Conformational Equilibrium of Cinchonidine in C6D12 Solution. Alternative NMR/DFT Approach.

1H NMR and 13C NMR chemical shifts as well as conformation dependent vicinal 1H-1H spin-spin coupling constants for cinchonidine in a dilute C6D12 solution have been measured. These data have been interpreted in detail exploiting the results of the extensive quantum chemistry calculations of molecular geometry and NMR parameters of the molecule, performed using the density functional theory (DFT) B3LYP/6-311++G(2d,p) polarizable continuum model (PCM) level of theory. The experimental values of NMR parameters for cinchonidine have been reproduced very well in terms of parameters calculated for key conformers of this molecule. Simultaneously, the analysis has provided us with a lot of information on conformational equilibrium of cinchonidine in the investigated solution. These findings remain in general agreement with the conclusions of other works, based on NOESY spectra or other physicochemical data. Thus, a careful quantitative interpretation of easily measurable NMR chemical shifts can be an independent and valuable source of structural information even in such complex cases as cinchonidine in solution.

Solvation of Amides in DMSO and CDCl3: An Attempt at Quantitative DFT-Based Interpretation of 1H and 13C NMR Chemical Shifts.

The study concerns N-methyl-2-pyrrolidinone, N,N-dimethylformamide, 2-pyrrolidinone, N-methylformamide, and formamide in DMSO-d6 and CDCl3 solutions. It has been shown that the results of DFT calculations [B3LYP and/or PBE0 6-311++G(2d,p), PCM] of molecular geometries and magnetic shielding are able to reproduce very well the amide 1H NMR and 13C NMR chemical shifts measured in these solvents provided that the specific solvation of the solute molecules and their association are taken into account and also that comparison of the experimental and theoretical data is carefully done. Analysis of the chemical shift data points out that in CDCl3 solutions primary and secondary amides are partially associated and that their carbonyl oxygen lone electron pairs are specifically solvated by solvent molecules. At the same time, association of the amides seems to be of minor importance in DMSO, while their N-H hydrogens form strong hydrogen bonds with solvent molecules.

Solvation of Uracil and Its Derivatives by DMSO: A DFT-Supported 1H NMR and 13C NMR Study.

1H NMR and 13C NMR spectra of uracil, thymine, 5-hydroxymethyluracil, 5,6-dihydrouracil, and 5,6-dihydrothymine in DMSO-d6 solutions have been measured. Additionally, molecular structures as well as NMR parameters of these compounds and their various solvates have been calculated using DFT B3LYP/6-311++G(2d,p) PCM(DMSO) method. The analysis of the chemical shift data for these compounds has shown that, indeed, in DMSO solutions they occur as equilibrium mixtures of free molecules and solvates in which solute and solvent molecules are joined by NH···O or OH···O hydrogen bonds. The populations of particular species present in the solutions have been estimated. Moreover, it has been found that 5,6-dihydrothymine exists in DMSO solution preferentially in conformation with the methyl group occupying the pseudoequatorial position. This finding is based on the molecular energy calculations and remains in full agreement with the interpretation of NMR data and theoretical calculations of NMR parameters.

Orotic acid in water solution, a DFT and (13)C NMR spectroscopic study.

Orotic acid, a biologically important compound, can exist in aqueous solutions in several ionic and tautomeric forms. Interpretation of the experimental (13)C NMR chemical shifts of this compound based on the results of energy and magnetic shielding calculations performed by DFT B3LYP/6-311++G(2d,p)/PCM method has shown that in water solutions the diketo tautomers are the dominant structural forms of this acid and its anions. For neutral molecules the anti conformation is preferable, monoanion occurs as the conventional carboxylate anion, whereas the orotic dianion exists in two tautomeric forms in the proportion of ca. 4:1. It has been found that the experimental (13)C NMR chemical shifts can be reproduced well by the results of DFT calculations, although for the orotate monoanion some small but characteristic divergences can be noticed. Similar divergences have been also observed for a few other aromatic carboxylates. It seems that the specific solute-solvent interactions occurring in our systems can be the cause of this inconsistency. To support this hypothesis, a simple and effective method of including the specific hydration into the theoretical calculations has been proposed.

