The effects of conformation and intermolecular hydrogen bonding on the structural and vibrational spectral data of naproxen molecule

The structural and vibrational properties of naproxen, an inhibitor of cyclooxygenase (COX) enzyme, were investigated by molecular modeling and experimental IR and Raman spectroscopic techniques. Possible conformers of the molecule were searched via a molecular dynamics simulation carried out with MM2 force field. The total energies, equilibrium geometries, force fields, IR and Raman spectral data of the found stable conformers were determined by means of geometry optimization and harmonic frequency calculations carried out using the B3LYP method and Pople-style basis sets of different size. The stability order obtained for the lowest-energy conformers was confirmed by high-accuracy thermochemistry calculations performed with G3MP2B3 composite method. Some electronic structure parameters of naproxen and the anharmonicity characters of its vibrational modes were determined by means of natural population analysis (NPA) and anharmonic frequency calculations at B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels of theory. A part of these calculations carried out for free naproxen molecule were repeated also for its energetically most favored dimer forms. Two different scaling procedures ((1) “SQM-FF methodology” and (2) “Dual scale factors”) were independently applied to the obtained harmonic vibrational spectral data to fit them to the corresponding experimental data. In the light of the obtained calculation results, which confirm the remarkable effects of conformation and intermolecular hydrogen bonding on the structural and vibrational spectral data, in particular, on those associated with the functional groups in the propanoic acid chain, a reliable assignment of the fundamental bands observed in the experimental IR and Raman spectra of the molecule was achieved.     

Infrared and ab initio studies of hydrogen bonding and proton transfer in the complexes formed by pyrazoles

The results of experimental studies and quantum mechanical calculations of vibrational spectra and structure of hydrogen bonded complexes formed by pyrazole (P) and 3,5-dimethylpyrazole (DMP) are presented. IR spectra of pyrazoles in solutions, gas phase, and solid state have been investigated in wide range of concentrations and temperatures. It has been found that in the gas phase both P and DMP reveal the equilibrium between monomers, dimers, and trimers. In solutions the equilibrium between monomers and trimers dominates, no bands, which can be attributed to dimers were detected. DMP retains the trimer structure in solid state, while in the case of pyrazole P, formation of the crystal provides another type of association. Geometrical and spectral characteristics of dimers and trimers, obtained by ab initio calculations, are presented and compared with experimental data.

IR spectra of solutions containing P and DMP with a number of acids (acetic and trifluoroacetic acids, pentachlorophenol, HBr) have been studied in parallel with ab initio calculations. It has been found that pentachlorophenol forms with pyrazoles complexes with one strong hydrogen bond O–HN, while NH pyrazole group remains unbonded. With carboxylic acids DMP forms 1:1 cyclic complexes with two hydrogen bonds. In the case of acetic acid, the complex in CH₂Cl₂ solution reveals molecular structure with OHN and C=OHN bonds, in accordance with results of the calculations. For trifluoroacetic acid, the calculations predict the molecular structure to be energetically more stable in the case of the isolated binary complex (in gas phase), while the experimental spectrum of CH₂Cl₂ solution gives an evidence of the proton transfer with formation of the cyclic ionic pair with two NH⁺O⁻ bonds. The agreement with experimental results can be improved by taking into account the influence of environment in the framework of Onsager or Tomasi models. The shape of proton potential function of the complexes and medium effect on its parameters, resulted from experimental data and calculations, are discussed. It has been found that the number of potential minima and their relative depth depend strongly on the method of calculations and the basic set. Under excess of trifluoroacetic acid, the formation of 2:1 acid–DMP complex has been detected. Spectral characteristics and results of calculations point to the cyclic structure of this complex, which includes homoconjugated bis-trifluoroacetate anion and DMPH⁺ cation. With HBr both studied pyrazoles were found to form ionic complexes including one or two pyrazole molecules per one acid molecule and correspondingly monocation or homoconjugated cation BHB⁺.     

