A molecular mechanics and ab initio prediction of the 1H chemical shifts of pinanes

Molecular mechanics calculations plus the application of a refined Karplus equation gave the conformations of 19 pinanes. These range from a Y‐shaped geometry in the apopinene and α‐pinene series to a pseudo chair conformation in β‐pinene, nopinone and verbanone, a flattened chair in pinocarvone and the pinocarveols and a distorted Y shape for iso‐verbanone. These structures were then used as input to predict the ¹H chemical shifts of these compounds by semi‐empirical (¹H‐NMR spectra (HSPEC)) and ab initio gauge‐invariant atomic orbital (GIAO) calculations, the latter at the B3LYP hybrid density functional theory level using 6‐31++G** basis set. The two methods gave generally good agreement with the 184 observed shifts with root mean square (RMS) errors 0.07 ppm (HSPEC) and 0.10 ppm (GIAO), but the GIAO calculations gave several significant (>0.25 ppm) errors. One was for the H₃ proton in apopinenone and other α,β unsaturated ketones; the others occurred for protons in close proximity to hydroxyl groups. To provide more information, smaller analogues of known geometry and chemical shifts were subject to the same analysis. In cyclopentenone, the Gaussian geometry gave good agreement with the observed shifts, but the MMFF94, MMX and MM3 geometries all gave errors for different protons. These results show clearly that the molecular geometries of the α,β unsaturated ketones are responsible for the errors. The errors for the alcohols were examined using ethanol as model and were shown to be due to the different possible conformations of the OH group. Similar GIAO calculations on substituted methanes gave good agreement for the methyl compounds but poor agreement for di and tri halosubstituted methanes. The aforementioned method of molecular mechanics plus GIAO calculations is shown to be a very useful tool for the investigation of molecular geometries and conformations. However, multihalogen compounds may require different basis sets for accurate calculations. Copyright © 2017 John Wiley & Sons, Ltd.     

Genistein complexes with amines. Part II: ab initio study of the complexes with piperazine and triethylamine

The piperazine and triethylamine complexes of genistein, exhibiting high immunosuppressant activity, were ab initio modeled at RHF/6-31G^** level and results were compared with those obtained for genistein–morpholine complexes by X-ray, NMR, and theoretical methods. The most stable genistein–piperazine complex is formed due to hydrogen bonding of genistein's OH group at position C7 to piperazine's nitrogen atom. In the most stable genistein–triethylamine complex genistein's OH group at position C4′ (position para to phenyl substituent) and trimethylamine nitrogen atom are engaged in hydrogen bond formation. The calculations confirmed our previous NMR conclusion that piperazine is more strongly complexed by genistein than is morpholine or triethylamine. The theoretical ¹³C NMR spectra correlate fairly well with the experimental spectra.     

The prediction of (1)H chemical shifts in amines: a semiempirical and ab initio investigation

Twenty one conformationally fixed amines and their N,N-dimethyl derivatives were obtained commercially or synthesized. These included cis and trans 4-t-butyl cyclohexylamine, 2-exo and 2-endo norbornylamine, 2-adamantylamine, 4-phenylpiperidine, 1-napthylamine and tetrahydro-1-napthylamine. The (1)H NMR spectra of these amines were measured in CDCl(3) solution, assigned and the (1)H chemical shifts given. This data was used to investigate the effect of the amino group on the (1)H chemical shifts in these molecules. These effects were analyzed using the CHARGE model. This calculates the electric field and steric effects of the amino group for protons more than three bonds removed, together with functions for the calculation of two-bond and three-bond effects. The rotational isomerism about the C--N bond of the amino group was investigated by ab initio calculations of the potential energy surface (PES) about this bond at the HF/3-21G level. The resulting conformers were then minimized at the B3LYP/6-311 + + G (d,p) level. These geometries were then used to calculate the (1)H chemical shifts in the above compounds by CHARGE and the ab initio gauge-invariant atomic orbital (GIAO) method at the B3LYP/6-311 + + G(d,p) level and the shifts were compared with those observed. The compounds investigated gave 170 (1)H chemical shifts ranging from 0.60 to 8.2 ppm. The rms errors (obs.-calc.) were ca 0.1 ppm (CHARGE) and ca 0.2 ppm (GIAO). Large deviations of ca 1.0 ppm were observed for the NH protons in the GIAO calculations. The complex spectra of alkyl and aryl amines can thus be successfully predicted by both ab initio and semiempirical methods except for the NH protons, for which the ab initio calculations are not sufficiently accurate.     

