Solid‐state nuclear magnetic resonance investigation of neurosteroid compounds and magnesium interactions

The neurosteroid trans‐dehydroandrosterone (DHEA) and its analogs with slightly different modifications in the side chain attached to C17, that is, (3S)‐acetoxypregn‐5‐en‐20‐one ( 1 ) and (3S,20R)‐acetoxypregn‐5‐en‐20‐ol ( 2 ), have been synthesized to investigate DHEA–cation interactions. In this study, we applied solid‐state ¹H/¹³C cross‐polarization/magic‐angle spinning (CP/MAS) nuclear magnetic resonance (NMR) spectroscopy to a series of DHEA analog/Mg²⁺ mixtures at different Mg²⁺ concentrations. The high‐resolution ¹³C NMR spectra of 1 /Mg²⁺ mixtures exhibit two distinct ¹³C spectral patterns, one attributable to 1 free from Mg²⁺, and the other attributable to 1 with bound Mg²⁺. For 2 , the ¹³C NMR spectra exhibit three distinct spectral patterns; besides that of the free form, the other two can be assigned to Mg²⁺‐bound forms. Based on the analysis of the chemical shift deviations (CSDs), we conclude that both 1 and 2 might be subject to a cation–π interaction via the C5–C6 double bond, in contrast to that observed previously for DHEA. As demonstrated, DHEA possesses two Mg²⁺ binding sites, that is, C17–O and C5–C6 double bond, in which the binding affinity of the former is at least three times stronger than that of the latter. The solid‐state ¹³C NMR investigation allows better understanding of the underlying cation binding effects of neurosteroid molecules in vitro.     

The Effect of C4H and C5H on the Microstructure of Aqueous Solutions of 1‐Alkyl‐3‐methylimidazolium Tetrafluoroborate Ionic Liquids

As is well‐known, the C2?H proton of 1‐ethyl‐3‐methylimidazolium tetrafluoroborate ([Emim]BF₄) and 1‐butyl‐3‐methylimidazolium tetrafluoroborate ([Bmim]BF₄) has a strong ability to form hydrogen bonds. The purpose of this work is to evaluate the effect of the interactions of the C4?H and C5?H protons on the microstructure of [Emim]BF₄ and [Bmim]BF₄ with water by using ¹H NMR spectroscopy. The differences between the relative ¹H NMR chemical shifts of C2?H, C4?H, and C5?H and between the interaction‐energy parameters obtained from these chemical shifts are minor, thus suggesting that the interactions of C4?H and C5?H may have a considerable effect on the microstructure. To confirm this, the viscosities of the systems are estimated by using the interaction‐energy parameters obtained from the ¹H NMR chemical shifts of the three studied aromatic protons and water, showing that the interactions of C4?H and C5?H also play an important role in the microstructure.     

Are there reliable DFT approaches for 13C NMR chemical shift predictions of fullerene C60 derivatives?

The relationships between experimental and theoretical ¹³C NMR chemical shifts of a pristine fullerene C₆₀, monoadducts from [2 + n] cycloaddition (n = 1–3), and one [2 + 1] bis‐adduct are systematically analyzed for the first time by using diverse quantum‐chemical levels of theory. These levels involved B3LYP, B3PW91, B97‐2, mPW1PW91, PBE1PBE, and X3LYP hybrid functionals combined with 3‐21G, 6‐31G, 6‐31G(d), 6‐31G(d,p), 6‐31G(d,2p), LanL2DZ, and SDDAll basis sets. X3LYP/6‐31G approach is determined to have the lowest deviations from the ¹³C NMR experimental data compared to the other methods for all the fullerene compounds (mean absolute error value is 0.856 ppm and root mean squared error value is 1.197 ppm). The highest deviations are characteristic for α (sp² C2/C5/C8/C10) and β (sp² C6/C7/C11/C12) carbon atoms relative to a functionalization site and for those (sp³ C1/C9) directly attached with a side fragment in the [2 + n] monoadducts (n = 1–3). A probable reason of such deviation is that the approaches do not take into account a contribution of paramagnetic ring currents to ¹³C NMR chemical shifts. The results will be useful in design of novel fullerene derivatives and in performing unambiguous ¹³C NMR chemical shift assignments with modern quantum chemistry calculations.     

