Conformation and configuration of tertiary amines via GIAO-derived (13)C NMR chemical shifts and a multiple independent variable regression analysis.

The (13)C chemical shifts of six tertiary amines of unambiguous conformational structure are compared to predicted (13)C NMR chemical shifts obtained via empirically scaled GIAO shieldings for geometries from MM3 molecular mechanics calculations. An average deviation, absolute value of Deltadelta(av), of 0.8 ppm and a maximum deviation, absolute value of Deltadelta(max), of 2.8 ppm between predicted and experimental (13)C shifts of the six tertiary amines of unambiguous structure are found. In several cases of tertiary amines subject to rapid exchange, where experimental (13)C shifts at room temperature are weighted averages of multiple conformers, a comparison of calculated (13)C shifts of all reasonable MM3 predicted conformers with experimental (13)C shifts via a multiple independent variable regression analysis provides an efficient method of determining the major and minor conformers. The examples presented are 2-methyl-2-azabicyclo[2.2.1]heptane and 1,6-diazabicyclo[4.3.1]decane, which each have two expected contributing structures, and 2-(diethylamino)propane and 1,8-diazabicyclo[6.3.1]dodecane, where ten and seven low-energy conformers, respectively, are predicted by MM3 calculations.     

Structure validation of natural products by quantum-mechanical GIAO calculations of 13C NMR chemical shifts

Geometry optimization and GIAO (gauge including atomic orbitals) (13)C NMR chemical shift calculations at Hartree-Fock level, using the 6-31G(d) basis set, are proposed as a tool to be applied in the structural characterization of new organic compounds, thus providing useful support in the interpretation of experimental NMR data. Parameters related to linear correlation plots of computed versus experimental (13)C NMR chemical shifts for fourteen low-polar natural products, containing 10-20 carbon atoms, were employed to assess the reliability of the proposed structures. A comparison with the hybrid B3LYP method was carried out to evaluate electron correlation contributions to the calculation of (13)C NMR chemical shifts and, eventually, to extend the applicability of such computational methods to the interpretation of NMR spectra in apolar solutions. The method was tested by studying three examples of revised structure assignments, analyzing how the theoretical (13)C chemical shifts of both correct and incorrect structures matched the experimental data.     

Computing the NMR spectrum of a bulk ionic liquid phase by QM/MM methods

The dependence of (1)H and (13)C NMR chemical shifts of 1-butyl-3-methylimidazolium ([bmim])-based room-temperature ionic liquids on the counteranion ([BF(4)], [MeSO(4)]) is investigated experimentally and computationally. The local structure of the ionic liquids is investigated by means of DFT calculations of the structure of ion pairs and molecular dynamics simulations. Clusters extracted from the simulation runs are used to calculate (1)H and (13)C chemical shifts by means of QM/MM methods with various partition schemes. Proton H2 of the imidazolium ring is the most sensitive to the counteranion; its chemical shift is strongly dependent on subtle details of the arrangement of the two closest anions. It is shown that a correct spacing of signals can be attained by including the two anions closest to C2 and H2 in the QM layer.     

Stereodivergent Synthesis and Stereochemical Reassignment of the C79–C104 Fragment of Symbiodinolide

We have synthesized eight possible diastereoisomers 3 a – h of the C79–C97 fragment of symbiodinolide ( 1 ) in a stereodivergent manner by utilizing a dithiane addition to the aldehyde as a key step. Comparison of the ¹³C NMR chemical shifts of the natural product 1 and the synthetic products 3 a – h indicated that the relative stereostructure of this fragment in symbiodinolide ( 1 ) is that represented in 3 a or f . We have stereodivergently synthesized eight possible diastereoisomers of the C94–C104 fragment 4 a – h , and we have compared their ¹³C NMR chemical shifts with those of the natural product, which established the relative stereochemistry of this fragment to be that described in diastereoisomers 4 a or e . By combining the stereostructural outcomes of the C79–C97 and C94–C104 fragments, we have proposed four candidate compounds of the C79–C104 fragment 2 a – d . We also synthesized diastereoisomers 2 a and b ( 2 a in the preceding article; Chem. Eur. J. 2015 , DOI: 10.1002/chem.201503880) by a Julia–Kocienski olefination and diastereoisomers 2 c and d by a Wittig reaction. By comparing the ¹³C NMR chemical shifts of natural symbiodinolide ( 1 ) with those of the synthetic products 2 a – d , we have reassigned the stereostructure of the C79–C104 fragment of natural product 1 to be that depicted in diastereoisomer 2 b .     