Interpretation of the longitudinal (13)C nuclear spin relaxation and chemical shift data for five bromoazaheterocycles supported by nonrelativistic and relativistic DFT calculations.

The longitudinal relaxation times of (13)C nuclei and NOE enhancement factors for 2-bromopyridine (1), 6-bromo-9-methylpurine (2), 3,5-dibromopyridine (3), 2,4-dibromopyrimidine (4), and 2,4,6-tribromopyrimidine (5) have been measured at 25 °C and B0 = 11.7 T. The most important contributions to the overall relaxation rates of nonbrominated carbons, i.e., the relaxation rates due to the (13)C-(1)H dipolar interactions and the shielding anisotropy mechanism, have been separated out. For 3 and 5, additionally, the T2,Q((14)N) values have been established from (14)N NMR line widths. All of these data have been used to determine rotational diffusion tensors for the investigated molecules. The measured saturation recovery curves of brominated carbons have been decomposed into two components to yield relaxation times, which after proper corrections provided parameters characterizing the scalar relaxation of the second kind for (13)C nuclei of (79)Br- and (81)Br-bonded carbons. These parameters and theoretically calculated quadrupole coupling constants for bromine nuclei have allowed the values of one-bond (13)C-(79)Br spin-spin coupling constants to be calculated. Independently, the coupling constants and magnetic shielding constants of the carbon nuclei have been calculated theoretically using the nonrelativistic and relativistic DFT methods F/6-311++G(2d,p)/PCM and so-ZORA/F/TZ2P/COSMO (F = BHandH or B3LYP), respectively. The agreement between the experimental and theoretical values of these parameters is remarkably dependent on the theoretical method used.

Scalar relaxation of the second kind. A potential source of information on the dynamics of molecular movements. 4. Molecules with collinear C-H and C-Br bonds.

Continuing studies based on measurements of the nuclear spin relaxation rates running via the SC2 mechanism (scalar relaxation of the second kind), we present in this work the results obtained for three molecules: 9-bromotriptycene, 1,3,5-tribromobenzene, and 1-(2-bromoethynyl)-4-ethynylbenzene in which C-Br bond and one of C-H bonds are collinear. Separation of saturation-recovery or inversion-recovery curves of (13)C NMR signals of bromine-bonded carbons in the investigated compounds on two components has provided the longitudinal SC2 relaxation rates of these carbons in (79)Br- and (81)Br-containing isotopomers. These data have enabled experimental determination of the bromine-carbon spin-spin coupling constants and relaxation rates of quadrupole bromine nuclei, hardly accessible by direct measurements. At the same time the rotational diffusion parameters describing the reorientation of the C-Br vectors have been determined for the investigated molecules on the basis of the dipolar relaxation of protonated carbons. These diffusion parameters are crucial for interpretation of the bromine relaxation rates. The values of the indirect (1)J((13)C,(79)Br) coupling constants, magnetic shielding of carbon nuclei and quadrupole coupling constants of bromines, determined for the investigated compounds, have been compared with the results of the theoretical calculations which take into account relativistic effects. The origin of some divergences between the results obtained by different methods has been discussed.

Scalar relaxation of the second kind. A potential source of information on the dynamics of molecular movements. 3. A (13)C nuclear spin relaxation study of CBrX3 (X = Cl, CH3, Br) molecules.

