Intramolecular interactions in ortho-substituted phenols: survey of DFT-B3LYP calculated data

Dynamic Role of the Intramolecular Hydrogen Bonding in the S1 State Relaxation Dynamics Revealed by the Direct Measurement of the Mode-Dependent Internal Conversion Rate of 2-Chlorophenol and 2-Chlorothiophenol

The dynamic role of the intramolecular hydrogen bond in the S1 relaxation of cis-2-chlorophenol (2-CP) or cis-2-chlorothiophenol (2-CTP) has been investigated in a state-specific manner. Whereas ultrafast internal conversion is dominant for 2-CP, the H-tunneling competes with internal conversion for 2-CTP even at the S1 origin. The S0-S1 internal conversion rate of 2-CTP could be directly measured from the S1 lifetimes of 2-CTP-d1 (Cl-C6H4-SD) as the D-tunneling is kinetically blocked, allowing distinct estimations of tunneling and internal conversion rates with increasing the energy. The internal conversion rate of 2-CTP increases by two times at the out-of-plane torsional mode excitation, suggesting that the internal conversion is facilitated at the nonplanar geometry. It then sharply increases at ∼600 cm-1, indicating that the S1/S0 conical intersection is readily accessible at the extended C-Cl bond length. The strength of the intramolecular hydrogen bond should be responsible for the distinct dynamic behaviors of 2-CP and 2-CTP.

Computational study of acylphloroglucinols: an investigation with many branches

Acylphloroglucinols (ACPLs) are a broad class of compounds structurally derived from phloroglucinol and characterised by the presence of a CRO group. They are interesting for their biological activities and their potentialities as lead compounds in drug development. The current review considers a series of works which, altogether, sum up to a systematic computational study of ACPLs in vacuo and in three solvents – chloroform, acetonitrile and water. An initial set of studies, focusing on ACPLs as a class and utilising an adequately representative selection of molecules, identified patterns in the conformational preferences and molecular properties of ACPLs, which appear valid for the whole class or for specific subclasses such as monomeric ACPLs, dimeric ACPLs, ACPLs with substituents containing C=C double bonds, etc. The validity of the identified patterns was further verified through the study of additional and significantly different ACPL molecules, as well as other molecular structures containing ACPL units. Furthermore, the computational study of ACPLs proved interesting for the insights into the factors stabilising their conformers, first of all intramolecular hydrogen bonding, which plays dominant roles in determining conformational preferences and energetics. The current review outlines the objectives, approaches and main results of these studies. The obtained information may be relevant for further studies aimed at a better understanding of the molecular bases of the biological activities of ACPLs.

The intramolecular H-bonding effect on the growth and stability of Schiff-base surface covalent organic frameworks

The introduction of intramolecular H-bonding by adding -OH functionalities adjacent to the Schiff base centers is considered to be a useful strategy to enhance the stability and crystallinity of bulk covalent organic frameworks (COFs). However, the influence of intramolecular H-bonding on the synthesis of surface COFs (SCOFs) have been barely explored. Herein, SCOFs based on the Schiff-base reaction between 1,3,5-tris(4-aminophenyl)benzene (TAPB) and terephthalaldehydes with symmetry or asymmetrically substituted hydroxyl functional groups are designed. In the absence of a solvent, hydroxyl substituents can be easily oxidized; thus argon protection is required to obtain high-quality SCOFs. Besides, an extended network with uniform pores can be achieved in spite of the symmetry of substituents. Both experimental results and theoretical calculations show that the influence of intramolecular hydrogen bonding on surface synthesis is not as important as that in bulk phase synthesis because the substrate itself can lead to the complanation of adsorbed molecules. The existence of intramolecular H-bonding can enhance the stability of the network in both acid and alkali environments.

Intramolecular Hydrogen Bonding and Conformational Preferences of Arzanol-An Antioxidant Acylphloroglucinol

Arzanol is a naturally-occurring prenylated acylphloroglucinol isolated from Helichrysum italicum and exhibiting anti-oxidant, antibiotic and antiviral activities. The molecule contains an α-pyrone moiety attached to the phloroglucinol moiety through a methylene bridge. The presence of several hydrogen bond donor or acceptor sites makes intramolecular hydrogen bonding patterns the dominant stabilising factor. Conformers with all the possible different hydrogen bonding patterns were calculated at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels with fully relaxed geometry in vacuo and in three solvents—chloroform, acetonitrile and water (these levels being chosen to enable comparisons with previous studies on acylphloroglucinols). Calculations in solution were performed with the Polarisable Continuum Model. The results show that the lowest energy conformers have the highest number of stronger intramolecular hydrogen bonds. The influence of intramolecular hydrogen bonding patterns on the other molecular properties is also analysed.

