π-Hydrogen bonding wins over conventional hydrogen bonding interaction: a jet-cooled study of indole···furan heterodimer

In this study, we have explored the conformational landscape of the indole···furan dimer in a supersonic jet by using resonant two-photon ionization (R2PI) and IR-UV double-resonance spectroscopic techniques combined with dispersion-corrected density functional theory (DFT) calculations. Only one conformer of the dimer has been observed in the experiment. DFT/B97-D level calculation shows that N-H···π hydrogen-bonded conformer (T') is energetically more stable than the N-H···O hydrogen-bonded conformer (HB). Natural bond orbital (NBO) calculation also shows that the hydrogen-bonding interaction in the HB conformer is very weak. Finally, the structure of the observed dimer has been determined to be tilted T-shaped N-H···π hydrogen-bonded (T') from very excellent agreement between experimental and theoretical N-H stretch frequency. The most significant finding of this study is the first-time observation of a N-H···π bound conformer of a dimer, which wins over a conventional hydrogen-bonded conformer of the dimer.     

Hydrogen-Bonding Interaction in a Complex of Amino Acid with <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethylformamide Studied by DFT Calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine and leucine) and N,N-dimethylformamide (DMF) in gas phase have been carried out using density functional theory (DFT) and ab initio calculations at the B3LYP/6-311++G** and MP2/6-311++G** theory levels. The structures, binding energy, stretching frequency and bond characteristics of the mentioned complexes were calculated. The NH₂ and COOH groups of amino acids form different types of hydrogen bonds with the DMF molecule, as well as alkyl side chains. High binding energy suggests multiple hydrogen bonds present in one complex. The nearly linear OH???O and NH???O contacts are stronger than a conventional hydrogen bond interaction with their H???O separation between 1.74 and 2.14 Å. The weaker CH???O H-bond is also discussed as being a crucial interaction in biological systems involving amino acids. The formation of this interaction results in a blue shift in the CH stretching frequency.     

Proton character of the peptide unit in the Ca2+-binding sites of calcium pump

The effect of forming calcium pump structures in biological systems on the proton character of the peptide unit has been studied theoretically using the density-functional theory calculations with a large basis set. One acetic acid, one acetate, and three acetamide molecules as well as the modeling peptide unit (MPU) have been employed to mimic the amino acid residues forming the Ca2+-binding sites. To highlight the limiting case of the Ca2+-binding effect on the proton property and the proton countertransport possibility in the direction opposite to the ion, the MPU bounded by the bare or the hydrated Ca2+ has also been investigated. The natural bond orbital (NBO) analysis indicates that the increase of the p-character of the (N-H) sigma orbital results in weakening of the N-H bond which is lengthened when a Ca2+ ion is introduced to the MPU. Calculated NMR shielding sigma(H1) of the MPU shifts upfield upon the Ca2+ ion combination, which reveals the donating of the electron from the amide H as represented by the increase of the calculated positive natural charge for amide H of the MPU. Moreover, the proton affinities (PA) and gas-phase basicities (GB) for the amide nitrogen active site of the MPU are reduced; that is, the acidity of the amide hydrogen gets stronger because of the influence of the Ca2+ ion. To prove the transport possibility of the N-H proton in the direction opposite to the Ca2+ ion along the N-H...O=C hydrogen bond in the helical peptide linkage, NH3 and H2O are used here to assist the dissociation of the amide H of the MPU, and the calculated results show the notable decrease of the deprotonation energies compared to that of the case without this assistance. Moreover, calculated results also reveal that the variation of the quantities discussed here for amide H of the MPU gets smaller when the acidity of Ca2+ ion decreases. Ionization states of the acidic residues forming the Ca2+-binding sites may influence the activity of the amide H of the MPU and further affect the transport tendency of the peptide unit proton in the direction opposite to Ca2+.     

