Monitoring structural fluctuations of discotic liquid crystal during phase transitions

The discotic liquid crystal 4-((2, 3, 4-tris (octyloxy) phenyl) diazenyl) benzoic acid, hereafter referred as DLC A8, exhibited in dimeric form has been studied using a combination of quantum chemical approaches and vibrational spectroscopy. This study investigates the structural alteration of DLC A8 associated with phase transition. The phase transitions of DLC A8 are Iso → Discotic nematic → Columnar → Crystalline, which have been investigated using differential scanning calorimetry (DSC) accompanied with polarized optical microscopy (POM). Monotropic columnar mesophase was observed during the cooling cycle while discotic nematic mesophase was observed in both the heating and cooling cycles. Density functional theory (DFT) along with IR and Raman spectroscopic techniques were utilized to study the dynamics of molecules during phase transition. To predict the most stable conformation of the molecule, one-dimensional PES scans have been performed along 31 flexible bonds using DFT/B3LYP/6-311G++(d,p) method. Vibrational normal modes were analyzed in detail, taking potential energy contribution into account. The spectral analysis of FT-IR and FT-Raman was done by deconvoluting the structural sensitive bands. The agreement between the calculated IR and Raman spectra and the observed FT-IR and Raman spectra at room temperature confirms our theoretically predicted molecular model of investigated discotic liquid crystal. Moreover, our studies have unraveled the existence of intact intermolecular H-bonding of dimers throughout the phase transitions.

Understanding the mechanism and regio- and stereo selectivity of [3 + 2] cycloaddition reactions between substituted azomethine ylide and 3,3,3-trifluoro-1-nitroprop-1-ene, within the molecular electron density theory

The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction between 2-(dimethylamino)-1H-indene-1,3(2H)-dione (AY11) and trans(E)-3,3,3-trifluoro-1-nitroprop-1-ene(FNP10) has been studied, in which the molecular electron density theory using density functional theory methods at the MPWB1K/6-31G(d) computational level was used. Analysis of the global reactivity indices permits us to characterize FNP10 as a strong electrophile and AY11 as a strong nucleophile. Four reactive pathways associated with the ortho/meta regioselective channels and endo/exo stereoselective approaches modes have been explored and characterized in the gas phase and in the benzene solvent. The analysis of the relative energies associated with the different reaction pathways indicates that the 32CA reactions of the azomethine ylide (AY) with the nitroalkene (FNP) is meta regioselective with high endo stereoselectivity. This result is in good agreement with the experimental observations. electron localization function topological analysis of the most favored reactive pathways allows for characterizing the mechanism of this 32CA reactions as a non-concerted two-stage one-step mechanism. Finally, non-covalent interactions and quantum theory of atoms in molecule analyses at the meta/endo transition state structure indicate that the presence of different several weak interactions, namely, CF and NH contributed in favoring the formation of a meta-endo cycloadduct.

Analysis of the Electron Density of a Water Molecule Encapsulated by Two Cholic Acid Residues

Cholic acid is a trihydroxy bile acid with a nice peculiarity: the average distance between the oxygen atoms (O7 and O12) of the hydroxy groups located at C7 and C12 carbon atoms is 4.5 Å, a value which perfectly matches with the O/O tetrahedral edge distance in Ih ice. In the solid phase, they are involved in the formation of hydrogen bonds with other cholic acid units and solvents. This fact was satisfactorily used for designing a cholic dimer which encapsulates one single water molecule between two cholic residues, its oxygen atom (Ow) being exactly located at the centroid of a distorted tetrahedron formed by the four steroid hydroxy groups. The water molecule participates in four hydrogen bonds, with the water simultaneously being an acceptor from the 2 O12 (hydrogen lengths are 2.177 Å and 2.114 Å) and a donor towards the 2 O7 (hydrogen bond lengths are 1.866 Å and 1.920 Å). These facts suggest that this system can be a nice model for the theoretical study of the formation of ice-like structures. These are frequently proposed to describe the water structure found in a plethora of systems (water interfaces, metal complexes, solubilized hydrophobic species, proteins, and confined carbon nanotubes). The above tetrahedral structure is proposed as a reference model for those systems, and the results obtained from the application of the atoms in molecules theory are presented here. Furthermore, the structure of the whole system allows a division into two interesting subsystems in which water is the acceptor of one hydrogen bond and the donor of another. The analysis of the calculated electron density is performed through its gradient vector and the Laplacian. The calculation of the complexation energy used correction of the basis set superposition error (BSSE) with the counterpoise method. As expected, four critical points located in the H…O bond paths were identified. All calculated parameters obey the proposed criteria for hydrogen bonds. The total energy for the interaction in the tetrahedral structure is 54.29 kJ/mol, while the summation obtained of the two independent subsystems and the one between the alkyl rings without water is only 2.5 kJ/mol higher. This concordance, together with the calculated values for the electron density, the Laplacian of the electron density, and the lengths of the oxygen atom and the hydrogen atom (involved in the formation of each hydrogen bond) to the hydrogen bond critical point, suggests that each pair of hydrogen bonds can be considered independent of each other.