A fast and easy computational method to calculate the (13)C NMR chemical shift of organic species adsorbed on the zeolite surface

Calculations of the 13C NMR chemical shifts for the methoxy and ethoxy groups adsorbed on Y and ZSM-5 zeolites were computed at GIAO/B3LYP/6-31+G*//MM+ level of theory, using a cluster representing a real part of the zeolites. The Y zeolite was represented by a cluster with 168 atoms, while ZSM-5 was represented by a cluster with 144 atoms. The calculated chemical shifts agreed well with reported experimental values, showing that the difference in chemical shifts is associated with differences in the geometry of the alkoxides on the two zeolites.     

新喜树碱衍生物的核磁共振谱分析与结构鉴定

以20(S)-喜树碱(CPT)为起始原料,对其进行结构修饰,合成了一种新的喜树碱衍生物CPT-A.并利用1D(~1H、~(13)C和DEPT135)和2D(异核单量子相关谱和异核多碳相关谱)核磁共振(NMR)技术对该化合物进行了结构确定,详细归属了CPT-A~1H和~(13)C NMR谱的化学位移,喜树碱骨架的指认结果与文献报道基本一致,并发现喜树碱骨架6位碳与取代基苯环3’位碳的化学位移相同,谱峰完全重叠,这在~(13)C谱中是不常见的.研究结果可为喜树碱类天然产物的发现和结构鉴定提供NMR数据支持和方法指引.     

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has been carried out. The present study is based on a recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach but the solvent effects are included by using the PB (Poisson-Boltzmann) model. Our calculated chemical shifts of (1)H and (13)C for these four proteins are in excellent agreement with experimentally measured values and represent clear improvement over that from the gas phase calculation. However, although the inclusion of the solvent effect also improves the computed chemical shifts of (15)N, the results do not agree with experimental values as well as (1)H and (13)C. Our study also demonstrates that AF-QM/MM calculated results accurately reproduce the separation of α-helical and β-sheet chemical shifts for (13)C(α) atoms in proteins, and using the (1)H chemical shift to discriminate the native structure of proteins from decoys is quite remarkable.     

Microenvironmental and conformational structure of triblock copolymers in aqueous solution by 1H and 13C NMR spectroscopy

1H and 13C nuclear magnetic resonance (NMR) spectra of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers in D2O solutions have been systematically investigated. The detailed assignments of various 1H and 13C NMR signals are presented. The hyperfine structure of PO -CH2- protons was clearly assigned, the arising reason of this hyperfine structure was attributed to the influence of the chiral center of -CHCH3- groups and the direct coupling between the PO -CH2- and -CH3 protons. The external standard 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS) was firstly applied in this system. Accurate chemical shift values referenced to the external standard DSS were obtained. 1H NMR chemical shift of PO -CH2- and -CH3 signals shows a larger decrease in ppm values than that of EO -CH2- signal with the increase of PPO/PEO ratio or temperature indicating that PO segments exist in a more hydrophobic microenvironment. A new resonance signal assigned to the PO -CH2- protons appeared when the temperature is above the CMT, which is attributed to the breakdown of the intra-molecular (C-H)...O hydrogen bond between the PO -CH2- protons and the ester oxygens. The breakdown of this intra-molecular hydrogen bond may result in a decrease of gauche conformers of the PPO chain. The increase of 13C NMR chemical shift of block copolymers validates this conformational change assumption. It can be inferred that the amount of gauche conformers decreases whereas that of trans conformers increases in both PO and EO chains when elevating the PPO/PEO ratio or temperature. The observed 13C NMR chemical shifts of PO segments show a bigger increase than those of EO segments, supporting the formation of a nonpolar microenvironment around PO segments.     