Theoretical study of hydrogen bonding interaction in nitroxyl (HNO) dimer: interrelationship of the two N-H...O blue-shifting hydrogen bonds

The hydrogen bonding interactions of the HNO dimer have been investigated using ab initio molecular orbital and density functional theory (DFT) with the 6-311++G(2d,2p) basis set. The natural bond orbital (NBO) analysis and atom in molecules (AIM) theory were applied to understand the nature of the interactions. The interrelationship between one N-H...O hydrogen bond and the other N-H...O hydrogen bond has been established by performing partial optimizations. The dimer is stabilized by the N-H...O hydrogen bonding interactions, which lead to the contractions of N-H bonds as well as the characteristic blue-shifts of the stretching vibrational frequencies nu(N-H). The NBO analysis shows that both rehybridization and electron density redistribution contribute to the large blue-shifts of the N-H stretching frequencies. A quantitative correlations of the intermolecular distance H...O (r(H...O)) with the parameters: rho at bond critical points (BCPs), s-characters of N atoms in N-H bonds, electron densities in the sigma*(N-H), the blue-shift degrees of nu(N-H) are presented. The relationship between the difference of rho (|Deltarho|) for the one hydrogen bond compared with the other one and the difference of interaction energy (DeltaE) are also illustrated. It indicates that for r(H...O) ranging from 2.05 to 2.3528 A, with increasing r(H...O), there is the descending tendency for one rho(H...O) and the ascending tendency for the other rho(H...O). r(H...O) ranging from 2.3528 to 2.85 A, there are descending tendencies for the two rho(H...O) with increasing r(H...O). On the potential energy surface of the dimer, the smaller the difference between one rho(H...O) and the other rho(H...O) is, the more stable the structure is. As r(H...O) increases, the blue-shift degrees of nu(N-H) decrease. The cooperative descending tendencies in s-characters of two N atoms with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H). Ranging from 2.05 to 2.55 A, the increase of the electron density in one sigma*(N-H) with elongating r(H...O) weakens the blue-shift degrees of nu(N-H), simultaneously, the decrease of the electron density in the other sigma*(N-H) with elongating r(H...O) strengthens the blue-shift degrees of nu(N-H). Ranging from 2.55 to 2.85 A, the cooperative ascending tendencies of the electron densities in two sigma*(N-H) with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H).     

The Effect of Intermolecular Hydrogen Bonding on the Polyaniline Water Complex

The polyaniline water hydrogen-bonded complex was studied by first-principles calculation. The density functional theory method was used to calculate the structure characters, natural bond orbital charge distribution, infrared spectra and the frontier molecular orbital. Results showed that the H–O···H–N and C–N···H–O type intermolecular hydrogen bonds were formed. The bonds involved in the intermolecular H-bond were all influenced by the hydrogen bonding interaction. During the hydrogen bond formation, the polymer chains in the complexes were all charged, which can be an important factor contributing to the increase of electrical conductivity. The N1–H vibration was strongly influenced, and the locations as well as the intensities of N1–H absorption bands were all changed in the complexes. In the orbital transition of HOMO to LUMO, the electron density transferred from benzenoid ring to quinoid ring.     

Photochemistry of <Emphasis Type="Italic">N</Emphasis>-substituted salicylic acid amides

The products of photolysis of N-substituted salicylic acid amides, viz., 2-hydroxy-3-tert-butyl-5-ethylbenzoic acid N-(4-hydroxy-3,5-di-tert-butylphenyl)amide (1) and 2-hydroxybenzoic acid N-[3-(4-hydroxy-3,5-di-tert-butylphenyl)prop-1-yl]amide (2), in heptane were studied by optical spectroscopy and stationary and nanosecond laser photolysis (Nd: YAG laser, 355 nm). It was shown by the method of partial deuteration of amides 1 and 2 that they exist in both the unbound state and as complexes with intraand intermolecular hydrogen bond. Amides 1 and 2 are subjected to photolysis, which results in the formation of a triplet state and phenoxyl radicals RO? presumably due to the absorption of the second photon by the excited singlet state. The formation of radical products due to N–H bond ionization was not observed. The main channel of decay of the triplet state and radicals RO? is triplet–triplet annihilation and recombination (k _r ≈ 2.3?10⁸ L mol^–1 s^–1), respectively. The UV irradiation of compounds 1 and 2 leads to the excitation of the amide groups, and no formation of radical products due to N–H bond ionization was observed.     