Manifestations of intramolecular H-bonds of CH… O and OH… C type in quercetin molecule: Analysis of IR spectra by mean of density functional theory

The IR spectra of 48 conformers of quercetin which represent full conformation space of its tautomers have been modeled at B3LYP/6-311++G(d,p) level of the density functional theory. The presence of intramolecular H-bonds C2'H/C6'H…O3 and O3H…C2'/C6' was characterized by their spectral manifestations. The C2'H/C6'H…O3 contacts were found to have a spectral blue-shift. The O3H…C2'/C6' contacts were mostly red-shifted. The stretching vibrations of H-bonds C2'H/C6'H…O3 demonstrate an increase in the intensity of the modes of stretching vibrations ν(C2'H)/ν(C6'H) and an increase in the frequency of their out-of-plane vibrations γ(C2'H)/γ(C6'H). Most of the spectral parameters correlate a little with the energy of the H-bonds.

Adjusting the balance between hydrogen and chalcogen bonds

A complex is assembled which pairs a carboxyl group of X₁COOH with a 1,2,5-chalcogenadiazole ring containing substituents on its C atoms. The OH of the carboxyl group donates a proton to a N atom of the ring to form a OH⋯N H-bond (HB), while its carbonyl O engages in a Y⋯O chalcogen bond (ChB) with the ring in which Y = S, Se, Te. The ChB is strengthened by enlarging the size of the Y atom from S to Se to Te. Placement of an electron-withdrawing group (EWG) X₁ on the acid strengthens the HB while weakening the ChB; the reverse occurs when EWGs are placed on the ring. By selection of the proper substituents on the two units, it is possible to achieve a near perfect balance between the strengths of these two bonds. These bond strengths are also reflected in the NMR spectroscopic properties of the chemical shielding of the various atoms and the coupling between the nuclei directly involved in each bond.

Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds

In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10-15% D and 80-90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400-4000 cm^-1 range, as a function of temperature (10-300 K). We provide assignments of the stretching and out-of-plane bending amine (NH₂) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine. In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader's quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.

Estimations of FH···X hydrogen bond energies from IR intensities: Iogansen's rule revisited

In this work the possibility of using the IR intensity of the stretching vibration ν_s of proton donor group for estimation of hydrogen bond strength was investigated. For a set of complexes with FH···X (X = F, N, O) hydrogen bonds in the wide range of energies (0.1-49.2 kcal/mol) vibrational frequencies ν_s and their intensities A were calculated (CCSD at complete basis set limit). The validity of the previously proposed linear proportionality between the intensification of the stretching vibration ν_s in IR spectra and hydrogen bond enthalpy -ΔH = 12.2 ∆ A (A. V. Iogansen, Spectrochimica Acta A 1999) was examined. It is shown that for a range of similar hydrogen bond types with complexation energies ∆E <15 kcal/mol the ∆E( ∆ A ) function remains similar to that proposed in the Iogansen's work, while upon strengthening this dependency becomes significantly nonlinear. We examined two other parameters ( ∆ A ν s and ∆ A ∙ m R ) related to IR intensity as descriptors of hydrogen bond strength which are proportional to transition dipole moment matrix element and mass-independent dipole moment derivative. It was found that the dependency ∆E( ∆ A ν s ) stays linear in the whole studied range of complexation energies and it can be used for evaluation of ∆E from infrared spectral data with the accuracy about 2 kcal/mol. The mass-independent product ∆ A ∙ m R is an appropriate descriptor for sets of complexes with various hydrogen bond types. Simple equations proposed in this work can be used for estimations of hydrogen bond strength in various systems, where experimental thermodynamic methods or direct calculations are difficult or even impossible.

Stretching force constants as descriptors of energy and geometry of F···HF hydrogen bonds

In this work applicability of proton donor group stretching vibration force constants k_s and intermolecular stretching force constants k_σ for evaluations of hydrogen bond strength and geometry are discussed. For a set of 30 complexes with F···HF hydrogen bonds in a wide range 0.5-48 kcal/mol by means of quantum chemical calculations equilibrium geometries, complexation energies, vibrational frequencies and corresponding force constants were calculated (MP2/aug-cc-pVTZ). It is shown, that properties of a hydrogen bond are more strictly correlated with the values of force constants than with vibrational frequencies. Easy-to-use equations for estimations of hydrogen bond energy ∆E and geometry (r_FH, r_FF) based on k_s and k_σ values are proposed.

The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C2H2⋯HF and C2H4⋯HF small dimers

The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C₂H₂⋯(HF), C₂H₂⋯2(HF), C₂H₂⋯4(HF), C₂H₄⋯(HF), C₂H₄⋯2(HF) and C₂H₄⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).

