Exploring the Dynamical Nature of Intermolecular Hydrogen Bonds in Benzamide,Quinoline and Benzoic Acid Derivatives

The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car–Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular hydrogen bonds (N-H…O, O-H…N and O-H…O). The time evolution of hydrogen bridges gave a deeper insight into bonds dynamics, showing that bridged protons are mostly localized on the donor side; however, the proton transfer phenomenon was registered as well. The vibrational features associated with O-H and N-H stretching were analyzed on the basis of the Fourier transform of the atomic velocity autocorrelation function. The spectroscopic effects of hydrogen bond formation were studied. The PIMD revealed quantum effects influencing the hydrogen bridges providing more accurate free energy sampling. It was found that the N…O or O…O interatomic distances decreased (reducing the length of the hydrogen bridge), while the O-H or N-H covalent bond was elongated, which led to the increase in the proton sharing. Furthermore, Quantum Theory of Atoms in Molecules (QTAIM) was used to give insight into electronic structure parameters. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was employed to estimate the energy contributions to the interaction energy of the selected dimers.     

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm−1–1700 cm−1 and 2300 cm−1–3400 cm−1 in the gas phase and 600 cm−1–1800 cm−1 and 2200 cm−1–3400 cm−1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm−1–1700 cm−1 and 2300 cm−1–3300 cm−1 for the gas phase and one broad absorption region in the solid state between 700 cm−1 and 3100 cm−1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.     

Exploring Intra- and Intermolecular Interactions in Selected N-Oxides—The Role of Hydrogen Bonds

Intra- and intermolecular interactions have been explored in selected N-oxide derivatives: 2-(N,N-dimethylamino-N-oxymethyl)-4,6-dimethylphenyl (1) and 5,5’-dibromo-3-diethylaminomethyl-2,2’-biphenol N-oxide (2). Both compounds possess intramolecular hydrogen bonding, which is classified as moderate in 1 and strong in 2, and resonance-assisted in both cases. Density Functional Theory (DFT) in its classical formulation as well as Time-Dependent extension (TD-DFT) were employed to study proton transfer phenomena. The simulations were performed in the gas phase and with implicit and explicit solvation models. The obtained structures of the studied N-oxides were compared with experimental data available. The proton reaction path was investigated using scan with an optimization method, and water molecule reorientation in the monohydrate of 1 was found upon the proton scan progress. It was found that spontaneous proton transfer phenomenon cannot occur in the electronic ground state of the compound 1. An opposite situation was noticed for the compound 2. The changes of nucleophilicity and electrophilicity upon the bridged proton migration were analyzed on the basis of Fukui functions in the case of 1. The interaction energy decomposition of dimers and microsolvation models was investigated using Symmetry-Adapted Perturbation Theory (SAPT). The simulations were performed in both phases to introduce polar environment influence on the interaction energies. The SAPT study showed rather minor role of induction in the formation of homodimers. However, it is worth noticing that the same induction term is responsible for the preference of water molecules’ interaction with N-oxide hydrogen bond acceptor atoms in the microsolvation study. The Natural Bond Orbital (NBO) analysis was performed for the complexes with water to investigate the charge flow upon the polar environment introduction. Finally, the TD-DFT was applied for isolated molecules as well as for microsolvation models showing that the presence of solvent affects excited states, especially when the N-oxide acceptor atom is microsolvated.     

Theoretical Studies on the Structure and Intramolecular Interactions of Fagopyrins—Natural Photosensitizers of Fagopyrum

Simple SummaryThe study determines the spatial structure and intramolecular interactions of fagopyrins—natural photosensitizers of Fagopyrum species. In silico calculations show many fagopyrin conformers characterized by the formation of strong intramolecular interactions.AbstractCompounds characterized by a double-anthrone moiety are found in many plant species. One of them are fagopyrins—naturally occurring photosensitizers of Fagopyrum. The photosensitizing properties of fagopyrins are related to the selective absorption of light, which is a direct result of their spatial and electronic structure and many intramolecular interactions. The nature of the interactions varies in different parts of the molecule. The aim of this study is to determine the structure and intramolecular interactions of fagopyrin molecules. For this purpose, in silico calculations were used to perform geometry optimization in the gas phase. QTAIM and NCI analysis suggest the formation of the possible conformers in the fagopyrin molecules. The presence of a strong OHO hydrogen bond was shown in the anthrone moiety of fagopyrin. The minimum energy difference for selected conformers of fagopyrins was 1.1 kcal∙mol⁻¹, which suggested that the fagopyrin structure may exist in a different conformation in plant material. Similar interactions were observed in previously studied structures of hypericin and sennidin; however, only fagopyrin showed the possibility of brake the strong OHO hydrogen bond in favor of forming a new OHN hydrogen bond.     

