Crystal Structure Refinements of Cellulose Polymorphs using Solid State 13C Chemical Shifts

Force field methods in combination with chemical shift target functions are used to investigate the structures of cellulose I and II. Since diffraction investigations of biopolymers like cellulose II are only of poor resolution, different models for the structure are discussed in the literature. These models were used as the starting point for force field optimizations with ¹³C chemical shift target functions. In these optimizations additionally to the total energy a pseudo-energy is minimized that depends harmonically on the difference between calculated and observed chemical shifts. In the case of cellulose II all four criteria: (i) total energy, (ii) pseudo-energy, (iii) chemical shift rms (root mean square) difference, and (iv) deviation from the diffraction data favour the structure model of Kolpak and Blackwell with two antiparallel carbohydrate chains. The CH₂–OH group of one chain is in tg and that of the other chain in gt conformation. The chemical shift optimized fractional coordinates for cellulose II, I and I are presented together with the calculated and experimental ¹³C chemical shifts.     

Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide,a model for polar side-chain containing peptides

Knowledge of chemical shift-structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For-L-Ser-NH(2), was studied. Using the GIAO-RHF/6-31+G(d) and GIAO-RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen ((1)H(N), (1)H(alpha), (1)H(beta1), (1)H(beta2)), carbon ((13)C(alpha), (13)C(beta), (13)C') and nitrogen ((15)N) atoms have been computed for all 44 stable conformers of For-L-Ser-NH(2). An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (omega(0), phi, psi, omega(1), chi,(1) and chi(2)). At both levels of theory a linear correlation can be observed between (1)H(alpha)/phi, (13)C(alpha)/phi, and (13)C(alpha)/psi. These results indicate that the backbone and side-chain structures of For-L-Ser-NH(2) have a strong influence on its chemical shifts.     

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.     

Study of the temperature‐dependent conformational averaging of 1H NMR resonances in vinylcyclopropane through the use of ab initio methodology and Boltzmann statistics

The temperature dependence of the ¹ H NMR resonance of the C‐4 olefinic proton in vinylcyclopropane was investigated through a combination of ab initio calculations and Boltzmann statistics. A torsional energy profile as a function of the 〈?〉 dihedral angle was obtained using HF methodology with a 6–311G** basis set, while the corresponding ¹ H chemical shift profiles for the C‐4 proton were computed using the GIAO approach and either HF, DFT (B3LYP) or MP2 methods at the 6–311G** level of theory. Chemical shifts at different temperatures calculated as canonical ensemble averages in which the different ab initio ¹ H chemical shift profiles and a Boltzmann factor defined by the HF/ 6–311G** energy function are employed reproduce remarkably well the temperature dependence observed experimentally. Attempts to perform a similar study using only the GIAO‐MP2 ¹ H chemical shift profile and 〈?〉 dihedral angle trajectories obtained from molecular dynamics simulations at different temperatures failed to reproduce the experimental trends. This shortcoming was attributed to the inability of the force fields employed, Tripos 6.0 and MMFF94, to reproduce properly the three‐well torsional potential of vinylcyclopropane. The application of both methodologies to the calculation of population‐dependent chemical shifts in other systems is discussed. Copyright © 2002 John Wiley & Sons, Ltd.     

Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement

Although difficult to analyze, NMR chemical shifts provide detailed information on protein structure. We have adapted the semi-empirical bond polarization theory (BPT) to protein chemical shift calculation and chemical shift driven protein structure refinement. A new parameterization for BPT amide nitrogen chemical shift calculation has been derived from MP2 ab initio calculations and successfully evaluated using crystalline tripeptides. We computed the chemical shifts of the small globular protein ubiquitin, demonstrating that BPT calculations can match the results obtained at the DFT level of theory at very low computational cost. In addition to the calculation of chemical shift tensors, BPT allows the calculation of chemical shift gradients and consequently chemical shift driven geometry optimizations. We applied chemical shift driven protein structure refinement to the conformational analysis of a set of Trypanosoma brucei (the causative agent of African sleeping sickness) tryparedoxin peroxidase Px III structures. We found that the interaction of Px III with its reaction partner Tpx seems to be governed by conformational selection rather than by induced fit.     