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.

Are the intramolecular O-H···F and O-H···Cl hydrogen bonds maintained in solution? A theoretical study

The present case study aims at calculating the equilibrium conformer compositions for 2X-ethanol and 2X-phenol (X = F, Cl) in solution, and exploring the effect of the applied theoretical method and basis set on the obtained results, as well as considering the usefulness of the continuum solvent approach in comparison with the explicit solvent Monte Carlo model utilizing the free energy perturbation method. Gas-phase optimizations at the DFT/B97D/aug-cc-pvtz and ab initio MP2/aug-cc-pvtz levels predicted structures in good agreement with the available experimental data for three test molecules. Because in-solution geometries change only slightly according to the IEF-PCM continuum solvent calculations in carbon tetrachloride and water, the two theoretical levels were applied further on, and complete basis set (CBS) relative internal free energies were estimated for the conformers under study. The predicted OCCF gauche/trans ratio for 2F-ethanol was well reproduced in comparison with available experimental compositions. The predominant gauche structure maintains an intramolecular hydrogen bond in carbon tetrachloride (HB structure), whereas HB and NoHB gauche conformers appear in nearly the same fraction in aqueous solution. The internally hydrogen-bonded conformer is predominant also for 2X-phenol species, as calculated on the basis of relative CBS internal free energies and IEF-PCM and FEP/MC solvation free energies. Use of a trihydrate supermolecule model for 2F-ethanol conformers leads to the prediction of the aqueous-solution composition in contrast to the experiment. Solution structure modeling predicts weak hydrogen-bond formation capacity for both the covalently bound F and Cl atoms, even in conformations where they are fully exposed to hydration.

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.

Scales of oxidation potentials, pK(a), and BDE of various hydroquinones and catechols in DMSO

The one-electron oxidation potentials [E(ox)(NHE)(H(2)Q)], pK(a) (pK(a1) and pK(a2)) values, and bond dissociation energies (BDE(1) and BDE(2)) of 118 important p- and o-dihydroquinones in DMSO were systematically predicted for the first time by using DFT method and the PCM cluster continuum model. The calculated results agree well with the available experimental determinations. The study shows that all the five thermodynamic parameters correlate well with the Hammett substituent parameters σ(p) (for p-H(2)Q, E(ox)(NHE)(H(2)Q(·+)/H(2)Q) = 1.66Σσ(p) + 0.54, pK(a1) = -5.69Σσ(p) + 16.54, pK(a2) = -5.19Σσ(p) + 23.91, BDE(1) = 3.43Σσ(p) + 82.29, BDE(2) = 4.64Σσ(p) + 67.70 and for o-H(2)Q, E(ox)(NHE)(H(2)Q(·+)/H(2)Q) = 1.85Σσ(p) + 0.46, pK(a1) = -5.53Σσ(p) + 13.28, pK(a2) = -5.24Σσ(p) + 26.70, BDE(1) = 3.54Σσ(p) + 82.08, BDE(2) = 3.82Σσ(p) + 75.93), which hints that we can get these thermodynamic parameters as long as the structure of the hydroquinones were known. The comparisons of the calculated five thermodynamic parameters between p-hydroquinones and o-hydroquinones and the number of the phenyl ring effects on these thermodynamic parameters were also studied. At last, intramolecular hydrogen bond energies in hydroquinones at neutral, radical cation, radical, anion different state were systematically calculated and analyzed. Combined with the papers published in our group before, we will have a systematic thermodynamic picture of the transfer details between different kinds of quinones and corresponding hydroquinones, which strongly promote the fast development of the understanding and applications of quinones.

An NMR, IR and theoretical investigation of (1)H chemical shifts and hydrogen bonding in phenols

The change in (1)H NMR chemical shifts upon hydrogen bonding was investigated using both experimental and theoretical methods. The (1)H NMR spectra of a number of phenols were recorded in CDCl(3) and DMSO solvents. For phenol, 2- and 4-cyanophenol and 2-nitrophenol the OH chemical shifts were measured as a function of concentration in CDCl(3). The plots were all linear with concentration, the gradients varying from 0.940 (phenol) to 7.85 (4-cyanophenol) ppm/M because of competing inter- and intramolecular hydrogen bonding. Ab initio calculations of a model acetone/phenol system showed that the OH shielding was linear with the H...O=C distance (R) for R < 2.1 A with a shielding coefficient of - 7.8 ppm/A and proportional to cos(2)phi where phi is the H...O=C--C dihedral angle. Other geometrical parameters had little effect. It was also found that the nuclear shielding profile is unrelated to the hydrogen bonding energy profile. The dependence of the OH chemical shift on the pi density on the oxygen atom was determined as ca 40 ppm/pi electron. This factor is similar to that for NH but four times the value for sp(2) hybridized carbon atoms. The introduction of these effects into the CHARGE programme allowed the calculation of the (1)H chemical shifts of the compounds studied. The CHARGE calculations were compared with those from the ACD database and from GIAO calculations. The CHARGE calculations were more accurate than other calculations both when all the shifts were considered and also when the OH shifts were excluded. The calculations from the ACD and GIAO approaches were reasonable when the OH shifts were excluded but not as good when all the shifts were considered. The poor treatment of the OH shifts in the GIAO calculations is very likely due to the lack of explicit solvent effects in these calculations.