Local protein backbone folds determined by calculated NMR chemical shifts

NMR chemical shifts (CSs: δN(NH), δC(α), δC(β), δC', δH(NH), and δH(α)) were computed for the amino acid backbone conformers (α(L), β(L), γ(L), δ(L), ε(L), α(D), γ(D), δ(D), and ε(D) [Perczel et al., J Am Chem Soc 1991, 113, 6256]) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single β-strands, hairpins with type I and II β-turns, as well as double- and triple-stranded β-sheet models. The so-called "capping effect" was analyzed: residues at the termini of a homoconformer sequence unit usually have different CSs than the central residues of an adequately long homoconformer model. In heteroconformer sequences capping effect ruins the direct applicability of several chemical shift types (δH(NH), δC', and δN(NH)) for backbone structure determination of the parent residue. Experimental δH(α), δC(α), and δC(β) values retrieved from protein database are in good agreement with the relevant computed data in the case of the common backbone conformers (α(L), β(L), γ(L), and ε(L)), even though neighboring residue effects were not accounted for. Experimental and computed ΔδH(α)-ΔδC(α), ΔδH(α)-ΔδC(β), and ΔδC(α)-ΔδC(β) maps give qualitatively the same picture, that is, the positions of the backbone conformers relative to each other are very similar. This indicates that the H(α), C(α), and C(β) chemical shifts of alanine depend considerably on the backbone fold of the parent residue also in proteins. We provide tabulated CSs of the chiral amino acids that may predict the various structures of the residues.     

An ab initio study of pyruvic acid

The geometries and vibrational frequencies of two conformers of pyruvic acid have been obtained at the ab initio second order Möller-Plesset level of theory using the 6-311++G^** basis set. While the calculated geometries have been compared to the experimental microwave data, the vibrational frequencies have been assigned, using the experimental gas phase IR spectra of 13 isotopes of pyruvic acid by a recently developed scaling procedure (IRPROG). An attempt has been made to explain the stability of the eclipsed conformation over the staggered conformation of pyruvic acid by taking account of the molecular orbitals.     

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.     

1H chemical shifts in NMR: Part 23, the effect of dimethyl sulphoxide versus chloroform solvent on 1H chemical shifts

The 1H chemical shifts of 124 compounds containing a variety of functional groups have been recorded in CDCl3 and DMSO-d6 (henceforth DMSO) solvents. The 1H solvent shift Delta delta = delta(DMSO) - delta(CDCl3) varies from -0.3 to +4.6 ppm. This solvent shift can be accurately predicted (rms error 0.05 ppm) using the charge model of alpha, beta, gamma and long-range contributions. The labile protons of alcohols, acids, amines and amides give both, the largest solvent shifts and the largest errors. The contributions for the various groups are tabulated and it is shown that for H.C.C.X gamma-effects (X = OH, NH, =O, NH.CO) there is a dihedral angle dependence of the gamma-effect. The group contributions are discussed in terms of the possible solvent-solute interactions. For protic hydrogens, hydrogen bonding is the dominant interaction, but for the remaining protons solvent anisotropy and electric field effects appear to be the major factors.     

Ab initio molecular modeling of 13C NMR chemical shifts of polymers. 1. Ethylene–norbornene copolymers

Cycloolefin copolymers (COC) have recently raised much interest because of their excellent thermal and optical properties, largely determined by the chain composition and stereochemistry. Previous force‐field computations allowed us to define the main conformational characteristics of ethylene–norbornene (E–N) copolymers and to contribute to the elucidation of their microstructure on the basis of empirical relationships between conformation and ¹³C nuclear magnetic resonance (NMR) chemical shifts. A thorough test of ab initio ¹³C chemical shifts computations [gauge‐invariant atomic orbitals (GIAO)] on known cases shows that the agreement with experimental data is quite good, especially with the MPW1PW91 density functional theory (DFT), using the 6‐311+G(2d,p) basis set on properly energy‐minimized structures. We applied this method on proper model compounds to confirm the signal assignment of the spectra of E–N copolymers in the presence of norbornene microblocks, where strong effects arising from ring distortions are expected to occur. The results nicely confirm the latest assignment of norbornene signals belonging to ENNE sequences. This shows the great potentialities of GIAO/DFT computations with regard to complex spectra interpretation and polymer microstructural investigations. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Computational modeling of polyoxotungstates by relativistic DFT calculations of (183)W NMR chemical shifts

