Effect of adjoining aromatic ring upon excited state proton transfer, o-hydroxybenzaldehyde

Influence of Internal Angular Arrangement on Pnicogen Bond Strength

The three Z-X covalent bonds of a ZX3 unit (Z = P, As, Sb, Bi) are normally arranged in a pyramidal structure. Quantum chemical calculations show that pnicogen bonds (ZBs) to the central Z are weakened if ZX3 is flattened, as in the opening of an umbrella. The partial closing of the umbrella has the opposite effect of substantially strengthening these ZBs, even amounting to a 2- or 3-fold magnification in certain cases. The strongest such bonds, wherein Sb and Bi are in a strained configuration within a ZO3CH model system, have interaction energies of 20 kcal/mol with an NH3 base. Most of these systems, whether flattened or more pyramidal, are capable of engaging in three ZBs simultaneously, despite a certain amount of negative cooperativity.

Transition between the Noncovalency and Covalency of σ-Hole Bonds

The properties of the bond between a N-ligand and a Lewis acid containing a σ-hole are studied by quantum chemical methods. Interactions considered include pnicogen bonds involving SbX5, PX5, and PX3, where X represents any of the halogen atoms F, Cl, Br, or I. Also studied are the tetrel bonds of PbX4 and SiX4, as well as the chalcogen bond involving TeOX4. Both NH3 and NCH are applied as two possible bases of differing potency. Some of the bonds are very strong with interaction energies easily exceeding 25 kcal/mol and with AIM bond critical point densities much higher than 0.04 au, suggesting their classification as coordinate covalent bonds. The pentavalent SbX5 and PX5 fall into this category when combined with NH3, as does TeOX4. Although the tetrel bonds involving PbX4 are only slightly weaker, they are probably better viewed as a strong noncovalent bond on the cusp of covalency. Changing the internal bonding of hypervalent SbX5 to the more conventional SbX3 weakens the interaction to a classical noncovalent pnicogen bond. Reducing the base nucleophilicity from NH3 to NCH weakens the bonds so that they are clearly noncovalent.

Influence of Internal Noncovalent Bonds on Rotational Dynamics

While a good deal of information has accumulated concerning the manner in which an intramolecular noncovalent bond can affect the relative energies of various conformers, less is known about how such bonds might affect the dynamics of interconversion between them. A series of molecules are constructed in which symmetrically equivalent conformers containing a noncovalent bond can be interconverted by a bond rotation, the energy barrier to which is computed by quantum chemical methods. The rotation of a CF3 group attached to a phenyl ring is speeded up if a Se··F chalcogen bond can be formed with a SeH or SeF group placed in an ortho position, a bond that is present in and stabilizes the rotational transition state. The analogous SnF3 group can, on the other hand, engage in a Sn··Se tetrel bond in its global minimum. The energetic cost of breakage of this bond is not fully compensated by the appearance of a Se··F chalcogen bond in the rotational transition state. Other systems were designed by placing two phenyl rings on opposite ends of an octahedrally disposed SeF4 group. A high barrier inhibits their rotation with bulky Br atoms in ortho positions, but this barrier is lowered if Br is replaced by groups that can engage in either chalcogen (SeH or SeF) or pnicogen (AsH2) bonds with the F atoms in the rotational transition state. The barrier reduction is closely related to the strength of these noncovalent bonds.

Competition between Binding to Various Sites of Substituted Imidazoliums

The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH₃ base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.

Factors contributing to halogen bond strength and stretch or contraction of internal covalent bond

The halogen bond formed by a series of Lewis acids TF₃X (T = C, Si, Ge, Sn, Pb; X = Cl, Br, I) with NH₃ is studied by quantum chemical calculations. The interaction energy is closely mimicked by the depth of the σ-hole on the X atom as well as the full electrostatic energy. There is a first trend by which the hole is deepened if the T atom to which X is attached becomes more electron-withdrawing: C > Si > Ge > Sn > Pb. On the other hand, larger more polarizable T atoms are better able to transmit the electron-withdrawing power of the F substituents. The combination of these two opposing factors leaves PbF₃X forming the strongest XBs, followed by CF₃X, with SiF₃X engaging in the weakest bonds. The charge transfer from the NH₃ lone pair into the σ*(TX) antibonding orbital tends to elongate the covalent TX bond, and this force is largest for the heavier X and T atoms. On the other hand, the contraction of this bond deepens the σ-hole at the X atom, which would enhance both the electrostatic component and the full interaction energy. This bond-shortening effect is greatest for the lighter X atoms. The combination of these two opposing forces leaves the T-X bond contracting for X = Cl and Br, but lengthening for I.

