Hydrogen Bonding Interactions of Radicals

Hydrogen bonding interactions of organic radicals are systematically studied using diverse ab initio and density functional theory (DFT) methods. It is found that open-shell hydrogen bonds with radical proton donors are more difficult to model than those with radical proton acceptors. The DFT methods perform significantly worse than the unrestricted second order Möller-Plesset perturbation (UMP2) method in both geometry optimization and interaction energy calculations for the open-shell hydrogen bonds. The UB3LYP method seriously underestimates the donor-acceptor distances and overestimates interaction energies for the open-shell hydrogen bonds with radical proton donors. Nevertheless, use of the UBH&HLYP functional to study the open-shell hydrogen bonds is still acceptable. Furthermore, it is necessary to use sufficiently flexible basis sets, such as 6-311++G(2df,2p), to get reliable interaction energies for the open-shell hydrogen bonds. The open-shell proton donors are stronger Lewis acids than the corresponding closed-shell proton donors. The open-shell proton acceptors are weaker Lewis bases than the corresponding closed-shell proton acceptors.     

The multieffects of DMF and DBU on the [5 + 1] benzannulation of nitroethane and α‐alkenoyl ketene‐(S,S)‐acetals: Hydrogen bonding and electrostatic interactions

A density functional theory (DFT) study was performed to elucidate the mechanism for the [5 + 1] benzannulation of nitroethane and α‐alkenoyl ketene‐(S,S)‐acetals. The calculation results are consistent with experimental findings, showing that the reaction proceeds via deprotonation of nitroethane, nucleophilic addition, intramolecular cyclization, elimination of HNO₂, and the keto‐enol tautomerization sequence. It was disclosed that N,N‐dimethylformamide (DMF) and 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) act as not only solvent and nonnucleophilic base, respectively, but also catalysts in the reaction by stabilizing the transition states (TSs) and intermediates via intermolecular hydrogen bonds and electrostatic interactions. Besides, the effective orbital interaction of the reaction site in TS also contributes to the intramolecular cyclization step. The new mechanistic insights obtained by DFT calculations highlight that the hydrogen bonds and electrostatic interactions are key factors for the [5 + 1] benzannulation of nitroethane and α‐alkenoyl ketene‐(S,S)‐acetals. © 2015 Wiley Periodicals, Inc.     

The Nature of Activated Non‐classical Hydrogen Bonds: A Case Study on Acetylcholinesterase–Ligand Complexes

Molecular recognition events in biological systems are driven by non‐covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH???Y type involving electron‐deficient CH donors using dispersion‐corrected density functional theory (DFT) calculations applied to acetylcholinesterase–ligand complexes. The strengths of CH???Y interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non‐activated CH???Y interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CH???Y interactions when analysing protein–ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.     

Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study

This article reports a combined quantum mechanics/molecular mechanics (QM/MM) investigation on the acid hydrolysis of cellulose in water using two different models, cellobiose and a 40‐unit cellulose chain. The explicitly treated solvent molecules strongly influence the conformations, intramolecular hydrogen bonds, and exoanomeric effects in these models. As these features are largely responsible for the barrier to cellulose hydrolysis, the present QM/MM results for the pathways and reaction intermediates in water are expected to be more realistic than those from a former density functional theory (DFT) study with implicit solvent (CPCM). However, in a qualitative sense, there is reasonable agreement between the DFT/CPCM and QM/MM predictions for the reaction mechanism. Differences arise mainly from specific solute–solvent hydrogen bonds that are only captured by QM/MM and not by DFT/CPCM. © 2015 Wiley Periodicals, Inc.     

Density functional theory study on the –SO3H functionalized acidic ionic liquids

In this work, the structures of the –SO₃H functionalized acidic ionic liquid 1-(3-sulfonic acid) propyl-3-methylimidazolium hydrogen sulfate ([C₃SO₃Hmim]HSO₄), including its precursor compound (zwitterion), cation, and cation–anion ion-pairs, were optimized systematically by the DFT theory at B3LYP/6-311++G** level, and their most stable geometries were obtained. The calculation results indicated that a great tendency to form strong intramolecular hydrogen bonds was present in the zwitterion, and this tendency was weakened in the cation that was the protonation product of zwitterion. The intramolecular hydrogen bonds and intermolecular hydrogen bonds coexisted in the ionic liquid, and they played an important role in the stability of the systems. The strongest interaction in the ionic liquid was found between the anion and the functional group. The transition state research and the intrinsic reaction coordinate analysis of the hydrogen transfer reaction showed that, when the cation and the anion interacted near the functional group by double O–H···O hydrogen bonds, the ionic liquid was inclined to exist in a form of the zwitterion and H₂SO₄.     

