Energetics of Intramolecular Hydrogen Bonding in Di-substituted Benzenes by the ortho−para Method

Formation of hydrogen bonding network of methane sulfonic acid at low degree of hydration (MSA)m·(H2O)n (m = 1-2 and n = 1-5)

This study employs ab initio calculations based on density functional theory (DFT) to investigate the structural properties, 1H-NMR spectra, and vibrational spectra of methane sulfonic acid (MSA) at low degree of hydration. The findings reveal that energetically stable structures are formed by small clusters consisting of one or two MSA molecules (m = 1 and 2) and one or two water molecules in (MSA)m·(H2O)n (m = 1-2 and n = 1-5).These stable structures arise from the formation of strong cyclic hydrogen bonds between the proton of the hydroxyl (OH) group in MSA and the water molecules. However, clusters containing three or more water molecules (n > 2) exhibit proton transfer from MSA to water, resulting in the formation of ion-pairs composed of CH3SO3- and H3O+species. The measured 1H-NMR spectra demonstrate the presence of hydrogen-bonded interactions between MSA and water, with a single MSA molecule interacting with water molecules. This interaction model accurately represents the hydrogen bonding network, as supported by the agreement between the experimental and calculated NMR chemical shift results.

Experimental and computational thermochemistry: how strong is the intramolecular hydrogen bond in alkyl 2-hydroxybenzoates (salicylates)

Hydrogen bonding (HB) is a fascinating phenomenon that exhibits unusual properties in organic and biomolecules. The qualitative manifestation of hydrogen bonds is known in numerous chemical processes. However, quantifying HB strength is a challenging task, especially in the case of intra-molecular hydrogen bonds. It is qualitatively well established that the alkyl 2-hydroxybenzoates have strong intra-HB. The thermochemical methods suitable for the determination of intra-HB strength were the focus of this study. The experimental gas phase formation enthalpies for alkyl 2-hydroxybenzoates (including methyl, ethyl, n-propyl and n-butyl) at 298.15 K were derived from a combination of vapour pressure measurements and high-precision combustion calorimetry and validated by the quantum chemical methods G3MP2 and G4. The intra-HB strength in methyl 2-hydroxybenzoate was determined from the evaluated gas-phase enthalpies of formation by comparing the energies of cis- and trans- conformers, by well-balanced reactions, the "para-ortho" method and the "HB and Out" method. All these methods give a common level of intra-molecular hydrogen bond strength of -43 kJ mol-1. The intra-HB strength was found to be independent of the chain length of the alkyl 2-hydroxybenzoates.

Synthesis, Structures, and Complexation with Phenolic Guests of Acridone-Incorporated Arylene-Ethynylene Macrocyclic Compounds

Acridone units were incorporated into the arylene-ethynylene structure as polar arene units. Cyclic trimers consisting of three acridone-2,7-diyl units and three 1,3-phenylene units were synthesized by Sonogashira couplings via stepwise or direct route. X-ray analysis revealed that the trimer had a nearly planar macrocyclic framework with a cavity surrounded by three carbonyl groups. In contrast, the corresponding tetramer had a nonplanar macrocyclic framework. ¹ H NMR measurements showed that the trimer formed a 1 : 1 complex as a macrocyclic host with dihydric phenol guests, and the association constants were determined to be ca. 1.0×10³  L mol^-1 for hydroquinone or resorcinol guests in CDCl₃ at 298 K. The calculated structures of these complexes by the DFT method supported the presence of two sets of OH⋅⋅⋅O=C hydrogen bonds between the host and guest molecules. The spectroscopic data of the cyclic trimers and tetramers are compared with those of reference acridone compounds.