Ability of Peripheral H Bonds to Strengthen a Halogen Bond

Quantum calculations study the manner in which the involvement of a halogen atom as a proton acceptor in one or more H bonds (HBs) affects the strength of the halogen bond (XB) it can form with a nucleophile aligned with the X σ-hole. A variety of Lewis acids wherein X = F, Cl, Br, and I are attached to a tetrel atom C or Ge engaged in a XB with nucleophile NH₃. One, two, and three HF molecules were positioned perpendicular to the XB axis so that they could form a HB to the X atom. Each such HB strengthened the XB by an increment of 1 kcal/mol or more that does not attenuate as each new HB is added, potentially increasing the interaction energy manyfold. Additionally, the presence of one or more HBs facilitates the formation of a XB by molecules which are reluctant to engage in such a bond in the absence of these auxiliary interactions. Even the F atom, which avoids such a XB, can be coaxed to participate in a XB of moderate strength by one or more of these external HBs.

Classification of So-Called Non-Covalent Interactions Based on VSEPR Model

The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.

Intramolecular Hydrogen Bond Energy and Its Decomposition—O–H∙∙∙O Interactions

The method to calculate the energy of intramolecular hydrogen bond is proposed and tested for a sample of malonaldehyde and its fluorine derivatives; the corresponding calculations were performed at the ωB97XD/aug-cc-pVTZ level. This method based on relationships found for related intermolecular hydrogen bonds is compared with other approaches which may be applied to estimate the intramolecular hydrogen bond energy. Particularly, methods based on the comparison of the system that contains the intramolecular hydrogen bond compared with corresponding conformations where such interaction does not occur are discussed. The function-based energy decomposition analysis, FB-EDA, of the intramolecular hydrogen bonds is also proposed here.

A Critical Overview of Current Theoretical Methods of Estimating the Energy of Intramolecular Interactions

This article is probably the first such comprehensive review of theoretical methods for estimating the energy of intramolecular hydrogen bonds or other interactions that are frequently the subject of scientific research. Rather than on a plethora of numerical data, the main focus is on discussing the theoretical rationale of each method. Additionally, attention is paid to the fact that it is very often possible to use several variants of a particular method. Both of the methods themselves and their variants often give wide ranges of the obtained estimates. Attention is drawn to the fact that the applicability of a particular method may be significantly limited by various factors that disturb the reliability of the estimation, such as considerable structural changes or new important interactions in the reference system.

Magnetic descriptors of hydrogen bonds in malonaldehyde and its derivatives

The nature of the hydrogen bond, HB, as such is still unknown, though a few of its most fundamental features has been uncovered during the last few decades. At the moment, it is possible to obtain reliable results for only a few of its broadest properties, like magnetic properties. They could give new insights into the physics underlying the strength and features of HBs. In this article we analyze the electronic origin of the NMR spectroscopic parameters of malonaldehyde, MA, and some substituted MAs. These substituted MAs are such that the H-bonds are assisted by one of two phenomena: resonance, RAHB, or charge, CAHB. We have studied the dependences of these parameters on two of the main factors which contribute the most to both phenomena, the geometrical and electronic factors, and found out how they can be used to characterize RAHB or CAHB by means of reliable theoretical calculations. We show that in the set of compounds analyzed here (i) the shielding of the proton of the H-bond can be used as a measure of the strength of the HB and (ii) the relation between the contact and non-contact mechanisms of J-couplings between donor and acceptor atoms is a reliable descriptor of whether the H-bond is resonance assisted or charge assisted.

Halogen Bonds Formed between Substituted Imidazoliums and N Bases of Varying N-Hybridization

Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp³, sp² and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with the H-bond generally similar in magnitude to the Br-bond. Methyl substitution on the N electron donor enhances the binding energy. Very little perturbation arises if the imidazolium is attached to a phenyl ring. The energetics are not sensitive to the hybridization of the N atom. More regular patterns appear in the individual phenomena. Charge transfer diminishes uniformly on going from amine to imine to nitrile, a pattern that is echoed by the elongation of the C-Z (Z=H, Cl, Br, I) bond in the Lewis acid. These trends are also evident in the Atoms in Molecules topography of the electron density. Molecular electrostatic potentials are not entirely consistent with energetics. Although I of the Lewis acid engages in a stronger bond than does H, it is the potential of the latter which is much more positive. The minimum on the potential of the base is most negative for the nitrile even though acetonitrile does not form the strongest bonds. Placing the systems in dichloromethane solvent reduces the binding energies but leaves intact most of the trends observed in vacuo; the same can be said of ∆G in solution.

