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

Calculated vibration spectrum of calcium hexahydroxodizincate dihydrate (qatranaite)

On the basis of first-principles electronic structure calculations, crystallographic parameters have been refined for calcium hydroxozincate (Qatranaite mineral), and the vibration properties (frequencies and eigenvectors) calculated. A detailed analysis of vibration modes is done, in the context of comparison with infrared and Raman spectra previously available. Special attention is paid to a posteriori symmetry analysis of vibration modes, discussing the latters' attribution to four irreducible representations of the P21/c space group, and to identifying stretchings and bendings of particular chemical bonds, pronounced in different vibrations. It turns out that high-frequency (>700 cm-1) vibrations of hydroxyl groups bridging the Ca or Zn cations differ quite considerably for crystallographically distinct hydroxyl positions. It is shown that the vibrations involving hydroxyl groups and crystalline water typically come about in quadruplets at very close frequencies, whereby different irreducible representations reflect different combinations of similar "molecular" vibrations of four identical entities (of each hydroxyl or water) present in the unit cell. However, some vibrations show exceptions from this rule. In addition to interpretation of earlier experimental investigations, our study indicates that the low-frequency (<700 cm-1) vibrations within the cation-hydroxyl connected skeleton are of more "solid-state-like" character and cannot be reasonably interpreted in terms of "molecular" vibrations within ZnO4 or CaO6 units.

Factors governing the protonation of Keggin-type polyoxometalates: influence of the core structure in clusters

Atomic substitution is a promising approach for controlling structures and properties for developing clusters with desired responses. Although many possible coordination candidates could be deduced for substitution, not all can be prepared. Therefore, predicting the correlation between structures and physical properties is important prior to synthesis. In this study, regarding Keggin-type polyoxometalates (POMs) as a model cluster, the dominant factors affecting the protonation were investigated by atomic substitutions and geometry changes. The valence of Keggin-type POMs and the constituent elements of the cluster shell structure affect the charge and potential distribution, which change the protonation sites. Furthermore, the valence of Keggin-type POMs and the bond length between the core and shell structure determine the protonation energy. These factors also affect the HOMO-LUMO gap, which governs photochemical and redox reactions. These governing factors derived from actual parameters of the α-isomer of Keggin-type POMs enabled us to deduce the protonation energy of the β-isomer, which is more difficult to prepare and isolate than the α-isomer.

Dissociation Kinetics and Antimicrobial Activity of Ofloxacin Antibiotic in Artificial Tears Via 1H-NMR, Raman, and UV-Vis Spectroscopic Analysis

Introduction: The hydrogen-bonded networks play a significant role in influencing several physicochemical properties of ofloxacin in artificial tears (ATs), including density, pH, viscosity, and self-diffusion coefficients. The activities of the ofloxacin antibiotic with Ats mixtures are not solely determined by their concentration but are also influenced by the strength of the hydrogen bonding network which highlight the importance of considering factors such as excessive tear production and dry eye conditions when formulating appropriate dosages of ofloxacin antibiotics for eye drops. Objectives: Investigating the physicochemical properties of ofloxacin-ATs mixtures, which serve as a model for understanding the impact of hydrogen bonding on the antimicrobial activity of ofloxacin antibiotic eye drops. Determine the antimicrobial activities of the ofloxacin-Ats mixture with different concentration of ofloxacin. Methods: The ofloxacin-ATs mixtures were analyzed using 1H-NMR, Raman, and UV-Vis spectroscopies, with variation of ofloxacin concentration to study its dissociation kinetics in ATs, mimicking its behavior in human eye tears. The investigation includes comprehensive analysis of 1H-NMR spectral data, self-diffusion coefficients, Raman spectroscopy, UV-Vis spectroscopy, liquid viscosity, and acidity, providing a comprehensive assessment of the physicochemical properties. Results: Analysis of NMR chemical shifts, linewidths, and self-diffusion coefficient curves reveals distinct patterns, with peaks or minima observed around 0.6 ofloxacin mole fraction dissociated in ATs, indicating a strong correlation with the hydrogen bonding network. Additionally, the pH data exhibits a similar trend to viscosity, suggesting an influence of the hydrogen bonding network on protonic ion concentrations. Antibacterial activity of the ofloxacin-ATs mixtures is evaluated through growth rate analysis against Salmonella typhimurium, considering varying concentrations with mole fractions of 0.1, 0.4, 0.6, 0.8, and 0.9. Conclusions: The antibiotic-ATs mixture with a mole fraction of 0.6 ofloxacin exhibited lower activity compared to mixtures with mole fractions of 0.1 and 0.4, despite its lower concentration. The activities of the mixtures are not solely dependent on concentration but are also influenced by the strength of the hydrogen bonding network. These findings emphasize the importance of considering tear over-secretion and dry eye problems when designing appropriate doses of ofloxacin antibiotics for eye drop formulations.

