Natural bond orbital analysis and vibrational spectroscopic studies of H-bonded N,N′-diphenylguanidinium nitrate

NIR-FT Raman and FT-IR spectra of the crystallized biologically active molecule N,N′-diphenylguanidinium nitrate (DGN) have been recorded and analyzed using quantum chemical computations based on density functional theory. The extraordinary basicity and strong stability of this novel bioactive compound has been discussed as the consequence of resonance stabilization leading to Y-aromaticity and hydrogen bonding. This peculiar Y-delocalization character of DGN is well reflected in the optimized geometry and bond order (BO) calculations. The observance of the equality of C–N bond lengths in the protonated species indicates delocalization of the π-electron system. The spectroscopic and natural bonds orbital (NBO) analysis confirms the occurrence of strong network of inter molecular hydrogen bonds. The changes in electron density in the global minimum and in the energy of hyperconjugative interactions of DGN calculated by second order perturbation theory have been studied extensively in comparison with the values of the neutral species. The observed characteristic ring vibrations are well fit with the theoretical values calculated at B3LYP/6-31G* level.     

Interaction in trans-2-halocyclohexanols — an infrared and theoretical study

The O–H and C–O stretching frequencies of trans-2-halocyclohexanols in CCl₄ solutions have been measured and theoretical calculations have been performed to elucidate the main interactions, which are responsible for the conformational equilibria in these systems. It can be concluded that hydrogen bonding is predominant for trans-2-fluorocyclohexanol, leading to a stabilization of the eq–eq conformation, while for the chlorine, bromine and iodine derivatives, besides hydrogen bonding, gauche and steric interactions are also present.     

Comparative Study of Halogen‐ and Hydrogen‐Bond Interactions between Benzene Derivatives and Dimethyl Sulfoxide

The halogen bond, similar to the hydrogen bond, is an important noncovalent interaction and plays important roles in diverse chemistry‐related fields. Herein, bromine‐ and iodine‐based halogen‐bonding interactions between two benzene derivatives (C₆F₅Br and C₆F₅I) and dimethyl sulfoxide (DMSO) are investigated by using IR and NMR spectroscopy and ab initio calculations. The results are compared with those of interactions between C₆F₅Cl/C₆F₅H and DMSO. First, the interaction energy of the hydrogen bond is stronger than those of bromine‐ and chlorine‐based halogen bonds, but weaker than iodine‐based halogen bond. Second, attractive energies depend on 1/rⁿ, in which n is between three and four for both hydrogen and halogen bonds, whereas all repulsive energies are found to depend on 1/r^8.5. Third, the directionality of halogen bonds is greater than that of the hydrogen bond. The bromine‐ and iodine‐based halogen bonds are strict in this regard and the chlorine‐based halogen bond only slightly deviates from 180°. The directional order is iodine‐based halogen bond>bromine‐based halogen bond>chlorine‐based halogen bond>hydrogen bond. Fourth, upon the formation of hydrogen and halogen bonds, charge transfers from DMSO to the hydrogen‐ and halogen‐bond donors. The CH₃ group contributes positively to stabilization of the complexes.     

N-(p-methoxyphenyl)-N-prop-2-ynyl-urea: a crystal structure with the rare Z′=5, and statistical data on Z′ values

The crystal structure of N-(p-methoxyphenyl)-N-prop-2-ynyl-urea contains five symmetry-independent molecules (Z′=5), which is a high and rarely occurring value. The five molecules have similar but not identical conformations, and form similar but not identical intermolecular interactions. The terminal alkyne groups of the five molecules are oriented differently, and form different hydrogen bond interactions (C–HO and C–Hπ). This is an example of how simple molecules can form a highly complicated solid state structure.     