Theoretical and spectroscopic studies on molecular structure and hydrogen bonding of 2-trifluoroacetylphenol

The molecular structure, intramolecular hydrogen bonding, and vibrational frequencies of 2-trifluoroacetylphenol (TFAP), were investigated by means of density functional theory (DFT) calculations and NMR, IR, and Raman spectroscopy techniques. The calculated theoretical and observed experimental results were compared with the corresponding data for salicylaldehyde (SA). Calculations were performed at the B3LYP level, using 6-311++G(**) basis set. The observed vibrational frequencies of TFAP were assigned with aid of theoretical calculations. The scaled frequencies at the B3LYP/6-311++G(**) level are in good agreement with the corresponding observed values by acceptable deviations. To investigate the effect of CF3 group on the hydrogen bond strength, the charge distributions, steric effects, and electron delocalization in TFAP and SA are studied using the natural bond orbital (NBO) analysis. The computations were further complemented with an atoms-in-molecules (AIM) topological analysis to characterize the nature of the intramolecular hydrogen bond, IHB, in the considered molecules. The contradiction between experimental and theoretical results was interpreted by considering the opposite effects of steric effect and electron withdrawing nature of CF3 group.

Intramolecular charge-assisted hydrogen bond strength in pseudochair carboxyphosphate

Carboxyphosphate, a suspected intermediate in ATP-dependent carboxylases, has not been isolated nor observed directly by experiment. Consequently, little is known concerning its structure, stability, and ionization state. Recently, carboxyphosphate as either a monoanion or dianion has been shown computationally to adopt a novel pseudochair conformation featuring an intramolecular charge-assisted hydrogen bond (CAHB). In this work, additive and subtractive correction schemes to the commonly employed open–closed method are used to estimate the strength of the CAHB. Truhlar’s Minnesota M06-2X functional with Dunning’s aug-cc-pVTZ basis set has been used for geometry optimization, energy evaluation, and frequency analysis. The CHARMM force field has been used to approximate the Pauli repulsive terms in the closed and open forms of carboxyphosphate. From our additive correction scheme, differential Pauli repulsion contributions between the pseudochair (closed) and open conformations of carboxyphosphate are found to be significant in determining the CAHB strength. The additive correction modifies the CAHB prediction (ΔE_{closed–open}) of −14 kcal/mol for the monoanion and −12 kcal/mol for the dianion to −22.9 and −18.4 kcal/mol, respectively. Results from the subtractive technique reinforce those from our additive procedure, where the predicted CAHB strength ranges from −17.8 to −25.4 kcal/mol for the monoanion and from −15.7 to −20.9 kcal/mol for the dianion. Ultimately, we find that the CAHB in carboxyphosphate meets the criteria for short-strong hydrogen bonds. However, carboxyphosphate has a unique energy profile that does not result in the symmetric double-well behavior of low-barrier hydrogen bonds. These findings provide deeper insight into the pseudochair conformation of carboxyphosphate, and lead to an improved mechanistic understanding of this intermediate in ATP-dependent carboxylases.

Interference of H-bonding and substituent effects in nitro- and hydroxy-substituted salicylaldehydes

Two intramolecular interactions, i.e., (1) hydrogen bond and (2) substituent effect, were analyzed and compared. For this purpose, the geometry of 4- and 5-X-substituted salicylaldehyde derivatives (X = NO₂, H or OH) was optimized by means of B3LYP/6-311 + G(d,p) and MP2/aug-cc-pVDZ methods. The results obtained allowed us to show that substituents (NO₂ or OH) in the para or meta position with respect to either OH or CHO in H-bonded systems interact more strongly than in the case of di-substituted species: 4- and 3-nitrophenol or 4- and 3-hydroxybenzaldehyde by ∼31%. The substituent effect due to the intramolecular charge transfer from the para-counter substituent (NO₂) to the proton-donating group (OH) is ∼35% greater than for the interaction of para-OH with the proton-accepting group (CHO). The total energy of H-bonding for salicylaldehyde, and its derivatives, is composed of two contributions: ∼80% from the energy of H-bond formation and ∼20% from the energy associated with reorganization of the electron structure of the systems in question.

Figure

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.