Predicting 195Pt NMR Chemical Shifts in Water-Soluble Inorganic/Organometallic Complexes with a Fast and Simple Protocol Combining Semiempirical Modeling and Machine Learning

Water-soluble Pt complexes are the key components in medicinal chemistry and catalysis. The well-known cisplatin family of anticancer drugs and industrial hydrosylilation catalysts are two leading examples. On the molecular level, the activity mechanisms of such complexes mostly involve changes in the Pt coordination sphere. Using ¹⁹⁵Pt NMR spectroscopy for operando monitoring would be a valuable tool for uncovering the activity mechanisms; however, reliable approaches for the rapid correlation of Pt complex structure with ¹⁹⁵Pt chemical shifts are very challenging and not available for everyday research practice. While NMR shielding is a response property, molecular 3D structure determines NMR spectra, as widely known, which allows us to build up 3D structure to ¹⁹⁵Pt chemical shift correlations. Accordingly, we present a new workflow for the determination of lowest-energy configurational/conformational isomers based on the GFN2-xTB semiempirical method and prediction of corresponding chemical shifts with a Machine Learning (ML) model tuned for Pt complexes. The workflow was designed for the prediction of ¹⁹⁵Pt chemical shifts of water-soluble Pt(II) and Pt(IV) anionic, neutral, and cationic complexes with halide, NO₂⁻, (di)amino, and (di)carboxylate ligands with chemical shift values ranging from −6293 to 7090 ppm. The model offered an accuracy (normalized root-mean-square deviation/RMSD) of 1.08 %/145.02 ppm on the held-out test set.     

Chemical mass shifts in resonance ejection experiments in the quadrupole ion trap

Chemical mass shifts were measured in a Paul ion trap operated in the mass-selective instability scan with resonance ejection using a custom-built instrument. These shifts, which can be as much as 2%, decrease with increasing endcap electrode separation owing to changes in the higher order contributions to the electric field. They also decrease with decreasing helium buffer gas pressure. Both of these effects are analogous to those found with boundary ejection. This suggests that the previously proposed chemical mass shift mechanism based on compound-dependent collisional modification of the ejection delay produced by field faults near the endcap electrode apertures holds true also for resonance ejection. The influence of the resonance frequency on chemical mass shifts was also investigated and it is shown that at certain working points (values of the Mathieu parameter q(z) and a(z)) non-linear resonances greatly reduce the ejection delay for all ions, regardless of their chemical structures, and thus reduce the magnitude of the chemical mass shift. Energetic collisions leading to dissociation can take place at an earlier stage during the ejection process in the mass analysis scan when using resonance ejection compared with boundary ejection. This leads to even larger chemical mass shifts of fragile ions in resonance ejection. Increasing the resonance voltage amplitude can enhance this effect. The chemical mass shifts of fragile ions increase with increase in the resonance voltage amplitude, whereas negligible changes occur for structurally stable ions.     

小环化合物中饱和碳质子化学位移的计算

小环化合物由于其张力、构型、构象和各向异性效应等原因,环碳上质子化学位移缺乏规律性,难以预测,对此作者曾提出一种近似算法。本文根据303种小环化合物中饱和碳质子的化学位移实验数据,将适于计算这类质子化学位移的公式表述为:     

Theoretical Study on a 42 T Model of Beta Zeolite by Density Functional Theory Simulation