Theoretical investigation on multinuclear NMR chemical shifts of some tris(trifluoromethyl)boron complexes

Tris(trifluoromethyl)boron complexes have unusual properties and may find applications in many fields of chemistry, biology, and physics. To gain insight into their NMR properties, the isotropic ¹¹B, ¹³C, and ¹⁹F NMR chemical shifts of a series of tris(trifluoromethyl)boron complexes were systematically studied using the gauge‐included atomic orbitals (GIAO) method at the levels of B3LYP/6‐31 + G(d,p)//B3LYP/6‐31G* and B3LYP/6‐311 + G(d,p)//B3LYP/6‐311 + G(d,p). Solvent effects were taken into account by polarizable continuum models (PCM). The calculated results were compared with the experimental values. The reason that the structurally inequivalent fluorine atoms in a specific species give a same chemical shift in experimental measurements is attributed to the fast rotation of CF₃ group around the B? C(F₃) bond because of the low energy barrier. The calculated ¹¹B, ¹³C(F₃), and ¹⁹F chemical shifts are in good agreement with the experimental measurements, while the deviations of calculated ¹³C(X, X = O, N) chemical shifts are slightly large. For the latter, the average absolute deviations of the results from B3LYP/6‐311 + G(d,p)//B3LYP/6‐311 + G(d,p) are smaller than those from B3LYP/6‐31 + G(d,p)//B3LYP/6‐31G*, and the inclusion of PCM reduces the deviation values. The calculated ¹⁹F and ¹¹B chemical shieldings of (CF₃)₃BCO are greatly dependent on the optimized structures, while the influence of structural parameters on the calculated ¹³C chemical shieldings is minor. Copyright © 2009 John Wiley & Sons, Ltd.     

15N and 13C NMR chemical shifts of 6‐(fluoro,chloro, bromo,and iodo)purine 2′‐deoxynucleosides: measurements and calculations

The ¹⁵N and ¹³C chemical shifts of 6‐(fluoro, chloro, bromo, and iodo)purine 2′‐deoxynucleoside derivatives in deuterated chloroform were measured. The ¹⁵N chemical shifts were determined by the ¹H? ¹⁵N HMBC method, and complete ¹⁵N chemical‐shift assignments were made with the aid of density functional theory (DFT) calculations. Inclusion of solvation effects significantly improved the precision of the calculations of ¹⁵N chemical shifts. Halogen‐substitution effects on the ¹⁵N and ¹³C chemical shifts of purine rings are discussed in the context of DFT results. The experimental coupling constants for ¹⁹F interacting with ¹⁵N and ¹³C of the 6‐fluoropurine 2‐deoxynuleoside are compared with those from DFT calculations. Copyright © 2009 John Wiley & Sons, Ltd.     

Effect of ring annelation on cations [M = H+, Li+, Na+, K+, Be2+, Mg2+, and Ca2+]…benzene interaction: A density functional theory investigation

Density functional theory calculation was carried out on cation‐π complexes formed by cations [M = H⁺, Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺] and π systems of annelated benzene. The cation‐π bonding energy of Be²⁺ or Mg²⁺ with annelated benzene is very strong in comparison with the common cation‐π intermolecular interaction, and the bonding energies follow the order Be²⁺ > Mg²⁺ > Ca²⁺ > Li⁺ > Na⁺ > K⁺. Similarly, the interaction energies follow the trend 1‐M < 2‐M < 3‐M for all the metal cations considered. These outcomes may be due to the weak interactions of the metal cations with C? H and the interactions of metal cations with π in addition to the nature of a metal cation. We have also investigated on all the possible substituted sites, and find that the metal ion tends to interact with all ring atoms while proton prefers to bind covalently to one of the ring carbons. The binding of metal cations with annelated benzenes has striking effect on nuclear magnetic resonance chemical shifts using the gauge independent atomic orbital method. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Theoretical Studies on the Infrared Vibrational Spectra ,Thermodynamic Properties and Nuclear Magnetic Resonance Spectra for Polynitro-1,3-bishomopentaprismanes

Based on the optimized molecular geometries at the DFT‐B3LYP/6‐31G?? level, IR spectra, thermodynamic functions, as well as ¹³C and ¹H NMR chemical shifts, were obtained and discussed for polynitro‐1,3‐bishomo‐pentaprismanes (PNBPP). The comparison of the calculated IR frequencies and NMR chemical shifts showed considerable agreements with the available experimental results. IR regions, ¹³C and ¹H NMR chemical shifts of PNBPP were assigned. The relationships of the thermodynamic functions with temperature and the number of nitro groups were discussed, and it was found that the latter showed a good group additivity rule. These calculated data and discussions would be helpful for the further study of PNBPP.     

