Hydrogen-bonded acetic acid dimers: Anharmonic coupling and linear infrared spectra studied with density-functional theory

Complexes of phosphine oxides with substituted phenols: hydrogen bond characterization based on shifts of PO stretching bands

In this work IR spectral characteristics of PO groups are used to evaluate the strength of OHO hydrogen bonds. Three phosphine oxides: triphenylphosphine oxide, tributylphosphine oxide and hexamethylphosphoramide are investigated as proton acceptors. The results of the experimental IR study and DFT calculation of 30 complexes formed by phosphine oxides with various substituted phenols or CF3CH2OH in CCl4 solution at room temperature are reported. We show that the PO vibrational frequency changes non-linearly upon hydrogen bond formation and strengthening and that the shift of the PO band could be used for the estimation of hydrogen bond strength in complexes with phosphine oxides. The accuracy of these estimations and the influence of solvation effects on the main characteristics of complexes are discussed.

Dimerization dynamics of carboxylic acids in helium nanodroplets

The dimerization of molecules in helium nanodroplets is known to preferentially yield structures of higher energy than the global energy minimum structure for a number of quite different monomers. Here, we explore dimerization in this environment using an atomistic model within statistically converged molecular dynamics (MD) trajectories, treating the solvent implicitly through the use of a thermostat, or more explicitly by embedding one monomer in a He₁₀₀ cluster. The focus is on the two simplest carboxylic acids, formic and acetic, both of which have been studied experimentally. While the global minimum structure, which comprises two CO⋯HO hydrogen bonds, is predicted to be the most abundant dimer in the absence of the helium solvent, this is no longer the case once helium atoms are included. The simulations confirm the importance of kinetic trapping effects and also shed light on the occurrence of specific dynamical effects, leading to the occasional formation of high-energy structures away from minima, such as saddle configurations. Theoretically predicted infrared spectra, based on the MD statistics, are in good agreement with the experimental spectra.

Self-association of diphenylpnictoginic acids in solution and solid state: covalent vs. hydrogen bonding

Triphenylpnictogens were oxidized to access diphenylpnictioginic acids Ph₂XOOH (X = P, As, Sb, Bi). It was shown that oxidation with chloramine-T does not lead to the cleavage of a C-pnictogen bond. The preliminary reductive cleavage with sodium in liquid ammonia followed by the oxidation with hydrogen peroxide was successfully utilised for the synthesis of diphenylphosphinic and diphenylarsinic acids. It was shown that in solid state (by means of XRD), all diphenylpnictoginic acids form polymeric chains. Diphenylbismuthinic and diphenylantimonic acids form polymeric covalent adducts, while diphenylphosphinic and diphenylarsinic chains are associated through hydrogen bonding. Unlike diphenylphosphinic acid, diphenilarsinic acid forms two polymorphs of hydrogen-bonded infinite chains. In solution in a polar aprotic solvent diphenylarsinic acid, similarly to dimethylarsinic, forms hydrogen-bonded cyclic dimers together with a small amount of cyclic trimers.

Aquaphotomics investigation of the state of water in oral liquid formulation of traditional Chinese medicine and its dynamics during temperature perturbation

Three types of bound water with different hydrogen bonding strengths were identified and elucidated by aquaphotomics.

Spectroscopic Manifestations of Indirect Vibrational State Mixing: Novel Anharmonic Effects on a Prereactive H Atom Transfer Surface