CAST/CNMR: highly accurate C NMR chemical shift prediction system considering stereochemistry

Accurate, practical prediction of ¹³C NMR chemical shifts has been achieved with a new system, CAST/CNMR, taking account of stereochemistry. The CAST/CNMR system has solved the critical problem of the accurate distinction of differences and similarities in stereochemical structures around a specific carbon, which has not yet been achieved by any other database-oriented system for prediction of ¹³C NMR chemical shifts. CAST/CNMR uses a three-dimensional structural database together with a ¹³C NMR spectral database. Absolute/relative configurational and conformational structural information are described by the CAST (CAnonical-representation of STereochemistry) coding method. This paper provides an overview of the CAST/CNMR system, and describes its application to two natural products as examples.     

Conformational study of cis-1,4-di-tert-butylcyclohexane by dynamic NMR spectroscopy and computational methods. Observation of chair and twist-boat conformations

[reaction: see text] Low-temperature 13C NMR spectra of cis-1,4-di-tert-butylcyclohexane (1) showed signals for the twist-boat (1a) and chair (1b) conformations. 13C NMR signals were assigned to specific carbons based on the different populations, different symmetries (time-averaged C(2v) for 1a and time-averaged C(s) for 1b), and calculated chemical shifts (GIAO, HF/6-311+G*). In addition to slow ring inversion and interconversion of the chair and twist-boat conformations, slow rotation of the tert-butyl groups was found. Most of the expected 13C peaks were observed. Free-energy barriers of 6.83 and 6.35 kcal/mol were found for interconversion of 1a (major) and 1b (minor) at -148.1 degrees C. Conformational space was searched with Allinger's MM3 and MM4 programs, and free energies were obtained for several low-energy conformations 1a-c. Calculations were repeated with ab initio methods up to the HF/6-311+G* level. Molecular symmetries, relative free energies, relative enthalpies and entropies, frequencies, and NMR chemical shifts were obtained. A boat conformation (1d; C(2v) symmetry) was generated and optimized as a transition state by ab initio, MM3, and MM4 calculations.     

15N NMR spectroscopy of labeled alkoxyamines. 15N-labeled model compounds for nitroxide-trapping studies in free-radical (Co)polymerization

Eight (15)N-labeled derivatives of 1-ethoxy-2,2,6,6-tetramethylpiperidine were synthesized in order to investigate the effects of their structural units on (15)N NMR spectra. A single peak is found for each alkoxyamine. The chemical shift depends extensively on the nature of the alpha carbon atom of the alkoxy group. The remote functional group attached to position 4 of the piperidine ring has a smaller but still significant effect. The results of the (15)N NMR measurements are supported by the detection of the N-H and N-C spin-spin coupling from the (1)H and (13)C NMR. The investigated alkoxyamines are model compounds for the radical-trapping products of styryl, methyl methacryloyl, alpha-methylstyryl, and methyl acryloyl radicals by (15)N-labeled nitroxides. The potential of (15)N NMR spectroscopy to analyze such products is discussed. In addition, it is shown that the (13)C chemical shifts of the alpha carbon atom of the alkoxy group fall in an empty part of the (13)C NMR spectrum, which allows the identification of trapped (macro)radicals via natural abundance (13)C NMR.     