Root‐mean‐square‐deviation‐based rapid backbone resonance assignments in proteins

We have shown that the methodology based on the estimation of root‐mean‐square deviation (RMSD) between two sets of chemical shifts is very useful to rapidly assign the spectral signatures of ¹H^N, ¹³C^α, ¹³C^β, ¹³C′, ¹H^α and ¹⁵N spins of a given protein in one state from the knowledge of its resonance assignments in a different state, without resorting to routine established procedures (manual and automated). We demonstrate the utility of this methodology to rapidly assign the 3D spectra of a metal‐binding protein in its holo‐state from the knowledge of its assignments in apo‐state, the spectra of a protein in its paramagnetic state from the knowledge of its assignments in diamagnetic state and, finally, the spectra of a mutant protein from the knowledge of the chemical shifts of the corresponding wild‐type protein. The underlying assumption of this methodology is that, it is impossible for any two amino acid residues in a given protein to have all the six chemical shifts degenerate and that the protein under consideration does not undergo large conformational changes in going from one conformational state to another. The methodology has been tested using experimental data on three proteins, M‐crystallin (8.5 kDa, predominantly β‐sheet, for apo‐ to holo‐state), Calbindin (7.5 kDa, predominantly α‐helical, for diamagnetic to paramagnetic state and apo to holo) and EhCaBP1 (14.3 kDa, α‐helical, the wild‐type protein with one of its mutant). In all the cases, the extent of assignment is found to be greater than 85%. Copyright © 2010 John Wiley & Sons, Ltd.     

Hydroacridines: Part 30. 1H and 13C NMR spectra of 9‐substituted 1,2,3,4,5,6,7,8‐octahydroacridines and of their N‐oxides

The ¹H and ¹³C NMR chemical shifts of 1,2,3,4,5,6,7,8‐octahydroacridine, 12 of its 9‐substituted derivatives, and of the corresponding N‐oxides were determined, assigned, and discussed in terms of 9‐substituent effects and effects of N‐oxidation. A good linear correlation was found between the ¹³C chemical shifts of the aromatic carbons in octahydroacridines and those of respective carbons in the corresponding N‐oxides. Copyright © 2009 John Wiley & Sons, Ltd.     

Stereospecificity of 1H, 13C and 15N shielding constants in the isomers of methylglyoxal bisdimethylhydrazone: problem with configurational assignment based on 1H chemical shifts

In the ¹³C NMR spectra of methylglyoxal bisdimethylhydrazone, the ¹³C‐5 signal is shifted to higher frequencies, while the ¹³C‐6 signal is shifted to lower frequencies on going from the EE to ZE isomer following the trend found previously. Surprisingly, the ¹H‐6 chemical shift and ¹J(C‐6,H‐6) coupling constant are noticeably larger in the ZE isomer than in the EE isomer, although the configuration around the –CH═N– bond does not change. This paradox can be rationalized by the C–H?N intramolecular hydrogen bond in the ZE isomer, which is found from the quantum‐chemical calculations including Bader's quantum theory of atoms in molecules analysis. This hydrogen bond results in the increase of δ(¹H‐6) and ¹J(C‐6,H‐6) parameters. The effect of the C–H?N hydrogen bond on the ¹H shielding and one‐bond ¹³C–¹H coupling complicates the configurational assignment of the considered compound because of these spectral parameters. The ¹H, ¹³C and ¹⁵N chemical shifts of the 2‐ and 8‐(CH₃)₂N groups attached to the –C(CH₃)═N– and –CH═N– moieties, respectively, reveal pronounced difference. The ab initio calculations show that the 8‐(CH₃)₂N group conjugate effectively with the π‐framework, and the 2‐(CH₃)₂N group twisted out from the plane of the backbone and loses conjugation. As a result, the degree of charge transfer from the N‐2– and N‐8– nitrogen lone pairs to the π‐framework varies, which affects the ¹H, ¹³C and ¹⁵N shieldings. Copyright © 2012 John Wiley & Sons, Ltd.     