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.

Stereoselective Synthesis of the O-antigen of A. baumannii ATCC 17961 Using Long-Range Levulinoyl Group Participation

Herein, we described the first synthesis of the pentasaccharide and decasaccharide of the A. baumannii ATCC 17961 O-antigen for developing a synthetic carbohydrate-based vaccine against A. baumannii infection. The efficient synthesis of the rare sugar 2,3-diacetamido-glucuronate was achieved using our recently introduced organocatalytic glycosylation method. We found, for the first time, that long-range levulinoyl group participation via a hydrogen bond can result in a significantly improved β-selectivity in glycosylations. This solves the stereoselectivity problem of highly branched galactose acceptors. The proposed mechanism was supported by control experiments and DFT computations. Benefiting from the long-range levulinoyl group participation strategy, the pentasaccharide donor and acceptor were obtained via an efficient [2+1+2] one-pot glycosylation method and were used for the target decasaccharide synthesis.

Hydrogen Bonding in Platinum Indolylphosphine Polyfluorido and Fluorido Complexes

The reaction of the Pt complexes cis-[Pt(CH₃ )(Ar){Ph₂ P(Ind)}₂ ] (Ind=2-(3-methyl)indolyl, Ar=4-tBuC₆ H₄ (1 a)_, 4-CH₃ C₆ H₄ (1 b), Ph (1 c), 4-FC₆ H₄ (1 d), 4-ClC₆ H₄ (1 e), 4-CF₃ C₆ H₄ (1 f)) with HF afforded the polyfluorido complexes trans-[Pt(F(HF)₂ )(Ar){Ph₂ P(Ind)}₂ ] 2 a-f, which can be converted into the fluoride derivatives trans-[Pt(F)(Ar){Ph₂ P(Ind)}₂ ] (3 a-f) by treatment with CsF. The compounds 2 a-f and 3 a-f were characterised thoroughly by multinuclear NMR spectroscopy. The data reveal hydrogen bonding of the fluorido ligand with HF molecules and the indolylphosphine ligand. Polyfluorido complexes 2 a-f show larger |¹ J(F,Pt)|, but lower ¹ J(H,F) coupling constants when compared to the fluorido complexes 3 a-f. Decreasing ¹ J(P,Pt) coupling constants in 2 a-f and 3 a-f suggest a cis influence of the aryl ligands in the following order: 4-tBuC₆ H₄ (a) ≈4-CH₃ C₆ H₄ (b)<Ph (c)≪4-FC₆ H₄ (d)<4-ClC₆ H₄ (e)<4-CF₃ C₆ H₄ (f). In addition, the larger cis influence of aryl ligands bearing electron-withdrawing groups in the para position correlates with decreasing magnitudes of |¹ J(F,Pt)| coupling constants. The interpretation of the experimental data was supported by quantum-chemical DFT calculations.

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 Δν_1/2  < 3 Hz, are required for the successful implementation of the ¹ H¹³ C heteronuclear multiple bond correlation (HMBC) technique.

Structure-based rational design of an enhanced fluorogen-activating protein for fluorogens based on GFP chromophore

“Fluorescence-Activating and absorption-Shifting Tag” (FAST) is a well-studied fluorogen-activating protein with high brightness and low size, able to activate a wide range of fluorogens. This makes FAST a promising target for both protein and fluorogen optimization. Here, we describe the structure-based rational design of the enhanced FAST mutants, optimized for the N871b fluorogen. Using the spatial structure of the FAST/N871b complex, NMR relaxation analysis, and computer simulations, we identify the mobile regions in the complex and suggest mutations that could stabilize both the protein and the ligand. Two of our mutants appear brighter than the wild-type FAST, and these mutants provide up to 35% enhancement for several other fluorogens of similar structure, both in vitro and in vivo. Analysis of the mutants by NMR reveals that brighter mutants demonstrate the highest stability and lowest length of intermolecular H-bonds. Computer simulations provide the structural basis for such stabilization.