Nearest-Neighbour and Non-Nearest-Neighbour Non-Covalent Interactions between Substituents in the Aromatic Systems: Experimental and Theoretical Investigation of Functionally Substituted Benzophenones

Benzophenone derivatives exhibit not only biological activity but also act as photo initiator and UV blocker. We carried out experimental and theoretical thermochemical studies of hydroxy- and methoxy-substituted benzophenones. Standard molar enthalpies of vaporisation were obtained from the temperature dependence of vapour pressures measured by the transpiration method. The thermodynamic data on phase transitions available in the literature (crystal-gas, crystal-liquid, and liquid-gas) were also collected and evaluated. High-level quantum chemical methods G3MP2 and G4 were used to estimate the standard molar enthalpies of formation of substituted benzophenones in the gas phase and establish agreement between experimental and theoretical results. The application of the "centrepiece" group-contribution approach to hydroxy- and methoxy-substituted benzophenones was demonstrated. A quantitative assessment of the hydrogen bond was carried out using various approaches based on experimental data and quantum chemical calculations.

Thermodynamic Stability of Fenclorim and Clopyralid

The present work reports an experimental thermodynamic study of two nitrogen heterocyclic organic compounds, fenclorim and clopyralid, that have been used as herbicides. The sublimation vapor pressures of fenclorim (4,6-dichloro-2-phenylpyrimidine) and of clopyralid (3,6-dichloro-2-pyridinecarboxylic acid) were measured, at different temperatures, using a Knudsen mass-loss effusion technique. The vapor pressures of both crystalline and liquid (including supercooled liquid) phases of fenclorim were also determined using a static method based on capacitance diaphragm manometers. The experimental results enabled accurate determination of the standard molar enthalpies, entropies and Gibbs energies of sublimation for both compounds and of vaporization for fenclorim, allowing a phase diagram representation of the (p,T) results, in the neighborhood of the triple point of this compound. The temperatures and molar enthalpies of fusion of the two compounds studied were determined using differential scanning calorimetry. The standard isobaric molar heat capacities of the two crystalline compounds were determined at 298.15 K, using drop calorimetry. The gas phase thermodynamic properties of the two compounds were estimated through ab initio calculations, at the G3(MP2)//B3LYP level, and their thermodynamic stability was evaluated in the gaseous and crystalline phases, considering the calculated values of the standard Gibbs energies of formation, at 298.15 K. All these data, together with other physical and chemical properties, will be useful to predict the mobility and environmental distribution of these two compounds.

Interaction-Deletion: A Composite Energy Method for the Optimization of Molecular Systems Selectively Removing Specific Nonbonded Interactions

The complex interactions between different portions of a large molecule can be challenging to analyze through traditional electronic structure calculations. Moreover, standard methods cannot easily quantify the physical consequences of individual pairwise interactions inside a molecule. By creating a set of molecular fragments, we propose a composite energy method to explore changes in a molecule caused by removing selected nonbonded interactions between different molecular portions. Energies and forces are easily obtained with this composite approach, allowing geometry optimizations that lead to chemically meaningful structures that describe how the omitted interactions contribute to changes in the local geometrical minima. We illustrate the application of our new hybrid scheme by computing the influence of intramolecular hydrogen-bonding interactions in two small molecules: 1,6-(tG⁺G⁺TG⁺G⁺g^-)-hexanediol and a cyclic analogue, cis-1,4-cyclohexanediol. The resulting structural and energetic changes are interpreted to yield key physical insights and quantify concepts such as "preparation energy" or "reorganization energy". We demonstrate that the composite method can be extended to larger molecular systems by showing its application on a Si(100) surface model containing interactions between dissociated ammonia molecules on adjacent surface dimers. The scheme's efficacy is also tested by applying it to systems having multiple intramolecular interactions, viz., 3₁₀-polyglycine and H⁺GPGG. Furthermore, the cooperative nature of intramolecular hydrogen bonds is explored by using interaction-deletion in 2-nitrobenzene-1,3-diol.

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.