Ground and excited states of the monomer and dimer of certain carboxylic acids

The ground-state properties of the monomer and the dimer of formic acid, acetic acid, and benzoic acid have been investigated using Hartree-Fock (HF) and density functional theory (DFT) methods using the 6-311++G(d,p) basis set. Some of the low-lying excited states have been studied using the time-dependent density functional theory (TDDFT) with LDA and B3LYP functionals and also employing complete-active-space-self-consistent-field (CASSCF) and multireference configuration interaction (MRCI) methodologies. DFT calculations predict the ground-state geometries in quantitative agreement with the available experimental results. The computed binding energies for the three carboxylic acid dimers are also in accord with the known thermodynamic data. The TDDFT predicted wavelengths corresponding to the lowest energy n-pi* transition in formic acid (214 nm) and acetic acid (214 nm) and the pi-pi* transition in benzoic acid (255 nm) are comparable to the experimentally observed absorption maxima. In addition, TDDFT calculations predict qualitatively correctly the blue shift (4-5 nm) in the excitation energy for the pi-pi* transition in going from the monomer to the dimer of formic acid and acetic acid and the red shift (approximately 19 nm) in pi-pi* transition in going from benzoic acid monomer to dimer. This also indicates that the electronic interaction arising from the hydrogen bonds between the monomers is marginal in all three carboxylic acids investigated.     

Theoretical study of the dimerization of rhodanine in various tautomeric forms

The density functional theory (DFT) was used to calculate the relative stability of rhodanine dimers and the energy of intermolecular interaction in them. Analysis of the electron density showed hydrogen bonding in the dimers. The energies of individual hydrogen bonds were determined for the symmetrical dimers. The polarizable continuum model was used to calculate the solvation (hydration) energies of the structures studied. The effect of dimerization on the position of infrared absorption bands was demonstrated.     

发光共价有机骨架LCOF-NDT1荧光识别甲醛的理论研究

基于密度泛函理论(DFT)和含时密度泛函理论(TD-DFT),探究了发光共价有机骨架LCOF-NDT1与甲醛之间的分叉氢键作用.发现LCOF-NDT1与甲醛氢键作用后发光机理发生改变.氢键复合物的电子激发能减小,激发态下的氢键键长变短,氢键质子供体的~1H-NMR移向高场,氢键质子供体和受体的振动频率发生红移,均表明电子激发态下的氢键增强.氢键复合物的荧光速率系数减小,内转换速率系数增大,阐明电子激发态下氢键的增强有利于非辐射跃迁,不利于辐射跃迁,从而导致LCOF-NDT1荧光减弱或猝灭.计算结果表明LCOF-NDT1在荧光识别甲醛方面有潜在的应用前景.     

Density Functional Theory Study of Hydrogen Bonding Dimers with 4-Pyridinecarboxylic Acid Hydrazine

The H‐bonding dimers of 4‐pyridinecarboxylic acid hydrazine were studied using density functional theory (DFT) at B3LYP/6‐311++G** level. The results showed that the most stable dimer D1 had two same linear N H···O hydrogen bonds, and the interaction energy between them was 51.038 kJ·mol⁻¹ which was corrected by the basis set superposition error and zero‐point. The stretching vibration frequency of N H bond had a red shift because of the hydrogen bonds. The natural bond orbital analysis showed that each N H···O hydrogen bond in D1 had the biggest interaction stabilization energy of 69.078 kJ·mol⁻¹. Thermodynamic analysis indicated that the formation process of D1 was exothermic and spontaneous at low and room temperatures.     