Structural analyses guide the rational design of mutant fluorogen-activating proteins with enhanced fluorescence.

Estimations of OH·N hydrogen bond length from positions and intensities of IR bands

In this computational work applicability of IR spectral parameters for evaluations of OH···N hydrogen bond length is discussed. For a set of 124 complexes with OH···N hydrogen bond formed by combinations of methanol/acetic acid and pyridine (and their fluorine substituted versions) geometries, energies and IR parameters were calculated at MP2/def2-TZVP level of theory. For a number of IR parameters (the shift of proton donor group stretching vibration Δν_s, increase of its intensity I, the low-frequency hydrogen bond stretching vibration ν_σ, bending in-plane δ and out-of-plane γ vibrations) equations linking them with interatomic distances are proposed, the robustness and accuracy of such equations are discussed. The enthalpy of OH···N hydrogen bond formation ΔH was also linked with electron density parameters in (3; -1) critical point.

Evaluating the conformational space of the active site of D2 dopamine receptor. Scope and limitations of the standard docking methods

We report here for the first time the potential energy surfaces (PES) of phenyletilamine (PEA) and meta-tyramine (m-OH-PEA) at the D₂ dopamine receptor (D2DR) binding site. PESs not only allow us to observe all the critical points of the surface (minimums, maximums, and transition states), but also to note the ease or difficulty that each local minima have for their conformational inter-conversions and therefore know the conformational flexibility that these ligands have in their active sites. Taking advantage of possessing this valuable information, we analyze how accurate a standard docking study is in these cases. Our results indicate that although we have to be careful in how to carry out this type of study and to consider performing some extra-simulations, docking calculations can be satisfactory. In order to analyze in detail the different molecular interactions that are stabilizing the different ligand-receptor (L-R) complexes, we carried out quantum theory of atoms in molecules (QTAIM) computations and NMR shielding calculations. Although some of these techniques are a bit tedious and require more computational time, our results demonstrate the importance of performing computational simulations using different types of combined techniques (docking/MD/hybrid QM-MM/QTAIM and NMR shielding calculations) in order to obtain more accurate results. Our results allow us to understand in details the molecular interactions stabilizing and destabilizing the different L-R complexes reported here. Thus, the different activities observed for dopamine (DA), m-OH-PEA, and PEA can be clearly explained at molecular level.

Analytical and Structural Tools of Lipid Hydroperoxides: Present State and Future Perspectives

Mono- and polyunsaturated lipids are particularly susceptible to peroxidation, which results in the formation of lipid hydroperoxides (LOOHs) as primary nonradical-reaction products. LOOHs may undergo degradation to various products that have been implicated in vital biological reactions, and thus in the pathogenesis of various diseases. The structure elucidation and qualitative and quantitative analysis of lipid hydroperoxides are therefore of great importance. The objectives of the present review are to provide a critical analysis of various methods that have been widely applied, and more specifically on volumetric methods, applications of UV-visible, infrared, Raman/surface-enhanced Raman, fluorescence and chemiluminescence spectroscopies, chromatographic methods, hyphenated MS techniques, NMR and chromatographic methods, NMR spectroscopy in mixture analysis, structural investigations based on quantum chemical calculations of NMR parameters, applications in living cells, and metabolomics. Emphasis will be given to analytical and structural methods that can contribute significantly to the molecular basis of the chemical process involved in the formation of lipid hydroperoxides without the need for the isolation of the individual components. Furthermore, future developments in the field will be discussed.

Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic resonance (NMR) spectroscopy is significantly complicated by the ability of apiose to cross-link via borate ester linkages to form RG-II dimers. Here, we developed a computational approach to gain insight into the structure–spectra relationships of apio–borate complexes in an effort to complement experimental assignments of NMR signals in RG-II. Our protocol involved structure optimizations using density functional theory (DFT) followed by isotropic magnetic shielding constant calculations using the gauge-invariant atomic orbital (GIAO) approach to predict chemical shifts. We evaluated the accuracy of 23 different functional–basis set (FBS) combinations with and without implicit solvation for predicting the experimental 1H and 13C shifts of a methyl apioside and its three borate derivatives. The computed NMR predictions were evaluated on the basis of the overall shift accuracy, relative shift ordering, and the ability to distinguish between dimers and monomers. We demonstrate that the consideration of implicit solvation during geometry optimizations in addition to the magnetic shielding constant calculations greatly increases the accuracy of NMR chemical shift predictions and can correctly reproduce the ordering of the 13C shifts and yield predictions that are, on average, within 1.50 ppm for 13C and 0.12 ppm for 1H shifts for apio–borate compounds.

Synergistic Effect in a Graphene Quantum Dot-Enabled Luminescent Skinlike Copolymer for Long-Term pH Detection

The alluring properties of a luminescent graphene quantum dot (GQD)-based nanocomposite are unquestionable to realize many advanced applications, such as sweat pH sensors. The well-suited hydrophilic polymers to host GQDs can face an unavoidable swelling behavior, which deteriorates the mechanical stability, whereas the hydrophobic polymers can prevent swelling but at the same time barricade the analyte pathways to GQDs. To resolve the two aforementioned obstacles, we develop a nanocomposite film containing nitrogen-doped GQDs (NGQDs) incorporated into a transparent, elastic, and self-healable polymer matrix, composed of a hydrophobic n-butyl acrylate segment and a hydrophilic N-(hydroxymethyl)acrylamide segment for wearable healthcare pH sensors on the human body. Besides serving as the fluorescence source, NGQDs are also designed as a nano-cross-linker to promote abundant chemical and physical interactions within the nanocomposite network. This synergetic effect gives rise to a 10-fold higher mechanical strength, 7-fold increment in Young's modulus, 4-fold increment in toughness, and 15-fold more sensitivity in pH detection (pH 3-10) compared to those of the pristine copolymer and NGQDs, respectively. Moreover, the mechanically enhanced nanocomposite possesses a high self-healing efficiency (94%) at room temperature even under water and demonstrates a stable sensing performance after repetitive usage for 30 days. Our work provides insights into the simple preparation of human skinlike nanocomposite elastomers usable for wearable pH sensors.

Covalence and π-electron delocalization influence on hydrogen bonds in proton transfer process of o-hydroxy aryl Schiff bases: A combined NMR and QTAIM analysis

Within the framework of the density functional theory approach, we studied the relationship between the chemical nature of intramolecular hydrogen bonds (HBs) and nuclear magnetic resonance (NMR) parameters, J-couplings and ¹H-chemical shifts [δ(¹H)], of the atoms involved in such bonds in o-hydroxyaryl Schiff bases during the proton transfer process. For the first time, the shape of the dependence of the degree of covalence in HBs on ¹J(N-H), ¹J(O-H), ^2hJ(O-N), and δ(¹H) during the proton transfer process in o-hydroxyaryl Schiff bases was analyzed. Parameters obtained from Bader's theory of atoms in molecules were used to assess the dependence of covalent character in HBs with both the NMR properties. The influence of π-electronic delocalization on ^2hJ(N-O) under the proton transfer process was investigated. ^2hJ(O-N) in a Mannich base was also studied in order to compare the results with an unsaturated system. In addition, substituent effects on the phenolic ring were investigated. Our results indicate that the covalent character of HBs on both sides of the transition state undergoes a smooth exponential increase as the δ(¹H) moves downfield. The degree of covalence of the N⋯H (O⋯H) bond increases linearly as ¹J(N-H) (¹J(O-H)) becomes more negative, even after reaching the transition state. Non-vanishing values of spin dipolar (SD) and paramagnetic spin orbital terms of ^2hJ(O-N) show that π-electronic delocalization has a non-negligible effect on tautomeric equilibrium and gives evidence of the presence of the resonance assisted HB.Variation of the SD term of ^2hJ(O-N) follows a similar pattern as the change in the para-delocalization aromaticity index of the chelate ring.

