Theoretical investigation of in-plane hydrogen-bonded complexes of ammonia with partially substituted fluorobenzenes

Systematic investigation of in-plane hydrogen-bonded complexes of ammonia with partially substituted fluorobenzenes has revealed that fluorobenzene, difluorobenzene, and trifluorobenzene favor formation of cyclic complexes with a C-H...N-H...F-C binding motif. On the other hand, tetrafluorobenzene and pentafluorobenzene favor formation of linear C-H...N hydrogen-bonded complexes. The complete absence of exclusively linear N-H...F hydrogen-bonded complexes for the entire series indicates that C-F bond in fluorobenzenes is a reluctant hydrogen-bond acceptor. However, fluorine does hydrogen bond when cooperatively stabilized with C-H...N hydrogen bonds for the lower fluoro analogues. The propensity of fluorobenzenes to adapt to the C-H...N-H...F-C binding motif decreases with the progressive fluorination of the benzene ring and disappears completely when benzene ring is substituted with five or more fluorine atoms.     

取代基对1-甲基尿嘧啶与N-甲基乙酰胺氢键复合物中氢键强度的影响

使用密度泛函理论B3LYP方法和二阶微扰理论MP2方法对由1-甲基尿嘧啶与N-甲基乙酰胺所形成的氢键复合物中的氢键强度进行了理论研究, 探讨了不同取代基取代氢键受体分子1-甲基尿嘧啶中的氢原子对氢键强度的影响和氢键的协同性. 研究表明: 供电子取代基使N－H…O＝C氢键键长r(H…O)缩短, 氢键强度增强; 吸电子取代基使N－H…O＝C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: 供电子基团使参与形成氢键的氢原子的正电荷增加, 使氧原子的负电荷增加, 使质子供体和受体分子间的电荷转移量增多; 吸电子基团则相反. 供电子基团使N－H…O＝C氢键中氧原子的孤对电子轨道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强, 吸电子基团使这种二阶相互作用稳定化能减弱. 取代基对与其相近的N－H…O＝C氢键影响更大.     

Factors controlling extremely strong AAA-DDD triply hydrogen-bonded complexes

Triply hydrogen-bonded complexes of the form AAA-DDD are shown to have the strongest interaction when the complex is substituted with electron withdrawing groups on the donor molecule (DDD) and electron donating groups on the acceptor molecule (AAA). In particular, the largest effects are observed when the withdrawing groups act through resonance. This serves to flatten the entire system resulting in more linear, and consequently stronger, hydrogen bonds. Furthermore, the present calculations show that the binding energy correlates with the electron density at the bond critical points and inversely with the hydrogen bond lengths.     

Supramolecular silanol chemistry in the gas phase. Topological (AIM) and population (NBO) analyses of hydrogen-bonded complexes between H3SiOH and selected O- and N-acceptor molecules

Hydrogen bonding of the type SiO-H...A (A = O, N) has been studied in the gas phase for simple H3SiOH.acceptor complexes with the acceptor molecules being O(H)SiH3, OH2, O(H)CH3, O(CH3)2, O(CH3)SiH3, O(SiH3)2, NH3, N(CH3)H2, N(CH3)2H, N(CH3)3, N(CH3)2C6H5, and NC5H5, respectively, at the B3LYP/6-311+(2d,p) level of theory, using Bader's atoms in molecules (AIM) and Weinhold's natural bond orbital (NBO) methodology. For all complexes (except H3SiOH.N(CH3)2C6H5) the complex energy Eadd. is a good estimate for the hydrogen bond energy EHB, which is generally higher in N-acceptor complexes (-5.52 to -7.17 kcal mol-1) than in O-acceptor complexes (-2.09 to -5.06 kcal mol-1). In case of H3SiOH.N(CH3)2C6H5, EHB and Eadd. differ by the energy associated with the loss of n(N)-->pi conjugation in N(CH3)2C6H5 upon complex formation. EHB shows no correlation with O...A distances and the red shifts Deltanu(OH) of the OH-stretching vibrations when different acceptors are compared, although both parameters are commonly used to estimate the strength of the hydrogen bond from spectroscopic and diffraction data. A good linear correlation of the hydrogen bond energy EHB has been established with parameters derived from the AIM and NBO analyses, namely, the electron densities rho(HA) and rho(OH) at the H...A and O-H bond critical points (BCPs) and the NLMO bond orders BONLMO(HA) of the H...A bonds of the H3SiOH.acceptor complexes as well as the change of natural charges DeltaqNPA(O) at the O-donor atom upon H3SiOH.acceptor complex formation. Hydrogen bonding of the type SiO-H...A (A = O, N) has been also studied in the related cyclic multiple H3SiOH.acceptor complexes (H3SiOH)3, (H3SiOH)2.NC5H5, and (H3SiOH)4, respectively, at the same level of theory. Cooperative hydrogen bonding is evident for all cyclic multiple H3SiOH.acceptor complexes, whereby the strongest concomitant strengthening of the hydrogen bonds is observed for (H3SiOH)4 and (H3SiOH)2.NC5H5.     