The NH stretch region of the IR spectrum of methyl anthranilate is modeled in the S₁ state to understand the connection between the absence of this fundamental in the fluorescence-dip infrared spectra of Blodgett et al. [Phys. Chem. Chem. Phys. 2020, 22, 14077] and its relevance to the H atom dislocation that occurs upon electronic excitation. A set of coordinates are chosen that highlight the role of certain low-frequency modes. A Hamiltonian is developed in which a large-amplitude two-dimensional surface describing the H-bonded H atom is linearly and quadratically coupled to the remaining degrees of freedom which are treated at the harmonic level. The surface is calculated within the time-dependent density functional theory framework by using the B3LYP/6-311++(d, p) level of theory with dispersion. Our spectral results show that indirect couplings lead to massive intensity sharing over hundreds of wavenumbers. This sharing is predicted to be dramatically reduced upon deuteration. The spectral broadening mechanism is found to involve off-resonant doorway states that are themselves strongly coupled to states nearly degenerate with the NH stretch fundamental and represents a complementary mechanism to previous explanations based on Fermi resonance or the presence of Franck-Condon like combination bands with low-frequency motions. Consistent with the spectra predictions, time-dependent calculations show that if the NH stretch fundamental were excited with an ultrafast laser, it would decay within 40 fs. The competition between H atom dislocation and vibrational relaxation is discussed.

Composition-Dependent Hydrogen-Bonding Motifs and Dynamics in Brønsted Acid-Base Mixtures

In recent years the interaction of organophosphates and imines, which is at the core of Brønsted acid organocatalysis, has been established to be based on strong ionic hydrogen bonds. Yet, besides the formation of homodimers consisting of two acid molecules and heterodimers consisting of one acid and one base, also multimeric molecular aggregates are formed in solution. These multimeric aggregates consist of one base and several acid molecules. The details of the intermolecular bonding in such aggregates, however, have remained elusive. To characterize composition-dependent bonding and bonding dynamics in these aggregates, we use linear and nonlinear infrared (IR) spectroscopy at varying molar ratios of diphenyl phosphoric acid and quinaldine. We identify the individual aggregate species, giving rise to the structured, strong, and very broad infrared absorptions, which span more than 1000 cm^–1. Linear infrared spectra and density functional theory calculations of the proton transfer potential show that doubly ionic intermolecular hydrogen bonds between the acid and the base lead to absorptions which peak at ∼2040 cm^–1. The contribution of singly ionic hydrogen bonds between an acid anion and an acid molecule is observed at higher frequencies. As common to such strong hydrogen bonds, ultrafast IR spectroscopy reveals rapid, ∼ 100 fs, dissipation of energy from the proton transfer coordinate. Yet, the full dissipation of the excess energy occurs on a ∼0.8–1.1 ps time scale, which becomes longer when multimers dominate. Our results thus demonstrate the coupling and collectivity of the hydrogen bonds within these complexes, which enable efficient energy transfer.

Dissecting intermolecular interactions in the condensed phase of ibuprofen and related compounds: the specific role and quantification of hydrogen bonding and dispersion forces

Ibuprofen is a well-established non-steroidal anti-inflammatory drug, inhibiting the prostaglandin-endoperoxide synthase. One of the key features defining the ibuprofen structure is the doubly intermolecular O-HO[double bond, length as m-dash]C hydrogen bond in cyclic dimers as know from carboxylic acids and confirmed by X-ray analysis. Until now, there was neither information about the vaporization enthalpy of ibuprofen nor about how this thermal property is determined by the subtle balance between different types of intermolecular interaction. In this study we derive the vaporization enthalpy of ibuprofen from thermochemical experiments to be . We dissected the hydrogen bond energy, EHB = 45.0 kJ mol-1, exclusively from measured vaporization enthalpies of related aliphatic carboxylic acids, their homomorph methyl esters and alkyl acetates, respectively. This contribution from hydrogen bonding could be confirmed almost quantitatively from quantum chemical calculations of ibuprofen clusters, which also suggest dispersion interaction of similar order (Edisp = 47 kJ mol-1). Following the full analysis of the gas-vapor transition enthalpy, we studied the changing structural components from the solid to the liquid phase of ibuprofen by means of Attenuated Total Reflection Infrared (ATR-IR) spectroscopy. The cyclic dimers as observed in the X-ray patterns are essentially preserved in the liquid state just above the melting point. However, with increasing temperature the doubly hydrogen-bonded cyclic dimers are replaced by singly hydrogen-bonded linear dimers in the liquid ibuprofen. The transfer enthalpy from the temperature-dependent equilibria of both dimers as obtained from the IR intensity ratios of the vibrational bands quantifies for the first time the energy of the released, single hydrogen bond to be EHB = 21.0 kJ mol-1. Overall, we show that a combination of thermodynamics, infrared spectroscopy and quantum chemistry provides quantification and detailed understanding of structure and molecular interaction in ibuprofen and related compounds.