The (183)W nuclear shielding in a variety of tungsten polyoxometalates (POM) (Lindqvist, Anderson, decatungstates, Keggin) of different shapes and charges has been modeled by DFT calculations that take into account relativistic effects, by means of the zero-order regular approximation (ZORA), and solvent effects, by the conductor-like screening model (COSMO) continuum method. The charge/surface area ratio (q/A) is proposed as an indicator of the charge density to which the solvation energies of all POMs are correlated in a satisfactory way. Among the various theoretical levels tested (ZORA scalar or spin-orbit, frozen-core or all-electron basis set, geometry optimization in the gas phase or in the continuum solvent, etc.), the best results are obtained when both geometry optimization in solvent and spin-orbit shielding are included (mean absolute error of delta=35 ppm). The quality of the computed chemical shifts depends systematically on the charge density as expressed by q/A; thus, POMs with low q/A ratios display the best agreement with experimental data. The performance of the method is such that computed values can aid the assignment of the (183)W NMR spectra of polyoxotungstates, as shown by the case of alpha-[PW(11)TiO(40)](5-), whose six signals are ranked computationally so as to almost reproduce the experimental ordering even though the signals are spaced by as little as 5 ppm.     

A physiochemical study of excited state intramolecular proton transfer process-Luminescent chemosensor by spectroscopic investigation supported by ab initio calculations

A group of novel Schiff base derivatives were synthesized and characterized by NMR spectra, X-ray, mass and CHN analysis. An excited state intramolecular proton transfer (ESIPT) process in hydroxy Schiff base (SB4) has been studied using emission spectroscopy and it was detected that the two distinct ground state isomers of I and II are responsible for the emission. The comparison of the emission wavelength in hydrocarbon solvent strongly supports that trans enol form predominates over the cis enol form for Schiff base (SB4). With increasing base concentration of the solutions of hydroxy substituted Schiff bases (SB4 and SB5), two isobestic points are found which confirm the equilibrium among the trans enol form, anion and the cis enol form. The fluorescence of (SB4) quenched markedly with the gradual addition of Cu(2+) but the fluorescence properties of (SB5) was influenced by other metal ions. Therefore Schiff base (SB5) can be used as a new fluorescence sensor to detect the quantity of Cu(2+) ion in any sample solution depending on the relative intensity change. DFT calculations on energy, dipole moment, charge distribution of the rotamers in the ground and excited states of the Schiff base derivatives were performed and discussed. PES calculation indicates that the energy barrier for the interconversion of two rotamers is too high in the excited state than the ground state.     

Temperature coefficient of NH chemical shifts of thioamides and amides in relation to structure

NH chemical shift temperature coefficients have been measured in a large series of N-substituted-3-piperidinethiopropionamides in which the NN distances are short but of varied length, as well as in a couple of the corresponding amides and in some simpler amides and thioamides. Geometries are calculated by means of ab initio DFT methods. The N-substituted-3-piperidinethiopropionamides show in most cases strong intramolecular N–HN hydrogen bonds according to IR spectra and ab initio calculations. For compounds with rather short NN distances the S=C–N–H moiety is non-planar. Dihedral angles as small as 160° are found. The NH chemical shift coefficients measured in non-polar solvents in all the N-substituted-3-piperidinethiopropionamides are more negative (−8 to −17 ppb/K) than in non-hydrogen bonded thioamides. For the latter in non-polar solvents like CDCl₃ and toluene the temperature coefficients are as small as −1 to −4 ppb/K. The large negative effects can be related not only to the non-planarity of the thioamide group in a way that the more pronounced the non-planarity the more negative the temperature coefficients, but also to strong hydrogen bonding and the fact that the acceptor is a nitrogen. For similar amides with non-planar amide groups and nitrogen acceptor large negative temperature coefficients are likewise seen. In polar solvents like DMF the effects in simple thioamides are uniform and close to −6 ppb/K, whereas in the more complex compound like 4p(t) the temperature coefficient is close to 0. An essential feature of measuring temperature coefficients of compounds without strong intramolecular hydrogen bonds in non-polar solvents and at low temperatures is to keep the concentration low enough to avoid dimerisation.     