Continuing studies based on measurements of the nuclear spin relaxation rates running via the SC2 mechanism (scalar relaxation of the second kind), we present in this work the results obtained for three bromo compounds: CBrCl3, (CH3)3CBr, and CBr4. A careful separation of saturation-recovery curves, measured for signals of (13)C nuclei at 7.05 and 11.7 T on two components, has provided the longitudinal SC2 relaxation rates of carbon signals in (79)Br and (81)Br containing isotopomers of the investigated compounds. These data have enabled experimental determination of spin-spin coupling constants and relaxation rates of quadrupole bromine nuclei, both types of parameters being hardly accessible by direct measurements. Investigation of the relaxation behavior of these molecules, being of similar size and shape, has provided quite different practical and interpretational problems which are likely to be encountered in relaxation studies of many other carbon-bromine systems. In order to evaluate the quality of the obtained experimental results, advanced theoretical calculations of the indirect (1)J((13)C,(79)Br) coupling constants, magnetic shielding of carbon nuclei, and quadrupole coupling constants of bromines in the investigated compounds have been performed and compared with the experimental values. Relatively small divergences between experiment and theory have been found. The contributions of the relativistic effects to the values of the discussed parameters have been tentatively estimated.

Scalar relaxation of the second kind - a potential source of information on the dynamics of molecular movements. 2. Magnetic dipole moments and magnetic shielding of bromine nuclei.

In this paper, we continue the exploration of possibilities, limitations, and methodological problems of the studies based on measurements of the nuclear spin relaxation rates running via the scalar relaxation of the second kind (SC2) mechanism. The attention has been focused on the (13)C-(79)Br and (13)C-(81)Br systems in organic bromo compounds, which are characterized by exceptionally small differences of Larmor frequencies, ΔωCBr, of the coupled nuclei. This unique property enables experimental observation of longitudinal SC2 relaxation of (13)C nuclei, which makes investigation of the SC2 relaxation rates an attractive experimental method of determination of spin-spin coupling constants and relaxation rates of quadrupole bromine nuclei, both types of parameters being hardly accessible by direct measurements. A careful examination of the methodology used in SC2 relaxation studies of carbon-bromine systems reveals, however, some disturbing facts that could burden the results with systematic inaccuracies. Namely, the way of calculating the Larmor frequency differences between (13)C and bromine isotopes, ΔωCBr, may cause some reservations. In this work, the values of (79)Br and (81)Br magnetogyric ratios have been rechecked using bromine NMR data for the KBr·Kryptofix 222 complex in acetonitrile solution and the results of the advanced calculations of the magnetic shielding of the bromine nucleus in the Br(-) anion. Moreover, it has been pointed out that in the case of (13)C-(79)Br, the magnetic shielding of the bromine nucleus in the investigated molecule must not be neglected during the calculation of the ΔωCBr parameter. Some recommendations concerning the exploitation of available theoretical methods to calculate bromine shielding constants for bromo compounds have also been formulated, keeping in mind relativistic effects.

The Influence of a Presence of a Heavy Atom on (13)C Shielding Constants in Organomercury Compounds and Halogen Derivatives.

(13)C nuclear magnetic resonance shielding constants have been calculated by means of density functional theory (DFT) for several organomercury compounds and halogen derivatives of aliphatic and aromatic compounds. Relativistic effects have been included through the four-component Dirac-Kohn-Sham (DKS) method, two-component Zeroth Order Regular Approximation (ZORA) DFT, and DFT with scalar effective core potentials (ECPs). The relative shieldings have been analyzed in terms of the position of carbon atoms with respect to the heavy atom and their hybridization. The results have been compared with the experimental values, some newly measured and some found in the literature. The main aim of the calculations has been to evaluate the magnitude of heavy atom effects on the (13)C shielding constants and to check what are the relative contributions of scalar relativistic effects and spin-orbit coupling. Another object has been to compare the DKS and ZORA results and to check how the approximate method of accounting for the heavy-atom-on-light-atom (HALA) relativistic effect by means of scalar effective core potentials on heavy atoms performs in comparison with the more rigorous two- and four-component treatment.

Detection of acylglycines in urine by 1H and 13C NMR for the diagnosis of inborn metabolic diseases.

A range of inborn metabolic diseases result in abnormal accumulation of acylglycines in body fluids. Therefore, detection of these metabolites is important for diagnostic purposes. (1)H and (13)C NMR spectroscopies have successfully been applied for both qualitative and quantitative determinations of various acylglycines in urine samples from patients suffering from metabolic diseases connected with excretion of these compounds. Various acylglycines were identified in test urine samples from 15 patients suffering from five different metabolic diseases, providing information which could be crucial for their diagnoses. The paper reports complete (1)H and (13)C NMR data of 11 acylglycines, which is essential for this type of NMR analysis of body fluids. NMR spectroscopy has been proven effective in determining the presence as well as the levels of acylglycines in urine. The proposed method is rapid, simple and requires minimal sample treatment.