Recognition of carboxylate and dicarboxylates by azophenol–thiourea derivatives: a theoretical host–guest investigation

Geometries of azophenol–thiourea derivative complexes with acetate, oxalate, malonate, succinate, glutarate, adipate, pimelate, suberate and azelate were carried out using the integrated MO:MO method. The binding and complexation energies of these complexes were derived from the ONIOM(B3LYP/6-31G(d):AM1) calculations. The relative stabilities of the complexes of azophenol–thiourea derivatives with carboxylate guests are reported. The binding interactions of the azophenol–thiourea receptor 1, 2 and carboxylate guests are described as multipoints hydrogen bonding, where the amine and phenolic hydrogen atoms of receptors act as hydrogen bond donors in complex with acetate and all amine-hydrogen and phenolic hydrogen atoms act as hydrogen bond donors in complex with dicarboxylate guests. Thermodynamic properties of binding interactions between receptors 1, 2 and their preorganizations and complexations are also reported.     

AB initio SCF LCAO MO study of the HOH…Cl− hydrogen bond

Ab initio SCF LCAO MO calculations for the [H₂O…Cl]^? complex have been performed. The energy of the linear hydrogen bond has been found to be lower than the energy of the bifurcated one. The difference of the energies is about 3 kcal/mole. The calculated equilibrium distance between the oxygen and chlorine atoms equals 5.75 au. The interaction energy of the chlorine anion and the rigid water molecule amounts to ?19 kcal/mole. The optimization of the OH bond length in the complex (linear hydrogen bond) leads to an interaction energy of ?19.5 kcal/mole (the experimental value equals ?13.1 kcal/mole). As a result of the hydrogen bond formation the OH bond length increases by 0.08 au.     

Basis set superposition error in N-body clusters

We present a new scheme for calculating the basis set superposition error (BSSE) in N-body clusters. It is based on the assumption that each n-body term can be expressed as a sum of only two-body contributions. The conventional Boys–Bernardi method can be used thus for calculating BSSE-corrected energy terms. The scheme is illustrated by some calculations on the hydrogen fluoride trimers and tetramers. The results are compared to the ones obtained with the site–site function counterpoise (SSFC), the hierarchical (Valiron–Mayer) function counterpoise (VMFC), the pairwise additive function counterpoise (PAFC), and the successive reaction counterpoise (SRCP) schemes.     

Reactions of N, N-dichloroalkylamines with solid base as studied by FTIR combined with DFT calculations

Products of vacuum gas–solid reactions of N, N-dichloroalkylamines with KOH have been identified by FTIR spectroscopy and DFT calculations. It has been found that the reactions consist of elimination of two Cl atoms accompanied with migration of an H atom, a ring carbon or a methyl group from the -carbon to the N atom and unstable imines with a C=N double bond are formed.     

Intramolecular hydrogen bonds with large proton polarizability in semisalts of mono- and di-N-oxides of N,N′-tetraalkyl-o-xylyldiamines

Heteroconjugated NO⁺H … N NO … H⁺N and homoconjugated NO⁺H … ON NO … H⁺ON intramolecular hydrogen bonds formed in semisalts of mono- and di-N-oxides of N,N′-tetraalkyl-o-xylyldiamines were studied by IR and NMR spectroscopy. All these hydrogen bonds show large proton polarizability. In the case of the heteroconjugated hydrogen bonds the proton transfer equilibrium shifts from compounds 1 to 3 to the left hand side since the interaction of the hydrogen bond with the solvent environment decreases in this series of compounds. With compound 1 the hydrogen bonds are slightly weaker and longer, hence the wavenumber dependence of the intensity of the continuum caused by these hydrogen bonds is slightly changed with compound 1 compared with compound 2. In the case of compound 3 the intensity of the continuum decreases because of increasing screening of the hydrogen bonds. In the series of homoconjugated hydrogen bonds, from compound 4 to 6 the intense continuum vanishes, and only the band of the 0–1 proton transition at 950 cm⁻¹ remains. The vanishing of the continuum is caused by increasing screening of the hydrogen bonds against their solvent environments by bulky groups, and thus, this change demonstrates again that the interaction of the hydrogen bond with large proton polarizabilities is a necessary prerequisite for IR continua to appear.     

