Ab initio conformational studies on diols and binary diol-water systems using DFT methods. Intramolecular hydrogen bonding and 1:1 complex formation with water

Nuclear quantum effects in gas-phase ethylene glycol

Path integral molecular simulations are used to explore the nuclear quantum effects (NQEs) on the structure, dihedral landscape and infrared spectrum of ethylene glycol. The simulations are carried out on a new reaction surface Hamiltonian-based model potential energy surface, with special focus on the role of the OCCO and HOCC dihedrals. In contrast with classical simulations, we analyse how the intramolecular interactions between the OH groups change due to zero-point effects as well as temperature. These are found to be weak. The NQEs on the free energy profile along the OCCO dihedral are analysed, where notable effects are seen at low temperatures and found to be correlated with the radii of gyration of the atoms. Finally, the power spectrum of the molecule from path integral simulations is compared with the experimental infrared spectrum, yielding a good agreement of band positions.

Subtle hydrogen bonds: benchmarking with OH stretching fundamentals of vicinal diols in the gas phase

The theoretical description of spectral signatures for weakly bound hydrogen contacts between alcohol groups is challenging and remains poorly characterised. By combining Raman jet spectroscopy with appropriately scaled harmonic DFT predictions and relaxation path analyses for 16 vicinal diols (ethylene glycol (ethane-1,2-diol), propane-1,2-diol, 3,3,3-trifluoro-propane-1,2-diol, rac-butane-2,3-diol, 2-methyl-propane-1,2-diol, 2-methyl-butane-2,3-diol, pinacol (2,3-dimethyl-butane-2,3-diol), 3-butene-1,2-diol, 1-phenyl-ethane-1,2-diol, trans-cyclobutane-1,2-diol, trans-cyclopentane-1,2-diol, trans-cyclohexane-1,2-diol, trans-cycloheptane-1,2-diol, cis-cyclohexane-1,2-diol, 1-(1-hydroxy-1-methylethyl)-cyclopentanol and [1,1'-bicyclopentyl]-1,1'-diol), 69 conformational assignments become possible in a two-tier approach with a 5 diol training and an 11 diol test set. The latter reveals systematic deviations for ring strain and secondary π interactions, but otherwise a remarkably robust correction and correlation model based on hybrid DFT with a minimally augmented triple-zeta basis set is obtained, whereas GGA functionals perform significantly worse. Raw experimental data in the 3560-3700 cm^-1 wavenumber range as well as computed geometries of all conformations invite further vibrational and structural benchmarking at the onset of hydrogen bonding. Beyond this diol-probed threshold, the accurate prediction of hydrogen bond induced shifts of different magnitudes remains one of the challenges for DFT functionals.

Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy

Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.

How many solvent molecules are required to solvate chiral 1,2-diols with hydrogen bonding solvents? A VCD spectroscopic study

A VCD spectroscopic analysis of selected model systems for solute–solvent interactions of chiral diols with hydrogen bonding solvents DMSO and ACN.

Can 2-X-Ethanols Form Intramolecular Hydrogen Bonds?

For 2-X-ethanols, where X = F, OH, or NH₂, the gauche conformer is favored over the trans conformer by at least 2 kcal/mol. Initially, this preference, ΔE, was attributed to an intramolecular hydrogen bond, IMHB, between the OH and X groups. Over the years, this conclusion has been challenged by two major arguments. One claim is that the entirety of ΔE can be accounted for by the gauche effect. Against this, calculations using five different methods show that the maximum contribution of the gauche effect to ΔE is less than 1 kcal/mol. A second argument employs the quantum theory of atoms in molecules to contend that the absence of a bond critical point (BCP) between the OH and X groups in 2-X-ethanols denotes the lack of an IMHB. By looking at the 2-X-ethanols at fixed XCCO torsional angles ranging from 0° to 60°, it is shown that the BCP criterion is inconsistent with other properties such as energy, bond lengths, and stretching frequencies. These inconsistencies are removed when the theory of noncovalent interactions is used. The IMHBs in 2-X-ethanols are found to be similar in form but smaller in magnitude than their intermolecular counterparts. This work concludes that 2-X-ethanols form IMHBs.