Excited state hydrogen atom transfer in micro-solvated dicoumarol: A TDDFT/EFP1 study

Ground (S₀) and excited (S₁) state properties of dicoumarol (DC) are investigated by applying density functional theory (DFT) and time dependent DFT (TDDFT) interfacing with the effective fragment potential (EFP) method of solvation. Benzene and pyrone rings of the each 4-hydroxy coumarin (4HC) moiety are in a plane and these planes are twisted by 180° with respect to each other. Two intra-molecular hydrogen bonds (HB) CO⋯HO exist between the carbonyl (CO) and hydroxyl (OH) groups of different 4HC moieties (4HC-1 and 4HC-2). DC(H₂O)₃ complex is formed using the original EFP model (EFP1). Four inter-molecular HBs are established by the carbonyl and hydroxyl oxygen atoms of 4HC-1 and 4HC-2 moieties; two HBs with two solvent molecules on one side of the complex and other two HBs with one solvent molecule at the other side. In S₁ state, the hydrogen atomtransfer takes place only from the hydroxyl group of 4HC-1 to the carbonyl group of 4HC-2. The natural charge analysis and the modification of HBs manifest the intra-molecular charge transfer (ICT) from one 4HC moiety to another. Theoretical and experimental studies of the absorption spectra, and the theoretical study of potential energy curves of OH bonds at both S₀ and S₁ states affirm the hydrogen atom transfer from the hydroxyl group of 4HC-1 to the carbonyl group of 4HC-2 moiety.

The Influence of the Position of the Double Bond and Ring Size on the Stability of Hydrogen Bonded Complexes

To study the influence of the position of the double bond and ring size on the stability of hydrogen bonded complexes, the 1:1 complexes formed between 2,2,2-trifluoroethanol (TFE) and three heterocyclic compounds including 2,3-dihydrofuran (2,3-DHF), 2,5-dihydrofuran (2,5-DHF) and 3,4-dihydropyran (3,4-DHP) were investigated systematically. The formation of hydrogen bonded TFE−2,3-DHF, TFE−2,5-DHF and TFE−3,4-DHP complexes were identified by gas phase FTIR spectroscopy at room temperature, and the OH-stretching fundamental transition of TFE was red shifted upon complexation. The competition between the O atom and π-electrons bonding sites within the complexes was studied, and the O−H···π type hydrogen bond was found to be less stable than the O−H···O in all three cases. The observed red shifts of the OH-stretching fundamental transitions in the complexes were attributed to the formation of O−H···O hydrogen bond. Equilibrium constants of the complexation reactions were determined from measured and calculated OH-stretching fundamental intensities. Both theoretical calculations and experimental results reveal that the hydrogen bond strengths in the complexes follow the sequence: TFE−2,5-DHF > TFE−2,3-DHF ≈ TFE−3,4-DHP, thus the position of the double bond exerts significantly larger influence than ring size on the stability of the selected hydrogen bonded complexes.

The interaction strengths and spectroscopy parameters of the C2H2∙∙∙HX and HCN∙∙∙HX complexes (X = F, Cl, CN, and CCH) and related ternary systems valued by fluxes of charge densities: QTAIM, CCFO, and NBO calculations

This theoretical work exhibits a new systematic study of structural parameters, electronic properties, infrared vibration modes, and molecular topography of hydrogen complexes, namely linear-type HCN⋯HX and T-type C₂H₂⋯HX (X = F, Cl, CN, and CCH). Ideally, the knowledge of the ternary systems of C₂H₂⋯HCN⋯HF and HCN⋯HCN⋯HF whose subparts integrate the linear and T-shaped complexes were used to give support in this current research. By means of computational calculations carried out in both levels B3LYP and MP2, the variations of the HX bond lengths are clearly overestimated in the HCN⋯HX linear complexes. In agreement with the analyses of the electrostatic potentials, the higher intermolecular energies of these complexes agree with the larger red-shifts in the stretch frequencies in HX. Also, the QTAIM descriptors and NBO calculations were used to inspect the interaction strength as well as to confirm the π cloud as a proton accepting center. By taking into account the absorption intensity ratio as a standard parameter to predict the interaction strength and intermolecular characterization, the formalism of the charge-charge flux-overlap modified (CCFO) was applied.

Variable Temperature Infrared Spectroscopy Studies of Aromatic Acid Adsorbate Effects on Montmorillonite Dehydration

Molecular interactions between benzoic, salicylic, and acetylsalicylic acids and water contained within montmorillonite clay interlayer spaces are characterized by using variable temperature diffuse reflection infrared Fourier transform spectroscopy (VT-DRIFTS). By using sample perturbation and difference spectroscopy, infrared (IR) spectral variations resulting from the removal of interlayer water are used to characterize aromatic acid local environment changes. Difference spectra features representing functional group perturbations are correlated with changes in IR absorptions associated with -O-H and -C = O stretching vibrations. Results suggest that adsorbate carboxylic acid functionalities participate in extensive hydrogen bonding and that the strengths of these interactions are diminished when clays are dehydrated. The nature of these interactions and their temperature-dependent properties are found to depend on adsorbate structure and concentration as well as the clay interlayer cation.

Toward a uniform description of hydrogen bonds and halogen bonds: correlations of interaction energies with various geometric, electronic and topological parameters

Correlations between interaction energies and various structural parameters were established to reveal the differences between hydrogen bonds and halogen bonds.