[NHN] and [OHO] hydrogen bonding in the adduct of 1,8-bis(dimethylamino)naphthalene (DMAN) with 1,8-dihydroxy-2,4-dinitronaphthalene (DHDNN)

X-Ray diffraction, IR and ¹H NMR studies were performed on the 1:1 adduct of 1,8-bis(dimethylamino)naphthalene (DMAN) with 1,8-dihydroxy-2,4-dinitronaphthalene (DHDNN). The adduct crystallizes in the triclinic system, space group , a = 9.911(2) Å, b = 11.212(2) Å, c = 11.194(2) Å, = 68.95(2)°, β = 79.72(2)°, γ = 73.78(2)°, Z = 2. Both [NHN]⁺ and [OHO]⁻ hydrogen bonds formed in the ion pairs are asymmetrical with lengths equal to 2.574(2) Å and 2.466(4) Å respectively. The [NHN]⁺ bridge shows a typical behaviour in the IR spectrum, i.e. a low-frequency absorption between 300 and 700 cm⁻¹. The coupling of [OHO]⁻ hydrogen bonds with the naphthalene π-electron system is so strong that no absorption related to the proton stretching vibrations can be detected in the high- and low-frequency regions. The ¹H NMR chemical shifts for the [NHN]⁺ and [OHO]⁻ bridge protons of 18.63 and 15.81 ppm respectively confirm the strong hydrogen bonds.     

Structure and hydrogen bonding in polyhydrated complexes of guanine

Abstract Molecular structure of complexes of guanine with 12, 13, 16, and 17 water molecules were calculated using B3LYP/6-311G(d,p) level of theory. Interaction with water results in some deformation of geometrical parameters of guanine, which can be described as contribution of zwitter-ionic resonant form into the structure of DNA base. Saturation of water binding sites within guanine creates possibilities for the formation of the N···H–O hydrogen bond where the nitrogen atom of amino group acts as proton acceptor. The NBO analysis of guanine–water interactions reveals that hydrogen bonds involving the N(3) and N(7) atoms of guanine represent a case of mixed N···H–O/π···H–O hydrogen bonds where contribution of π-system into total energy of interaction varies from 3% to 41%. This contribution significantly depends on orientation of the hydrogen atom of water molecule with respect to plane of purine bicycle and influence of neighboring water molecules. Graphical Abstract      

Aramidocalix[4]arenes as new anion receptors

Calix[4]arenes bearing aromatic amide (aramid) moieties at the upper rim display interesting recognition properties toward anions and in particular versus planar trigonal nitrate and Y-shaped benzoate. Molecular modeling and DFT calculations indicate that the high affinity displayed by aramidocalix[4]arenes 3 and 4 for nitrate anion is likely due to the planar arrangement of the NH groups, which form an unusual six-hydrogen-bond scheme with nitrate anion.     

FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil

FT-IR and FT-Raman spectra of the biomolecule 5-aminouracil were recorded in the regions 400–4000 cm⁻¹ and 10–3500 cm⁻¹, respectively. The observed vibrational wavenumbers were analyzed and assigned to different normal modes of vibration of the molecule. Density functional calculations were performed to support wavenumber assignments of the observed bands. A comparison with the molecule of uracil was made, and specific scale factors were employed in the predicted wavenumbers of 5-aminouracil. With the purpose of study the important molecule 5-aminouracil, its equilibrium geometry and harmonic wavenumbers were calculated for the first time by the B3LYP DFT method. The vibrational wavenumbers were compared with IR and Raman experimental data. Also good reproduction of the experimental wavenumbers is obtained and the % error is very small. All the tautomeric forms of 5-aminouracil were determined and optimized. The dimer forms were also simulated. The energy, atomic charges and dipole moments were discussed and several general conclusions were underlined.     

FT-IR, FT-Raman vibrational spectra and molecular structure investigation of 2-chloro-4-methylaniline: A combined experimental and theoretical study

In this work, the experimental and theoretical vibrational spectra of 2-chloro-4-methylaniline (2Cl4MA, C₇H₈NCl) were studied. FT-IR and FT-Raman spectra of 2Cl4MA in the liquid phase have been recorded in the region 4000–400 cm⁻¹ and 3500–50 cm⁻¹, respectively. The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree-Fock (HF) and density functional method (B3LYP) with the 6-31G(d), 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p) and 6-311G(d), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p) basis sets. The vibrational frequencies have been calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The DFT-B3LYP/6-311++G(d,p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 2Cl4MA. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of aniline and p-methylaniline molecules.     