Density functional theory was applied to study the structure of Beta zeolite. A model cluster containing 41Si atoms, 1 Al atom, 70 O atoms and 29 H atoms was constructed. The model structures were optimized using the Becke＇s three-parameter hybrid method with the Lee-Yang-Parr correlation functional （B3LYP） and the 6-31G basis set applying the Gaussian03 program package. The NMR parameters were calculated to validate the rationality of the model. It was found that in the optimization models, all O-H bond lengths were in range of 0.984-0.985A^°, among which the model with O-H bond length of 0.98478A^° was more stable than the others. The ^1H and ^27Al chemical shifts of the most stable model were 4.03434 and 55.74 ppm, which were pretty consistent with Larry＇ s experimental data of 4.1 and 54 ppm. The relationship between other structure parameters and total relative electric energy has also been found. All the results exhibit that the 42 T （the total number of Si and Al atoms is 42） model has common properties of the standard of zeolite Beta.     

Toward direct determination of conformations of protein building units from multidimensional NMR experiments VI: chemical shift analysis of his to gain 3D structure and protonation state information

NMR--chemical shift structure correlations were investigated by using GIAO-RB3LYP/6-311++G(2d,2p) formalism. Geometries and chemical shifts (CSI values) of 103 different conformers of N'-formyl-L-histidinamide were determined including both neutral and charged protonation forms. Correlations between amino acid torsional angle values and chemical shifts were investigated for the first time for an aromatic and polar amino acid residue whose side chain may carry different charges. Linear correlation coefficients of a significant level were determined between chemical shifts and dihedral angles for CSI[(1)H(alpha)]/phi, CSI[(13)C(alpha)]/phi, and CSI[(13)C(alpha)]/psi. Protonation of the imidazole ring induces the upfield shift of CSI[(13)C(alpha)] for positively charged histidines and an opposite effect for the negative residue. We investigated the correspondence of theoretical and experimental (13)C(alpha), (13)C(beta), and (1)H(alpha) chemical shifts and the nine basic conformational building units characteristic for proteins. These three chemical shift values allow the identification of conformational building units at 80% accuracy. These results enable the prediction of additional regular secondary structural elements (e.g., polyProlineII, inverse gamma-turns) and loops beyond the assignment of chemical shifts to alpha-helices and beta-pleated sheets. Moreover, the location of the His residue can be further specified in a beta-sheet. It is possible to determine whether the appropriate residue is located at the middle or in a first/last beta-strand within a beta-sheet based on calculated CSI values. Thus, the attractive idea of establishing local residue specific backbone folding parameters in peptides and proteins by employing chemical shift information (e.g., (1)H(alpha) and (13)C(alpha)) obtained from selected heteronuclear correlation NMR experiments (e.g., 2D-HSQC) is reinforced.     

Solid-state 13C NMR and quantum chemical investigation of metal diene complexes

This paper presents novel measurements and calculations of the olefinic (13)C chemical shift tensor principal values in several metal diene complexes. The experimental values and the calculations show shifts as large as 70 ppm with respect to the values in the parent olefinic compounds. These shifts are highly anisotropic, with the largest ones observed in the less shielded principal components and the smallest ones in the most shielded principal components of the tensor. The orientations of the principal components of the tensors remain, within 10 degrees , at their directions in ethylene and other olefinic compounds. The calculations, performed using the GIAO method and the LanDZ pseudopotential basis set, show good agreement with the experiments, and were used to establish definite evidence for the existence of a Cl-bridge structure in the bicyclo[2.2.1]hepta-2,5-diene (BCHD)dichlororuthenium(II) polymer.     

NMR hyperfine shifts in blue copper proteins: a quantum chemical investigation

We present the results of the first quantum chemical investigations of 1H NMR hyperfine shifts in the blue copper proteins (BCPs): amicyanin, azurin, pseudoazurin, plastocyanin, stellacyanin, and rusticyanin. We find that very large structural models that incorporate extensive hydrogen bond networks, as well as geometry optimization, are required to reproduce the experimental NMR hyperfine shift results, the best theory vs experiment predictions having R2 = 0.94, a slope = 1.01, and a SD = 40.5 ppm (or approximately 4.7% of the overall approximately 860 ppm shift range). We also find interesting correlations between the hyperfine shifts and the bond and ring critical point properties computed using atoms-in-molecules theory, in addition to finding that hyperfine shifts can be well-predicted by using an empirical model, based on the geometry-optimized structures, which in the future should be of use in structure refinement.     