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, δ_exp(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 δ_exp(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 δ_calc(OH) of minimum energy solvation clusters were shown to be in reasonable agreement with the pattern in experimental δ_exp(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.

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.

Accurate location of hydrogen atoms in hydrogen bonds of tizoxanide from the combination of experimental and theoretical models

To obtain detailed information about the position of hydrogen atoms in hydrogen bonds, HBs, of crystalline organic molecular compounds is not an easy task. In this work we propose a combination of ssNMR experimental data with theoretical procedures to get such information. Furthermore, the combination of experimental and theoretical models provides us with well-defined grounds to analyse the strength of π-stacking interactions between layers of hydrogen bonded molecules. Two different theoretical models were considered, both approaches being quite different. The first one is a solid-state model, so that the periodicity of a crystalline system underlies calculations of the electronic energy, the electronic density and NMR parameters. The other one is a molecular model in which molecules are taken as isolated monomers, dimers and tetramers. These two models were applied to the tizoxanide, TIZ, molecular crystal though it can widely be applied to any other molecular crystal. By the application of the quantum molecular model it was possible to learn about the way the intermolecular HBs affect the position of hydrogen atoms that belong to HBs in TIZ. This molecule has two intermolecular HBs that stabilize the structure of a basic dimer, but it also has an intramolecular HB in each monomer whose position should be optimized together with the other ones. We found that by doing this it is possible to obtain reliable results of calculations of NMR spectroscopic parameters. Working with the solid-state model we found that any local variation of the TIZ crystalline structure is correlated with the variation of the values of the NMR parameters of each nucleus. The excellent agreement between experimental and calculated chemical shifts leads to the conclusion that the N10-H10 bond distance should be (1.00 ± 0.02) Å.

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.

Cooperativity in a cycloalkane-1,2/1,3-polyol corona: Topological hydrogen bonding in 1,2-diol motifs

A corona, consisting of 18 carbon atoms bearing 12 hydroxy groups in a continuous hydrogen-bonded chain, is built up by alternating degenerate conformations of alternating alkane-1,2-diol and 1,3-diol motifs. Geometries, proton nuclear magnetic resonance shifts and interaction energies for the dodecahydroxycyclo-octadecane and selected fragments are determined by density functional calculations at the B3LYP/6-311+G(d,p) level. Cooperative effects of O-H⋯O-H bonding are evident from the simple juxtaposition of these two motifs with a common OH group in butane-1,2,4-triol conformers. Bracketing a 1,2-diol motif with two 1,3-diol motifs in hexane-1,3,4,6-tetrol leads to a structure in which the 1,2-diol motif displays a bond critical point for hydrogen bonding. This is associated with enhancement of the shift of the hydrogen-bonded OH proton and of the corresponding H⋯O interaction energy. The full corona has a complete outer ring of O-H⋯O-H bond paths, and an inner ring of bond paths, due to C-H⋯H-C hydrogen-hydrogen bonding, which result in a central ring critical point. The topological O-H⋯O-H hydrogen bond, never seen in simple alkane-1,2-diols, is associated with cooperative enhancement of the H⋯O interaction energy, but this is not a necessary condition for a bond path: values for topological C-H⋯H-C hydrogen-hydrogen bonds can be as low as -0.4 kcal mol^-1 .

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.

Impact of donor acidity and acceptor anharmonicity on vc=o spectral shifts in O-H···O=C H-bonded ketone-alcohol complexes: An IR spectroscopic investigation