Theoretical Studies on the Mechanism of deNOx Process in Cu–Zn Bimetallic System—Comparison of FAU and MFI Zeolites

In the present study we propose a more promising catalyst for the deNOx process to eliminate harmful nitrogen oxides from the environment. The study was performed with a computer calculation using density functional theory (DFT) based on an ab initio method. Two zeolite catalysts, FAU and MFI, were selected with additional Cu–O–Zn bimetallic dimer adsorbed inside the pores of both zeolites. Based on the analysis of preliminary studies, the most probable way of co-adsorption of nitric oxide and ammonia was selected, which became the initial configuration for the reaction mechanism. Two types of mechanisms were proposed: with hydroxyl groups on a bridged position of the dimer or a hydroxyl group on one of the metal atoms of the dimer. Based on the results, it was determined that the FAU zeolite with a bimetallic dimer and an OH group on the zinc atom was the most efficient configuration with a relatively low energy barrier. The real advantage of the Cu–Zn system over FAU and MFI in hydrothermal conditions has been demonstrated in comparison to a conventional Cu–Cu catalyst.     

有机π共轭配体溶剂化效应与分子间相互作用的理论研究

采用可极化的连续介质模型(PCM), 运用密度泛函理论(DFT), 在B3LYP/6-31+G^**水平下研究了溶剂极性对有机π共轭配体N,N'-Bis-(3-pyridyl)ethylene-bis-urea(BPEBU)中syn-anti构象的分子几何和电子结构的影响, 并借助分子动力学模拟的方法, 采用明确溶剂模型研究了溶质-溶剂分子间的相互作用. 密度泛函理论计算结果表明, 随着溶剂极性的增强, BPEBU中尿素基上的CO键和N-H键以及吡啶环上的C-N键被明显极化, 使羰基氧原子和吡啶氮原子的电负性明显增强, 尿素基的N-H键上氢原子的正电荷也显著增加. 分子动力学模拟统计的结果表明, 在极性较强的乙醇溶液中, 有明确的O…H-O, N…H-O和N-H…O等3种氢键作用存在, 而在丙酮溶液中, 只有N…H-O一种氢键作用存在, 而且与乙醇溶液中的N…H-O作用相比要弱些. 另外, 采用密度泛函理论方法结合连续/明确的混合溶剂模型, 优化得到了溶质-溶剂三聚体的超分子簇结构, 与分子动力学模拟的第一溶剂层中的超分子结构相比, 两者定性一致.     

A Combined Experimental and Theoretical Electron Density Study of Intra‐ and Intermolecular Interactions in Thiourea S,S‐Dioxide

The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has C_s symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρ_b and H_b of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom.     

Theoretical study of bifurcated hydrogen bonding effects on the 1J(N,H), 1hJ(N,H), 2hJ(N,N) couplings and 1H, 15N shieldings in model pyrroles

According to the density functional theory calculations, the X···H···N (X?N, O) intramolecular bifurcated (three‐centered) hydrogen bond with one hydrogen donor and two hydrogen acceptors causes a significant decrease of the ^1hJ(N,H) and ^2hJ(N,N) coupling constants across the N? H···N hydrogen bond and an increase of the ¹J(N,H) coupling constant across the N? H covalent bond in the 2,5‐disubsituted pyrroles. This occurs due to a weakening of the N? H···N hydrogen bridge resulting in a lengthening of the N···H distance and a decrease of the hydrogen bond angle at the bifurcated hydrogen bond formation. The gauge‐independent atomic orbital calculations of the shielding constants suggest that a weakening of the N? H···N hydrogen bridge in case of the three‐centered hydrogen bond yields a shielding of the bridge proton and deshielding of the acceptor nitrogen atom. The atoms‐in‐molecules analysis shows that an attenuation of the ^1hJ(N,H) and ^2hJ(N,N) couplings in the compounds with bifurcated hydrogen bond is connected with a decrease of the electron density ρ_H···N at the hydrogen bond critical point and Laplacian of this electron density ?²ρ_H···N. The natural bond orbital analysis suggests that the additional N? H···X interaction partly inhibits the charge transfer from the nitrogen lone pair to the σ*_{N? H} antibonding orbital across hydrogen bond weakening of the ^1hJ(N,H) and ^2hJ(N,N) trans‐hydrogen bond couplings through Fermi‐contact mechanism. An increase of the nitrogen s‐character percentage of the N? H bond in consequence of the bifurcated hydrogen bonding leads to an increase of the ¹J(N,H) coupling constant across the N? H covalent bond and deshielding of the hydrogen donor nitrogen atom. Copyright © 2010 John Wiley & Sons, Ltd.     