Assessment of O-H⋯O and O-H⋯S intramolecular hydrogen bond energies in some substituted pyrimidines using quantum chemistry methods

Resonance-assisted hydrogen bond (RAHB) theory was studied in some substituted pyrimidines in which encompass O-H⋯Y unit (Y= O and S). Alteration of substituents (R ₁, R₂, R₃ = H, C₂H, C₂F) on pyrimidine ring changes properties of electron charge density at this ring and influences indirectly on strength of intramolecular hydrogen bond (IHB) interactions in the mentioned structures. Then, IHB energies were estimated using cis-trans method (CTM), related rotamers method (RRM), Espinosa' method (EM), and a viewpoint based on properties of electron charge densities at ring critical point (RCP) of RAHB ring. Moreover, the estimated IHB energies with these methods were compared with those obtained using modified Espinosa' method (MEM), Iogansen's relationship, and chemical shift-based method to find more consistent method with the proposed viewpoint based on RCP characteristics. The linear correlations between the all estimated IHB energies and some hydrogen bonding descriptors such as geometrical, spectroscopic, topological, and molecular orbital factors were examined. Results indicated that the IHB energies that obtained by way of MEM and Iogansen's relationship have better correlations with hydrogen bonding descriptors. Also, there are good consistencies between results of these two methods with viewpoint based on properties of RCPs. Therefore, IHB energies can suitably estimate using properties of RCPs in heterocyclic molecular systems especially in cases that rotation around C-C/CC bonds makes additional interactions in isomers and influences on accuracy of calculated IHB energies using approaches such as CTM and RRM.

The Effect of Intramolecular Hydrogen Bond Type on the Gas-Phase Deprotonation of ortho-Substituted Benzenesulfonic Acids. A Density Functional Theory Study

Structural factors have been identified that determine the gas-phase acidity of ortho-substituted benzenesulfonic acid, 2-XC6H4-SO3H, (X = -SO3H, -COOH, -NO2, -SO2F, -C≡N, -NH2, -CH3, -OCH3, -N(CH3)2, -OH). The DFT/B3LYP/cc-pVTZ method was used to perform conformational analysis and study the structural features of the molecular and deprotonated forms of these compounds. It has been shown that many of the conformers may contain anintramolecular hydrogen bond (IHB) between the sulfonic group and the substituent, and the sulfonic group can be an IHB donor or an acceptor. The Gibbs energies of gas-phase deprotonation ΔrG0298 (kJ mol-1) were calculated for all compounds. It has been set that in ortho-substituted benzenesulfonic acids, the formation of various types of IHB is possible, having a significant effect on the ΔrG0298 values of gas-phase deprotonation. If the -SO3H group is the IHB donor, then an ion without an IHB is formed upon deprotonation, and the deprotonation energy increases. If this group is an IHB acceptor, then a significant decrease in ΔrG0298 of gas-phase deprotonation is observed due to an increase in IHB strength and the A- anion additional stabilization. A proton donor ability comparative characteristic of the -SO3H group in the studied ortho-substituted benzenesulfonic acids is given, and the ΔrG0298 energies are compared with the corresponding values of ortho-substituted benzoic acids.

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.

Structural and Energetic Insights on Two Dye Compounds: 1-Acetyl-2-Naphthol and 2-Acetyl-1-Naphthol

The energy involved in the structural switching of acyl and hydroxyl substituents in the title compounds was evaluated combining experimental and computational studies. Combustion calorimetry and Knudsen effusion techniques were used to determine the enthalpies of formation, in the crystalline state, and of sublimation, respectively. The gas-phase enthalpy of formation of both isomers was derived combining these two experimental data. Concerning the computational study, the G3(MP2)//B3LYP composite method was used to optimize and determine the energy of the isomers in the gaseous state. From a set of hypothetical reactions it has been possible to estimate the gas-phase enthalpy of formation of the title compounds. The good agreement between the experimental and computational gas-phase enthalpies of formation of the 1-acetyl-2-naphthol and 2-acetyl-1-naphthol isomers, provided the confidence for extending the computational study to the 2-acetyl-3-naphthol isomer. The structural rearrangement of the substituents in position 1 and 2 in the naphthalene ring and the energy of the intramolecular hydrogen bond are the factors responsible for the energetic differences exhibited by the isomers. The gas phase tautomeric keto ↔ enol equilibria of the o-acetylnaphthol isomers were analyzed using the Boltzmann’s distribution.