Structural and Optical Characteristics of Aqueous Solutions of Acetic Acid

A refractometric method, coupled with molecular dynamics study, attenuated total reflection Fourier transform infrared (ATR FT-IR), and Raman spectroscopy, was used to determine optical characteristics of concentration features of aqueous solutions of acetic acid. Measurements of the refractive index of aqueous solutions of acetic acid in the wide range of acetic acid concentrations (∼ 0 ÷ 1 mole fraction) in a solution at a room temperature were conducted. Maximum value of refractive index was detected at a concentration of ∼0.3 mole fraction. The deviation from the parabolic form of the dependence of the refractive index on the concentration occurs at a concentration of ∼0.8 mole fraction. As far as we know, this deviation has been observed for the first time. The maximum is attributed to the largest number of molecular interactions between water and acetic acid molecules, while the deviation is associated with the parallel orientation of acetic acid molecules. To identify the reconstructing of molecules in the system, FT-IR and Raman spectra of these solutions at a concentration of ∼0.3 and ∼0.8 mole fraction were recorded and compared with pure solutions. The data obtained by using ATR FT-IR and Raman spectroscopy support the idea that the refractometric method is sensitive to determine the structural states of aqueous solutions of acetic acid.

IR Spectra of Hydrogen-Bonded Complexes of Trifluoroacetic Acid with Acetone and Diethyl Ether in the Gas Phase. Interaction between CH and OH Stretching Vibrations

The spectra of complexes of trifluoroacetic acid (TFA) with acetone and diethyl ether (DEE) and their perdeuterated isotopologues were extracted from the spectra of the mixture of the compounds recorded at room temperature. The ν(OH) bands of the complexes with protiated and deuterated acetone notably differ from each other, whereas these ν(OH) bands are practically not affected by the deuteration of DEE. An assumption about the interaction of CH and OH groups in the (CH₃)-C═O···HO fragment is made. According to density functional theory calculations, complexes of TFA with both acetone and DEE have a cyclic structure with one strong ═O···HO hydrogen bond and one weak CH···O═ bond. The structural, spectroscopic, and electronic properties indicate an essential role of weak bonds in the total complexation energy of the systems studied.

Carboxylic acids in aqueous solutions: Hydrogen bonds, hydrophobic effects, concentration fluctuations, ionization, and catalysis

In the frequency range between 100 kHz and 2 GHz, ultrasonic absorption spectra have been measured for a series of carboxylic acids from formic to enanthic acid, including constitutional isomers. Also investigated have been the spectra for mixtures with water of short-chain formic, acetic, propionic, butyric, and isobutyric acid, in each case covering the complete composition range. The neat carboxylic acids feature two Debye-type relaxation terms with relaxation times between 5.6 and 260 ns as well as 0.14 and 1.4 ns, respectively, at room temperature. Depending on the composition, mixtures with water reveal an additional Debye relaxation term in the intermediate frequency range (acetic acid) or a term subject to a relaxation time distribution (propionic, butyric, and isobutyric acid). The relaxations of the neat acids are assigned to the equilibrium between monomers and single-hydrogen-bonded linear dimers and between linear and twofold-hydrogen-bonded cyclic dimers. The latter equilibrium is considerably catalyzed by hydronium and carboxylate ions. Several mixtures with water indicate one of the up to three Debye relaxations to reflect the protolysis of the organic acid. The term with underlying relaxation time distribution is due to noncritical fluctuations in the local concentrations. The Debye relaxations are evaluated to yield the parameters of the relevant elementary chemical reactions, such as the rate and equilibrium constants and the isentropic reaction volumes. A comparison of the correlation length of concentration fluctuations with data for other aqueous systems confirms the idea that the hydrophobic part of the organic constituent promotes the formation of a micro-heterogeneous liquid structure, whereas the hydrophilic moiety is of minor importance in this respect. The high-frequency limiting absorption suggests the equilibrium between conformers of linear dimers to contribute to the spectra well above the frequency range of measurements.