DFT, FT-Raman and FT-IR investigations of 5-methoxysalicylic acid

FT-IR and FT-Raman spectra of 5-methoxysalicylic acid (5MeOSA) have been experimentally reported in the region of 4000–10 cm⁻¹ and 4000–50 cm⁻¹, respectively. The optimized geometric parameters, conformational equilibria, normal mode frequencies and corresponding vibrational assignments of 5MeOSA (C₈H₈O₄) are theoretically examined by means of B3LYP hybrid density functional theory (DFT) method together with 6-31++G(d,p) basis set. Furthermore, reliable vibrational assignments have made on the basis of potential energy distribution (PED) calculated and the thermodynamics functions, highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) of 5MeOSA have been predicted. Calculations are employed for different conformations of 5MeOSA, both in gas phase and in solution. Solvent effects are investigated using chloroform and dimethylsulfoxide. All results indicate that B3LYP method is able to provide satisfactory results for predicting vibrational frequencies and the structural parameters, vibrational frequencies and assignments, IR and Raman intensities of 5MeOSA are solvent dependent.     

Metal-free synthesis of azacalix[4]arenes

The facile preparation of N(H)-bridged azacalix[4]arenes has been achieved by stepwise nucleophilic aromatic substitutions assisted by hydrogen bonding interactions. The synthesis is uncatalyzed and affords previously unknown tetranitroazacalix[4]arenes.     

Hydrogen bonding in 2-hydroxybenzoyl and 2-hydroxythiobenzoyl compounds: Spectroscopic characterization and spectroscopic bond strength sequences

Summary A survey of IR and NMR spectroscopic data is given for 30 2-hydroxybenzoyl and 2-hydroxy-thiobenzoyl compounds, which are representative for various kinds of (thio)carbonyl groups. The data shall provide a basis for a comparison between corresponding intramolecular O-H··O and O-H··S hydrogen bonds and for the evaluation of systematic dependencies. Correlations between v_OH frequencies, which are considered as the main characteristic of hydrogen bond strengths, and several other spectroscopic quantities are shown. For O-H··O type associations the bond strength sequence is acid chloridesOH-Frequenzen, die als wesentliches Kriterium zur Charakterisierung der Bindungsstärken herangezogen werden, und verschiedenen anderen spektroskopischen Daten werden gezeigt. Bei den Wasserstoffbrückenbindungen des Typs O-H··O nehmen die Bindungsstärken in der Reihenfolge SäurechlorideCO-Frequenzen. Die auffällige Sonderstellung der tertiären Amide ist auf sterische Effekte zurückzuführen. Die v_OH-Frequenzen der O-H··S Wasserstoffbrückenbindungen sind denen der entsprechenden O-H··O Bindungen sehr ähnlich, ausgenommen Thiosäuren und Thioester, für die wesentlich niedrigere Frequenzen gefunden wurden.     

Regioselective deuteration of 25,27-dialkoxycalix[4]arenes

A direct deuteration of the upper rim of calix[4]arene has been carried out for the first time. 25,27-Dialkoxy derivatives of calix[4]arene (R = Me, Et, n-Pr, n-Bu) were regioselectively deuterated at the para positions of unsubstituted phenolic rings using DCl/D₂O in tetrachloroethane. Interestingly, identical reaction conditions do not lead to deuteration of mono- or tri-substituted derivatives where only simple cleavage of alkyl substituents was observed.     

Pyrrolamidocalix[4]arenes: new receptors for anion recognition

Pyrrolamidocalix[4]arenes 1-4, members of a new class of anion receptors bearing pyrrolic units at the upper rim of calix[4]arene macrocycle, have been readily synthesized in good yields. Derivatives 1 and 3, with unsubstituted pyrrole units, show a good selectivity for over F⁻ and AcO⁻, while the presence of electron-withdrawing NO₂ substituents in 2 and 4 inverts the selectivity favoring more basic AcO⁻ and F⁻. In addition, it is demonstrated that the flexibility of calix[4]arene skeleton, present in 1 but absent in 3, is very important in the fitting process that leads the amidopyrrole moieties to wrap the tetrahedral guest.     