A theoretical study of the intramolecular proton transfer and calculation of the nucleus independent chemical shift in juglone and some of its derivatives

In the present study, first, the intramolecular proton transfer (IPT) process of juglone and its derivatives were theoretically investigated in the gas phase and the effect of electron-withdrawing and electronreleasing substituents in different positions of the phenyl and benzoquinone rings of juglone on the IPT process was studied in which the geometries, energies and thermodynamic functions of the compounds were obtained using DFT calculations at the B3LYP/6-31+G(2d,p) level. Next, the influence of IPT on changing the aromaticity of the phenyl and benzoquinone rings was investigated. To determine the aromaticity of the rings, nuclear independent chemical shift (NICS) values were calculated for the ground state and transition state structures (GS1,TS,GS2) using the continues set of gauge transformations (CSGT) procedure at the B3LYP/6-311+G(2d,p) level.

Estimates of the energy of intramolecular hydrogen bonds

A method for the estimation of the energy of intramolecular hydrogen bonds in conjugated systems existing in a variety of conformations is presented. The method is applied to determine the intramolecular hydrogen bond energy in 3-aminopropenal and 3-aminopropenthial. According to the proposed estimation scheme, the intramolecular H-bond energies are found to be of the order of 5-7 kcal/mol. These results are compared with those obtained by using other estimation schemes as well as with the recent results by other authors. Also, the H-bond energies in dimers and trimers of the two molecules are calculated and compared with the corresponding data for internally hydrogen-bonded monomers. This comparison shows that the bond equalization effect is primarily due to proton donor-proton acceptor proximity. In comparison with intermolecular hydrogen bonds, the rigidity of the chelate skeleton enhances this proximity effect. The same effect can be seen in systems with intermolecular hydrogen bonds, although its magnitude is diminished because of the absence of additional forces which pull the proton donor and proton acceptor groups toward each other. No specific resonance-assisted origin of the intramolecular hydrogen bond energy seems to be needed to elucidate the energetics of these bonds.

Excited-state intramolecular proton transfer: a survey of TDDFT and RI-CC2 excited-state potential energy surfaces

TDDFT and RI-CC2 calculations have been performed on the excited-state intramolecular proton transfer in malonaldehyde, o-hydroxybenzaldehyde, salicylic acid, 7-hydroxy-1-indanone, and 2-(2'-hydroxyphenyl)benzothiazole. Vertical and adiabatic excitation energies have been computed for the npi and pipi states. Overall, we have found that both RI-CC2 and TDDFT methods are good candidates for the description of ESIPT potential energy surfaces. Proton transfer (PT) curves have been computed for both excited states. An essentially barrierless and very shallow energy profile has been found for the pi pi* state. For the n pi* state the keto minimum is more pronounced than for the pi pi* state and, depending on the case, energy barriers ranging from values <0.1 eV up to 0.5 eV were found. From the computed PT curves we conclude that extended crossing regions between the two excited states will occur.

Cannabinoid CB2/CB1 selectivity. Receptor modeling and automated docking analysis

Three-dimensional models of the CB1 and CB2 cannabinoid receptors were constructed by means of a molecular modeling procedure, using the X-ray structure of bovine rhodopsin as the initial template, and taking into account the available site-directed mutagenesis data. The cannabinoid system was studied by means of docking techniques. An analysis of the interaction of WIN55212-2 with both receptors showed that CB2/CB1 selectivity is mainly determined by the interaction in the CB2 with the nonconserved residues S3.31 and F5.46, whose importance was suggested by site-directed mutagenesis data. We also carried out an automated docking of several ligands into the CB2 model, using the AUTODOCK 3.0 program; the good correlation obtained between the estimated free energy binding and the experimental binding data confirmed our binding hypothesis and the reliability of the model.

Vibrational assignment, structure and intramolecular hydrogen bond of 4-methylamino-3-penten-2-one

The molecular structure, intramolecular hydrogen and vibrational frequencies of 4-methylamino-3-penten-2-one were investigated by a series of density functional theoretical (DFT) calculations and ab initio calculation at the post-Hartree-Fock (MP2) level. Fourier transform infrared and Fourier transform Raman spectra of this compound and its deuterated analogue were clearly assigned. The calculated geometrical parameters show a strong intramolecular hydrogen bond with a N...O distance of 2.622-2.670 A. This bond length is about 0.02 A shorter than that in its parent, 4-amino-3- penten-2-one which is in agreement with spectroscopic results. Furthermore, the conformations of methyl groups with respect to the plane of the molecule and with respect to each other were investigated.

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.