Dimers of acetic acid in helium nanodroplets

Two metastable dimers are created inside superfluid helium and studied using infrared spectroscopy to provide insight into condensed phase structures.

Anharmonicity in a double hydrogen transfer reaction studied in a single porphycene molecule on a Cu(110) surface

Anharmonicity plays a crucial role in hydrogen transfer reactions in hydrogen-bonding systems, which leads to a peculiar spectral line shape of the hydrogen stretching mode as well as highly complex intra/intermolecular vibrational energy relaxation. Single-molecule study with a well-defined model is necessary to elucidate a fundamental mechanism. Recent low-temperature scanning tunnelling microscopy (STM) experiments revealed that the cis↔cis tautomerization in a single porphycene molecule on Cu(110) at 5 K can be induced by vibrational excitation via an inelastic electron tunnelling process and the N-H(D) stretching mode couples with the tautomerization coordinate [Kumagai et al. Phys. Rev. Lett. 2013, 111, 246101]. Here we discuss a pronounced anharmonicity of the N-H stretching mode observed in the STM action spectra and the conductance spectra. Density functional theory calculations find a strong intermode coupling of the N-H stretching with an in-plane bending mode within porphycene on Cu(110).

Understanding the influence of low-frequency vibrations on the hydrogen bonds of acetic acid and acetamide dimers

Low-frequency vibrations coupled to high-frequency modes are known to influence the hydrogen bond strengths in a weakly interacting dimer.

Spectroscopic and Computational Study of Acetic Acid and Its Cyclic Dimer in the Near-Infrared Region

Anharmonic vibrational analysis of near-infrared (NIR) spectra of acetic acid was carried out by anharmonic quantum chemical calculation in a wide concentration range of its CCl4 solution. By predicting vibrational spectra of acetic acid for the first time over a wide NIR region, it was possible to elucidate the influence of the formation of acetic acid cyclic dimer on its NIR spectrum. Quantum chemical simulations were based on coupled cluster and density functional theory quantum methods. Additionally, Møller-Plesset perturbation theory was employed for the additional calculation of hydrogen bonding stabilization energies. An anharmonic vibrational analysis was performed with the use of generalized second-order vibrational perturbation theory (GVPT2). A hybrid approach was assumed, in which monomeric species was treated by CCSD(T)/aug-cc-pVDZ (harmonic approximation) and B3LYP/SNSD (anharmonic approximation) methods. For the cyclic dimer, B3LYP and B2PLYP single and double hybrid functionals, paired with an SNSD basis set, were employed. DFT calculations were augmented with additional empirical dispersion correction. It was found that quantum chemically calculated vibrational modes in the NIR region are in a good agreement with experimental data. The results of anharmonic vibrational analysis were supported by a harmonic shift analysis, for elucidating the very strong anharmonic coupling observed between stretching modes of hydrogen bonded bridge in the cyclic dimer. However, the calculated wavenumbers for combination modes of double hydrogen bonded bridge in the cyclic dimer, which are very sensitive to the formation of hydrogen bonding, were found to be underestimated by quantum chemical methods. Therefore, by band fitting, the wavenumbers and shape parameters for these bands were found, and the modeled spectra were adjusted accordingly. A high accuracy of simulated spectra was achieved, and a detailed analysis of the experimental NIR spectra of acetic acid was possible, with successful identification of numerous experimental bands, including those which originate from concentration effects. It was also found that the main spectral features observed in the NIR spectra of carboxylic acid upon the formation of hydrogen bond should be accounted for combination modes of the stretching and bending vibrations of double hydrogen-bonded bridge in the cyclic dimers of acetic acid.