Molecular Structures and Properties of the Complete Series of Bromophenols: Density Functional Theory Calculations

The complete series of 19 bromophenols have been studied by density functional theory (DFT) calculations at the B3LYP/6-311G++(d,p) level. The molecular structures and properties of bromophenols are strongly influenced by intramolecular hydrogen bonding of ortho-bromine, steric and inductive effects of substituted bromine, and other intramolecular electrostatic interactions. Systematic trends in several structural parameters and molecular properties of bromophenols have been found with the increasing number of bromine substitutions, including increase in O-H bond length, decrease in C-O bond length, red shift in O-H stretching frequency, and blue shift in O-H torsional frequency. Correlations among several key molecular parameters as well as those with available aqueous pKa values are examined. Comparisons with chlorophenols have indicated that the inductive effect of substituted bromine appears larger and bromophenols are slightly stronger acids than chlorophenols.

PCM Study of the Solvent and Substituent Effects on the Conformers, Intramolecular Hydrogen Bonds and Bond Dissociation Enthalpies of 2-Substituted Phenols

A PCM continuum model, at the DFT/B3LYP level, is used to study the solvent and substituent effects on the conformers, intramolecular hydrogen bond (HB) enthalpies, (Delta H(intra)s), and O-H bond dissociation enthalpies, (BDEs), in 2-substituted phenols, 2-X-ArOH, in the liquid phase. Two electron-donating (edg) and three electron-withdrawing (ewg) substituents are chosen, involved in a variety of biochemical transformations. Seven solvents, differing in their H-bonding ability and polarity, are selected to model different environmental situations. Very good correlations are found between the computed R(O-H) and nu(O-H) values in solution for all non-HB 2-X-ArOH, showing that the former can be used as an universal molecular descriptor for the latter and vice-versa. In all 2-X-ArOH, the HB parent conformer is the most stable in all media, closely matching frequency experimental data in CCl4. However, for all 2-X-ArO*, the most stable conformer either forms a "reverse"-HB or a HB is not formed, due to the long distance or steric effects. Changes in the stability, in solution, are observed for some of the 2-X-ArO* conformers. The intramolecular HB-strength in solution, Delta H(S,intra), varies significantly with the size of the HB ring formed and the nature of the substituents. Reasonable correlations, derived between the two energetic parameters (BDE(aw,sol) and Delta H(S,intra)) and the solvent ( and a), and/or molecular, [R(O-H) and nu(O-H)] ones, allow for an approximate estimation of the two former from the four latter. 2-X(edg) decrease BDEs (hence, increase the antioxidant efficiency of the solute, too) in all media; 2-X(ewg) present an opposite result. Moreover, an isodesmic reactions study affords total stabilization effect (TSE) values (identical to the Delta[BDE(aw)]s), which are mainly governed by the stabilization of the phenolic radical (SPR) than that of the parent molecule (SPP). Quantitative correlations between the two effects in the TSE in both the gas and the liquid phases are also given. Unlike in the protic solvents, the better stabilization of the radical than the parent species, derived for the 2-X(edg)-ArOH in the aprotic, apolar, and/or low polar solvents, could account well for their smaller BDE(sol)s. An effective antioxidant in solution should involve either one of the two edg in any one of the two latter solvents.

Theoretical vibrational analysis of monohalogenated phenols

Harmonic vibrational frequencies of a representative series of X-phenols (X = F, Cl, Br) in ortho, meta and para positions are determined using density functional theory (B3LYP) in conjunction with 6-311 + + G(d,p), 6-311 + + G(2d,2p), and 6-311 + + G(2df,2p) basis sets. Their complete and clear-cut vibrational assignment based on the concept of the potential energy distribution is carried out. Such assignment allows to resolve a number of uncertainties appeared in the previous studies and to propose a new explanation of frequency alterations of particular vibrational modes in this series.