Structural Studies of Monounsaturated and ω-3 Polyunsaturated Free Fatty Acids in Solution with the Combined Use οf NMR and DFT Calculations-Comparison with the Liquid State.

Molecular structures, in chloroform and DMSO solution, of the free fatty acids (FFAs) caproleic acid, oleic acid, α-linolenic acid, eicosapentanoic acid (EPA) and docosahexaenoic acid (DHA) are reported with the combined use of NMR and DFT calculations. Variable temperature and concentration chemical shifts of the COOH protons, transient 1D NOE experiments and DFT calculations demonstrate the major contribution of low molecular weight aggregates of dimerized fatty acids through intermolecular hydrogen bond interactions of the carboxylic groups, with parallel and antiparallel interdigitated structures even at the low concentration of 20 mM in CDCl3. For the dimeric DHA, a structural model of an intermolecular hydrogen bond through carboxylic groups and an intermolecular hydrogen bond between the carboxylic group of one molecule and the ω-3 double bond of a second molecule is shown to play a role. In DMSO-d6 solution, NMR and DFT studies show that the carboxylic groups form strong intermolecular hydrogen bond interactions with a single discrete solvation molecule of DMSO. These solvation species form parallel and antiparallel interdigitated structures of low molecular weight, as in chloroform solution. This structural motif, therefore, is an intrinsic property of the FFAs, which is not strongly affected by the length and degree of unsaturation of the chain and the hydrogen bond ability of the solvent.

Density functional theory calculations of δ(13 C) and δ(1 H) chemical shifts and 3 J(13 COO1 H) coupling constants as structural and analytical tools in hydroperoxides: Prospects and limitations of 1 H13 C heteronuclear multiple bond correlation experiments.

Density functional theory (DFT) calculations of δ(13 C) and δ(1 H) chemical shifts and 3 J(13 COO1 H) coupling constants of three model hydroperoxides of the naturally occurring cis-11-OOH and trans-9-OOH isomers of oleate and 9-cis, 11-trans-16-OOH endo hydroperoxide of methyl linolenate are reported. The computational δ(OOH) for various functionals and basis sets were found to be nearly identical for the cis/trans geometric isomers. The chemical shifts of the methine CHOOH protons and carbons, on the contrary, are highly diagnostic for the identification of cis/trans geometric isomerism. The chemical shifts of the olefinic protons and carbons strongly depend on the orientation of the hydroperoxide unit relative to the double bond and, thus, of importance in conformational analysis. The results are in very good agreement with the available experimental data. For the various diastereomeric pairs of the model endo-hydroperoxide, the strongly deshielded OOH resonances, due to the presence of an intramolecular hydrogen bond between the hydroperoxide proton and an oxygen of the endo-peroxide ring, along with the δ(CHOOH), are highly diagnostic for identification and structure elucidation of complex erythro- and threo- diastereomeric pairs of endo-hydroperoxides; the computational results are in very good agreement with the available experimental data. The 3 J(13 COO1 H) coupling constants were found to be < 2  Hz for the cis-trans geometric models and < 0.5  Hz for the endo-hydroperoxide and, thus, unimportant in stereochemical analysis. Sharp resonances of the hydroperoxide protons, with Δν1/2 < 3 Hz, are required for the successful implementation of the 1 H13 C heteronuclear multiple bond correlation (HMBC) technique.

DFT Calculations of 1H NMR Chemical Shifts of Geometric Isomers of Conjugated Linolenic Acids, Hexadecatrienyl Pheromones, and Model Triene-Containing Compounds: Structures in Solution and Revision of NMR Assignments.