精氨酸侧链和核酸碱基间离子氢键作用强度分析

采用MP2/6-31+G(d,p)方法优化得到了22个由精氨酸侧链与碱基尿嘧啶、 胸腺嘧啶、 胞嘧啶、 鸟嘌呤及腺嘌呤形成的氢键复合物的气相稳定结构, 使用包含BSSE校正的MP2/aug-cc-pVTZ方法计算得到了复合物的气相结合能, 通过MP2/6-31+G(d,p)方法和PCM模型优化得到了复合物的水相稳定结构, 采用MP2/aug-cc-pVTZ方法和PCM模型计算得到了复合物的水相结合能. 研究发现, 精氨酸侧链与碱基间的离子氢键作用强度与单体间电荷转移量、 氢键临界点电子密度及二阶作用稳定化能密切相关. 与中性氢键相比, 离子氢键作用具有更显著的共价作用成分. 研究还发现, 精氨酸侧链和碱基间形成的氢键复合物的稳定性次序可以通过氢键受体碱基分子上氧原子和氮原子的质子化反应焓变进行预测, 质子化反应焓变越负, 形成的氢键复合物越稳定.     

A TD-DFT study on the hydrogen bonding of three esculetin complexes in electronically excited states: strengthening and weakening

Time-dependent density functional theory (TD-DFT) method was used to study the excited-state hydrogen bonding of three esculetin complexes formed with aprotic solvents. The geometric structures, molecular orbitals (MOs), electronic spectra and the infrared (IR) spectra of the three doubly hydrogen-bonded complexes formed by esculetin and aprotic solvents dimethylsulfoxide (DMSO), tetrahyrofuran (THF) and acetonitrile (ACN) in both ground state S(0) and the first singlet excited state S(1) were calculated by the combined DFT and TD-DFT methods with the COSMO solvation model. Two intermolecular hydrogen bonds can be formed between esculetin and the aprotic solvent in each hydrogen-bonded complex. Based on the calculated bond lengths of the hydrogen bonds and the groups involved in the formation of the intermolecular hydrogen bonds in different electronic states, it is demonstrated that one of the two hydrogen bonds formed in each hydrogen-bonded complex is strengthened while the other one is weakened upon photoexcitation. Furthermore, it is found that the strength of the intermolecular hydrogen bonds formed in the three complexes becomes weaker as the solvents change from DMSO, via THF, to ACN, which is suggested to be due to the decrease of the hydrogen bond accepting (HBA) ability of the solvents. The spectral shifts of the calculated IR spectra further confirm the strengthening and weakening of the intermolecular hydrogen bonds upon the electronic excitation. The variations of the intermolecular hydrogen bond strengths in both S(0) and S(1) states are proposed to be the main reasons for the gradual spectral shifts in the absorption and fluorescence spectra both theoretically and experimentally.     

Switching binding sites: low-temperature NMR studies on adenosine-aspartic acid interactions

Low-temperature NMR experiments were performed on mixtures of adenine nucleosides and aspartic acid derivatives in a freonic solvent. By acquiring spectra at temperatures as low as 123 K, the regime of slow hydrogen bond exchange is reached and hydrogen-bonded complexes can be characterized in detail. With 2'-deoxyadenosine lacking a 2'-substituent, N-Boc-protected aspartic acid benzyl ester binds through its carboxylic acid side chain to the Watson-Crick site of the adenine base, forming a strong hydrogen bond with the proton located close to the center between the oxygen donor and adenine N1 nitrogen acceptor. However, in the case of 2'-O-silylated adenine ribofuranosides, noncovalent interactions of the 2'-substituent with protecting groups on the amino acid shift the binding mode toward a Hoogsteen geometry with only a moderately strong hydrogen bond involving adenine N7.     