Shielding and indirect spin-spin coupling tensors in the presence of a heavy atom: an experimental and theoretical study of bis(phenylethynyl)mercury.

Magnetic shielding and indirect spin-spin coupling phenomena are tensorial properties and both their isotropic and anisotropic parts do affect NMR spectra. The involved interaction tensors, σ and J, can nowadays be theoretically calculated, although the reliability of such methods in the case of anisotropic parameters, Δσ and ΔJ, in systems involving heavy nuclei, yet demands testing. In this communication the results of the experimental and theoretical investigations of bis(phenylethynyl)mercury (I) labeled with (13)C isotope at positions neighboring Hg are reported. The theoretical calculations of molecular geometry and values of NMR parameters for I have been performed by the ZORA/DFT method, including the relativistic scalar and spin-orbit coupling contributions, using the PBE0 functional and TZP (or jcpl) basis set. These values have been confronted with the experimentally measured ones. The isotropic parameters have been measured by the standard (13)C and (199)Hg NMR spectra. The shielding anisotropies for the atoms in the central part of molecule I have been determined in a liquid sample using magnetic relaxation measurements. The relaxation data have been interpreted within the rotational diffusion theory, assuming the symmetrical top reorientation model. The anisotropies of one-bond (13)C-(199)Hg and two-bond (13)C-Hg-(13)C spin-spin couplings have been determined exploiting the temperature-dependent (13)C NMR spectra of I in the ZLI1167 liquid-crystal phase. We have found that our theoretical calculations reproduce experimental values of both isotropic and anisotropic NMR parameters very well.

Scalar relaxation of the second kind: a potential source of information on the dynamics of molecular movements. 1. Investigation of solution reorientation of N-methylpyridone and 1,3-dimethyluracil using measurements of longitudinal relaxation rates in the rotating frame.

The practical utility of the method of retrieving the relaxation rate of a quadrupole nucleus via the scalar relaxation of the second kind (SC2) of an I = 1/2 spin nucleus has been considered once again. The study was motivated by the fact that such data are frequently very useful in investigations of reorientational movements of molecules in solutions. At the same time, the parameters describing spin-spin and quadrupolar couplings, necessary in such studies, have become relatively easily accessible owing to a remarkable progress in theoretical methods. It was shown that even in the case of small N-C coupling constants ((1)J = 7-8 Hz) the classical method of approaching SC2 relaxation effects by measurements of the longitudinal relaxation rates in the rotating frame, although somewhat tedious, can yield acceptably accurate results. The whole procedure has been successfully applied in the investigation of molecular movements of N-methylpyridone (1) and 1,3-dimethyluracil (2) in acetone solution.

Structure of neutral molecules and monoanions of selected oxopurines in aqueous solutions as studied by NMR spectroscopy and theoretical calculations.

A methodology enabling investigation of a multicomponent tautomeric and acid-base equilibria by (13)C NMR spectroscopy supported by theoretical calculations has been proposed. The effectiveness of this method has been illustrated in a study of 2-oxopurine, 6-oxopurine (hypoxanthine), 8-oxopurine, and 2,6-dioxopurine (xanthine) in neutral and alkaline aqueous solutions. For each compound a series of (13)C NMR spectra were recorded at pH ranges in which neutral molecules, monoanions and/or dianions occurred in dynamic equilibrium. The carbon chemical shifts for these three forms of the investigated compounds were retrieved from the analysis of pH-dependence of the measured, dynamically averaged values of these parameters. The structures of several stable tautomers of the neutral and monoanionic oxopurine forms were predicted from theoretical calculations and nuclear magnetic shielding constants for (13)C nuclei in these tautomers were calculated. At both calculation steps (molecular geometry optimization and calculation of NMR parameters) the PBE1PBE/6-311++G(2d,p) level of theory was used. The populations of the most stable tautomers were determined from the experimental data analysis exploiting the fact that they were population-weighted averages of the chemical shifts of particular tautomers. It has been shown that only the oxo forms of the investigated oxopurines are present in aqueous solutions and that the determined populations in most cases remain in a qualitative agreement with the calculated free energies of the appropriate tautomers. The obtained results are in general agreement with other literature reports on oxopurine tautomerism and confirm importance of the hydration phenomena for the investigated systems. The data analysis has shown that the best compliance between theory and experiment is obtained when the hydration phenomenon is modeled by discrete hydration augmented by PCM (polarizable continuum solvation model).