A DFT study of the 1H NMR chemical shifts, δ(1H), of geometric isomers of 18:3 conjugated linolenic acids (CLnAs), hexadecatrienyl pheromones, and model triene-containing compounds is presented, using standard functionals (B3LYP and PBE0) as well as corrections for dispersion interactions (B3LYP-D3, APFD, M06-2X and ωB97XD). The results are compared with literature experimental δ(1H) data in solution. The closely spaced "inside" olefinic protons are significantly more deshielded due to short-range through-space H…H steric interactions and appear close to or even beyond δ-values of aromatic systems. Several regularities of the computational δ(1H) of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest-energy DFT-optimized single conformer for all functionals used and are in very good agreement with experimental δ(1H) in solution. Examples are provided of literature studies in which experimental resonance assignments deviate significantly from DFT predictions and, thus, should be revised. We conclude that DFT calculations of 1H chemical shifts of trienyl compounds are powerful tools (i) for the accurate prediction of δ(1H) even with less demanding functionals and basis sets; (ii) for the unequivocal identification of geometric isomerism of conjugated trienyl systems that occur in nature; (iii) for tackling complex problems of experimental resonance assignments due to extensive signal overlap; and (iv) for structure elucidation in solution.

On the molecular basis of H2O/DMSO eutectic mixtures by using phenol compounds as molecular sensors: a combined NMR and DFT study.

NMR and DFT studies of phenol compounds as molecular sensors were carried out to investigate H2O/DMSO eutectic mixtures at a molecular level. The experimental 1H NMR chemical shifts of the OH groups, δexp(OH), of phenol, paracoumaric acid, and vanillic acid show maximum deshielding and, thus, hydrogen bond interactions in the range of mole fractions 0.20 < χ(DMSO) < 0.33. In the mole fractions χ(DMSO) < 0.2, a progressive decrease in δexp(OH) was observed which demonstrates a decrease in hydrogen bond interactions at infinite dilution in H2O, despite the increase in the number of available hydrogen bond acceptor and donor sites. DFT calculated δcalc(OH) of minimum energy solvation clusters were shown to be in reasonable agreement with the pattern in experimental δexp(OH) data. The chemical shift deshielding and, thus, increased hydrogen bond interactions in the natural product + DMSO + nH2O (n = 2, 3) solvation clusters, relative to complexes in DMSO or H2O solutions, cannot be attributed to a single structural parameter of the cooperative interactions between H2O and DMSO molecules with the phenol OH groups of the natural products. The minimum energy conformers of phenol compounds + 2H2O + DMSO complexes are in excellent agreement with a recent low temperature neutron diffraction experiment of 3D2O + DMSO and demonstrate a general structural motif of solvation complexes. The combined use of 1H NMR and DFT studies with emphasis on δ(OH) of phenol compounds, as molecular sensors, can provide an effective method for the study of solute-solvent interactions at the atomic level.

NMR and Computational Studies as Analytical and High-Resolution Structural Tool for Complex Hydroperoxides and Diastereomeric Endo-Hydroperoxides of Fatty Acids in Solution-Exemplified by Methyl Linolenate.

A combination of selective 1D Total Correlation Spectroscopy (TOCSY) and 1H-13C Heteronuclear Multiple Bond Correlation (HMBC) NMR techniques has been employed for the identification of methyl linolenate primary oxidation products without the need for laborious isolation of the individual compounds. Complex hydroperoxides and diastereomeric endo-hydroperoxides were identified and quantified. Strongly deshielded C-O-O-H 1H-NMR resonances of diastereomeric endo-hydroperoxides in the region of 8.8 to 9.6 ppm were shown to be due to intramolecular hydrogen bonding interactions of the hydroperoxide proton with an oxygen atom of the five-member endo-peroxide ring. These strongly deshielded resonances were utilized as a new method to derive, for the first time, three-dimensional structures with an assignment of pairs of diastereomers in solution with the combined use of 1H-NMR chemical shifts, Density Functional Theory (DFT), and Our N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) calculations.

DFT Calculations of 1H- and 13C-NMR Chemical Shifts of Geometric Isomers of Conjugated Linoleic Acid (18:2 ω-7) and Model Compounds in Solution.