Ab initio quantum chemical and NMR study of the symmetric monooximes of 1,2,3-phenalenetrione and 1,2,3-indantrione

The possibility for nitroso-oxime tautomerism in symmetric monooximes of 1,2,3-phenalenetrione and 1,2,3-indantrione is studied by means of ab initio quantum chemical methods and NMR spectroscopy. For both compounds, ab initio calculations with different basis sets predict the oxime tautomer as most stable in agreement with the ¹H- and ¹³C-NMR results in CDCl₃ and DMSO-d₆ solutions. A coalescence of the signals for the carbon atoms from carbonyl groups of 1,2,3-phenalenetrione monooxime in DMSO-d₆ solution at temperature 360 K is observed. This coalescence may be attributed to rotation of the hydrogen atom from the hydroxyl group around the N---O bond. The rotational transition structures for both compounds at different computational levels were located in the gas phase and in solution.     

o-Alkyl-substituted aromatic phosphanes for hydroformylation studies: synthesis, spectroscopic characterization and ab initio investigations

In earlier hydroformylation studies modification of the rhodium catalyst with o-methyl-substituted or o-ethyl-substituted phosphane ligands have increased regioselectivity to branched aldehydes. The promising results achieved created a need for further studies. Hence, a wider group of o-substituted arylphosphane ligands, e.g. (2-cyclohexylphenyl)diphenylphosphane, (2-isopropylphenyl)diphenylphosphane, (2-methylnaphthyl)diphenylphosphane, (2,5-dimethylphenyl)diphenylphosphane and (2-phenylphenyl)diphenylphosphane were synthesized and tested in rhodium-catalyzed hydroformylation to support the previous findings. Characterization of the ligands was made by NMR spectroscopy (¹H, ³¹P{¹H}, ¹³C{¹H}, HSQC, COSY-90 and COLOC). Additional parameters for evaluation of the stereoelectronic properties of the ligands were provided by quantum mechanical calculations and by synthesizing Rh(acac)(CO)(PR₃) complexes. In the rhodium-catalyzed hydroformylation of propene and 1-hexene the ligands increased the formation of branched aldehydes compared to triphenylphosphane. Additionally the increasing size of the o-alkyl-substituent was found to effect favorably to the iso-selectivity.     

An ab initio study of solvent polarity and hydrogen bonding effects on the nitrogen NMR shieldings of N,N‐dimethylacetamidine

Density functional theory combined with the polarizable continuum model (PCM) and continuous set of gauge transformations method is applied to investigate the effects of solvent polarity on the nitrogen NMR shieldings of N, N‐dimethylacetamidine. Hydrogen bonding effects on shielding are likewise calculated using a supermolecule approach, where the imino group of the solute is hydrogen bonded with solvent. Theoretical results are compared with published experimental data. The PCM shielding calculations utilizing PCM‐optimized solute geometries yield results comparable to those obtained with the supermolecule approach. Geometry optimization of the solute appears to be more important in PCM shielding calculations than in the supermolecule approach. The large solvent shifts observed in water can only be reproduced when the N·H distance used in the calculation indicates full proton transfer from water to the imino nitrogen of the solute. Copyright © 2002 John Wiley & Sons, Ltd.     

Complete basis set ab initio computational study of three-dimensional aromaticity in highly symmetric hydrogen clusters

The aromaticity of planar and highly symmetric three-dimensional hydrogen clusters were evaluated with the complete basis set ab initio computational method. The energy of formation of the hydrogen clusters from the hydrogen molecule and hydrogen molecular ions were used in comparison to their relative stabilities. The aromaticity of planar hydrogen clusters, as well as hydrogen clusters in the three dimensions, arranged as highly symmetric regular polyhedra (Plato's polyhedras), were discussed with respect to the Hückel and Möbius aromatic rules.     

Comparison of the substituent effects on the 13C NMR with the 1H NMR chemical shifts of CHN in substituted benzylideneanilines

Fifty‐two samples of substituted benzylideneanilines XPhCH?NPhYs (XBAYs) were synthesized, and their NMR spectra were determined in this paper. Together with the NMR data of other 77 samples of XBAYs quoted from literatures, the ¹H NMR chemical shifts (δ_H(CH?N)) and ¹³C NMR chemical shifts (δ_C(CH?N)) of the CH?N bridging group were investigated for total of 129 samples of XBAYs. The result shows that the δ_H(CH?N) and δ_C(CH?N) have no distinctive linear relationship, which is contrary to the theoretical thought that declared the δ_H(CH?N) values would increase as the δ_C(CH?N) values increase. With the in‐depth analysis, we found that the effects of σ_F and σ_R of X/Y group on the δ_H(CH?N) and the δ_C(CH?N) are opposite; the effects of the substituent specific cross‐interaction effect between X and Y (Δσ²) on the δ_H(CH?N) and the δ_C(CH?N) are different; the contributions of parameters in the regression equations of the δ_H(CH?N) and the δ_C(CH?N) [Eqns 4 and 7), respectively] also have an obvious difference. Copyright © 2015 John Wiley & Sons, Ltd.     