Blue-shifted hydrogen-bonded complexes. II. CH3F(HF)1 n 3 and CH2F2(HF)1 n 3

The equilibrium structures, binding energies, and vibrational spectra of the clusters CH₃F(HF)_{1 n 3} and CH₂F₂(HF)_{1 n 3} have been investigated with the aid of large-scale ab initio calculations performed at the Møller–Plesset second-order level. In all complexes, a strong C–FH–F halogen–hydrogen bond is formed. For the cases n = 2 and n = 3, blue-shifting C–HF–H hydrogen bonds are formed additionally. Blue shifts are, however, encountered for all C–H stretching vibrations of the fluoromethanes in all complexes, whether they take part in a hydrogen bond or not, in particular also for n = 1. For the case n = 3, blue shifts of the ν(C–H) stretching vibrational modes larger than 50 cm⁻¹ are predicted. As with the previously treated case of CHF₃(HF)_{1 n 3} complexes (A. Karpfen, E. S. Kryachko, J. Phys. Chem. A 107 (2003) 9724), the typical blue-shifting properties are to a large degree determined by the presence of a strong C–FH–F halogen–hydrogen bond. Therefore, the term blue-shifted appears more appropriate for this class of complexes. Stretching the C–F bond of a fluoromethane by forming a halogen–hydrogen bond causes a shortening of all C–H bonds. The shortening of the C–H bonds is proportional to the stretching of the C–F bond.     

DFT study on the intermolecular interactions between Aun (n = 2–4) and thymine

Density functional B3LYP method with 6-31++G** basis set is applied to optimize the geometries of the luteolin, water and luteolin–(H₂O)_n complexes. The vibrational frequencies are also studied at the same level to analyze these complexes. We obtained four steady luteolin–H₂O, nine steady luteolin–(H₂O)₂ and ten steady luteolin–(H₂O)₃, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) are used to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are within −13.7 to −82.5 kJ/mol. The strong hydrogen bonding mainly contribute to the interaction energies, Natural bond orbital analysis is performed to reveal the origin of the interaction. All calculations also indicate that there are strong hydrogen bonding interactions in luteolin–(H₂O)_n complexes. The OH stretching modes of complexes are red-shifted relative to those of the monomer.     

UV/Vis Spectroscopic Properties of N -(2′-Hydroxy-4′- N , N -dimethyl-aminobenzylidene)-4-nitroaniline in Various Solvents and Solid Environments

 N-(2′-Hydroxy-4′-N,N-dimethylaminobenzylidene)-4-nitroaniline [HDBN] has been used as a model for investigating intra- and intermolecular D–A (donor–acceptor) interactions in various environments by means of UV/Vis spectroscopy. UV/Vis spectra of HDBN have been measured in various solvents, ethanolic solutions of different pH, adsorbed on silica, and in the solid state. A bathochromic shift of ν_max is observed with increasing the dipolarity/polarizability and HBD (hydrogen bond donor) capacity of the solvent, which is described by means of a multiple LSE (linear solvation energy) relationship in terms of the empirical Kamlet-Taft solvent polarity parameters. The adsorption of HDBN on Aerosil^? 300-silica particles in non-HBA (hydrogen bond acceptor) solvents is explained in the same sense. Mobile protons and sol–gel entrapping cause a hypsochromic shift due to protonation of the lone electron pair of the 4′-N,N-dimethylamino group. Hydroxide ions attack the 2′-hydroxy group which causes a bathochromic shift. A strong intramolecular hydrogen bond between the 2′-hydroxyl hydrogen and the imine nitrogen atom is present in the solid-state structure causing an unprecedented bathochromic shift.     