Hydrogen bonding in 2-hydroxybenzoic, 2-hydroxythiobenzoic,and 2-hydroxydithiobenzoic acid. A structural and spectroscopic study

Summary X-ray structural data are reported for 2-hydroxythiobenzoic acid (T=200 K;P2₁/a;a=14.903(5) Å,b=5.203(3) Å,c=9.114(6) Å, =92.40(4)°;Z=4;R=0.049) and 2-hydroxydithiobenzoic acid (T=297 K;P2₁/a;a=14.416(3) Å,b=13.447(3) Å,c=3.947(1) Å, =90.96(2)°;Z=4;R=0.047). In 2-hydroxythiobenzoic acid, each two molecules form cyclic dimersvia S-H...O=C hydrogen bonds, analogous to the association pattern of 2-hydroxybenzoic acid. In 2-hydroxydithiobenzoic acid, the molecules are linked to chains by S-H...O(H)-C hydrogen bonds. Solid state IR, and solution IR and NMR spectroscopic data of 2-hydroxybenzoic acid, 2-hydroxythiobenzoic acid, and 2-hydroxydithiobenzoic acid are summarized. The main characteristics of the intramolecularly associated phenolic O-H groups of the three title compounds are for the solids, for solutions (CCl₄), and _OH=10.21, 10.53, 12.20 ppm for solutions (CCl₄:CDCl₃=5:1).Dedicated to Prof.O. Olaj on the occasion of his 60^th birthday     

Infrared and Raman bands of phytantriol as markers of hydrogen bonding and interchain interaction

Hydrogen bonding and interchain interactions in phytantriol, 3,7,11,15-tetramethyl-1,2,3-hexadecanetriol, have been studied by Fourier transform infrared (FT-IR) and Raman spectroscopies. Assignments of the bands were performed based on the OH/OD isotopic substitution, molecular modeling, and measurements of polarized Raman spectra. Marker bands were evaluated from the temperature-dependent spectral changes. It is shown that Raman spectroscopy provides sensitive markers, namely I(delta(CH2))/I(deltas(CH3)), tau(CH)2, I(nus(CH3)(FR))/I(nus(CH2)), and nus(CH2) for probing the interactions between the hydrocarbon chains. Hydrogen bonding interaction might be studied through the difference Raman spectroscopy by the analysis of polarized band at 811 cm-1. Relationship is found between the frequencies of IR bands at 883-873 and 1097-1086 cm-1, associated with the vibrations localized at the primary COH site, and the frequencies of OH stretching mode, making these bands specific markers in the analysis of hydrogen bonding. Evaluated marker bands may be of utility to probe the interchain and hydrogen bonding interaction of phytantriol with guest molecules in the practically important aqueous liquid-crystalline phases of this lipid.     

DFT study of the IR and Raman spectra of a fluorescent dendron built from cyclotriphosphazene core

Combined experimental and theoretical studies on molecular structure of the zero generation dendron, built from the hexafunctional cyclotriphosphazene core, with five OC₆H₄(CH₂)₂NHSO₂C₁₀H₆N(CH₃)₂ terminal groups and one oxybenzaldehyde group G₀ are reported. The Fourier transform Raman and IR spectra of G₀ have been recorded. Conformations of low energy isomers of G₀ have been studied at quantum-chemical level. The optimized geometry has been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. The theoretical geometrical parameters, harmonic vibrational frequencies, IR intensities and Raman scattering activities are predicted in a good agreement with the experimental data. It was found that dendron molecule G₀ has a concave lens structure with planar OC₆H₄CHO fragments and slightly non-planar cyclotriphosphazene core. Relying on DFT calculations the bands of the core and terminal groups were assigned. The frequencies of ν(NH) bands in the IR spectrum reveal the presence of the H-bonds in the dendron.     