Understanding sterol-membrane interactions part I: Hartree-Fock versus DFT calculations of 13C and 1H NMR isotropic chemical shifts of sterols in solution and analysis of hydrogen-bonding effects

1H and 13C NMR chemical shifts are exquisitely sensitive probes of the local environment of the corresponding nuclei. Ultimately, direct determination of the chemical shifts of sterols in their membrane environment has the potential to reveal their molecular interactions and dynamics, in particular concerning the hydrogen-bonding partners of their OH groups. However, this strategy requires an accurate and efficient means to quantify the influence of the various interactions on chemical shielding. Herein the validity of Hartree-Fock and DFT calculations of the 13C and 1H NMR chemical shifts of cholesterol and ergosterol are compared with one another and with experimental chemical shifts measured in solution at 500 MHz. A computational strategy (definition of basis set, simpler molecular models for the sterols themselves and their molecular complexes) is proposed and compared with experimental data in solution. It is shown in particular that the effects of hydrogen bonding with various functional groups (water as a hydrogen-bond donor and acceptor, acetone) on NMR chemical shifts in CDCl3 solution can be accurately reproduced with this computational approach.     

Computational studies of 13C NMR chemical shifts of saccharides

The (13)C NMR chemical shifts for alpha-D-lyxofuranose, alpha-D-lyxopyranose (1)C(4), alpha-D-lyxopyranose (4)C(1), alpha-D-glucopyranose (4)C(1), and alpha-D-glucofuranose have been studied at ab initio and density-functional theory levels using TZVP quality basis set. The methods were tested by calculating the nuclear magnetic shieldings for tetramethylsilane (TMS) at different levels of theory using large basis sets. Test calculations on the monosaccharides showed B3LYP(TZVP) and BP86(TZVP) to be cost-efficient levels of theory for calculation of NMR chemical shifts of carbohydrates. The accuracy of the molecular structures and chemical shifts calculated at the B3LYP(TZVP) level is comparable to those obtained at the MP2(TZVP) level. Solvent effects were considered by surrounding the saccharides by water molecules and also by employing a continuum solvent model. None of the applied methods to consider solvent effects was successful. The B3LYP(TZVP) and MP2(TZVP)(13)C NMR chemical shift calculations yielded without solvent and rovibrational corrections an average deviation of 5.4 ppm and 5.0 ppm between calculated and measured shifts. A closer agreement between calculated and measured chemical shifts can be obtained by using a reference compound that is structurally reminiscent of saccharides such as neat methanol. An accurate shielding reference for carbohydrates can be constructed by adding an empirical constant shift to the calculated chemical shifts, deduced from comparisons of B3LYP(TZVP) or BP86(TZVP) and measured chemical shifts of monosaccharides. The systematic deviation of about 3 ppm for O(1)H chemical shifts can be designed to hydrogen bonding, whereas solvent effects on the (1)H NMR chemical shifts of C(1)H were found to be small. At the B3LYP(TZVP) level, the barrier for the torsional motion of the hydroxyl group at C(6) in alpha-D-glucofuranose was calculated to 7.5 kcal mol(-1). The torsional displacement was found to introduce large changes of up to 10 ppm to the (13)C NMR chemical shifts yielding uncertainties of about +/-2 ppm in the chemical shifts.     

15N nuclear magnetic resonance spectroscopy. Natural abundance 15N NMR of monosubstituted indoles

¹⁵N chemical shifts of twenty-four substituted indoles have been determined in natural abundance (in organic solvents) using Fourier transform NMR. The overall chemical shift range is 27 ppm, with groups in the 2-, 3- and 5-ring positions showing the largest substituent effects. Substituents capable of resonance interaction with the indole nitrogen give shifts in the expected directions but they cannot be correlated with known substituent parameters. Compounds measured in DMSO give 0·2 to 10·2 ppm downfield shifts with respect to the same compound measured in CDCl₃. ¹³C NMR data for previously unreported compounds are also reported.     