Caffeine interactions with nucleic acids. Molecular mechanics calculations of model systems for explanation of mechanisms of biological actions

To understand the molecular mechanisms of the influence of caffeine (CAF) on DNA functioning, molecular mechanics calculations of the interaction energy of CAF with nucleic acid bases and base pairs have been performed. The calculations reveal three types of mutual CAF–base (and CAF–base pair) arrangements corresponding to minima of the interaction energy. Besides well-known stacking mutual positions of the molecules, two other types of arrangements are revealed and studied. One of these arrangements corresponds to the nearly in-plane position of CAF and base (or base pair) and the formation of a single hydrogen bond. Another type of minimum corresponds to nearly perpendicular arrangements of the molecular planes and the formation of intermolecular hydrogen bonds. These two arrangements are possible both for individual nucleic acid monomers and for DNA duplexes. The calculations suggest the molecular mechanisms of the influence of CAF on DNA interactions with other biologically active molecules.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 20002).     

Vibrational spectroscopic and density functional theory studies on ion solvation and ion association of lithium tetrafluoroborate in N,N-dimethylcarbamoyl chloride-based solvents

Solvation and association interactions in solutions of LiBF₄/DMCC (DMCC for N,N-dimethylcarbamoyl chloride) and LiBF₄/DMCC–DME (DME for 1,2-dimethoxyethane) have been studied as a function of concentration of lithium tetrafluoroborate by infrared and Raman spectroscopy. Strong interactions between Li⁺ and solvent molecules or BF₄⁻ anions are observed. The apparent solvation numbers of Li⁺ in LiBF₄/DMCC solutions were deduced. Band-fitting to the B–F stretching band of BF₄⁻ anion permits detailed assess of the ion pairing. Based on the calculations of density function theory, optimal structures of Li⁺(DMCC)_n (n = 1–3) were suggested. It is found that the lithium ion was preferentially solvated by DME in DMCC–DME binary solvents. This finding is supported by quantum chemistry calculations.     

A theoretical study of the hydrogen bond donor capability and co-operative effects in the hydrogen bond complexes of the diaza-aromatic betacarbolines

In this work, we present a quantum mechanical investigation on the hydrogen bond interactions of N(9)-methyl-9H-pyrido[3,4-b]indole, MBC, and N(2)-methyl-9H-pyrido[3,4-b]indole, BCA, with different hydrogen bond donors. Thus, it has been analysed the influence that the hydrogen bond donor strength and the co-operative effect of the increasing number of donor molecules have on the shape of the potential energy surfaces versus the N···H distances, r(N–H). To rationalize the nature of the interactions, the Bader theory has been applied and the characteristics of the bond critical points analysed. The results show that two different hydrogen bond complexes can be formed depending on the donor capabilities or the number of donor molecules included in the calculations. The topological parameters from the Bader theory are used to justify the statement that the analysed interactions can be classified as weak or partially covalent hydrogen bond interactions, respectively. As experimentally observed, weak hydrogen bond donors form weak hydrogen bond complexes, called HBC. Upon the increase of the donor strength the N···H proton is shifted nearest to the nitrogen atom giving rise to the observation of a stronger hydrogen bond complex, the proton transfer complex, PTC. The most outstanding result of these studies is the fact that the formation of the PTC can also be managed just by changing the number of donor molecules, that is, by a co-operative effect of the hydrogen bonds.     

Quantum mechanical study of tautomerism of methimazole and the stability of methimazole–I2 complexes

DFT and ab initio theoretical methods were used to calculate the relative stability of tautomers in the methimazole (MMI). The calculations show that the thione form of MMI 1 is more stable than the thiol tautomer in good agreement with the experimental results. The DFT and ab initio calculations were also used to determine the stability of MMI–I₂ complexes. All methods suggest that the methimazole in the MMI–I₂ complex exists almost exclusively as the thione tautomer. The Gibbs free energy difference between planar and perpendicular forms of thione tautomer of MMI–I₂ complex indicates that the planar form is the predominant complex. The counterpoise corrected Gibbs free energy also shows that the MMI–I₂(plan.) complex is more stable than the MMI–I₂(perp.) complex. These predictions are in good agreement with the experimental results. By using the natural bond orbital (NBO) approach, the effects of charge transfer interactions on the stability of MMI–I₂ complexes were investigated. The LP₃(S)→σ*(I–I) and LP₃(I)→σ*(N–H) charge transfer interactions may be very important in the stability of the planar form. The results show that the LP₃(S)→σ*(I–I) charge transfer interaction causes a greater increase in the σ*(I–I) antibond occupation number, and concomitantly, a greater increase in the corresponding I–I bond length in the planar complex with respect to the perpendicular complex. The LP₃(S)→σ*(I–I) charge transfer interaction is assisted by NHI intermolecular hydrogen bonding. The atom in molecule (AIM) analysis shows that the charge density and its Laplacian at the SI bond critical point of the planar complex is greater than the perpendicular complex.     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