An intramolecular 1,5-chalcogen bond on the conformational preference of carbonyl thiocarbamate species

Two closely related carbamothioates were prepared by the reaction of benzoyl isothiocyanates and methanol. The crystal structures show the occurrence of 1,5-O⋯O intramolecular short distance that determines the conformational preference.

Buffer gas additives (modifiers/shift reagents) in ion mobility spectrometry: Applications, predictions of mobility shifts, and influence of interaction energy and structure

Ion mobility spectrometry (IMS) is an analytical technique used for fast and sensitive detection of illegal substances in customs and airports, diagnosis of diseases through detection of metabolites in breath, fundamental studies in physics and chemistry, space exploration, and many more applications. Ion mobility spectrometry separates ions in the gas-phase drifting under an electric field according to their size to charge ratio. Ion mobility spectrometry disadvantages are false positives that delay transportation, compromise patient's health and other negative issues when IMS is used for detection. To prevent false positives, IMS measures the ion mobilities in 2 different conditions, in pure buffer gas or when shift reagents (SRs) are introduced in this gas, providing 2 different characteristic properties of the ion and increasing the chances of right identification. Mobility shifts with the introduction of SRs in the buffer gas are due to clustering of analyte ions with SRs. Effective SRs are polar volatile compounds with free electron pairs with a tendency to form clusters with the analyte ion. Formation of clusters is favored by formation of stable analyte ion-SR hydrogen bonds, high analytes' proton affinity, and low steric hindrance in the ion charge while stabilization of ion charge by resonance may disfavor it. Inductive effects and the number of adduction sites also affect cluster formation. The prediction of IMS separations of overlapping peaks is important because it simplifies a trial and error procedure. Doping experiments to simplify IMS spectra by changing the ion-analyte reactions forming the so-called alternative reactant ions are not considered in this review and techniques other than drift tube IMS are marginally covered.

A Critical Check for the Role of Resonance in Intramolecular Hydrogen Bonding

Although resonance-assisted H-bonds (RAHBs) are well recognized, the role of π resonance in RAHBs is controversial, as the seemingly enhanced H-bonds in unsaturated compounds may result from the constraints imposed by the σ skeleton. Herein the block-localized wave function (BLW) method, which can derive optimal yet resonance-quenched structures with related physiochemical properties, was employed to examine the correlation between π resonance and the strength of intramolecular RAHBs. Examination of a series of paradigmatic molecules with RAHBs and their saturated analogues showed that it is inappropriate to compare a conjugated system with its saturated counterpart, as they may have quite different σ frameworks. Nevertheless, comparison between a conjugated system and its resonance-quenched (i.e., electron-localized) state, which have identical σ skeletons, shows that in all studied cases, π resonance unanimously reduces the bonding distance by 0.111-0.477 Å, strengthens the bonding by 40-56 %, and redshifts the D-H vibrational frequency by 104-628 cm^-1 . Furthermore, there is an excellent correlation between hydrogen-bonding strength and the classical Coulomb attraction between the hydrogen-bond donor and the acceptor, which suggests that the dominant role of the electrostatic interaction in H-bonds and RAHBs originates from the charge flow from H-bond donors to acceptors through π conjugation.

The Origin of the Non-Additivity in Resonance-Assisted Hydrogen Bond Systems

The concept of resonance-assisted hydrogen bond (RAHB) has been widely accepted, and its impact on structures and energetics can be best studied computationally using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently. In this work, we use the BLW method to examine a few molecules that result from the merging of two malonaldehyde molecules. As each of these molecules contains two hydrogen bonds, these intramolecular hydrogen bonds may be cooperative or anticooperative, depended on their relative orientations, and compared with the hydrogen bond in malonaldehyde. Apart from quantitatively confirming the concept of RAHB, the comparison of the computations with and without π resonance shows that both σ-framework and π-resonance contribute to the nonadditivity in these RAHB systems with multiple hydrogen bonds.