Solution structure of succinylacetone, an unsymmetrical beta-diketone, as studied by 13C NMR and GIAO-DFT calculations.

The enolization degrees of succinylacetone, an important heme biosynthesis inhibitor, have been determined in CDCl(3) and water solutions using (1)H NMR. The solution structures of SA have been investigated using a combined NMR/theoretical [GIAO DFT PBE1PBE/6-311++G(2d, p) PCM] approach. The populations of both enolic forms undergoing enol-enol equilibriums for SA and a series of unsymmetrical beta-diketones have been established by a quantitative comparison of the experimental (13)C NMR chemical shifts and calculated shielding constants. Moreover, using the same method and considering various trial structures differing in conformation and/or hydration of neutral SA molecule as well as its monoanion and dianion the structures of the most abundant species being present in the investigated water solutions have been deduced.

Inhibition of 4-hydroxyphenylpyruvate dioxygenase by 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione.

Triketone herbicides are inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD), a key enzyme of the tyrosine transformation pathway, common for plants and animals. One of these herbicides, 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC), is so selective and efficient that it can be applied as a medicine in a hereditary metabolic disease - tyrosinemia type I. In this paper the available information concerning the molecular mechanism of HPPD inhibition by NTBC, originating from experimental investigations as well as theoretical modeling, has been collected. It is supplemented by results of additional theoretical DFT and/or MP2 calculations of the energetic effects of individual elementary molecular transformations. All these data are discussed and a consistent picture of HPPD inhibition by NTBC is proposed.

Remarks on GIAO-DFT predictions of 13C chemical shifts.

Predicting (13)C chemical shifts by GIAO-DFT calculations appears to be more accurate than frequently expected provided that: (a) the comparison between experimental and theoretical data is performed using the linear regression method, (b) a sufficiently high level of theory [e.g. B3LYP/6-311 + + G(2d,p)//B3LYP/6-311 + + G(2d,p) or PBE1PBE/6-311 + G(2df,p)//B3LYP/6-311 + + G(2d,p)] is used, (c) the experimental data originate from the measurements performed in one solvent whose influence is taken into account at the molecular geometry optimization step and, first of all, during the shielding calculation, (d) the experimental data are free of heavy atom effects or such effects are appropriately treated in calculations, and finally (e) the conformational compositions of the investigated objects are known.

Identification of 2-[2-nitro-4-(trifluoromethyl)benzoyl]- cyclohexane-1,3-dione metabolites in urine of patients suffering from tyrosinemia type I with the use of 1H and 19F NMR spectroscopy.

Organic extracts of six urine samples from children treated with nitisinone, a medicine against tyrosinemia type I, were investigated by (1)H and (19)F NMR spectroscopy. The presence of unchanged 2-[2-nitro-4-(trifluoromethyl)benzoyl]cyclohexane-1,3-dione (NTBC), 6-hydroxy-2-[2-nitro-4-(trifluoromethyl)benzoyl]cyclohexane-1,3-dione (NTBC-OH) and 2-nitro-4-trifluoromethylbenzoic acid (NTFA) as well as a few other unidentified compounds containing CF(3) group was documented.

Investigation of a wide spectrum of inherited metabolic disorders by 13C NMR spectroscopy.