Investigation of C–HX (X=N, O, S) intramolecular hydrogen bond in 1-vinyl-2-(2′-heteroaryl)pyrroles by ab initio calculations

The C–HX (X=N, O, S) intramolecular hydrogen bond between the α-hydrogen of the vinyl group and the corresponding heteroatom in the series of 1-vinyl-2-(2′-heteroaryl)pyrroles was examined by ab initio calculations at the B3LYP/6-311(d,p) level. It was shown that the C–HN hydrogen bond is stronger than the C–HO hydrogen bond and the latter is, in turn, stronger than the C–HS hydrogen bond. This conclusion is supported by calculations of ¹H NMR chemical shieldings.     

Conformational dependence of the intrinsic acidity of the aspartic acid residue sidechain in N-acetyl- -aspartic acid-N′-methylamide

The sidechain conformational potential energy hypersurfaces (PEHS) for the γ_L, β_L, α_L, and α_D backbone conformations of N-acetyl- -aspartate-N′-methylamide were generated. Of the 81 possible conformers initially expected for the aspartate residue, only seven were found after geometric optimizations at the B3LYP/6-31G(d) level of theory. No stable conformers could be located in the δ_L, _L, γ_D, δ_D, and _D backbone conformations. The ‘adiabatic’ deprotonation energies for the endo and exo forms of N-acetyl- -aspartic acid-N′-methylamide were calculated by comparing their optimized relative energies against those found for the seven stable conformers of N-acetyl- -aspartate-N′-methylamide. Sidechain conformational PEHSs were also generated for the estimation of ‘vertical’ deprotonation energies for both endo and exo forms of N-acetyl- -aspartic acid-N′-methylamide. All backbone–sidechain (N–H⁻O–C) and backbone–backbone (N–HO=C) hydrogen bond interactions were analyzed. A total of two backbone–backbone and four backbone–sidechain interactions were found for N-acetyl- -aspartate-N′-methylamide. The deprotonated sidechain of N-acetyl- -aspartate-N′-methylamide may allow the aspartyl residue to form strong hydrogen bond interactions (since it is negatively charged) which may be significant in such processes as protein–ligand recognition and ligand binding. As a primary example, the molecular geometry of the aspartyl residue may be important in peptide folding, such as that in the RGD tripeptide.     

Density functional and multiphoton ionization studies of N,N-dimethylformamide–(methanol)n clusters

The multiphoton ionization of the hydrogen-bonded clusters N,N-dimethylformamide–(methanol)_n (DMF–(CH₃OH)_n) was studied using a time-of-flight mass spectrometer at the wavelengths of 355 and 532 nm. At both wavelengths, a series of protonated DMF–(CH₃OH)_nH⁺ ions was obtained. The clusters were also investigated by density functional theory B3LYP method in conjunction with basis sets 6-31+G(d,p) and 6-311+G(2d,p). Equilibrium geometries of both neutral and ionic DMF–CH₃OH clusters, and dissociation channels and dissociation energies of the ionic clusters are presented. The results show that when DMF–CH₃OH is vertically ionized and dissociated, DMFH⁺ and CH₃O are the dominant products via proton transfer reaction. A high energy barrier makes another channel corresponding to the production of DMFH⁺ and CH₂OH disfavored. In the DMF–(CH₃OH)H⁺ ion, the proton prefers to link with the O atom of DMF molecule. Variation of atomic charges during proton transfer in hydrogen bond of the protonated cluster DMF–(CH₃OH)H⁺ ion is also discussed.