Ab initio EOM-CCSD spin-spin coupling constants for hydrogen-bonded formamide complexes: bridging complexes with NH3, (NH3)2, H2O, (H2O)2, FH, and (FH)2

EOM-CCSD spin-spin coupling constants across hydrogen bonds have been computed for complexes in which NH3, H2O, and FH molecules and their hydrogen-bonded dimers form bridging complexes in the amide region of formamide. The formamide one-bond N-H coupling constant [(1)J(N-H)] across N-H...X hydrogen bonds increases in absolute value upon complexation. The signs of the one-bond coupling constants (1h)J(H-X) indicate that these complexes are stabilized by traditional hydrogen bonds. The two-bond coupling constants for hydrogen bonds with N-H as the donor [(2h)J(N-X)] and the carbonyl oxygen as the acceptor [(2h)J(X-O)] increase in absolute value in the formamide/dimer relative to the corresponding formamide/monomer complex as the hydrogen bonds acquire increased proton-shared character. The largest changes in coupling constants are found for complexes of formamide with FH and (FH)2, suggesting that bridging FH monomers and dimers in particular could be useful NMR spectroscopic probes of amide hydrogen bonding.     

Theoretical study of the effects of substitution,solvation, and structure on the interaction between nitriles and methanol

We report an investigation on intermolecular interactions in R? CN ··· H? OCH₃ (R = H, CH₃, F, Cl, NO₂, OH, SH, SCH₃, CHO, COCH₃, CH₂Cl, CH₂F, CH₂OH, CH₂COOH, CF₃, SCOCH₃, SCF₃, OCHF₂, CH₂CF₃, CH₂OCH₃, and CH₂CH₂OH) complexes using density functional theory. The calculations were conducted on B3LYP/6‐311++G** level of theory for optimization of geometries of complexes and monomers. An improper hydrogen bonding (HB) in the H₃CO? H ··· NC? R complexes was observed in that N atom of the nitriles functions acts as a proton acceptor. Furthermore, quantum theory of “Atoms in Molecules” (AIM) and natural bond orbital (NBO) method were applied to analyze H‐bond interactions in respective complexes. The electron density (ρ) and Laplacian (?²ρ) properties, estimated by atoms in molecules calculations, indicate that H ··· N bond possesses low ρ and positive ?²ρ values, which are in agreement with partially covalent character of the HBs, whereas O? H bonds have negative ?²ρ values. In addition, the weak intermolecular force due to dipole–dipole interaction (U) is also considered for analysis. The examination of HB in these complexes by quantum theory of NBO method fairly supports the ab initio results. Natural population analysis data, the electron density, and Laplacian properties, as well as, the ν(O? H) and γ(O? H) frequencies of complexes, calculated at the B3LYP/6‐311++G** level of theory, are used to evaluate the HB interactions. The calculated geometrical parameters and conformational analysis in water phase solution show that the H₃CO? H ··· NC? R complexes in water are more stable than that in gas phase. The obtained results demonstrated a strong influence of the R substituent on the properties of complexes. Numerous correlations between topological, geometrical, thermodynamic properties, and energetic parameters were also found. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

取代基对N—H…O＝C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N-H…O=C氢键强度,探讨了氢键受体分子中不同取代基对N-H…O=C氢键强度的影响.研究表明,不同取代基对氢键三聚体中N-H…O=C氢键强度的影响是不同的:取代基为供电子基团,氢键键长r(H…O)缩短,氢键强度增强;取代基为吸电子基团,氢键键长r(H…O)伸长,氢键强度减弱.自然键轨道(NBO)分析表明,N-H…O=C氢键强度越强,氢键中氢原子的正电荷越多,氧原子的负电荷越多,质子供体和受体分子间的电荷转移越多.供电子基团使N-H…O=C氢键中氧原子的孤对电子n(O)对N-H的反键轨道σ~*(N-H)的二阶相互作用稳定化能增加,吸电子基团使这种二阶相互作用稳定化能减小.取代基对与其相近的N-H…O=C氢键影响更大.     