A DFT study on the mechanism of phosphodiester cleavage mediated by monozinc complexes

Density functional theory (DFT), Tao-Perdew-Staroverov-Scuseria (TPSS), is employed to study the reaction mechanism for the zinc-mediated phosphodiester cleavage reaction. The calculations indicate a general base catalysis mechanism. The flexibility of Zn(II) ion's coordination number (5 and 6) as well as the formation of hydrogen bonds between the coordinating water and the ester are responsible for the trapping (namely, coordinating to the Zn complexes) of the phosphodiester. The hydrogen bonds, between the water, the ester, and the nitrogen-ligand, tris(6-amino-2-pyridylmethyl)amine, not only stabilize the key five-coordinated phosphorus intermediates with a trigonal pyramidal PO5 unit but also lower the energy barriers for the proton transfer within the complexes by gaining stronger solvation energies.     

A computational investigation of the different intermediates during organoalkoxysilane hydrolysis

Using a combination of atomistic molecular dynamics (MD) simulations and density functional theory (DFT) calculations, the four steps of hydrolysis of aminopropyl-, thiolpropyl-, and butyltrimethoxysilane have been studied. Large box MD simulations at constant pressure and temperature yield appropriate pair distribution functions--which allows us to quantify the number of surrounding water molecules--as well as the density of the systems. These densities serve as input for small box DFT calculations, which allow further geometry optimization and calculation of the electronic structure of the systems. The periodic DFT calculations are compared with gas-phase simulations. In all cases, the first step of hydrolysis is exothermic with the extent depending on the type of silane as well as on the number of hydrogen bonds in the initial stage.     

A Theoretical Study on the Photochromic Mechanism of 1-Phenyl-3-methyl-4-（6-hydro-4-amino-5-sulfo-2,3-pyrazine）-pyrazole-5-one

The photochromic mechanism of 1-phenyl-3-methyl-4-（6-hydro-4-amino-5-sulfo-2,3- pyrazine）-pyrazole-5-one has been investigated using the density functional theory（DFT）. The solvent effect is simulated using the polarizable continuum model（PCM） of the self-consistent reaction field theory. According to the crystal structure of the title compound, an intramolecular proton transfer mechanism from enol to keto form was proposed to interpret its photochromism. Bader＇s atom-in-molecule（AIM） theory is used to investigate the nature of hydrogen bonds and ring structures. Time-dependent density functional theory（TDDFT） calculation results show that the photochromic process from enol to keto form is reasonable. The conformation and molecular orbital analysis of enol and keto forms explain why only intramolecular proton transfer is possible. The results from analyzing the energy and dipole moments of enol form, transition state and keto form in the gas phase and in different solvents have been used to assess the stability of the title compound.     

Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors

The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.     

Electronic structure of oligoaniline doped by inorganic and organic acids

The electronic structure of doped‐oligoaniline with various dopants is investigated by means of DFT method. After doping by hydrochloric acid (HCl) and camphorsulfonic acid (HCSA), the alternation of bond‐lengths is decreased and the co‐planarity of adjacent aromatic rings is increased. The π‐conjugating effect is increased in the electronic nature of Ph‐N system because the electrons can be delocalized along the backbone of oligoaniline where the hydrogen bonds as a bridge transfer the electrons. The electronic structure of polaron and bipolaron conformation and their relative stability is discussed, indicating that the preferable conformation is dependant on various dopants. The calculation results reveal that there is a relatively stronger interaction between the organic dopant of HCSA and N atoms of PANI, and more charge transfer between PANI and HCSA is a reason for the fact that the conductivity of HCSA‐doped PANI is higher than that of HCl‐doped PANI. The doping mechanism is proposed based on the calculation results. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

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.     

CO在Pt及其合金表面电化学氧化和吸附的理论研究

文本综述了CO在Pt及其它过渡金属上电化学氧化机理的量子化学研究现状。系统论述了密度泛函理论计算在催化剂对CO电氧化的作用机制和CO与金属间吸附、成键及振动频率方面所给出的详细信息, 并指出了量子化学计算结果对于电极催化剂设计的指导意义。最后, 指出了目前量子化学计算的局限性并展望来其未来发展趋势。     

Binaphthol-derived bisphosphoric acids serve as efficient organocatalysts for highly enantioselective 1,3-dipolar cycloaddition of azomethine ylides to electron-deficient olefins