The viscous consequence of different trends in clustering of 1,2-diol and 1,n-diol molecules

This paper presents the molecular basis for the quite different behavior of the viscosity of 1,2- and 1,n-diols in dependence of the length of the alkyl part of the molecules of these compounds. The experimental data on the dipolar orientational effects revealed a decidedly different role of that part of the molecules in creating a microstructure of both the hydrogen-bonded liquids. In the case of 1,n-diols, an increase in the alkyl radical length, i.e. an increasing of the distance between the OH groups within the molecule, highly stimulates molecular self-assembly in form of gradually longer and wider ribbon-like clusters. This effect yields a quite important increase in the viscosity of 1,n-diols as n increases. In the case of 1,2-diols, due to gradual separation of the hydrophilic and hydrophobic parts of the molecules, the situation is quite different. Two OH groups situated on one of the ends of the hydrocarbon radical form the clusters of a micelle-like shape, however, the dipole moment is not compensated. Along with an increase in the hydrocarbon part in 1,2-diol molecules, one only observes an increase in the intermolecular consolidation within the micelle-like entities. This manifests as a gradual decrease in the polarity of these clusters. So, actually, there are no relevant reasons for essential differences of viscosities in the series of 1,2-diols.

How much different are thermochemical properties of enantiomers and their racemates? Thermochemical properties of enantiopure and racemate of methyl- and butyl lactates

This work is a contribution to the molecular understanding of the thermodynamic properties of the chiral compounds. A comprehensive thermochemical study of the liquid enantiopure and racemate pairs of optically active alkyl lactates has been performed. Vapor pressures of DL-(±)-, L-(-)-methyl-, and DL-(±)-, L-(-)-n-butyl esters of lactic acid were measured by the transpiration method. The liquid phase standard molar enthalpies of formation of these esters were measured by using the high-precision combustion calorimetry. The standard molar enthalpies of vaporization of alkyl lactates at 298.15 K were derived from vapor pressure temperature dependencies. Thermochemical data of these compounds were collected, evaluated, and tested for internal and external consistency. The high-level G4 quantum-chemical method was used for mutual validation of the experimental and theoretical gas phase enthalpies of formation of alkyl lactates. A critical review of the available thermochemical data for the liquid and crystalline enantiopure and racemate pairs of optically active compounds has been performed. Useful general trends in energetics of sublimation, vaporization, and formation of optically active compounds have been revealed. This knowledge is required for evaluation of new and already available experimental data for the chiral compounds, and it can be helpful to assess volatility or feasibility of processes to separate enantiomers.

Calculation of anharmonic effect on the dissociation of ethylene glycol

The unimolecular dissociation rate constants of ethylene glycol were examined using the MP2/6-311[Formula: see text]G(d,p) method based on the Rice–Ramsperger–Kassel–Marcus (RRKM) theory. The effect of anharmonicity on the dissociation rate constants was evaluated at 500–4000[Formula: see text]K temperatures of the canonical system and 25,182–50,235[Formula: see text]cm[Formula: see text] total energies of the microcanonical system. The comparison of the results showed that the H2O elimination reaction played a critical role in the decomposition processes of ethylene glycol. The results of the rate constant calculations indicated that the H2O elimination reaction dominated at low temperatures, whereas the direct C–C bond dissociation reaction (CH2OHCH2OH [Formula: see text] CH2OH[Formula: see text][Formula: see text][Formula: see text]CH2OH) dominated at high temperatures. For channel 1, CH2OH[Formula: see text][Formula: see text][Formula: see text]CH2OH, the anharmonic effect of the canonical system was not observed, while it became more obvious with the increasing total energies in the microcanonical system. For channels 2–5, CH3CHO[Formula: see text][Formula: see text][Formula: see text]H2O, CH2CHOH[Formula: see text][Formula: see text][Formula: see text]H2O, CH3OH[Formula: see text][Formula: see text][Formula: see text]CHOH, and CH2OHCHO[Formula: see text][Formula: see text][Formula: see text]H2, the anharmonic effect of canonical and microcanonical systems became more obvious with increasing temperatures and total energies. The comparison showed that, for channels 1 and 4, C–C bond dissociation and the anharmonic effect of the microcanonical system were more evident, whereas the anharmonic effect of the canonical system was more predominant for channels 2 (CH3CHO[Formula: see text][Formula: see text][Formula: see text]H2O), 3 (CH2CHOH[Formula: see text][Formula: see text][Formula: see text]H2O), and 5 (CH2OHCHO[Formula: see text][Formula: see text][Formula: see text]H2).