Density functional calculations of the physicochemical properties of formamidyl radicals

The geometric, spectroscopic, and thermodynamic parameters of the HNC(O)H radical were studied by the DFT B3L YP/6-311++G(3df, 3pd) method. The structure of its conformers was established. Electron and spin density distributions were analyzed. The potential function of internal hindered rotation was calculated. The enthalpies of dissociation were determined for the O-H bond in HNC(OH)H and N-H bond in H₂NC(O)H.     

Solvatochromism of heteroaromatic compounds: XXX. <Emphasis Type="Italic">N</Emphasis>-Methyltrifluoromethanesulfonamide as hydrogen-bond donor

In two-centered H-complexes with protophilic solvents, the monomer of N-methyltrifluoromethanesulfonamide I behaves as a strong H-bond donor, stronger than 4-fluorophenol and ranking second after 4-nitrophenol. In protophilic media, amide I exists as monomeric H-complexes with a two-centered H-bond and 1:2 H-complexes of the open-chair dimer with a bifurcated (three-centered) hydrogen bond. The formation of a strong bifurcated H-bond weaken the bridging N-H.‥O=S bond.     

Crystal and molecular structures of (3Z)-(±)-4-(2′-hydroxypropyl)amino-and (3Z)-4-(2′-hydroxyethyl)amino-pent-3-en-2-ones

An X-ray study of (3Z)-(±)-4-(2′-hydroxypropyl)amino-and (3Z)-4-(2′-hydroxyethyl)amino-pent-3-en-2-ones is reported. The bond lengths inside the H ring are equalized due to the classical N-H...O hydrogen bond between the carbonyl oxygen and the amino group. In the 4-(2′-hydroxyethyl)amino-pent-3-en-2-one crystal, due to the classical N-H...O bonds, infinite zigzag chains are formed along the 0b axis and arranged into a layered structure due to the weak C-H...O interactions. In (±)-4-(2′-hydroxypropyl)aminopent-3-en-2-one crystal, however, centrosymmetric dimers are formed, which are then linked by weak C-H...O intermolecular interactions to form a layered structure along the a0b plane.     

Theoretical study on coordination of methanol clusters to 3-methyl-4-pyrimidone

Density functional theory (DFT), MP2, and couple cluster ab initio methods were employed to investigate the microsolvation of 3-methyl-4-pyrimidone (3M4P) surrounded by methanol (MeOH) molecules. Structures are analyzed based on hydrogen bonds with a focus on relative energies, interaction energies, hydrogen bond cooperativity, hydrogen bonding geometries, and redshifts in the frequencies of O–H and C=O stretching modes. Our results show that there is no preferential orientation of MeOH attacks on the carbonyle site of 3M4P; both trans and cis 3M4P-MeOH complexes have same chance to be observed. cis 3M4P-MeOH and 3M4P-MeOH complex in which MeOH is located on N lie 0.56 and 3.11 kJ/mol at CCSD(T)/6-31+G(d,p) (0.63 and 1.67 kJ/mol at MP2/6-311++G(d,p)) above trans 3M4P-MeOH. MeOH dimers form more stable 3M4P-(MeOH)₂ complexes compare to 3M4P-(MeOH)₂ complexes in which individual MeOH molecules bind to carbonyl and N. Relative energies of 3M4P-(MeOH)₃ computed using various DFT methods point out the complex formed by linear MeOH trimer along methyl group of 3M4P (cis 3M4P-(MeOH)₃) as lowest. Carbonyl group is predicted as preferential site for hydrogen bond interaction. Besides O–H…O and O–H…N hydrogen bonds, 3M4P-(MeOH)₂ and 3M4P-(MeOH)₃ complexes are also stabilized by H–O…H–C weak interactions.     