Effects of Structure and Environment on the Spectroscopic Properties of (3-Amino-Substituted-Thieno[2,3-b] Pyridine-2-yl)Pyridine/Quinolin-2-yl)(Phenyl)Methanones: Experimental and Theoretical Study

The electronic absorption, excitation and fluorescence properties of two 3-amino-substituted-thieno[2,3-b]pyridine/quinolin-2-yl)(phenyl)methanones; (referred to as compounds 1-2: where 3-amino-4,5,6-trimethyl-thieno[2,3-b]pyridin-2-yl)(phenyl)methanone (1); and 3-amino-5,6,7,8-tetrahydro-thieno[2,3-b]quinolin-2-yl)(phenyl)methanone (2)) have been investigated in solvents of various polarity and hydrogen-bonding abilities. Results based on the electronic absorption, excitation and emission study of these compounds; indicated that singlets (S1 and S2) excited-states are populated in non-polar and polar protic/aprotic solvents giving dual fluorescence with weak charge transfer separation. The experimental results were interpreted with the aid of quantum chemistry calculations carried out with the DFT and TD-DFT/B3lyp/6-31 + G(d,p) methods. Based on these calculations, compounds 1-2 exist in two rotamers: anti and syn, separated by ca. 5-6 kcal mol(-1) energy barriers in favor of the anti-conformer. The anti-structure, was shown to be stabilized through existence of intramolecular NH…O hydrogen bond (H-b), which plays a dominant role in affecting the energy of the HOMO-1 molecular orbital. Further, methyl/alkyl substitution in the pyridyl-thiophene ring was shown to involve in σ-π hyper-conjugation and destabilization of the HOMO-1 MO's.

Slow Photoelectron Velocity-Map Imaging Spectroscopy of the ortho-Hydroxyphenoxide Anion

We report high-resolution photodetachment spectra of cryogenically cooled ortho-hydroxyphenoxide anions (o-HOC6H4O(-)) using slow photoelectron velocity-map imaging spectroscopy (cryo-SEVI). We observe transitions to the three lowest-lying electronic states of the ortho-hydroxyphenoxy radical, and resolve detailed vibrational features. Comparison to Franck-Condon simulations allows for clear assignment of vibronic structure. We find an electron affinity of 2.3292(4) eV for the neutral X̃(2)A″ ground state, improving upon the accuracy of previous experiments. We measure term energies of 1.4574(7) eV and 1.5922(48) eV for the Ã(2)A' and B̃(2)A″ excited states respectively, representing their first resolution and clear assignment. Photodetachment threshold effects are considered to explain the structure of these bands.

The nature of NO-bonding in N-oxide group

The nature of the NO-bond in the N-oxide group was investigated by means of combined theoretical calculations (including QTAIM and NBO approaches) and statistical analyses of the contents of crystal structure databases. The N-O bond in the N-oxide group should be classified as the NO donating bond with an important contribution of ON back-donation (of the π-electron type, when available). The visualization of the Laplacian of electron density in the region of an oxygen valence sphere suggests the presence of two lone pairs for the imine-N-oxide group (characterized by effective ON back-donation). A detailed bonding analysis performed by means of natural resonance theory indicates that the N→O bond is of an order of magnitude clearly greater than 1. In addition, the stability of the N→O bond in various N-oxides was estimated. The analyses of the hydrogen- and halogen-bonded complexes of the N-oxides reveal strong Lewis basicity of the N-oxide group. The formation of H- and X-bonding leads to N→O bond elongation due to its structural, topological and spectroscopic characteristics. Moreover, in pyridine-N-oxide, the electron-withdrawing -NO2 group additionally stabilizes the N→O bond, whereas the opposite effect can be observed for the electron-donating-NH2 substituent. This is due to a substituent effect on the π-type ON back-donation. As a result, the oxygen atom in pyridine-N-oxide may change its availability during intermolecular interaction formation, as revealed in the interaction energy, which changes by about half of the estimated total interaction energy.