18-冠-6与Eu(fod)3+在CCl4中的化学平衡及其配合物的结构

在室温下测定了CCl_4溶液中,18-冠-6的亚甲基、Eu(fod)的t—丁基质子的PMR化学位移与溶液组成的相互关系。提出了生成配合物RS,R_2S,R_2,R_3(S为18-冠-6,R为Eu(fod)_3)的模式。求得了平衡常数值(升/摩):K_1=[RS]/([R][S])=2.O×10~5,K_2=[R_2S]/([R][RS])=1.0×10~3,Q_1=[R_2]/[R]~2=4.2×10~2,Q_2=[R_3]/([R_2][R])=4.0×10~1。并测得在配合物RS,R_2S中18-冠-6质子的平均化学位移分别为4.90,10.84(ppm,相对于纯18-冠-6); 在配合物R,R_2,R_3,RS,R_2中t-丁基质子平均化学位移分别为1.53,2.33,0.54,1.02,2.42(ppm,相对于TMS)。 根据配合物的化学位移值,并考虑分子及分子轨道的对称性、位阻等因素提出了配合物R_2,RS,R_2S的可能的结构模型。     

Calculating nuclear magnetic resonance chemical shifts in solvated systems

The nuclear magnetic resonance (NMR) chemical shift is extremely sensitive to molecular geometry, hydrogen bonding, solvent, temperature, pH, and concentration. Calculated magnetic shielding constants, converted to chemical shifts, can be valuable aids in NMR peak assignment and can also give detailed information about molecular geometry and intermolecular effects. Calculating chemical shifts in solution is complicated by the need to include solvent effects and conformational averaging. Here, we review the current state of NMR chemical shift calculations in solution, beginning with an introduction to the theory of calculating magnetic shielding in general, then covering methods for inclusion of solvent effects and conformational averaging, and finally discussing examples of applications using calculated chemical shifts to gain detailed structural information.     

Introducing krypton NMR spectroscopy as a probe of void space in solids

A wealth of information about porous materials and their void spaces has been obtained from the chemical shift data in (129)Xe NMR spectroscopy during the past decades. In this contribution, the only NMR active, stable krypton isotope (83)Kr (spin I = (9)/(2)) is explored as a novel probe for porous materials. It is demonstrated that (83)Kr NMR spectroscopy of nanoporous or microporous materials is feasible and straightforward despite the low gyromagnetic ratio and low abundance of the (83)Kr isotope. The (83)Kr line width in most of the studied cases is quadrupolar dominated and field-strength independent. A significant exception was found in calcium-exchanged zeolites where the field dependence of the line width indicates a distribution of isotropic chemical shifts that may be caused by long-range disorder in the zeolite structure. The (83)Kr chemical shifts observed in the investigated materials display a somewhat different behavior than that of their (129)Xe counterparts and should provide a great resource for the verification or refinement of current (129)Xe chemical shift theory. In contrast to xenon, krypton with its smaller atomic radius has been demonstrated to easily penetrate the porous framework of NaA. Chemical shifts and line widths of (83)Kr are moderately dependent on small fluctuations in the krypton loading but differ strongly between some of the studied samples.     

Substituent Effect on Mercury-199 Chemical Shifts in Some Bisarylmercurials and Aryl(2-benzothiazolylthio) mercurials

The present paper covers the 199 Hg NMR chemical shifts of 24 substituted diphenylmercurials and phenyl(2-benzothiazolylthio)mercurials. There is a good linear relationship between the chemical shift and the Hammett constant of the substituents for both series of compounds, and electron donating substituents cause the chemical shift towards downfield.     