Standard free energy of the equilibrium between the trans-monomer and the cyclic-dimer of acetic acid in the gas phase from infrared spectroscopy

Survey jet-cooled spectra of acetic acid have been recorded in the infrared region (200-4000 cm(-1)) over a wide range of expansion conditions. From the variations of the relative intensities of the signals, vibrational transitions have been assigned unambiguously to the trans-monomer and cyclic-dimer. The IR-active fundamental frequencies have been determined at the instrumental accuracy of 0.5 cm(-1). This analysis of the jet-cooled spectra supported by electronic structure calculations permitted us to characterize the trans-monomer/cyclic-dimer equilibrium. From static cell spectra at 298 K, variations of the molar fractions ratio as a function of the total pressure were used to estimate the equilibrium constant and the Gibbs free energy of dimerization at 298 K. The very good agreement with the literature data shows that the present method is able to produce, from a single study, a free energy value as reliable as the one obtained from a large collection of data. In addition, the semi-empirical free energy value was used to estimate the accuracy of electronic structure calculations and in turn the accuracy of the derived useful information such as the dissociation energy of the complex (i.e. the strength of the hydrogen bonds) or the relative energies within the conformational landscape.

Encasing of Na+ ion in dimer-formed acetic acid clusters

Peaks with anomalous abundance found in the mass spectra are associated with ions with enhanced stability. Among the scientific community focused on mass spectrometry, these peaks are called 'magic peaks' and their stability is often because of suggestive symmetric structures. Here, we report findings on ionised Na-acetic acid clusters [Na(+) -(AcA)n ] produced by Na-doping of (AcA)n and UV laser ionisation. Peaks labelled n = 2, 4, 8 are clearly distinguishable in the mass spectra from their anomalous intensity. Ab initio calculations helped elucidate cluster structures and energetic. A plausible interpretation of the magic peaks is given in terms of (AcA)n formed by dimer aggregation. The encasing of Na(+) by twisted dimers is proposed to be the origin of the enhanced cluster stability. A conceivable dimer-formed tube-like closed structure is found for the Na(+) -(AcA)8 .

Direct observation of the cyclic dimer in liquid acetic acid by probing the C=O vibration with ultrafast coherent Raman spectroscopy

We present a comparison of spontaneous Raman and ultrafast coherent anti-Stokes Raman scattering (CARS) spectra of the C=O vibration of liquid acetic acid. The former technique cannot clearly reveal the number of contributions in the spectrum. However, the additional time and spectrally resolved CARS experiment supports strictly the existence of four modes, which proves the coexistence of more than one H-bonded configuration in liquid acetic acid. A comparably slowly dephasing mode which is obscured by a broad band in the linear Raman spectrum is assigned to the cyclic dimer and can be observed freed from all other contributions by ultrafast CARS.

Spectroscopic signatures and structural motifs in isolated and hydrated theophylline: a computational study

Optimized geometry of newly characterized theophylline dimer Form IV at MP2/6-311++G(d,p) level.

IR spectroscopy as a probe for C–H⋯X hydrogen bonded supramolecular synthons

We describe a five step IR spectroscopic method that identifies supramolecular synthons in weak hydrogen bonded dimer assemblies, bifurcated systems, and π-electron mediated synthons.

