Theoretical infrared spectral density of H-bonds in liquid and gas phases: Anharmonicities and dampings effects

IR absorption band of weak H-Bonded systems: Showcasing the signature of the quantum indirect damping within the framework of a new approach using non-Hermitean Hamiltonian formalism

Herein, we investigate the effects of the irreversible action of the medium on the theoretical elucidation of the IR spectrum of weakly H-bonded systems, a prototypical model which provides a rigorous treatment of the relaxation mechanisms impacts on the IR spectral density. The attention will be focused particularly on the effect of indirect damping on the IRυS(X-H⃗) spectrum beyond the harmonic and adiabatic approximations. The ultimate objective of the present investigation is the treatment of the action of the surrounding of the intermonomer modes of H-bonded systems, which must induce a broadening of the Dirac delta peaks, the nature of which, as shown by Maréchal and Witkowski theory, is a Franck-Condon progression. The quantum treatment of the IR absorption band reveals that quantum relaxation of the intermonomer mode of H-bonded complexes could be successfully approached by a non-Hermitian Hamiltonian formalism. Motivated by development of a second method that will be able to validate the first approach, a computationally efficient algorithm was proposed for elucidating the quantum indirect relaxation using Hermitean Hamiltonians. The real eigenvalues, corresponding to different energies of the system are considered to be complex by adjunction of the imaginary parts, which reflects the action of the indirect irreversible action of the medium. These two crude approaches may pave the way for the incorporation of the mechanism of indirect relaxation in more physical and complex situations dealing, particularly, with tunnelling effects in strong H-bonded species, Fermi resonances, and Davydov coupling for cyclic H-bonds dimers beyond the harmonic and adiabatic assumptions.

Breaking the Structure of Liquid Hydrogenated Alcohols Using Perfluorinated tert-Butanol: A Multitechnique Approach (Infrared, Raman, and X-ray Scattering) Analyzed by DFT and Molecular Dynamics Calculations

The state of aggregation at room temperature of tert-butanol (TBH) and perfluoro tert-butanol (TBF) liquid mixtures is assessed by vibrational spectroscopy (Raman and infrared) and X-ray diffraction and analyzed using density functional theory (DFT) and molecular dynamics (MD) simulations. It is shown that larger clusters (mostly tetramers) of TBH are destroyed upon dilution with TBF. Small oligomers, monomers, and mainly heterodimers are present at the equimolar concentration. At variance with slightly interacting solvents, the signature of hetero-oligomers is shown by the appearance of a new broad band detected in the infrared region. The same spectral observation is detected for mixtures of other hydrogenated alcohols (methanol and 1-butanol). The new infrared feature is unaffected by dilution in a polar solvent (CDCl3) in a high-concentration domain, allowing us to assign it to the signature of small hetero-oligomers. MD simulations are used to assess the nature of the species present in the mixture (monomers and small hetero-oligomers) and to follow the evolution of their population upon the dilution. Combining MD simulations with DFT calculations, the infrared spectral profile is successfully analyzed in equimolecular mixtures. This study shows that TBF is a structure breaker of hydrogen-bonded alcohol networks and that the TBF (donor)-TBH (acceptor) heterodimer is the dominant species in an extended range of concentration, centered in the vicinity of the equimolar fraction.

How far the vibrational exciton interactions are responsible for the generation of the infrared spectra of oxindole crystals?