A variety of chiral bisphosphoric acids derived from binaphthols have been evaluated for enantioselective 1,3-dipolar cycloaddition reactions, revealing that the feature of the linker in the catalysts exerted great impact on the stereoselectivity. Among them, the oxygen-linked bisphosphoric acid 1a provided the highest level of stereoselectivity for the 1,3-dipolar cycloaddition reaction tolerating a wide range of substrates including azomethine ylides, generated in situ from a broad scope of aldehydes and α-amino esters, and various electron-deficient dipolarophiles such as maleates, fumarates, vinyl ketones, and esters. This reaction actually represents one of the most enantioselective catalytic approaches to access structurally diverse pyrrolidines with excellent optical purity. Theoretical calculations with DFT method on the formation of azomethine ylides and on the transition states of the 1,3-dipolar cycloaddition step showed that the dipole and dipolarophile were simultaneously activated by the bifunctional chiral bisphosphoric acids through the formation of hydrogen bonds. The effect of the bisphosphoric acids on reactivity and stereochemistry of the three-component 1,3-dipolar cycloaddition reaction was also theoretically rationalized. The bisphosphoric acid catalyst 1a may take on a half-moon shape with the two phosphoric acid groups forming two intramolecular hydrogen bonds. In the case of maleates, one phosphate acts as a base to activate the 1,3-dipole, and simultaneously, the two hydroxyl groups in the catalyst 1a may respectively form two hydrogen bonds with the two ester groups of maleate to make it more electronically deficient as a much stronger dipolarophile to participate in a concerted 1,3-dipolar cycloaddition with azomethine ylide. However, in the cases involving acrylate and fumarate dipolarophiles, only one hydroxyl group forms a hydrogen bond with the ester functional group to lower the LUMO of the C-C double bond and another one is remained to adjust the acidity and basicity of two phosphoric acids to activate the dipole and dipolarophile more effectively.     

The Role of Amino Acid Esters and the Amide Group in the Chiral Induction Process by a Novel Monoamide‐Linked Monozinc Bisporphyrinate

A monoamide‐linked monozinc bisporphyrinate for monodentate chiral guests was designed and synthesized. It was used as a host to complex with amino acid esters; the resulting CD spectra showed typical bisignate shape, which suggest the ability to transfer chirality from amino acid esters. The molecular structure of the host indicates that amino acid esters function as monodentate ligands in the host‐guest complex. ¹H NMR spectroscopic studies suggest formation of a hydrogen bond between the amide NH and the carbonyl oxygen groups of the amino acid ester. The possible mechanism of the chiral induction process was further studied by DFT calculations.     

N-磷酰化肽酯及小肽与氨基酸相互作用的ESI-MS研究

采用ESI-MS研究了一系列结构具有可比性的N-二异丙氧基磷酰化肽酯及小肽同20种蛋白氨基酸及3种D型氨基酸(D-Ala、D-Ser、D-Phe)的非共价相互作用.结果表明,可形成π-π共轭体系的芳香环,可显著增强磷酰化肽酯及小肽与氨基酸的相互作用力,π-π堆积力是首要的非共价相互作用力;可形成氢键的极性基团有利于形成复合物,但能否形成氢键还要受到分子柔顺性的影响;另外,分子大小、空间位阻对复合物的形成也有影响;而氨基酸的手性对它们的相互作用在质谱条件下没有表现出影响.     

Density Functional Theory Study of Hydrogen Bonds of Bipyridine with 1,3,5-Benzenetricarboxylic Acid

The hydrogen‐bonded dimer and trimer formed between 1,3,5‐benzenetricarboxylic acid and bipyridine have been investigated using a density functional theory (DFT) method and 6‐31++G** basis set. The interaction energies are ?45.783 and ?89.998 kJ·mol^?1 for the most stable dimer and trimer, respectively, after the basis set superposition error and zero‐point corrections. The formation of O–H...N hydrogen bonds makes O–H symmetric stretching modes in the dimer and trimer red‐shifted relative to those of the 1,3,5‐benzenetricarboxylic acid monomer. The natural bond orbit analysis shows that the inter‐molecular charge transfers are 0.60475e and 1.20225e for the dimer and trimer, respectively. Thermodynamic analysis indicates that the formation of trimer is an exothermic and spontaneous process at low and room temperature. A supramolecule can be constructed through the strong N···H–O intermolecular hydrogen bonds between bipyridine and 1,3,5‐benzenetricarboxylic acid, which is in good agreement with the experimental results.