Theoretical Studies on the Fe-M Interactions and 31P NMR in Fe(CO)3(EtPhPpy)2MX2 (X=NCS,SCN, Cl; M=Zn,Cd, Hg)

To study the Fe?M interactions and their effects on 31P NMR, the structures of Fe(CO)3(EtPhPpy)2 1,Fe(CO)3(EtPhPpy)2M(NCS)2 (2: M=Zn, 3: M=Cd, 4: M=Hg) and Fe(CO)3(EtPhPpy)2CdX2 (5: X=Cl,6: X=SCN) were investigated by density functional theory (DFT) PBE0 method. The stabilities S of complexes follow S(2)>S(3)>S(4) and S(3)≈S(6)>S(5), indicating that 6 is stable and may be synthesized.The complexes with thiocyanate are more stable than that with chloride in Fe(CO)3(EtPhPpy)2CdX2.The strength I of Fe-M interactions follows I(2)≈I(3)相似文献   

Interaction of the important species HNO and HFSO2 in the atmosphere: Theoretical study of the N?H and S?H blue‐shifted hydrogen bonds

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the N? H…O and S? H…O blue‐shifted H‐bonds in the HNO…HFSO₂ complex. The geometric structures, vibrational frequencies, and interaction energies were calculated by both standard and CP‐corrected methods. Natural bond orbital (NBO) analysis was used to investigate the origin of blue‐shifted H‐bonds, showing that the decrease in the σ*(N? H) and σ*(S? H) is due to the electron density redistribution effect. The structure reorganization effect on the blue‐shifted hydrogen bonds was discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

On the Coexistence of the Carbene⋯H-D Hydrogen Bond and Other Accompanying Interactions in Forty Dimers of N-Heterocyclic-Carbenes (I,IMe2, IiPr2, ItBu2, IMes2, IDipp2, IAd2; I = imidazol-2-ylidene) and Some Fundamental Proton Donors (HF,HCN, H2O,MeOH, NH3)

The subject of research is forty dimers formed by imidazol-2-ylidene (I) or its derivative (IR2) obtained by replacing the hydrogen atoms in both N-H bonds with larger important and popular substituents of increasing complexity (methyl = Me, iso-propyl = iPr, tert-butyl = tBu, phenyl = Ph, mesityl = Mes, 2,6-diisopropylphenyl = Dipp, 1-adamantyl = Ad) and fundamental proton donor (HD) molecules (HF, HCN, H2O, MeOH, NH3). While the main goal is to characterize the generally dominant C⋯H-D hydrogen bond engaging a carbene carbon atom, an equally important issue is the often omitted analysis of the role of accompanying secondary interactions. Despite the often completely different binding possibilities of the considered carbenes, and especially HD molecules, several general trends are found. Namely, for a given carbene, the dissociation energy values of the IR2⋯HD dimers increase in the following order: NH3< H2O < HCN ≤ MeOH ≪ HF. Importantly, it is found that, for a given HD molecule, IDipp2 forms the strongest dimers. This is attributed to the multiplicity of various interactions accompanying the dominant C⋯H-D hydrogen bond. It is shown that substitution of hydrogen atoms in both N-H bonds of the imidazol-2-ylidene molecule by the investigated groups leads to stronger dimers with HF, HCN, H2O or MeOH. The presented results should contribute to increasing the knowledge about the carbene chemistry and the role of intermolecular interactions, including secondary ones.     

Substrate‐Dependent H/D Kinetic Isotope Effects and the Role of the Di(μ‐oxo)diiron(IV) Core in Soluble Methane Monooxygenase: A Theoretical Study

Soluble methane monooxygenase (sMMO) is an enzyme that converts alkanes to alcohols using a di(μ‐oxo)diiron(IV) intermediate Q at the active site. Very large kinetic isotope effects (KIEs) indicative of significant tunneling are observed for the hydrogen transfer (H‐transfer) of CH₄ and CH₃CN; however, a relatively small KIE is observed for CH₃NO₂. The detailed mechanism of the enzymatic H‐transfer responsible for the diverse range of KIEs is not yet fully understood. In this study, variational transition‐state theory including the multidimensional tunneling approximation is used to calculate rate constants to predict KIEs based on the quantum‐mechanically generated intrinsic reaction coordinates of the H‐transfer by the di(μ‐oxo)diiron(IV) complex. The results of our study reveal that the role of the di(μ‐oxo)diiron(IV) core and the H‐transfer mechanism are dependent on the substrate. For CH₄, substrate binding induces an electron transfer from the oxygen to one Fe^IV center, which in turn makes the μ‐O ligand more electrophilic and assists the H‐transfer by abstracting an electron from the C?H σ orbital. For CH₃CN, the reduction of Fe^IV to Fe^III occurs gradually with substrate binding and H‐transfer. The charge density and electrophilicity of the μ‐O ligand hardly change upon substrate binding; however, for CH₃NO₂, there seems to be no electron movement from μ‐O to Fe^IV during the H‐transfer. Thus, the μ‐O ligand appears to abstract a proton without an electron from the C?H σ orbital. The calculated KIEs for CH₄, CH₃CN, and CH₃NO₂ are 24.4, 49.0, and 8.27, respectively, at 293 K, in remarkably good agreement with the experimental values. This study reveals that diverse KIE values originate mainly from tunneling to the same di(μ‐oxo)diiron(IV) core for all substrates, and demonstrate that the reaction dynamics are essential for reproducing experimental results and understanding the role of the diiron core for methane oxidation in sMMO.     