A density functional theory (DFT) study of the 1H- and 13C-NMR chemical shifts of the geometric isomers of 18:2 ω-7 conjugated linoleic acid (CLA) and nine model compounds is presented, using five functionals and two basis sets. The results are compared with available experimental data from solution high resolution nuclear magnetic resonance (NMR). The experimental 1H chemical shifts exhibit highly diagnostic resonances due to the olefinic protons of the conjugated double bonds. The "inside" olefinic protons of the conjugated double bonds are deshielded than those of the "outside" protons. Furthermore, in the cis/trans isomers, the signals of the cis bonds are more deshielded than those of the trans bonds. These regularities of the experimental 1H chemical shifts of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest energy DFT optimized single conformer, for all functionals and basis sets used. The other low energy conformers have negligible effects on the computational 1H-NMR chemical shifts. We conclude that proton NMR chemical shifts are more discriminating than carbon, and DFT calculations can provide a valuable tool for (i) the accurate prediction of 1H-NMR chemical shifts even with less demanding functionals and basis sets; (ii) the unequivocal identification of geometric isomerism of CLAs that occur in nature, and (iii) to derive high resolution structures in solution.

The unique catalytic role of water in aromatic C-H activation at neutral pH: a combined NMR and DFT study of polyphenolic compounds.

Direct activation of aromatic C-H bonds in polyphenolic compounds in a single step, without the use of late transition metals, is demonstrated with the use of D2O and common phosphate buffer at neutral pD and near ambient temperatures. Detailed variable temperature and pD 1H NMR studies were carried out to investigate, for the first time, the Gibbs activation energy (ΔG‡), the activation enthalpy (ΔH‡), and activation entropy (TΔS‡) of H/D exchange reactions of the natural product catechin and the model compounds resorcinol and phloroglucinol. NMR and DFT calculations support a catalytic cycle comprising two water molecules in a keto-enol tautomeric process. The reduction of ΔG‡ values due to the catalytic role of two molecules of water by a factor of 20-30 kcal mol-1 and the resulting acceleration of the H/D exchange rate by a factor of 1020-1030 should be compared with a minor reduction in ΔG‡ of 0.4 to 4.5 kcal mol-1 due to the effect of an additional electron donating oxygen group and the deprotonation of OH groups. It can therefore be concluded that although the H/D exchange process can be accelerated by a small amount of an acid or a base to break a C-H bond, water as a catalyst plays the major role. This approach opens a new vistas for the combined use of NMR and DFT studies as tools to understand the molecular basis of the catalytic role of water.

Solvent-Dependent Structures of Natural Products Based on the Combined Use of DFT Calculations and 1H-NMR Chemical Shifts.

Detailed solvent and temperature effects on the experimental 1H-NMR chemical shifts of the natural products chrysophanol (1), emodin (2), and physcion (3) are reported for the investigation of hydrogen bonding, solvation and conformation effects in solution. Very small chemical shift of │Δδ│ < 0.3 ppm and temperature coefficients │Δδ/ΔΤ│ ≤ 2.1 ppb/K were observed in DMSO-d6, acetone-d6 and CDCl3 for the C(1)-OH and C(8)-OH groups which demonstrate that they are involved in a strong intramolecular hydrogen bond. On the contrary, large chemical shift differences of 5.23 ppm at 298 K and Δδ/ΔΤ values in the range of -5.3 to -19.1 ppb/K between DMSO-d6 and CDCl3 were observed for the C(3)-OH group which demonstrate that the solvation state of the hydroxyl proton is a key factor in determining the value of the chemical shift. DFT calculated 1H-NMR chemical shifts, using various functionals and basis sets, the conductor-like polarizable continuum model, and discrete solute-solvent hydrogen bond interactions, were found to be in very good agreement with the experimental 1H-NMR chemical shifts even with computationally less demanding level of theory. The 1H-NMR chemical shifts of the OH groups which participate in intramolecular hydrogen bond are dependent on the conformational state of substituents and, thus, can be used as molecular sensors in conformational analysis. When the X-ray structures of chrysophanol (1), emodin (2), and physcion (3) were used as input geometries, the DFT-calculated 1H-NMR chemical shifts were shown to strongly deviate from the experimental chemical shifts and no functional dependence could be obtained. Comparison of the most important intramolecular data of the DFT calculated and the X-ray structures demonstrate significant differences for distances involving hydrogen atoms, most notably the intramolecular hydrogen bond O-H and C-H bond lengths which deviate by 0.152 tο 0.132 Å and 0.133 to 0.100 Å, respectively, in the two structural methods. Further differences were observed in the conformation of -OH, -CH3, and -OCH3 substituents.