Infrared absorption of methanol-water clusters (CH3OH)n(H2O), n = 1-4, recorded with the VUV-ionization/IR-depletion technique

We recorded infrared (IR) spectra in the CH- and OH-stretching regions of size-selected clusters of methanol (M) with one water molecule (W), represented as M_nW, n = 1-4, in a pulsed supersonic jet using the photoionization/IR-depletion technique. Vacuum ultraviolet emission at 118 nm served as the source of ionization in a time-of-flight mass spectrometer to detect clusters M_nW as protonated forms M_n-1WH⁺. The variations in intensities of M_n-1WH⁺ were monitored as the wavelength of the IR laser light was tuned across the range 2700-3800 cm^-1. IR spectra of size-selected clusters were obtained on processing of the observed action spectra of the related cluster-ions according to a mechanism that takes into account the production and loss of each cluster due to IR photodissociation. Spectra of methanol-water clusters in the OH region show significant variations as the number of methanol molecules increases, whereas those in the CH region are similar for all clusters. Scaled harmonic vibrational wavenumbers and relative IR intensities predicted with the M06-2X/aug-cc-pVTZ method for the methanol-water clusters are consistent with our experimental results. For dimers, absorption bands of a structure WM with H₂O as a hydrogen-bond donor were observed at 3570, 3682, and 3722 cm^-1, whereas weak bands of MW with methanol as a hydrogen-bond donor were observed at 3611 and 3753 cm^-1. For M₂W, the free OH band of H₂O was observed at 3721 cm^-1, whereas a broad feature was deconvoluted to three bands near 3425, 3472, and 3536 cm^-1, corresponding to the three hydrogen-bonded OH-stretching modes in a cyclic structure. For M₃W, the free OH shifted to 3715 cm^-1, and the hydrogen-bonded OH-stretching bands became much broader, with a weak feature near 3179 cm^-1 corresponding to the symmetric OH-stretching mode of a cyclic structure. For M₄W, the observed spectrum agrees unsatisfactorily with predictions for the most stable cyclic structure, indicating significant contributions from branched isomers, which is distinctly different from M₅ of which the cyclic form dominates.

Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet

Adsorption of carbohydrates on graphene has the potential to improve graphene dispersibility in water. Here we assess the ability of DFTB-based and NDDO-based quantum chemical methods to model β-cyclodextrin conformations and interactions with graphene.

Free-energy patterns in inclusion complexes: the relevance of non-included moieties in the stability constants

A MD/PMF-based procedure is designed for quantification of the interaction and respective components, guiding complex formation in water between β-CD and several naphthalene derivatives, highlighting the relevance of substituents.

Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of 1 H NMR chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen-bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge-including atomic orbital method to geometry-optimized conformers. For certain conformers, intramolecular OH···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms-in-molecules and non-covalent interaction plots. The computed OH and CH proton shifts for the diol and the two complexes correlate well with values obtained by analysing data from the NMR titration of the diols in benzene against pyridine. Shift values for the diols in neat pyridine are calculated by weighting the shifts of the various protons in the three forms (free diol, 1 : 1 and 1 : 2 diol/pyridine complexes) according to the experimentally determined association constants. The results are in good agreement with those observed, and after empirical scaling, the root mean square difference is 0.18 ppm. Copyright © 2016 John Wiley & Sons, Ltd.