Tautomerism and isotopic multiplets in the 13C NMR spectra of partially deuterated 3‐arylpyrimido[4,5‐c]pyridazine‐5,7(6H,8H)‐diones and their sulfur analogs—evidence for elucidation of the structure backbone and tautomeric forms

The tautomerism of the synthesized 3‐arylpyrimido[4,5‐c]pyridazine‐5,7(6H,8H)‐diones ( 1a–d ) and 3‐aryl‐7‐thioxo‐7,8‐dihydro‐6H‐pyrimido[4,5‐c]pyridazine‐5‐ones ( 2a–d ) was studied in dimethyl sulfoxide (DMSO)‐d₆. ¹H NMR spectra of 1a–d showed a clustered water molecule in the structure backbone that is attached by strong intermolecular H bonding. The relation between the temperature and H bonding of the clustered water molecule with 1a was also studied as representative. The relation between the electronegativity (χ) of the substituent on phenyl ring and the chemical shifts of clustered water protons in 1a–d was also studied. All of 1a–d and also 2d compounds existed in lactam ( I ) form, whereas 2a–c compounds have two distinguished tautomers in DMSO‐d₆ [lactam ( I ) and lactim ( II ) forms]. The solvent‐substrate proton exchange was examined in compounds 1a–d and 2a–d by adding one drop of D₂O. All compounds (except 1d ) showed proton/deuterium exchange of the clustered water protons in DMSO by adding one drop of D₂O. Some compounds (but not all of them) that are easily soluble in DMSO‐d₆ containing D₂O showed isotopic splitting (β‐isotope effect) in their ¹³C NMR spectra. Among them, compound 1a was the best evidence to help the spectral assignments and structure determination of predominant tautomer by carbon‐13 splitting (β‐isotope effect). Copyright © 2010 John Wiley & Sons, Ltd.     

Intermolecular hydrogen bonding in the binary mixture [(C2H5)2CO + CH3OH] probed by polarized Raman measurements and DFT calculations

The Raman spectra of neat (C₂H₅)₂CO (pentanone) and its binary mixtures with hydrogen donor solvent (CH₃OH), [(C₂H₅)₂CO + CH₃OH] having different mole fractions of the reference system, (C₂H₅)₂CO in the range 0.1-0.9 at a regular interval of 0.1 were recorded in the CO stretching region. In neat liquid, the Raman peak appears asymmetric. The asymmetric nature of the peak has been attributed to the CO stretching mode of the two conformers of (C₂H₅)₂CO having C₂ and C_2v point groups and the corresponding bands at ∼1711 and ∼1718 cm⁻¹, respectively. A careful analysis of the I_iso (isotropic component of the Raman scattered intensity) at different concentrations reveals that upon dilution with methanol, at mole fraction C = 0.6, an additional peak in the CO stretching region is observed at ∼1703 cm⁻¹ which is attributed to the hydrogen bonding with methanol. A peculiar feature in this study is that upon dilution, the peak at ∼1718 cm⁻¹ shows a minimum at C = 0.6, but on further dilution it shows a blue shift. However, the other peak at ∼1711 cm⁻¹ shows a continuous red shift with dilution as well as a maximum at C = 0.7 in the linewidth vs. concentration plot, which is essentially due to competition between motional narrowing and diffusion phenomena. A significant amount of narrowing in the Raman band at ∼1718 cm⁻¹ can be understood in terms of caging effect of the reference molecule by the solvent molecules at high dilution. A density functional theoretic (DFT) calculation on optimized geometries and vibrational frequencies of two conformers of neat (C₂H₅)₂CO in C₂ ad C_2v forms and the complexes with one and two CH₃OH molecules with both the conformers was performed. The experimental results and theoretical calculations together indicate a co-existence of two conformers as well as hydrogen bonded complex with methanol in the binary mixture, [(C₂H₅)₂CO + CH₃OH] at intermediate concentrations.