Refinement of labile hydrogen positions based on DFT calculations of 1H NMR chemical shifts: comparison with X-ray and neutron diffraction methods.

Numerous gas phase electron diffraction, ultra-fast electron diffraction, X-ray and neutron diffraction experiments on ß-dicarbonyl compounds exhibiting enol-enol tautomeric equilibrium, with emphasis on acetylacetone and dibenzoylmethane, have so far been reported with conflicting results on the structural details of the O-HO intramolecular hydrogen bond and resulted in alternative hypotheses on the intramolecular hydrogen bond potential function either a double minimum potential corresponding to two tautomeric forms in equilibrium or a single symmetrical one. We demonstrate herein, firstly, that the DFT calculated OH 1H NMR chemical shifts of acetylacetone and dibenzoylmethane exhibit a strong linear dependence on the computed OO hydrogen bond length of ∼-50 ppm Å-1 and as a function of the O-HO bond angle of ∼1 ppm per degree, upon the transfer of the hydrogen atom from the ground state toward the transition state. Secondly, the refinement of labile hydrogen atomic positions in intramolecular hydrogen bonds based on the root-mean-square deviation between experimentally determined and DFT calculated 1H NMR chemical shifts in solution can provide high resolution structures of O-H and O(H)O bond lengths and O-HO bond angles with an accuracy of ∼10-2 Å and ∼0.5°, respectively. Thirdly, the calculated 1H NMR chemical shifts in solution of the two ground state tautomers in equilibrium of acetylacetone and dibenzoylmethane are in excellent agreement with the experimental value, even for moderate basis sets for energy minimization. In contrast, the single symmetrical structure in a strongly delocalized system is a transition state with calculated 1H NMR chemical shifts which strongly deviate from the experimental value. Fourth, the DFT calculated ground state O-H bond lengths of acetylacetone and dibenzoylmethane are in quantitative agreement with the literature data which take into account the effect of quantum nuclear motion. The DFT structural results are critically discussed with respect to the state-of-the-art variable temperature X-ray and neutron diffraction methods.

Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

Accurate ab initio calculations of O-HO and O-H(-)O proton chemical shifts: towards elucidation of the nature of the hydrogen bond and prediction of hydrogen bond distances.

The inability to determine precisely the location of labile protons in X-ray molecular structures has been a key barrier to progress in many areas of molecular sciences. We report an approach for predicting hydrogen bond distances beyond the limits of X-ray crystallography based on accurate ab initio calculations of O-HO proton chemical shifts, using a combination of DFT and contactor-like polarizable continuum model (PCM). Very good linear correlation between experimental and computed (at the GIAO/B3LYP/6-311++G(2d,p) level of theory) chemical shifts were obtained with a large set of 43 compounds in CHCl3 exhibiting intramolecular O-HO and intermolecular and intramolecular ionic O-H(-)O hydrogen bonds. The calculated OH chemical shifts exhibit a strong linear dependence on the computed (O)HO hydrogen bond length, in the region of 1.24 to 1.85 Å, of -19.8 ppm Å(-1) and -20.49 ppm Å(-1) with optimization of the structures at the M06-2X/6-31+G(d) and B3LYP/6-31+G(d) level of theory, respectively. A Natural Bond Orbitals (NBO) analysis demonstrates a very good linear correlation between the calculated (1)H chemical shifts and (i) the second-order perturbation stabilization energies, corresponding to charge transfer between the oxygen lone pairs and σ antibonding orbital and (ii) Wiberg bond order of the O-HO and O-H(-)O hydrogen bond. Accurate ab initio calculations of O-HO and O-H(-)O (1)H chemical shifts can provide improved structural and electronic description of hydrogen bonding and a highly accurate measure of distances of short and strong hydrogen bonds.