Complete assignment of the 1H and 13C NMR spectra of antimicrobial 4‐arylamino‐ 3‐nitrocoumarin derivatives

Herein, we describe the synthesis and complete assignment of the ¹H and ¹³C NMR chemical shifts of a series of antimicrobial 4‐arylamino‐3‐nitrocoumarin derivatives based on a combination of ¹H and ¹³C NMR, ¹H‐¹H‐COSY, NOESY, HSQC and HMBC experiments. Conformational effects upon the chemical shifts of the coumarin moiety arising from the anisotropy of the aryl side group are briefly discussed. This study provides the first complete and fully assigned NMR data for this important group of antimicrobial compounds and bridges the gap existing in the literature with regard to NMR structural data for 4‐arylamino‐3‐nitrocoumarins. Copyright © 2010 John Wiley & Sons, Ltd.     

Crucial Roles of Two Hydrated Mg2+ Ions in Reaction Catalysis of the Pistol Ribozyme

Pistol ribozymes constitute a new class of small self‐cleaving RNAs. Crystal structures have been solved, providing three‐dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre‐catalytic state, a vanadate mimic of the transition state, and the product. The results led to the proposed underlying chemical mechanism. Importantly, a hydrated Mg²⁺ ion remains innersphere‐coordinated to N7 of G33 in all three states, and is consistent with its likely role as acid in general acid base catalysis (δ and β catalysis). Strikingly, the new structures shed light on a second hydrated Mg²⁺ ion that approaches the scissile phosphate from its binding site in the pre‐cleavage state to reach out for water‐mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg²⁺ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme‐catalyzed backbone cleavage.     

Isotopic effect on tautomeric behavior of 5‐(2,6‐disubstituted‐aryloxy)‐tetrazoles

Isotopic effect on tautomeric behaviors of the synthesized 5‐phenoxy‐ (1a), 5‐(2,6‐dimethylphenoxy)‐ (1b), 5‐(2,6‐diisopropylphenoxy)‐ (1c), 5‐(2,6‐dimethoxyphenoxy)‐ (1d) and 5‐(4‐methylphenoxy)‐tetrazole (1e) were investigated in DMSO‐d₆ by adding one drop of D₂O. Among 1a–e, 1a, 1d and 1e show small rotational barrier around C5? O1 and O1? C6 while in 1b and 1c there are distinguishable rotational barrier about that bonds. The ¹H NMR spectra of 1b and 1c show slightly different chemical shifts for two methyl and isopropyl groups on those phenyl ring, respectively, while the chemical shifts difference (Δδ) between two methyl and two isopropyl groups were enhanced by adding D₂O. The ¹³C NMR spectra of 1b show two overlapped singlets for methyl groups after adding D₂O. Representatively, the calculations of compound 1c were performed with GAUSSIAN‐03and the rotational barrier about C5? O1 and between isopropyl group and phenyl ring in 1c was calculated with B3LYP/6‐31G(d) basis set. Copyright © 2011 John Wiley & Sons, Ltd.     

Novel 13C‐detected NMR Experiments for the Precise Detection of RNA Structure

Up to now, NMR spectroscopic investigations of RNA have utilized imino proton resonances as reporters for base pairing and RNA structure. The nucleobase amino groups are often neglected, since most of their resonances are broadened beyond detection due to rotational motion around the C–NH₂ bond. Here, we present ¹³C‐detected NMR experiments for the characterization of all RNA amino groups irrespective of their motional behavior. We have developed a C(N)H‐HDQC experiment that enables the observation of a complete set of sharp amino resonances through the detection of proton‐NH₂ double quantum coherences. Further, we present an “amino”‐NOESY experiment to detect NOEs to amino protons, which are undetectable by any other conventional NOESY experiment. Together, these experiments allow the exploration of additional chemical shift information and inter‐residual proton distances important for high‐resolution RNA secondary and tertiary structure determination.     

