NMR experiments. The conformations of the carotenoporphyrins varied from extended ones with the carotenoid well away from the porphyrin ring to tightly folded species, depending on molecular constitution. The analytical method can be extended to other porphyrin-based systems.     

High-resolution NMR spectra of n-alkanes penetrating into carbon fibers and of protons in carbon fibers

We present a simple NMR method for microscopically exploring the local environment in carbon fibers. The method utilizes n-alkanes as probe molecules, where the n-alkanes penetrate carbon fibers of interest. The high-resolution (1)H NMR spectra for a mixture of a carbon fiber and n-alkanes acquired by this method show a shift of the resonance line, which is due to the local structure of the fiber. The utility of this method is discussed on the basis of the (1)H NMR spectra obtained. In addition, the (1)H distribution and the local motion in the structure of the carbon fiber are revealed in view of the (1)H NMR spectra.