High-resolution (1)H NMR spectroscopy of body fluids has proved to be very useful in diagnostics of inherited metabolic diseases, whereas (13)C NMR remains almost unexploited. In this paper the application of (13)C NMR spectroscopy of fivefold concentrated urine samples for diagnosis of selected metabolic diseases is reported. Various marker metabolites were identified in test urine samples from 33 patients suffering from 10 different diseases, providing information which could be crucial for their diagnoses. Spectra were accumulated for 2 h or overnight when using spectrometers operating at 9.4 or 4.7 T magnetic fields, respectively. Interpretation of the measurement results was based on a comparison of the peak positions in the measured spectrum with reference data. The paper contains a table with (13)C NMR chemical shifts of 73 standard compounds. The method can be applied individually or as an auxiliary technique to (1)H NMR or any other analytical method.

Anisotropic reorientation of 9-methylpurine and 7-methylpurine molecules in methanol solution studied by combining 13C and 14N nuclear spin relaxation data and quantum chemical calculations.

Reorientation of 9-(trideuteromethyl)purine and 7-(trideuteromethyl)purine molecules in methanol-d4 solutions has been investigated on the basis of the interpretation of the nuclear spin relaxation rates of their 14N (or 1H) and 13C nuclei. The transverse quadrupole relaxation rates of 14N nuclei have been obtained from the line shape analysis of their 14N NMR spectra. Alternatively, the information on the longitudinal 14N relaxation rates has been obtained via the scalar relaxation of the second kind of protons coupled to 14N. The longitudinal dipolar relaxation rates of the protonated 13C nuclei in the investigated molecules have been determined by measuring their overall relaxation rates and NOE enhancement factors. The molecular geometries, scalar coupling constants, and EFG tensors needed for quantitative interpretation of the above data have been calculated theoretically [DFT B3LYP/6-311++G(2d,p) or B3PW91/6-311+G(df,pd)] including the impact of the solvent by using discrete solvation and the polarizable continuum model. The reorientation of the investigated purines has been described as rotational diffusion of an asymmetrical top. It has been found that to get a fully consistent interpretation of the relaxation data, effective C-H bond lengths being 3% longer than the calculated ones had to be used in analysis to compensate for the ground-state vibrations. The obtained rotational diffusion coefficients and orientations of the principal diffusion axes show that the investigated molecules reorient anisotropically and that the mode of their solvation is remarkably different, in spite of their structural similarity.

1H NMR, 13C NMR, and computational DFT studies of the structure of 2-acylcyclohexane-1,3-diones and their alkali metal salts in solution.

1H and 13C NMR spectra of 2-acyl-substituted cyclohexane-1,3-diones (acyl = formyl, 1; 2-nitrobenzoyl, 2; 2-nitro-4-trifluoromethylbenzoyl, 3) and lithium sodium and potassium salts of 1 have been measured. The compound 3, known as NTBC, is a life-saving medicine applied in tyrosinemia type I. The optimum molecular structures of the investigated objects in solutions have been found using the DFT method with B3LYP functional and 6-31G** and/or 6-311G(2d,p) basis set. The theoretical values of the NMR parameters of the investigated compounds have been calculated using GIAO DFT B3LYP/6-311G(2d,p) method. The theoretical data obtained for compounds 1-3 have been exploited to interpret their experimental NMR spectra in terms of the equilibrium between different tautomers. It has been found that for these triketones an endo-tautomer prevails. The differences in NMR spectra of the salts of 1 can be rationalized taking into account the size of the cation and the degree of salt dissociation. It seems that in DMSO solution the lithium salt exists mainly as an ion pair stabilized by the chelation of a lithium cation with two oxygen atoms. The activation free energy the of formyl group rotation for this salt has been estimated to be 51.5 kJ/mol. The obtained results suggest that in all the investigated objects, including the free enolate ions, all atoms directly bonded to the carbonyl carbons lie near the same plane. Some observations concerning the chemical shift changes could indicate strong solvation of the anion of 1 by water molecules. Implications of the results obtained in this work for the inhibition mechanism of (4-hydroxyphenyl) pyruvate dioxygenase by NTBC are commented upon.