O-H···O=C Hydrogen bonding (H-bonding) results in spectral shifts in both ν_O-H and ν_C=O modes. A large number of investigations exist in literature that focuses on how the spectral shifts vary with certain properties of the donors and acceptors. However information on how the magnitude of spectral shift is dictated individually by the donor and acceptor is not yet clear to us. Here, IR spectroscopy in room temperature CCl₄ solution has been used to investigate how ν_C=O spectral shifts of ketones in H-bonded complexes with alcohols are influenced by change in donor and acceptor properties. For this purpose 25 number of O-H···O=C H-bonded complexes formed by 5 different ketones and 5 alcohols have been studied. The magnitude of red-shifts shown by the ν_C=O bands were found to show systematic trends with changing donor and acceptor species. It was found that for a particular ketone, the magnitude of shift increases monotonically with acidity of the alcohols. Spectral shifts were found to increase in a linear fashion with decreasing p^K_a of the donor alcohols. On the other hand, when the alcohol were kept fixed, the spectral shift was found to be dependent on the CO bond strength of the ketones. We found spectral shifts to linearly increase with increasing anharmonicity constant and decreasing dissociation energy of CO bond. Finally, it has been shown that there exist concomitant correlations of the spectral shifts with donor p^K_a and acceptor ν_C=O anharmonicity constant/bond dissociation energy. The relations have been validated for H-bonded complexes of 1,4-cyclohexanedione with the above mentioned five alcohols.

Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects

Electronic and nuclear quantum effects determine the symmetry and highly downfield ¹H NMR chemical shifts of short hydrogen bonds.

Relationships between NMR shifts and interaction energies in biphenyls, alkanes, aza-alkanes, and oxa-alkanes with X─H… H─Y and X─H… Z (X, Y = C or N; Z = N or O) hydrogen bonding

Hydrogen-hydrogen C─H^… H─C bonding between the bay-area hydrogens in biphenyls, and more generally in congested alkanes, very strained polycyclic alkanes, and cis-2-butene, has been investigated by calculation of proton nuclear magnetic resonance (NMR) shifts and atom-atom interaction energies. Computed NMR shifts for all protons in the biphenyl derivatives correlate very well with experimental data, with zero intercept, unit slope, and a root mean square deviation of 0.06 ppm. For some congested alkanes, there is generally good agreement between computed values for a selected conformer and the experimental data, when it is available. In both cases, the shift of a given proton or pair of protons tends to increase with the corresponding interaction energy. Computed NMR shift differences for methylene protons in polycyclic alkanes, where one is involved in a very short contact ("in") and the other is not ("out"), show a rough correlation with the corresponding C─H^… H─C exchange energies. The "in" and "in,in" isomers of selected aza- and diaza-cycloalkanes, respectively, are X─H^… H─N hydrogen bonded, whereas the "out" and "in,out" isomers display X─H^… N hydrogen bonds (X = C or N). Oxa-alkanes and the "in" isomers of aza-oxa-alkanes are X─H^… O hydrogen bonded. There is a very good general correlation, including both N─H^… H─Y (Y = C or N) and N─H^… Z (Z = N or O) interactions, for NH proton shifts against the exchange energy. For "in" CH protons, the data for the different C─H^… H─Y and C─H^… Z interactions are much more dispersed and the overall shift/exchange energy correlation is less satisfactory.

Crystal structure and Hirshfeld surface analysis of 2-hy-droxy-7-meth-oxy-1,8-bis-(2,4,6-tri-chloro-benzo-yl)naphthalene

In the title compound, C25H12Cl6O4, the two carbonyl groups are oriented in a same direction with respect to the naphthalene ring system and are situated roughly parallel to each other, while the two 2,4,6-tri-chloro-benzene rings are orientated in opposite directions with respect to the naphthalene ring system: the carbonyl C-(C=O)-C planes subtend dihedral angles of 45.54 (15) and 30.02 (15)° to the naphthalene ring system are. The dihedral angles formed by the carbonyl groups and the benzene rings show larger differences, the C=O vectors being inclined to the benzene rings by 46.39 (16) and 79.78 (16)°. An intra-molecular O-H⋯O=C hydrogen bond forms an S(6) ring motif. In the crystal, no effective inter-molecular hydrogen bonds are found; instead, O⋯Cl and C⋯Cl close contacts are observed along the 21 helical-axis direction. The Hirshfeld surface analysis reveals several weak interactions, the major contributor being Cl⋯H/H⋯Cl contacts.

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.