A comparison of the structure and bonding in the aliphatic boronic R–B(OH)<Subscript>2</Subscript> and borinic R–BH(OH) acids (R=H; NH<Subscript>2</Subscript>, OH,and F): a computational investigation

Boronic acids, R–B(OH)₂, play an important role in synthetic, biological, medicinal, and materials chemistry. This investigation compares the structure and bonding surrounding the boron atoms in the simple aliphatic boronic acids, R–B(OH)₂ (R=H; NH₂, OH, and F), and the analogous borinic acids, R–BH(OH). Geometry optimizations were performed using second-order Møller–Plesset perturbation theory (MP2) with the Dunning–Woon aug-cc-pVTZ, aug-cc-pVQZ, and aug-cc-pV5Z basis sets; single-point CCSD(FC)/aug-cc-pVTZ//MP2(FC)/aug-cc-pVTZ level calculations were used to generate a QCI density for natural bond orbital analyses of the bonding. The optimized boron–oxygen bond lengths for the X–B–O_t–H trans-branch of the endo-exo form of the boronic acids and for the X–B–O–H cis-branch of the boronic and borinic acids (X=N, O, and F, respectively) decrease as the electronegativity of X increases. The boron–oxygen bond lengths are generally longer in the endo-exo or anti forms of the boronic acids than in the corresponding borinic acids. NBO analyses suggest the boron–oxygen bond in H₂BOH is a double bond; the boron–oxygen bonding in the remaining boronic and borinic acids in this study has a significant contribution from dative pπ–pπ bonding. Values for Δ\({\text{H}}_{298}^{0}\) for the highly balanced reaction, R–B(OH)₂ + R–BH₂ → 2 R–BH(OH), suggest that the bonding surrounding the boron atom is stronger in the borinic acid than in the corresponding boronic acid.     

Propagator quantum chemical study of <Emphasis Type="Italic">S</Emphasis>-<Emphasis Type="Italic">cis</Emphasis>-(<Emphasis Type="Italic">Z</Emphasis>)-2-(2-formylethenyl)pyrrole: electronic structure and aspects of intramolecular hydrogen bond manifestation in ionization spectra

For the purpose of investigation of the electronic structures of functionalized pyrroles with potential biological activity the electronic structures and ionization spectra of S-cis-(Z)-2-(2-formylethenyl)pyrrole (FP) were calculated by the propagator quantum chemical method. The calculations were performed using the third-order algebraic diagrammatic construction method (ADC(3)) for one-particle Green´s function (electronic propagator) and the 6–31G** basis set. Going from FP (possessing the intramolecular hydrogen bond H?O) to its conformation FPR (without H?O bonding), the O1s-ionization energy and the ionization energy of the σ-type lone electron pair orbital of the O atom decrease by ~0.2 eV, which is a consequence of stopping the electron density transfer from the O atom. A strong electron density transfer through the hydrogen bond from the O atom to the NH group occurs in the nitrogen core level ionization spectrum as evidenced by a lower N1s-ionization energy of FP (by ~0.7 eV ) compared to that of FPR. The valence shell ionization spectra of FP and FPR calculated using the ADC(3) method are characterized by a high density of the satellite states. The results obtained indicate that the electronic structures of the compounds of the considered class are characterized by pronounced effects of electron correlation.     