Tautomeric and conformational equilibrium of 2-nitrosophenol and 9,10-phenanthrenequinonemonooxime: ab initio and NMR study

The tautomeric and conformational equilibrium of 2-nitrosophenol and 9,10-phenanthrenequinonemonooxime was studied by ab initio methods. The geometry optimizations of the structures investigated were done without any geometrical restrictions at HF/6-31G** and MP2/6-31G** levels of theory. The transition structures for tautomeric and rotameric conversions were located. To correct for electron correlation, single-point calculations were carried out up to MP4/6-311G*//MP2/6-31G* level of theory.

Ab initio calculations for 2-nitrosophenol in agreement with the available experimental data define the nitroso form as more stable. It was found that the influence of the correlation energy on the relative stabilities is smaller for the rotamers of the nitroso tautomer but substantially (4–6 kcal/mol) for the oxime forms. It was found that the barrier height of tautomerization reaction is 10.24 kcal/mol.

The structure of the 9,10-phenanthrenequinonemonooxime was studied by solid and liquid state NMR spectroscopy. Ab initio calculations in agreement with our experimental data predict that the compound exists as oxime tautomer and the syn-oxime is most stable. It was found that the solvent influence on the relative stabilities of both isomers: syn- and anti-oxime. While in chloroform solution the syn-oxime is preferred but in DMSO anti-oxime is more stable in energy.

At the MP4/6-311G*//MP2/6-31G**+ZPE level of theory the barrier of tautomerization was predicted to be 10.96 kcal/mol and the rotational barrier around the single C–O bond in the syn-oxime was found to be 7.57 kcal/mol. The rotation is facile and this explains the absence of nitroso tautomers in solution.     

烷基锂分子中化学键的 ab initio 研究

本文用6-13G基函对3-12G基优化构型进行单点ab initio (从头计算法) 计算, 并根据轨道的组合系数、电荷密度图和键强参数等详尽地分析了烷基锂分子的成键情况。烷基锂的易挥发、易聚合、聚合物易溶于烃类溶剂中等物理、化学性质主要是其C－Li键具有显著的共价性缘故。由于烷基锂的C-Li键比C－H和C－C键的强度要小,故C-Li键易于断裂,使烷基锂表现有高的化学反应活性。     

Ab initio analysis of the interaction of CO2 with acetylated d-glucopyranose derivatives

Peracetylated d-glucopyranose has a high solubility in CO₂ and can be a promising phase-change physical solvent or absorbent for CO₂, as reported recently. However, peracetylated d-glucopyranose is unstable under acidic atmospheres, especially in sulfur-containing waste gases, and the possibly major decomposition products are 2,3,4,6-tetra-O-acetyl-d-glucopyranose, 1-thiol-d-glucopyranose tetraacetate, and 1-mercaptoethyl-d-glucopyranose tetraacetate. Therefore, it is highly interesting to investigate the interaction between CO₂ and these three compounds using ab initio calculations, including geometry optimizations with HF/3-21G, B3LYP/6-31+G** and single-point energy calibration with MP2/aug-cc-pVDZ. The results indicate that the electrostatic interactions between the substrates and CO₂ are mainly influenced by the interaction distance and the numbers of negative charge donors or the interacting pairs involved in the complex. It is furthermore found that ΔE increases significantly if S and O atoms could interact with CO₂ simultaneously. The binding energy is irrelevant if one considers the chemical environment of the O atom (i.e. O_Ac, O_E or O_S) or the S atom (i.e. SEt or SH), and the electronegativity difference between the S and O atoms. The three substrates studied are still excellent CO₂-philes, although their average ΔE (–20 kJ/mol) is slightly lower than that of peracetylated d-glucose (–22 kJ/mol), which has one more O atom that can interact with CO₂. Therefore, the applications of carbohydrates can be expanded to include adsorbents for CO₂, SO₂ or both, and the functional groups attached to the carbohydrate can vary from those to the acetyl groups.