Conformational stability and intramolecular hydrogen bonding in 1,2-ethanediol and 1,4-butanediol

The gas-phase infrared spectra of 1,2-ED and 1,4-BD have been recorded at three different temperatures using a multipass gas cell of 6 m optical path length. DFT calculation has also been carried out using 6-311++G** and aug-cc-pVDZ basis sets to look for the existence of intramolecular hydrogen bonding in them from the red shift and infrared absorption intensity enhancement of the bonded O-H band compared to that of the free O-H band. Equilibrium population analysis with 10 conformers of 1,2-ED and 1,4-BD at experimental temperatures were carried out for the reconstruction of the observed vibrational spectra at that temperature using standard statistical relationships. The most abundant conformer at experimental temperatures was identified. In 1,2-ED a red shift of 45 cm(-1) in the intramolecularly interacting O-H stretching vibrational band position and no significant intensity enhancement compared to that of the free O-H have been observed. On the contrary, in one of the hydrogen-bonded conformers of 1,4-BD, a 124 cm(-1) red shift in the O-H stretching frequency and a 8.5 times intensity enhancement for the "bonded" O-H compared to that of the "free" O-H is seen. On the basis of this comparative study, we have concluded that strong intramolecular hydrogen bonding exists in 1,4-BD. But there appears to be weak intramolecular hydrogen bonding in 1,2-ED at temperatures of 303, 313, and 323 K in the gas phase. We have found that most stable hydrogen-bonded conformers of 1,4-BD are less populated than some of the non-hydrogen-bonded conformers. Even for the 1,4-BD, the relative population of the g'GG'Gt conformer, which has a strong intramolecular hydrogen bond, is less than what is predicted. Perhaps the intramolecular hydrogen bond plays a less significant role in the relative stability of the various conformers than what has been predicted from calculations and prevails in the literature.

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond

In this discussion, we show that a static definition of a ‘bond’ is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan,Phys. Chem. Chem. Phys.2009,11, 8974) which showed a practical way to differentiate ‘hydrogen bonding’ from ‘van der Waals interaction’. We report results fromab initioand atoms in molecules theoretical calculations for a series of Rg⋯HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg⋯HX/DX complexes show that Rg⋯DX could have a ‘deuterium bond’ even when Rg⋯HX is not ‘hydrogen bonded’, according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an ‘intra-molecular hydrogen bond’ can appear during a normal mode vibration which is dominated by the O⋯O stretching, though a ‘bond’ is not found in the equilibrium structure. This dynamical ‘bond’ formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration ‘breaks’ an existing bond and in the later case, a vibration leads to ‘bond’ formation. In both cases, the molecule/complex stays bound irrespective of what happens to this ‘hydrogen bond’. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunanet al. Pure. Appl. Chem.2011,831637) and justify the inclusive nature of the definition.

Competing intramolecular vs. intermolecular hydrogen bonds in solution

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.

Molecular structure and hydrogen bonding in pure liquid ethylene glycol and ethylene glycol-water mixtures studied using NIR spectroscopy

The molecular structure and hydrogen bonding of ethylene glycol (EG) and EG-water mixtures in the liquid phase were studied by using near-infrared (NIR) spectroscopy. The spectra were evaluated using a two-dimensional (2D) correlation approach, moving-window 2D correlation analysis and chemometric methods. The minor changes for the CH stretching bands indicate that the structures of pure liquid EG and EG-water mixtures are determined by the intermolecular hydrogen bonding through the OH groups. The analysis of the ν2 + ν3 combination band of water reveals that in EG-rich solutions the molecules of water are predominantly bonded with two molecules of EG and this cooperative hydrogen bonding is stronger than that in bulk water. Further increase in the water content leads to formation of small water clusters around OH groups of EG. Comparing results for the binary mixtures of water with different organic solvents one can conclude that the total amount and distribution of the polar groups are the most important factors determining the solubility of water in the organic phase. The distribution of these groups depends on the length and structure of the hydrocarbon chain. Due to high population and relatively uniform distribution of the OH groups of EG water has unlimited solubility in liquid EG.