NMR 1H-Shielding Constants of Hydrogen-Bond Donor Reflect Manifestation of the Pauli Principle

NMR spectroscopy is one of the most useful methods for detection and characterization of hydrogen bond (H-bond) interactions in biological systems. For H bonds X-H···Y, where X and Y are O or N, it is generally believed that a decrease in ¹H-shielding constants relates to a shortening of H-bond donor-acceptor distance. Here we investigated computationally the trend of ¹H-shielding constants for hydrogen-bonded protons in a series of guanine C8-substituted GC pair model compounds as a function of the molecular structure. Furthermore, the electron density distribution around the hydrogen atom was analyzed with the Voronoi deformation density (VDD) method. Our findings demonstrate that ¹H-shielding values of the hydrogen bond are determined by the depletion of charge around the hydrogen atom, which stems from the fact that electrons obey the Pauli exclusion principle.

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 β-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.

A new fluorescent–colorimetric chemosensor for cobalt(ii) ions based on bis-benzimidazolium salt with three anthraquinone groups

A novel colorimetric chemosensor was prepared, and its recognition performance for Co²⁺ was investigated by the fluorescence method and color change.

High Resolution NMR Spectroscopy as a Structural and Analytical Tool for Unsaturated Lipids in Solution

Mono- and polyunsaturated lipids are widely distributed in Nature, and are structurally and functionally a diverse class of molecules with a variety of physicochemical, biological, medicinal and nutritional properties. High resolution NMR spectroscopic techniques including 1H-, 13C- and 31P-NMR have been successfully employed as a structural and analytical tool for unsaturated lipids. The objective of this review article is to provide: (i) an overview of the critical 1H-, 13C- and 31P-NMR parameters for structural and analytical investigations; (ii) an overview of various 1D and 2D NMR techniques that have been used for resonance assignments; (iii) selected analytical and structural studies with emphasis in the identification of major and minor unsaturated fatty acids in complex lipid extracts without the need for the isolation of the individual components; (iv) selected investigations of oxidation products of lipids; (v) applications in the emerging field of lipidomics; (vi) studies of protein-lipid interactions at a molecular level; (vii) practical considerations and (viii) an overview of future developments in the field.

NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds

For the purpose of this review, strong hydrogen bonds have been defined on the basis of experimental data, such as OH stretching wavenumbers, νOH, and OH chemical shifts, δOH (in the latter case, after correction for ring current effects). Limits for O-H···Y systems are taken as 2800 > νOH > 1800 cm-1, and 19 ppm > δOH > 15 ppm. Recent results as well as an account of theoretical advances are presented for a series of important classes of compounds such as β-diketone enols, β-thioxoketone enols, Mannich bases, proton sponges, quinoline N-oxides and diacid anions. The O···O distance has long been used as a parameter for hydrogen bond strength in O-H···O systems. On a broad scale, a correlation between OH stretching wavenumbers and O···O distances is observed, as demonstrated experimentally as well as theoretically, but for substituted β-diketone enols this correlation is relatively weak.

Energy of Intramolecular Hydrogen Bonding in ortho-Hydroxybenzaldehydes, Phenones and Quinones. Transfer of Aromaticity from ipso-Benzene Ring to the Enol System(s)

Intramolecular hydrogen bonding (HB) is one of the most studied noncovalent interactions of molecules. Many physical, spectral, and topological properties of compounds are under the influence of HB, and there are many parameters used to notice and to describe these changes. Hitherto, no general method of measurement of the energy of intramolecular hydrogen bond (EHB) has been put into effect. We propose the molecular tailoring approach (MTA) for EHB calculation, modified to apply it to Ar-O-H∙∙∙O=C systems. The method, based on quantum calculations, was checked earlier for hydroxycarbonyl-saturated compounds, and for structures with resonance-assisted hydrogen bonding (RAHB). For phenolic compounds, the accuracy, repeatability, and applicability of the method is now confirmed for nearly 140 structures. For each structure its aromaticity HOMA indices were calculated for the central (ipso) ring and for the quasiaromatic rings given by intramolecular HB. The comparison of calculated HB energies and values of estimated aromaticity indices allowed us to observe, in some substituted phenols and quinones, the phenomenon of transfer of aromaticity from the ipso-ring to the H-bonded ring via the effect of electron delocalization.

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.

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.

Toward a uniform description of hydrogen bonds and halogen bonds: correlations of interaction energies with various geometric, electronic and topological parameters

Correlations between interaction energies and various structural parameters were established to reveal the differences between hydrogen bonds and halogen bonds.