Spatial substituent effects of various fluorinated groups on the 13C chemical shifts in cyclohexanes

The effect of introduction of fluorinated groups (CH(2)F, CHF(2), CF(3), C(2)F(5), OCF(3), SCF(3)) on the (13)C NMR chemical shifts in cyclohexanes is examined. The two main effects are caused by location at the alpha and gamma carbon positions. Comparison of the various data allowed the calculation of increments corresponding to the introduction of fluorinated groups at axial or equatorial positions on the cyclohexane ring. The introduction of fluorine atoms in methoxy and thiomethoxy groups has only a slight effect through the heteroatom on the (13)C chemical shifts.     

NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study

We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.     

Estimation and prediction of 13C NMR chemical shifts of carbon atoms in both alcohols and thiols

Quantitative structure-spectrum relationship calculations of ¹³C NMR chemical shifts of both 302 carbon atoms in 56 alcohols and 62 carbon atoms in 15 thiols are described using several parameters: the atomic ionicity index (INI), the polarizability effect index (PEI), and stereoscopic effect parameters (?) of the compounds. The ¹³C NMR chemical shifts for these compounds of both alcohols and thiols can be estimated through the multiple linear regression (MLR). A MLR model was built with variable screening by the stepwise multiple regression and examined by validation on its stability. The correlation coefficient of the established model as well as the leave-one-out cross-validation was 0.9724 and 0.9716 respectively. The results obviously indicate that INI and ? are linearly related with ¹³C NMR chemical shifts, which provides a new method for calculating ¹³C NMR chemical shifts in the compounds of both alcohols and thiols.     

The increment scheme for the prediction of13C NMR chemical shifts in polychlorinated dibenzo-p-dioxins

A topological method for the calculation of¹³C NMR chemical shifts was developed for polychlorinated dibenzo-p-dioxins (PCDD). Based on previous results for polychlorinated benzenes and polyhydroxybenzenes, the collective influence of the substituents on carbon chemical shifts is presented as the sum of two-particle increments. The increments only of two new monosubstituted graphs have to be added to those known for PCDD spectra: 1-Cl-DD and 2-Cl-DD. All structural situations in the¹³C NMR chemical shifts of the whole class of 75 PCDD can be covered with a few model compounds. The coefficients of the increment scheme are independent of the change of CDCl₃ for acetone-d₆, so it may be a new reliable criterion for recognizing PCDD by¹³C NMR, in spite of the close resemblance of NMR spectra of aromatic compounds.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 280–284, February, 1995.     

A density functional study of the 13C NMR chemical shifts in functionalized single-walled carbon nanotubes

The 13C NMR chemical shifts for functionalized (7,0), (8,0), (9,0), and (10,0) single-walled carbon nanotubes (SWNTs) have been studied computationally using gauge-including projector-augmented plane-wave (GIPAW) density functional theory (DFT). The functional groups NH, NCH3, NCH2OH, and CH2NHCH2 have been considered, and different sites where covalent addition or substitution may occur have been examined. The shifts of the carbons directly attached to the group are sensitive to the bond which has been functionalized and may, therefore, be used to identify whether the group has reacted with a parallel or a diagonal C-C bond. The addition of NH to a parallel bond renders the functionalized carbons formally sp3-hybridized, yielding shifts of around 44 ppm, independent of the SWNT radius. Reaction with a diagonal bond retains the formal sp2 hybridization of the substituted carbons, and their shifts are slightly lower or higher than those of the unsubstituted carbon atoms. The calculated 1H NMR shifts of protons in the functional groups are also dependent upon the SWNT-group interaction. Upon decreasing the degree of functionalization for the systems where the group is added to a parallel bond, the average chemical shift of the unfunctionalized carbons approaches that of the pristine tube. At the same time, the shifts of the functionalized carbons remain independent upon the degree of functionalization. For the SWNTs where N-R attaches to a parallel bond, the average shift of the sp2 carbons was found to be insensitive to the substituent R. Moreover, the shifts of the functionalized sp3 carbons, as well as of the carbons within the group itself, are independent of the SWNT radius. The results indicate that a wealth of knowledge may be obtained from the 13C NMR of functionalized SWNTs.