Theoretical and experimental investigation of the oxidized and oxygenated forms of pyrocatechuic acid (2,3-dihydroxybenzoic acid)

The catecholic derivative 2,3-dihydroxybenzoic acid (2,3-DHBA or pyrocatechuic acid) represents a diversity of actions in enzymatic processes. In the present study DFT calculations (at the B3LYP/TZVP level of theory) have been performed for neutral 2,3DHBA and its dimer (models 1-1a), several semiquinone forms of 2,3-DHBA, namely the neutral (models 2-4), the monoionized (models 5-7), the di-ionized (models 8) and the dimer 7a. The more stable species in each case are those with the carboxyl group protonated. Oxygenated adducts were also constructed (models 10-15) in which the dioxygen is either H-bonded to the catecholic or carboxylic hydrogen or it is concerned to act on the intradiol or extradiol carbon atoms. The side-on placement of O(2) on C(2) facilitates the intradiol C-C cleavage. Protonation of the oxygenated on C(1) adduct leads to decarboxylation of 2,3-DHBA. Isolation in the solid state and characterization by ESMS, IR, NMR, electronic spectra of the blue-green oxidized product of 2,3-DHBA (solid 1) supports the possibility of the existence of the semiquinone form or the hydroperoxide-adduct. Experimental spectroscopic data are correlated to the calculated spectroscopic parameters. In the ESMS the decarboxylation and degradation products as well a peroxo-adduct have been detected. Oxygenated species may also account for the plethora of redox signals in the cyclic voltammograms of solid 1 (in DMSO solutions).

Theoretical studies of the solvent effect on the conformation of the HO-C-C-X (X = F, NH2, NO2) moiety with competing intra- and intermolecular hydrogen bonds

Theoretical calculations up to the ab initio IEF-PCM/CCSD(T)/CBS//IEF-PCM/B3LYP/6-311++G** and IEF-PCM/B97D/aug-cc-pvtz levels have been performed for 2X-ethanol and 2X-phenol systems with X = F, NH(2), NO(2) in chloroform and aqueous solution. The calculated relative free energies by means of the IEF-PCM continuum dielectric method do not differ very much at the DFT and ab initio levels. Application of explicit solvent models and the FEP/MC method for determining relative solvation free energies causes, however, large deviations in the predicted equilibrium compositions, although the predominant conformation for the solute is generally in agreement with that from the corresponding IEF-PCM calculations. Existence of an intramolecular hydrogen bond (HB structure) for species with the HO-C-C-X moiety is preferred compared with a conformation when the hydrogen bond is disrupted (NoHB) for the considered F- and NO(2)-substituted molecules both in chloroform and aqueous solution. For 2NH(2)-ethanol, the HB structure is predominant in chloroform, whereas the 93:7 ratio for the OCCN trans/gauche species was obtained in aqueous solution. 2NH(2)-phenol exhibits a subtle equilibrium of the HB and NoHB conformations in both solvents. Potential of mean force calculations predict about a 10% solute association for the trans 2NH(2)-ethanol solute even in the fairly dilute 0.22 molar solution, whereas direct MC simulations do not support the maintenance of a doubly hydrogen-bonded dimer. Aqueous solution characteristics, as coordination numbers and numbers of strongly bound water molecules to the solute at T = 298 K and p = 1 atm, correspond reasonably to the derived molecular structures.

Gas-phase basicities of polyfunctional molecules. Part 2: Saturated basic sites

The present article is the second part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules. The first part of the review (Mass Spectrom. Rev., 2007, 26:775-835) was devoted to the description of the physico-chemical concepts and of the methods of determination, both experimental and theoretical, of gas-phase basicity. Several clues concerning the structural and energetic aspects of the protonation of isolated species have been emphasized. In the present article, specific examples are examined. The field of investigation is limited to molecules containing a "saturated" basic site, that is, nitrogen or oxygen atoms engaged in simple σ bonds with their neighboring. Aliphatic, cyclic and aromatic poly-amines, amino alcohols, alcohols, ethers, and hydroxyl-ethers, are successively presented.