Conformational preferences of 3,4-dihydroxyphenylacetic acid (DOPAC)

The conformational space of 3,4-dihydroxyphenylacetic acid (DOPAC), an important dopamine metabolite, has been investigated by quantum chemical methods (B3LYP and MP2, with the 6-311++G(d,p) basis set) and matrix-isolation infrared spectroscopy. Detailed analysis of the calculated potential energy surfaces of the molecule led to identification of thirteen unique conformers, all of them showing the acetic acid side chain out of the aromatic ring plane by 60-95°. According to the calculated Gibbs energies, the five lowest energy conformers make up 99.7% of the conformational mixture at 298.15K, exhibiting individual populations falling between 16% and 24%. The main conformational trends of this molecule were interpreted on the grounds of a thorough analysis of the structural parameters and by the application of the Natural Bond Orbital theory. The role of the intramolecular interactions on the relative stability and structure of the conformers was also investigated. The infrared spectrum of DOPAC was registered after isolation of its monomers in argon and xenon matrices. Only one of DOPAC forms populated in the gas phase could be trapped in both matrix gases. This result is in agreement with the predicted low energy barriers for conformational isomerization and is also supported by annealing experiments. The spectra of matrix-isolated model compounds, phenylacetic acid and catechol, were studied under the same experimental conditions. These data were used as references and assisted in the interpretation of the results obtained for DOPAC.

Stability of conformationally locked free fructose: theoretical and computational insights

Total stabilization is governed by three predominant factors viz. the sum of energy of all H-bonds, ring strain and anomeric stabilization.

Intramolecular resonance-assisted hydrogen bonds: a theoretical description by means of atomic charges and charge fluxes

The characterization of intramolecular H-bonds in terms of atomic charges and charge fluxes (at the B3LYP/cc-pVTZ level of theory) has been extended to the case of the so called resonance-assisted (RA) H-bonds. A quadratic correlation between the charge fluxes φH and the molecular IR absorption coefficients E that includes the entire family of the studied systems (31 of them) containing both intra- and intermolecular hydrogen bonds (O-H···O/N) confirmed the critical importance of the charge fluxes on the IR intensity enhancements. Since they reflect changing of the atomic charge distribution during the normal modes of vibrations, the dynamic nature of hydrogen bonding properties has been re-emphasized. The changes of the charge flux of the hydroxyl hydrogen in an RA intramolecular H-bond are between those for "free" OH bonds and the values calculated for intermolecular H-bonds. The transition "free"→intramolecular→intermolecular is gradual and therefore the hydrogen charge flux can be considered as practically sufficient to give quantitative measure to the intuitively obvious statement that "intramolecular H-bonding is somehow in between no H-bonding situation and intermolecular H-bonding" and thus provide a quantitative and yet simple parameterization of H-bond strength. In strictly planar molecules, the difference of the sums of charges of atoms participating in the 6-membered H-bond ring ΔΣ can serve as a measure of the charge delocalization after the H-bond is formed. The electronic charge is withdrawn from the group of six atoms when the H-bond is formed in nitrophenol (ΔΣ=-0.07), while the opposite is true (ΔΣ=+0.03) for 2-hydroxy benzylidene amine. The corresponding values of the geometrical resonance parameter Δ are 0.39 and 0.37, respectively, similar to those found for 2-hydroxy acetophenone and 2-hydroxy benzaldehyde. The extent of the π-electron delocalization as measured by the resonance parameter Δ does not follow the strength of H-bond as measured by the charge flux φH.

Diffusion Studies of Phenylenediamine Isomers in Water-Monohydric-Alcohol Systems

The study of isomer diffusion provides useful information regarding solvent effects for mixture analysis. Isomers, particularly those with similar hydrodynamic radii, provide a mechanism for probing solute–solvent interactions. Here nuclear magnetic resonance was used to measure the self-diffusion of phenylenediamine isomers in various water–monohydric-alcohol (i.e. methanol, ethanol, 1-propanol, and tert-butanol) solvents. These systems allowed the effect of solvent modulation on isomer diffusion to be examined. It was found that the resonances of phenylenediamine isomers in a mixture were separable via diffusion, with the separation becoming greater at higher concentration of monohydric-alcohols. Unlike previously shown for dihydroxybenzene isomers, all three phenylenediamine isomers were differentiable via diffusion.