Investigation of solute-solvent interactions in phenol compounds: accurate ab initio calculations of solvent effects on 1H NMR chemical shifts.

Accurate (1)H chemical shifts of the -OH groups of polyphenol compounds can be calculated, compared to experimental values, using a combination of DFT, polarizable continuum model (PCM) and discrete solute-solvent hydrogen bond interactions. The study focuses on three molecular solutes: phenol, 4-methylcatechol and the natural product genkwanin in DMSO, acetone, acetonitrile, and chloroform. Excellent linear correlation between experimental and computed chemical shifts (with the GIAO method at the DFT/B3LYP/6-311++G(2d,p) level) was obtained with minimization of the solvation complexes at the DFT/B3LYP/6-31+G(d) and DFT/B3LYP/6-311++G(d,p) level of theory with a correlation coefficient of 0.991. The use of the DFT/B3LYP/6-31+G(d) level of theory for minimization could provide an excellent means for the accurate prediction of the experimental OH chemical shift range of over 8 ppm due to: (i) strong intramolecular and solute-solvent intermolecular hydrogen bonds, (ii) flip-flop intramolecular hydrogen bonds, and (iii) conformational effects of substituents of genkwanin. The combined use of ab initio calculations and experimental (1)H chemical shifts of phenol -OH groups provides a method of primary interest in order to obtain detailed structural, conformation and electronic description of solute-solvent interactions at a molecular level.

2D and 3D photoreactive lanthanide MOFs of trans,trans-muconic acid.

Three 2D and 3D photoreactive MOFs of trans,trans-muconic acid with Er(3+) and their corresponding isomorphous Y(3+) phases were synthesized and their photoreactivity was studied as a function of the crystal environment.

Photoreactive 3D microporous lanthanide MOFs: formation of a strained ladderane in a partial single crystal-to-single crystal manner.

The assembly of Er(3+) and Y(3+) cations with trans,trans-muconic acid affords a photoreactive 3D microporous MOF that, upon UV irradiation, undergoes a cycloaddition reaction (SCSC up to 55%), with in situ formation of a strained ladderane.

Free electron transfer from xanthenyl- and fluorenylsilanes (Me3 or Ph3) to parent solvent radical cations: effects of molecule dynamics.

Parent radical cations of nonpolar solvents (alkanes and alkyl chlorides) ionize 9-(trimethylsilyl)xanthenes and 9-(trimethylsilyl)fluorenes in a diffusion-controlled electron transfer. The actual electron jump as the deciding part of the process does not require a defined encounter complex, and therefore the reactants are not subjected to any geometry optimization. Considering the molecule dynamics of the donors, bending motions of the silyl group are concerted with fluctuations of the highest occupied molecular orbital electrons. Ionizing such a standing conformer mixture creates metastable (microsecond) as well as dissociative donor radical cations. A mobility restriction of the benzylic silane group in positions vertical to the phenyl plane stabilizes the radical cations and accounts for a declining amount of dissociative radical cations, which undergo C-Si bond fragmentation in the order benzylsilane > xanthenylsilane > fluorenylsilane.

Triplet- vs. singlet-state imposed photochemistry. The role of substituent effects on the photo-Fries and photodissociation reaction of triphenylmethyl silanes.