On the perturbation of the H-bonding interaction in ethylene glycol clusters upon hydration

Ab initio and density functional methods have been employed to study the structure, stability, and spectral properties of various ethylene glycol (EG(m)) and ethylene glycol-water (EG(m)W(n)) (m = 1-3, n = 1-4) clusters. The effective fragment potential (EFP) approach was used to explore various possible EG(m)W(n) clusters. Calculated interaction energies of EG(m)W(n) clusters confirm that the hydrogen-bonding interaction between EG molecules is perturbed by the presence of water molecules and vice versa. Further, energy decomposition analysis shows that both electrostatic and polarization interactions predominantly contribute to the stability of these clusters. It was found from the same analysis that ethylene glycol-water interaction is predominant over the ethylene glycol-ethylene glycol and water-water interactions. Overall, the results clearly illustrate that the presence of water disrupts the ethylene glycol-ethylene glycol hydrogen bonds.

Theoretical calculation of the OH vibrational overtone spectra of 1,5-pentanediol and 1,6-hexanediol

It is well-known that intramolecular hydrogen bonding affects the relative energetics of conformers, as well as the OH stretching peak positions, intensities, and width. In this study we simulated the Δv(OH) = 3, 4 overtone spectra of 1,5-pentanediol (PeD) and 1,6-hexanediol (HD) using the peak positions, intensities, and width calculated from the B3LYP/6-31+G(d,p) method. Furthermore, room temperature free energy calculations were performed using B3LYP/6-31+G(d,p) MP2/6-31+G(d,p), and MP2/6-311++G(3df,3pd) to obtain the relative population of the conformers. From the calculation of 109 and 381 distinct conformers for PeD and HD, respectively, we find that for these long chain diols the intramolecular hydrogen bonded conformers are not the most dominant conformation at room temperature. This is in stark contrast with shorter chain diols such as ethylene glycol for which the hydrogen bonded conformer dominates the population at room temperature. On the other hand, we found that the correlation between the hydrogen bonded OH red shift versus the homogeneous width, Γ = 0.0155(Δω)(1.36), which was derived for shorter chain diols, is valid even for these longer chain diols. We also showed that the intramolecular hydrogen bonded OH initially decays through the CCOH torsion and COH bending mode no matter how long the alkanediol chain length is for 1,n-alkanediols for n up to 6.

Intramolecular OH···π interactions in alkenols and alkynols

The vibrational overtone spectra of propargyl alcohol (prop-2-yn-1-ol, PA), allyl alcohol (prop-2-en-1-ol, AA), propargyl carbinol (but-3-yn-1-ol, PC) and allyl carbinol (but-3-en-1-ol, AC) were recorded with intracavity laser photoacoustic spectroscopy (ICL-PAS) in the Δv(OH) = 3, 4 and 5 regions for propargyl alcohol and allyl alcohol and in the Δv(OH) = 4 and 5 regions for propargyl carbinol and allyl carbinol. Local mode anharmonic oscillator calculations were performed with explicitly correlated coupled cluster methods to guide spectral assignment. Atoms in molecules (AIM) and non-covalent interactions (NCI) calculations were carried out to analyze the interactions between the OH-group and the π-electrons of the carbon-carbon multiple bonds. We ascertain the effect of the carbon chain length and saturation on the conformation and spectroscopy of the four alcohols in relation to intramolecular hydrogen bonding interactions.

Wavelet Transform for Spectroscopic Analysis: Application to Diols in Water

Wavelet transform has been used to correlate spectroscopic and structural properties from trajectories obtained by ab initio molecular dynamics simulations. This method has been applied to hydrogen bond dynamics of glycols in heavy water solutions, showing how the stretching frequency of the intramolecular O-H bond changes with the intermolecular hydrogen-bond distance. The resulting wavelet spectrograms have been interpreted according to H-bond strength and stability.