Structure of isolated 1,4-butanediol: combination of MP2 calculations, NBO analysis, and matrix-isolation infrared spectroscopy

Theoretical calculations at the MP2 level, NBO and AIM analysis, and matrix-isolation infrared spectroscopy have been used to investigate the structure of the isolated molecule of 1,4-butanediol (1,4-BDO). Sixty-five structures were found to be minima on the potential energy surface, and the three most stable forms are characterized by a folded backbone conformation leading to the formation of an intramolecular H-bond. To better characterize the intramolecular interactions and particularly the hydrogen bonds, natural bond orbital analysis (NBO) was performed for the four most stable conformers, and was further complemented with an atoms-in-molecules (AIM) topological analysis. Infrared spectra of 1,4-BDO isolated in low-temperature argon and xenon matrixes show a good agreement with a population-weighted mean theoretical spectrum, and the spectral features of the conformers expected to be trapped in the matrixes were observed experimentally. Annealing the xenon matrix from 20 to 60 K resulted in significant spectral changes, which were interpreted based on the barriers to intramolecular rotation. An estimation of the intramolecular hydrogen bond energy was carried out following three different methodologies.

Computation of the bond dissociation enthalpies and free energies of hydroxylic antioxidants using the ab initio Hartree-Fock method

INTRODUCTION

A new method for calculating theoretical bond dissociation enthalpy (BDE) and bond dissociation free energy (BDFE) of hydroxylic antioxidants is forwarded. BDE and BDFE may be understood as activation energies accompanying the formation of transition states, which may undergo downhill homolytic dissociation. The new method does not involve the complete fission of O-H bonds.

METHOD

Theoretical gas phase BDE values were calculated with the ab initio unrestricted Hartree-Fock (UHF) method, as changes in enthalpy between ground singlet states (GS) and triplet dissociative states (DS). Similarly, gas phase BDFEs were estimated from the corresponding changes in Gibbs free energy. The results were then compared with reliable experimental reports.

RESULTS

The proposed theoretical approach of BDE and BDFE determination was tested using 10 simple phenols, 5 flavonoids, and l-ascorbic acid derivatives. The agreement between our calculated gas phase results and the adopted experimental values were generally within 0.5 kcal mol(-1), with a very few exceptions.

DISCUSSION

Generally, steric interactions as well as intramolecular hydrogen bonding involving the dissociating OH group should be minimized in the GS. The DS are both electronically and vibrationally exited transition states. They have one unpaired electron on the carbon atom, which bears the homolytically dissociating OH group and are second order saddle points with a fixed <C-O-H bond angel of 180°.

CONCLUSION

It was concluded that ab initio UHF was well suited for the estimation of gas phase BDE and BDFE. The method presented has a good potential for application across a range of hydroxylic antioxidants. Currently, work is underway to extend its application in other class of antioxidants.

Different zeroes of interaction energies as the cause of opposite results on the stabilizing nature of C-H···O intramolecular interactions

The interaction energy of the C-H···O intramolecular interaction is estimated by several methods for a large group of systems possessing a quasi-cyclic six-membered ring. In the case of the geometry corrected method (GCM), the related rotamers method (RRM), and Espinosa's method (EM), the linear correlations between interaction energies and the electron density at the bond critical point have close slopes. The first and the last two methods yield almost systematically opposite results concerning the stabilizing/destabilizing character of the interaction, and their main difference is their zero of the interaction energy. An investigation on the limitations of reference energies has led to the introduction of the geometry corrected related rotamers method (GCRRM), estimating both stabilizing and destabilizing C-H···O interactions. An extension of EM is proposed.