The photochemistry of three structurally very similar triphenylmethylsilanes 1, 2, 3 [p-X-C(6)H(4)-CPh(2)-SiMe(3): X = PhCO, 1; H, ; Ph(OCH(2)CH(2)O)C, 3] is described by means of 248 and 308 nm nanosecond laser flash photolysis (ns-LFP), femtosecond LFP, EPR spectroscopy, emission spectroscopy (fluorescence, phosphorescence), ns-pulse radiolysis (ns-PR), photoproduct analysis studies in MeCN, and X-ray crystallographic analysis of the two key-compounds 1 and 2. The photochemical behavior of 1, 2 and 3 is discussed and compared with that of a fourth one, 4, bearing on the p-position an amino group (X = Me(2)N) and whose detailed photochemistry we reported earlier (J. Org. Chem., 2000, 65, 4274-4280). Silane 1 undergoes on irradiation with 248 and 308 nm laser light a fast photodissociation of the C-Si bond giving the p-(benzoyl)triphenylmethyl radical (1*) with a rate constant of k(diss)= 3 x 10(7) s(-1). The formation of 1* is a one-quantum process and takes place via the carbonyl triplet excited state with high quantum yield (Phi(rad)= 0.9); the intervention of the triplet state is clearly demonstrated through the phosphorescence spectrum and quenching experiments with ferrocene (k(q)= 9.3 x 10(9) M(-1) s(-1)), Et(3)N (1.1 x 10(9) M(-1) s(-1)), and styrene (3.1 x 10(9) M(-1) s(-1)) giving quenching rate constants very similar to those of benzophenone. For comparative reasons radical 1* was generated independently from p-(benzoyl)triphenylmethyl bromide via pulse radiolysis in THF and its absorption coefficient at lambda(max)= 340 nm was determined ([epsilon]= 27770 M(-1) cm(-1)). We found thus that the p-PhCO-derivative 1 behaves similar to the p-Me(2)N one (the latter giving the p-(dimethylamino)triphenylmethyl radical with Phi(rad)= 0.9), irrespective of their completely different ground state electronic properties. In contrast, compounds 2, 3 that bear only the aromatic chromophore give by laser or lamp irradiation both, (i) radical products [Ph(3)C* and p-Ph(OCH(2)CH(2)O)C-C(6)H(4)-C(*)Ph(2), respectively] after dissociation of the central C-Si bond (Phi(rad)= 0.16), and (ii) persistent photo-Fries rearrangement products (of the type of 5-methylidene-6-trimethylsilyl-1,3-cyclohexadiene) absorbing at 300-450 nm and arising from a 1,3-shift of the SiMe(3) group from the benzylic to the ortho-position of the aromatic ring (Phi approximately 0.85 for 2). Using fs-LFP on 2 we showed that the S(1) state recorded at 100 fs after the pulse decays on a time scale of 500 fs giving Ph(3)C* through C-Si bond dissociation. In a second step and within the next 10 ps trityl radicals either escape from the solvent cage (the quantum yield of Ph(3)C* formation Phi(rad)= 0.16 was measured with ns-LFP), or undergo in-cage recombination to photo-Fries products. Thus, singlet excited states (S(1)) of the aromatic organosilanes (2, 3) prefer photo-Fries rearrangement products, while triplet excited states (1, 4) favor free radicals. Both reactions proceed via a common primary photodissociation step (C-Si bond homolysis) and differentiate obviously in the multiplicity of the resulting geminate radical pairs; singlet radical pairs give preferably photo-Fries products following an in-cage recombination, while triplet radical pairs escape the solvent cage (MeCN). The results demonstrate the crucial role which is played by the chromophore which prescribes in a sense, (i) the multiplicity of the intervening excited state and consequently that of the resulting geminate radical pair, and (ii) the dominant reaction path to be followed: the benzophenone- and anilino-chromophore present in silanes 1 and 4, respectively, impose effective intersystem crossing transitions (k(isc)= 10(11) s(-1) and 6 x 10(8) s(-1), respectively) leading to triplet states and finally to free radical products, while the phenyl chromophore in 2 and 3, possessing ineffective isc (k(isc)= 6 x 10(6) s(-1)) leads to photo-Fries product formation via the energetic high lying S(1) state [approximately 443 kJ mol(-1)(106 kcal mol(-1))].

Assembly of a photoreactive coordination polymer containing rectangular grids.

We describe the synthesis, crystal structure and solid state reactivity of cadmium fumarate dihydrate, which is made up of planar H-bonded metal-organic layers and undergoes, upon irradiation, a topochemical [2 + 2] cycloaddition reaction.