Universal prediction of intramolecular hydrogen bonds in organic crystals

A complete exploration of intramolecular hydrogen bonds (IHBs) has been undertaken using a combination of statistical analyses of the Cambridge Structural Database and computation of ab initio interaction energies for prototypical hydrogen-bonded fragments. Notable correlations have been revealed between computed energies, hydrogen-bond geometries, donor and acceptor chemistry, and frequencies of occurrence. Significantly, we find that 95% of all observed IHBs correspond to the five-, six- or seven-membered rings. Our method to predict a propensity for hydrogen-bond occurrence in a crystal has been adapted for such IHBs, applying topological and chemical descriptors derived from our findings. In contrast to intermolecular hydrogen bonding, it is found that IHBs can be predicted across the complete chemical landscape from a single optimized probability model, which is presented. Predictivity of 85% has been obtained for generic organic structures, which can exceed 90% for discrete classes of IHB.

Theoretical and experimental investigation of the semiquinone forms of protocatechuic acid. The effect of manganese

Ten oxidized, oxygenated and dimeric forms of protocatechuic acid (PCA, 3,4-dihydroxybenzoic acid, 3,4-DHBA) have been studied using DFT calculations (at the B3LYP/TZVP level of theory) and their structural and spectroscopic parameters (electronic transitions, NMR resonances) have been calculated. Combination with experimental results (under anaerobic or aerobic environment) determines the conditions for the existence of protonated, fully deprotonate and/or oxygenated semiquinones of PCA. Several energy optimized conformers containing manganese-(PCA-semiquinones) and water or/and peroxo-groups have been drawn (species 11-16) and their structural and spectroscopic properties have been calculated at the same level of theory. Experimental parallel to the theoretical results provide evidence for the existence of Mn(II)- and Mn(III)-[PCA-semiquinone] as well the conditions of dioxygen activation. Two of the blue solids (17 and 18) isolated from these solutions, have been characterized. Elemental analyzes, TGA, IR and ESR spectra support the formulation Mn(2)(PCA)(2)(O(2))(OH)(2)(AcO)(ClO(4))(2)(H(2)O)(3) (17), and Mn(2)(PCA)(2)(O(2))(2)(OH)(2)(AcO)H(2)O (18). Their ESR spectra, in solution (blue solutions), are almost identical and indicative of Mn(IV) existence. From the whole investigation, the activation of dioxygen by the PCA, its relocation on manganese and the oxidation of the metal ion have been provided.

Conformational cooling dynamics in matrix-isolated 1,3-butanediol

The complete conformational space of monomeric 1,3-butanediol has been characterized theoretically, and 73 unique stable conformers were found at the MP2/6-311++G(d,p) level. These were classified into nine families whose members share the same heavy atom backbone configurations and differ in the hydrogen atom orientations. The first and third most populated backbone families are governed by the formation of an intramolecular hydrogen bond; however, the second precludes this type of interaction and was frequently overlooked in previous studies. Its stability is determined by the relatively high entropy of its main conformers. The hydrogen bonding of four of the most important conformers was characterized by means of atoms in molecules (AIM, also known as QTAIM) and natural bond orbital (NBO) analyses. Using appropriate isodesmic reactions, hydrogen bonding energy stabilizations of 12-14 kJ mol(-1) have been found. Experimentally, monomeric molecules of 1,3-butanediol were isolated in low-temperature inert matrixes, and their infrared spectra were analyzed from the viewpoint of the conformational distribution. All the relevant transition states for the conformational interconversion reaction paths were characterized at the same level of theory to interpret the conformational cooling dynamics observed in the low-temperature matrixes. The energy barriers for rotation of the OH groups were calculated to be very low (<3 kJ mol(-1)). These barriers were overcome in the experiments at 10 K (Ar matrix), in the process of matrix deposition, and population within each family was reduced to the most stable conformers. Further increase in the substrate temperature (up to 40 K, Xe matrix) resulted in conformational cooling where the medium-height barriers (approximately 13 kJ mol(-1)) could be surmounted and all conformational population converted to the ground conformational state. Remarkably, this state turned to consist of two forms of the most stable hydrogen bonded family, which were predicted by calculations to be accidentally degenerated and were found in the annealed matrix in equal amounts. All of these experimentally observed conformational cooling processes were analyzed and supported by full agreement with the theoretical calculations.