Oxindole (indolin-2-one, Ox) is a unique and a crucial molecular system in spectroscopic studies. Indole is the core structure of many substances found in the human body (tryptophan, serotonin) and the indole alkaloids have highly differentiated pharmacological properties such as analgesic, anti-fever and anti-inflammatory. The Ox's structural results given in the Cambridge Structural Database revealed the existence of only one crystalline form of Ox, referred to the α-form. However, we have experimentally noticed the existence of two polymorphic forms during the crystallization of Ox. Furthermore, the significant spectral differences that we have observed in the solid state infrared spectra of these two forms additionally confirm the existence of the polymorphism phenomenon. Of the four polymorphic forms of Ox, two of them - α - and β-forms - were of particular interest. In the crystalline lattices of both polymorphs, we observed a similar pattern of molecular arrangements giving rise to the supramolecular synthon according to the terminology of Etter. Moreover, hydrogen bonds in the dimer of the α-form are found to be non-equivalent (non-centrosymmetric dimers), having a length of 2797 Å and 2979 Å, respectively. Comparatively, in the most densely packed crystalline structure of Ox, the β-form, the dimer is formed by a pair of almost identical intermolecular hydrogen bonds and consequently the crystals of β-form exhibited spectral properties typical to centrosymmetric hydrogen bond dimers. In addition, the spectroscopic studies that we have conducted to polymorphic forms of Ox, isotopically diluted with deuterium, show the dramatic influence of isotopic substitution in the hydrogen bridge on the infrared spectra of hydrogen bonding. Thus, the main goal of this work is the proposition of a theoretical approach that can describe the main features of the crystalline infrared spectra of the Ox polymorphs. The proposed approach is based on the phenomenon of the exciton coupling results directly from intermolecular interactions in the vibrationally excited state which leads to the delocalization of the excitation over the molecules in the lattice and to the Davydov splitting effect in the crystalline spectra.

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.

Understanding the vibrational spectra of crystalline isoniazid: Raman, IR and INS spectroscopy and solid-state DFT study

This work presents a comprehensive spectroscopic analysis of crystalline isoniazid, one of the main drugs in tuberculosis chemotherapy, using a blend of spectroscopic and computational methods. Mid- and far-infrared, Raman, and inelastic neutron scattering spectroscopies, with contribution of isotopic substitution are combined with discrete and periodic DFT quantum chemical calculations. This combined approach successfully reproduces the whole spectral range, allowing a sound assignment of all the vibrational bands. Previous misassignments have been corrected and several spectral features of isoniazid crystal are reported for the first time. Virtues and limitations of the computational approach (periodic and discrete) are also discussed in light of the present state-of-the-art in the field.

Equivalence between the Classical and Quantum IR Spectral Density Approaches of Weak H-Bonds in the Absence of Damping

The aim of this paper is to overhaul the quantum elucidation of the spectral density (SD) of weak H-bonds treated without taking into account any of the damping mechanisms. The reconsideration of the SD is performed within the framework the linear response theory. Working in the setting of the strong anharmonic coupling theory and the adiabatic approximation, the simplified expression of the classical SD, in the absence of dampings, is equated to be I_Cl(ω) = Re[∫₀^∞G_Cl(t)e^-iΩt dt] in which the classical-like autocorrelation function (ACF), G_Cl(t), is given by G_Cl(t) = tr{ρ(β){μ(0)}{μ(t)}^†}. With this consideration, we have shown that the classical SD is equivalent to the line shape obtained by F(ω) = ΩI_Cl(ω), which in turn is equivalent to the quantum SD given by I_Qu(ω) = Re[∫₀^∞G_Qu(t)e^-iΩt dt], where G_Qu(t) is the corresponding quantum ACF having for expression G_Qu(t) = (1/β) tr{ρ∫₀^β[μ(0)}{μ(t + iλℏ)}^† dλ}. Thus, we have shown that for weak H-bonds dealt without dampings, the SDs obtained by the quantum approaches are equivalent to the SDs geted by the classical approach in which the incepation ACF is, however, of quantum nature and where the line shape is the Fourier transform of the ACF times the angular frequency. It is further shown that the classical approach dealing with the SD of weak H-bonds leads identically to the result found by Maréchal and Witkowski in their pioneering quantum treatment where they ignored the linear response theory and dampings.

Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac

Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO₂^-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO₂^- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO₂^- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO₂^- group of bioactive molecules with the water molecules in dilute aqueous solutions.