Spectroscopic study of hydrogen exchange processes and structure of intermediate complexes with intermolecular hydrogen bonds

The kinetics of hydrogen exchange in molecular systems with H-bonds has been studied by means of kinetic IR spectroscopy and low-temperature NMR spectroscopy. The experimental values of the rate constants and activation energies for molecules capable of forming H-bonds as both proton donors and proton acceptor are collected and analyzed from the point of view of the influence of H-bond formation ability of the molecules-partners. The evidence available testifies to a molecular mechanism of the H-exchange reactions in inert solvents and in the gas phase via the formation of cyclic bimolecular intermediates. The different mechanisms and the structure of intermediate complex of molecular H-exchange process in inert media are discussed and the possible paths of experimental elucidation of reaction mechanism are offered.     

Vibrational spectra and structures of urazole and 4-methylurazole: DFT calculations of the normal modes in aqueous solution and in the solid state,and the influence of hydrogen bonding

Solid-state IR and Raman as well as aqueous solution state Raman spectra are reported for urazole, 4-methylurazole and their deuterated derivatives. DFT calculations, at the B3-LYP/cc-pVTZ level, established that the structures and vibrational spectra of the molecules can be interpreted using models with hydrogen-bonded water molecules, in conjunction with the polarizable continuum solvation method. The vibrational spectra were computed at the optimised molecular geometry in each case, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments. Solid-state pseudopotential-plane-wave DFT calculations, using the PW91 functional were also carried out, reflecting the importance of intermolecular hydrogen bonding in the solid state.     

Strong intramolecular hydrogen bonds. Part I. Vibrational frequencies of the OH group in some picolinic acid N-oxides predicted from DFT calculated potentials and located in the infrared spectra

Hydrogen bonding in picolinic acid N-oxide (I), its 4-nitro (III), 4-methoxy (IV), 4-amino (V) derivatives and in quinaldic acid N-oxide (II) was characterized by calculations (B3LYP/6-31G(d)) of metric parameters, H-bond energies and one-dimensional proton potential functions with vibrational energy levels. Solvent effects were estimated by the SCRF PCM method of Tomasi and coworkers (J. Tomasi, M. Persico, Chem. Rev. 94 (1994) 2027). The potential functions are strongly asymmetric with the energy minimum placed near the carboxylic oxygen. The inflection near the NO oxygen develops into a second, shallower minimum under the SCRF.

Empirical assignments of the OH stretching and bending modes were made for (I)–(IV). The stretchings of (I, II) and (IV) in various solvents are observed in the region 1600–1300 cm⁻¹, but near 2600 cm⁻¹ for (III). The calculated and observed frequencies are in fairly good agreement with theoretical predictions reflecting the electronic effects of the substituents upon the H-bond strength. The observed trends in the solvent effects upon various parameters characterizing the H-bonding also correspond to predictions.     

Scaled quantum chemical calculations and FTIR, FT-Raman spectral analysis of 3,4-diamino benzophenone

The vibrational spectra of 3,4-diamino benzophenone (DABP) have been computed using B3LYP methodology and 6-31G* and 6-31G** basis sets. The solid phase FTIR and FT-Raman spectra were recorded in the region 4000-400 cm-1 and 3500-100 cm-1, respectively. A close agreement was achieved between the observed and calculated frequencies by employing normal coordinate calculations. The observed and simulated spectra were found to be well comparable.     

Kemp's triacid attached to octa-O-methyl resorc[4]arenes: conformations in solution and comparative binding studies with various 2-amino pyridines

We synthesized the new supramolecular host molecules 7 and 13 based on functionalized resorcarenes bearing Kemp's triacid. Conformations in solution have been investigated and the influence of intra- and intermolecular hydrogen bonds from the triacid was shown by low temperature and DOSY NMR experiments. The results of host 7 are supported by DFT calculations. The binding behaviour of 7 towards different 2-amino pyridines in chloroform has been investigated by NMR titrations. The association constants reach from K=207 M⁻¹ for 2-amino-5-cyano pyridine to K=1551 M⁻¹ for 2-amino-4-methyl pyridine. The association constants of the formed complexes of 7 with 2-amino pyridines were compared with those of the simple host systems 14 and 15 in order to evaluate the influence of the attached resorcarene host.