ESTIMATION ON THE INTRAMOLECULAR 8- AND 12-MEMBERED RING N–H…O=C HYDROGEN BONDING ENERGIES IN β-PEPTIDES

Computation of accurate hydrogen bonding energies in peptides is of great importance in understanding the conformational stabilities of peptides. In this paper, the intramolecular 8- and 12-membered ring N – H … O = C hydrogen bonding energies in β-peptide structures were evaluated. The optimal structures of the β-peptide conformers were obtained using MP2/6-31G(d) method. The MP2/6-311++G(d,p) calculations were then carried out to evaluate the single-point energies. The results show that the intramolecular 8-membered ring N – H … O = C hydrogen bonding energies in the five β-dipeptide structures β-di, β-di-R1, β-di-R2, β-di-R3, and β-di-R4 are -5.50, -5.40, -7.28, -4.94, and -6.84 kcal/mol with BSSE correction, respectively; the intramolecular 12-membered ring N – H … O = C hydrogen bonding energies in the nine β-tripeptide structures β-tri, β-tri-R1, β-tri-R2, β-tri-R3, β-tri-R4, β-tri-R1', β-tri-R2', β-tri-R3' and β-tri-R4' are -10.23, -10.32, -9.53, -10.30, -10.32, -10.55, -10.09, -10.51, and -9.60 kcal/mol with BSSE correction, respectively. Our calculation results further indicate that for the intramolecular 8-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "a–a" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "e–e", while for the intramolecular 12-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "e–e" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "a–a". The method is also applied to estimate the individual intermolecular hydrogen bonding energies in the dimers of amino-acetaldehyde, 2-amino-acetamide, 2-oxo-acetamide, and oxalamide, each dimer having two identical intermolecular hydrogen bonds. According to our method, the individual intermolecular hydrogen bonding energies in the four dimers are calculated to be -1.71, -1.50, -4.67, and -3.22 kcal/mol at the MP2/6-311++G(d,p) level, which are in good agreement with the values of -1.84, -1.72, -4.93, and -3.26 kcal/mol predicted by the supermolecular method.

Charge-assisted intramolecular hydrogen bonds in disubstituted cyclohexane derivatives

In this paper, the N(+)-H···N, N(+)-H···O, and O-H···O(-) charge-assisted intramolecular hydrogen bonds (CAHBs) are investigated using different theoretical approaches. Monocharged cyclohexyldiamines (CHDA), aminocyclohexanols (ACHO), and cyclohexanediols (CHDO) are used as model compounds. Geometry optimizations at the MP2/aug-cc-pVDZ level are used to find the equilibrium structures for all possible H-bonded conformers. CAHBs are characterized geometrically and spectroscopically, and their energy is evaluated by means of homodesmic reactions. By comparison with the neutral forms, the presence of the charge is found to have a deep influence on the geometric and energetic H-bond parameters. In addition, these parameters are strongly dependent on the type of the groups involved as well as on their relative position in the cyclohexyl ring. For the systems under study, the H-bond energies vary from -23 to -113 kJ mol(-1), being classified from moderate to strong H-bonds. These H-bonds are also characterized by the application of the NBO and AIM theories. NBO analysis reveals that the energy corresponding to the charge transfer between the lone-pairs of the electron donor group and the antibonding orbitals of the acceptor group represents an important contribution in the H-bond stabilization. From the application of the AIM theory it is possible to see that these H-bonds possess some covalence which varies according to the type and relative position of the intervenient groups.

Mapping the catechol binding site in dopamine D₁ receptors: synthesis and evaluation of two parallel series of bicyclic dopamine analogues

A novel class of isochroman dopamine analogues, originally reported by Abbott Laboratories, have >100-fold selectivity for D₁-like over D₂-like receptors. We synthesized a parallel series of chroman compounds and showed that repositioning the oxygen atom in the heterocyclic ring decreases potency and confers D₂-like receptor selectivity to these compounds. In silico modeling supports the hypothesis that the altered pharmacology for the chroman series is due to potential intramolecular hydrogen bonding between the oxygen in the chroman ring and the meta-hydroxy group of the catechol moiety. This interaction realigns the catechol hydroxy groups and disrupts key interactions between these ligands and critical serine residues in TM5 of the D₁-like receptors. This hypothesis was tested by the synthesis and pharmacological evaluation of a parallel series of carbocyclic compounds. Our results suggest that if the potential for intramolecular hydrogen bonding is removed, D₁-like receptor potency and selectivity are restored.

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.