Electrical anharmonicity in hydrogen bonded systems: complete interpretation of the IR spectra of the Cl-H[combining right harpoon above] stretching band in the gaseous (CH3)2OHCl complex

Following the previous developments to simulate the fully infrared spectra of weak hydrogen bond systems within the linear response theory, an extension of the adiabatic model is presented here. A general formulation including the electrical anharmonicities in the calculation of the damped autocorrelation function of weak H-bonds is adopted to facilitate the support of the additional properties, and thus the IR spectra of the Cl-H[combining right harpoon above] stretching band in the gaseous (CH₃)₂OHCl complex. We have explored the origins of the broadening of the Cl-H[combining right harpoon above] stretching band. We found that the main features of the lineshape are attributed to electrical anharmonicity as a consequence of the large mixed second derivatives of the dipole moment with respect to the Cl-H[combining right harpoon above] bond and of the intermonomer elongations . In addition to providing more accurate theoretical band shapes, inclusion of the electrical anharmonicity in the present model paves the way for a more complete interpretation by generating three new Franck-Condon superposed distributions.

H/D isotopic recognition mechanism in hydrogen-bonded crystals of 3-methylacetanilide and 4-methylacetanilide

Polarized IR spectra of 3- and 4-methylacetanilide as well as their deuterium derivative crystals were measured at 293K and at 77K by a transmission method. The obtained results were interpreted within the limits of the "strong-coupling" theory. This approach facilitated the understanding of the H/D isotopic, temperature and dichroic effects observed in the hydrogen bond IR spectra. The existence of H/D isotopic "self-organization" phenomenon, depending on the non-random distribution of protons and deuterons in the crystal lattices of isotopically diluted samples of a compound was ascertained. This effect resulted from the dynamical co-operative interactions involving the closely spaced hydrogen bonds, each belonging to a different chain of associated 3- and 4-methylacetanilide molecules. In the case of 4-methylacetanilide crystals weaker but non-negligible exciton coupling also involved adjacent hydrogen bonds in each molecular chain and the H/D isotopic "self-organization" mechanism concerned at least four hydrogen bonds from each unit cell. The source of these phenomena was ascribed to the molecular electronic properties determined by aromatic rings linked to nitrogen atoms of the amide fragments.

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.

H/D isotopic recognition in hydrogen-bonded systems: strong dynamical coupling effects in the polarized IR spectra of 3-methylthioacetanilide and 4-methylthioacetanilide crystals

This paper presents the investigation results of the polarized IR spectra of the hydrogen bond in crystals of 3- and 4-methylthioacetanilide. The spectra were measured at 293 and 77 K by a transmission method, with the use of polarized light. The main spectral properties of the crystals can be interpreted satisfactorily in terms of the "strong-coupling" theory, on the basis of the hydrogen bond centrosymmetric dimer model. The spectra revealed that the strongest vibrational exciton coupling involved the closely spaced hydrogen bonds, each belonging to a different chain of associated 3- and 4-methylthioacetanilide molecules. A weaker exciton coupling involved the adjacent hydrogen bonds in each individual chain. It was proven that a nonrandom distribution of the protons and deuterons took place in the lattices of isotopically diluted crystalline samples of 3- and 4-methylthioacetanilide. In each case, the H/D isotopic "self-organization" mechanism involved all four hydrogen bonds from each unit cell.

Localization and anharmonicity of the vibrational modes for GC Watson-Crick and Hoogsteen base pairs

We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson-Crick and Hoogsteen base pair configurations. The results are obtained by using two different implementations of the DFT method. We assign the vibrational frequencies to cytosine or to guanine using the vibrational density of states. Next, we investigate the importance of anharmonic corrections for the vibrational modes. In particular, the unusual anharmonic effect of the H(+) vibration in the case of the Hoogsteen base pair configuration is discussed.