Standardization of chemical shifts of TMS and solvent signals in NMR solvents

The standard for chemical shift is dilute tetramethylsilane (TMS) in CDCl3, but many measurements are made relative to TMS in other solvents, the proton resonance of the solvent peak or relative to the lock frequency. Here, the chemical shifts of TMS and the proton and deuterium chemical shifts of the solvent signals of several solvents are measured over a wide temperature range. This allows for the use of TMS or the solvent and lock signal as a secondary reference for other NMR signals, as compared with dilute TMS in CDCl3 at a chosen temperature; 25 degrees C is chosen here. An accuracy of 0.02 ppm is achievable for dilute solutions, provided that the interaction with the solvent is not very strong. The proton chemical shift of residual water is also reported where appropriate.     

Trends in shift rules in carbon-13 nuclear magnetic resonance spectroscopy and computer-aided shift prediction

A major problem in the use of ¹³C-NMR spectroscopy for structure identification is to estimate the ¹³C shifts of compounds known or suspected to be present in the spectrum. The substituent chemical shifts of different functional groups were studied and new, detailed empirical rules are reported. Trends in these shift parameters are noted. It appears that for functional groups containing more than one nucleus, the observed shift parameters (x=α, β, γ, δ shifts) can be approximated by the shift parameters of the component nuclei (x_comp) in the functional group, i.e., x_obs ≈ x_comp. The detailed shift behavior and shift additivity rules were computerized. The resulting program (CSPEC) has many user friendly features, e.g., ease of input, modification of structure, storage and retrieval of known shifts, and rapid computation.     

15N-, 1H-, and 13C-NMR chemical shifts and electronic properties of aromatic diamines and dianhydrides

We measured the ¹⁵N-, ¹H-, and ¹³C-NMR chemical shifts for a series of aromatic diamines and aromatic tetracarboxylic dianhydrides dissolved in DMSO-d₆, and discuss the relationships between these chemical shifts and the rate constants of acylation (k) as well as such electronic-property-related parameters such as ionization potential (IP), electronic affinity (EA), and the energy ε of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). The ¹⁵N chemical shifts of the amino group of diamines (δ_N) depend monotonically on the logarithm of k (log k) and on IP. We inferred the reactivities of diamines whose acylation rates have not been measured from their δ_N, and we propose an arrangement of diamines in the order of their reactivity. The ¹H chemical shift of amino hydrogens (δ_H) and the ¹³C chemical shift of carbons bonded to nitrogen (δ_C) are roughly proportional to δ_N, but these shifts are not as closely correlated with log k and IP. Although the ¹³C chemical shifts of the carbonyl carbon of dianhydrides (δ_C,) varies much less than the δ_C and δ_N of diamines, δ_C, can be an index of acylation reactivity for dianhydrides because it is closely correlated with ε_LUMO. These facts indicate that the chemical shifts of diamines and dianhydrides are displaced according to their electron-donor and electron-acceptor properties, and that these chemical shifts can be used as indices of the electronic properties of monomers. Changes in reactivity caused by the introduction of trifluoromethyl groups into diamines and dianhydrides are inferred from the displacements of δ_N and δ_C © 1992 John Wiley & Sons, Inc.     

Interpretation of Spectroscopic Markers of Hydrogen Bonds

Quantum calculations are used to examine whether an AH???D H‐bond is unambiguously verified by a downfield shift of the bridging proton's NMR signal or a red (or blue) shift of the AH stretching frequency in the IR spectrum. It is found that such IR band shifts will occur even if the two groups experience weak or no attractive force, or if they are drawn in so close together that their interaction is heavily repulsive. The mere presence of a proton‐acceptor molecule can affect the chemical shielding of a position occupied by a protondonor by virtue of its electron density, even if there is no H‐bond present. This density‐induced shielding is heavily dependent on position around the proton–acceptor atom, and varies from one group to another. Evidence of a hydrogen bond rests on the measurement of a proton deshielding in excess of what is caused purely by the presence of the proton acceptor species.