Strong intermolecular vibrational coupling through cyclic hydrogen-bonded structures revealed by ultrafast continuum mid-IR spectroscopy

Cyclic hydrogen-bonded structures are common motifs in biological systems, providing structural stability and mediating proton transfer for redox reactions. The mechanism of proton transfer across hydrogen-bonded interfaces depends on the strength of the intermolecular coupling between bridging OH/NH vibrational modes. Here we present a novel ultrafast continuum mid-IR spectroscopy experiment to study the vibrational dynamics of the 7-azaindole-acetic acid (7AI-Ac) heterodimer as a model system for asymmetric cyclic hydrogen-bonded structures. In addition to spreading of the excitation across the whole OH band within the time resolution of the experiment, excitation of a 300 cm(-1) region of the ∼1000 cm(-1) broad OH stretching mode of the acetic acid monomer leads to a frequency shift in the NH stretching mode of the 7AI monomer. This indicates that the NH and OH stretching modes located on the two monomers are strongly coupled despite being separated by 750 cm(-1). The strong coupling further causes the OH and NH bands to decay with a common decay time of ∼2.5 ps. This intermolecular coupling is mediated through the hydrogen-bonded structure of the 7AI-Ac heterodimer and is likely a general property of cyclic hydrogen-bonded structures. Characterizing the vibrational dynamics of and the coupling between the high-frequency OH/NH modes will be important for understanding proton transfer across such molecular interfaces.

Ultrafast optical nonlinearity, electronic absorption, vibrational spectra and solvent effect studies of ninhydrin

FT-IR, FT-Raman and UV-Vis spectra of the nonlinear optical molecule ninhydrin have been recorded and analyzed. The equilibrium geometry, bonding features, and harmonic vibrational wavenumbers have been investigated with the help of B3LYP density functional theory method. A detailed interpretation of the vibrational spectra is carried out with the aid of normal coordinate analysis following the scaled quantum mechanical force field methodology. Solvent effects have been calculated using time-dependent density functional theory in combination with the polarized continuum model. Natural bond orbital analysis confirms the occurrence of strong intermolecular hydrogen bonding in the molecule. Employing the open-aperture z-scan technique, nonlinear optical absorption of the sample has been studied in the ultrafast and short-pulse excitation regimes, using 100 fs and 5 ns laser pulses respectively. It is found that ninhydrin exhibits optical limiting for both excitations, indicating potential photonic applications.

N-H stretching excitations in adenosine-thymidine base pairs in solution: pair geometries, infrared line shapes, and ultrafast vibrational dynamics

We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes.

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.

Ultrafast vibrational frequency shifts induced by electronic excitations: naphthols in low dielectric media

We study the solvent-induced frequency shifts of the OH-stretching mode of 1-naphthol and 2-naphthol in nonpolar/weakly polar solvents, subject to electronic excitation, with ultrafast UV/mid-infrared pump-probe spectroscopy and theoretical modeling based on Pullin's perturbative treatment of vibrational solvatochromic effects. The model is parametrized at the density functional theory (DFT) level, including the B3LYP/TZVP and TD-B3LYP/TZVP descriptions, for the naphthol chromophores in the S(0)- and (1)L(b)-states and accounts for both the static and the optical dielectric response of the solvent on time scales comparable to that of the OH-stretching vibrational motions. The favorable comparison between experimental and theoretical values of the solvent-induced vibrational frequency shifts suggests that the ultrafast dielectric response of the solvent contributes predominantly to the solvatochromic shifts in solvents of moderate polarity where specific solute-solvent interactions are absent.

Effect of the resonance of the C-H and O-H bond stretching vibrations on the IR spectra of the hydrogen bond in formic and acetic acid

It is shown that the resonance of the O-H and C-H bond stretching vibrations is responsible for a noticeable intensity redistribution effect in the IR spectra of associated formic acid molecules in the gaseous phase. This effect is manifested by a considerably high growth in intensity of the νC-H band, which overlaps the νO-H band contour in the spectra. A vibronic coupling of the Herzberg-Teller-type expressed by the second order term in the perturbation theory is the most probable source of these spectral effects. The presented mechanism explains the variation of the effect magnitude accompanying the phase transitions. The proposed model also facilitates the understanding of the H/D isotopic effects in the spectra as well as the essential difference in the corresponding spectral properties between the formic and the acetic acid.