A theoretical study of the strong interactions between carbon dioxide and OH<Superscript>+</Superscript> and NH<Subscript>2</Subscript><Superscript>+</Superscript> products resulting from protonation of 1,2-dioxirane-3-one and 1,2-oxaziridine-3-one,respectively

In this work, we investigate the nature of the O–O and O–N interactions in protonated 1,2-dioxirane-3-one derivatives and protonated 1,2-oxaziridine-3-one derivatives, respectively. The quantum theory of atoms in molecules and the natural bond orbital (NBO) method in conjunction with the localized molecular orbital energy decomposition analysis (LMOEDA) have been used. LMOEDA and NBO analyses reveal that the O–O and O–N interactions exhibit characteristics of dative covalent bonds. In addition, the L(r) = ??² ρ(r) function reveals that the O–O and O–N interactions can be categorized as strong hole–lump interactions.     

Molecular Adducts of Isoniazid: Crystal Structure,Electronic Properties,and Hirshfeld Surface Analysis

Three molecular adducts of the antituberculosis drug isoniazid (INH) are synthesized with γ-resorcylic acid (γRA), phloroglucinol (PG), and gallic acid (GA). The new solid phases are preliminarily characterized by the thermal analysis (DSC/TGA) and powder X-ray diffraction. The formation of new solid phases is confirmed by single crystal X-ray diffraction, infrared (FT-IR) and Raman spectroscopy. All three new solid crystalline forms are stabilized by various hydrogen bonding interactions such as N⁺···H–O^–, N···H–O, O···H–O, and π–π stacking. The FT-IR analysis puts forward that the solid form of INH1 is a salt whereas the INH2 and INH3 molecular complexes are cocrystals. We have also investigated the density of states (DOS), band structure, and atomic orbit projected density of state (PDOS) of title compounds by adopting the density functional theory (DFT) technique in the local density approximation (LDA). The electronic structure calculations show that energy states are delocalized in the k-space due the hydrogen and covalent bonds in the crystals. The frontier molecular orbital (FMO) analysis reveals that charge transfer takes place within the compounds. The Hirshfeld analysis shows that H–H and N?H–O hydrogen bonding interactions are dominant in all three molecular adducts of INH.     

Hydrogen-bonding interaction in a complex of amino acid with urea studied by DFT calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine, and leucine) and urea in gas phase have been carried out using density functional theory (DFT) and ab initio methods at the B3LYP/6-311++g** and MP2/6-311++g** theory levels. The structures, binding energy, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution, and bond characteristics of the mentioned complexes were calculated. Urea is a good H-bond donor and an excellent receptor for highly electronegative atoms like O and N, through the formation of two or more hydrogen bonds. The NH₂ and COOH groups of amino acids can form several different types of H-bonds with urea molecular, as well as C^αH and alkyl side chains. The calculated high binding energy also suggests multiple H-bonds formed in one complex. The OH···O contact is the strongest hydrogen bond interaction with H···O separation around 1.65 Å and its relevant angle close to 176°. The closely linear amide H-bonds NH···O and OH···N strongly stabilize the amino acid–urea complex with H···O separation between 1.89 and 2.38 Å. The weaker CH···O/N H-bonds are also discussed as significant interaction in biological systems involving amino acids.     

A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.     

Homodesmotic method of determining the O–H bond dissociation energies in phenols

The dissociation energy of the O–H bond has been calculated by the homodesmotic reaction method for phenolic compounds, which are well-known antioxidants, including for natural phenols. Use of moderately complex computational levels, such as B3LYP/6-31G(d), is sufficient for reliably estimating the D(O–H) value for phenols within the homodesmotic approach. The O–H bond dissociation energy for monosubstituted phenols has been calculated, and the additive character of the effect of methyl groups on D(O–H) in methylphenols has been demonstrated: the introduction of a CH₃ group into the aromatic ring decreases the D value by 7.8 kJ/mol (ortho position), 1.8 kJ/mol (meta position), and 7.6 kJ/mol (para position). The O–H bond strength has been calculated for a number of ubiquinols, selenophens, flavonoids, and chromanols. The D(O–H) value recommended for α-tocopherol is 328.0 ± 1.3 kJ/mol.