Putative One‐Pot Prebiotic Polypeptides with Ribonucleolytic Activity

KIA7, a peptide with a highly restricted set of amino acids (Lys, Ile, Ala, Gly and Tyr), adopts a specifically folded structure. Some amino acids, including Lys, Ile, Ala, Gly and His, form under the same putative prebiotic conditions, whereas different conditions are needed for producing Tyr, Phe and Trp. Herein, we report the 3D structure and conformational stability of the peptide KIA7H, which is composed of only Lys, Ile, Ala, Gly and His. When the imidazole group is neutral, this 20‐mer peptide adopts a four‐helix bundle with a specifically packed hydrophobic core. Therefore, one‐pot prebiotic proteins with well‐defined structures might have arisen early in chemical evolution. The Trp variant, KIA7W, was also studied. It adopts a 3D structure similar to that of KIA7H and its previously studied Tyr and Phe variants, but is remarkably more stable. When tested for ribonucleolytic activity, KIA7H, KIA7W and even short, unstructured peptides rich in His and Lys, in combination with Mg⁺⁺, Mn⁺⁺ or Ni⁺⁺ (but not Cu⁺⁺, Zn⁺⁺ or EDTA) specifically cleave the single‐stranded region in an RNA stem–loop. This suggests that prebiotic peptide–divalent cation complexes with ribonucleolytic activity might have co‐inhabited the RNA world.     

1H NMR spectra. Part 29§: proton chemical shifts and couplings in esters—the conformational analysis of methyl γ‐butyrolactones

The ¹H NMR spectra of 35 cyclic and acyclic esters are analysed to give the ¹H chemical shifts and couplings. The substituent chemical shifts of the ester group were analysed using three‐bond (γ) effects for near protons and the electric field, magnetic anisotropy and steric effect of the ester group for more distant protons. The electric field is calculated from the partial atomic charges on the O?C = O atoms, and the asymmetric magnetic anisotropy of the carbonyl group acts at the midpoint of the C = O bond. The values of the anisotropies Δχ_parl and Δχ_perp were for the aliphatic esters 10.35 and ?18.84 and for the conjugated esters 7.33 and ?15.75 (×10^?6 ų/molecule). The oxygen steric coefficients found were 104.4 (aliphatic C = O), 45.5 (aromatic C = O) and 16.0 (C–O) (×10^?6 Å⁶/molecule). After parameterisation, the overall RMS error for the data set of 280 entries was 0.079 ppm. The strongly coupled ¹H NMR spectra of the 2‐methyl, 3‐methyl and 4‐methyl γ‐butyrolactones were analysed and the methyl conformational equilibrium obtained from the observed couplings. The observed versus calculated density functional theory (DFT) ΔG(ax‐eq) was 1.0 (1.01), 0.34 (0.54) and 0.65 (0.71) kcal/mol res. The shielding effect of a methyl cis to a proton in the five‐membered lactone rings is ?0.40 ±0.05 ppm and deshielding trans effect 0.12 ±0.05 ppm, which is common to both five and six membered rings. The cis/trans isomerism in the vinyl esters methyl acrylate, crotonate and methacrylate and methyl furoate was examined using the ¹H chemical shifts. The calculated shifts of both the cis and trans isomers were in good agreement with the observed shifts. Copyright © 2012 John Wiley & Sons, Ltd.     

NMR study of phthalide‐type poly(phenylene)s. Symmetry and additivity

All ¹H and ¹³C NMR signals of the four poly(phenylenephthalides): polydiphenylenephthalide ( P(DPh)‐1 ), polyterphenylenephthalide ( P(TPh)‐2 ) and two sequentially ordered polymers with different ratios of alternating diphenylenephthalide and terphenylenephthalide units ( P(DTPh)‐3, P(DDTPh)‐4 ) were assigned unequivocally with two‐dimensional NMR techniques (¹H–¹H COSY and NOESY; ¹H–¹³C HSQC and HMBC). There are four types of polyphenylene fragments: not symmetrical end, symmetrical inner, symmetrical pre‐end and formally symmetric pre‐end. The equivalent carbon atoms in these fragments have different chemical shifts. A full additivity of the chemical shifts for the side phthalide and polyphenylene carbon atoms was revealed. A new structure of diads with a mirror symmetry plane, passing through the middle of aromatic moieties, is proposed. Copyright © 2017 John Wiley & Sons, Ltd.     

Comparison of structural,thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations

The prevalence of Mg²⁺ ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg²⁺ ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion‐centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg²⁺ model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion–water and ion–solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single‐site Mg²⁺ ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12‐6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12‐6‐4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg²⁺ ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next‐generation models that target specific binding sites in biomolecules. © 2015 Wiley Periodicals, Inc.