Time-Dependent Density Functional Theory Study on Electronic Excited-State Hydrogen Bonding of Benzonitrile in Methanol Solution

In this work, the time dependent density functional theory (TDDFT) method was used to investigate the hydrogen bonding dynamics of benzonitrile (PhCN) as hydrogen acceptor in hydrogen donating solvent methanol (MeOH). The ground-state geometry optimizations and the electronic transition energies of the isolated PhCN and MeOH monomers and the two hydrogen-bonded PhCN–MeOH dimers are calculated by the DFT and TDDFT method respectively. According to the results, the hydrogen bond takes the responsibility of the geometric structure change and electronic transfer of the molecules involved. As well, the intermolecular hydrogen-bond C≡N···H–O is strengthened in electronically excited states of the hydrogen-bonded PhCN–MeOH^a (planar structure) and PhCN–MeOH^b (perpendicular structure) as a result of the lower excitation energy and the electronic spectral redshifts. Despite the different structure, the effects of hydrogen bond on PhCN–MeOH^a and PhCN–MeOH^b are considered the same, which serves as a proof that geometric structure has little contribution to the structural and energy change in hydrogen-bonded complexes. However, in high-lying singlet states, the structure can cause the divergence of electronic transition rate between the two hydrogen-bonded complexes, even if within the same transition path. What’s more, the extent of hydrogen bond effect on PhCN and MeOH is different between the low-lying excited states and the high-lying excited states.     

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.     

Fluorescence solvatochromism in lumichrome and excited-state tautomerization: a combined experimental and DFT study

Fluorescence solvatochromism of lumichrome (LC) was studied by steady-state and time-resolved fluorescence spectroscopy. The excited-state properties of LC do not show any correlation with solvent polarity, however, reasonably good correlation with solvent E(T)(30) parameter was observed. A quantitative estimation of contribution from different solvatochromic parameters, like solvent polarizability (π*), hydrogen bond donor (α), and hydrogen bond acceptor (β) ability of the solvent, was made using linear free energy relationship on the basis of Kamlet-Taft equation. The analysis reveals that hydrogen bond donating ability (acidity) of the solvent is the most important parameter that characterizes the excited-state behavior of lumichrome. Quantum mechanical calculations using density functional theory (DFT) were done to study the most stable structure and excited-state tautomerization process of LC toward the formation of isoalloxazines. Charge localization in the excited state and formation of hydrogen-bonded cluster through solvent hydrogen bond donation on the N10 atom of alloxazine moiety were predicted to be the key step toward this water-catalyzed tautomerization process.     

The effect of hydrogen bonding on structural parameters : IV. An ab initio study of formamide—ammonia complexes

Four hydrogen-bonded formamide—ammonia complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is acceptor. In all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond. Potential functions for the N—HN and N—HO hydrogen bonds have been derived.     

Influence of intramolecular hydrogen bond strength on OH-stretching overtones

Vapor-phase OH-stretching overtone spectra of 1,3-propanediol and 1,4-butanediol were recorded and compared to the spectra of ethylene glycol to investigate the effect of increased intramolecular hydrogen bond strength on OH-stretching overtone transitions. The spectra were recorded with laser photoacoustic spectroscopy in the second and third OH-stretching overtone regions. The room-temperature spectra of each molecule are dominated by two conformers that show intramolecular hydrogen bonding. Anharmonic oscillator local-mode calculations of the OH-stretching transitions have been performed to aid assignment of the different conformers in the spectra and to illustrate the effect of the intramolecular hydrogen bonding. The hydrogen bond strength increases in the order ethylene glycol, 1,3-propanediol, and 1,4-butanediol. The overtone transitions of the hydrogen-bonded hydroxyl groups are more difficult to observe with increasing intramolecular hydrogen bond strength. We suggest that the bandwidth of these transitions increases with increasing hydrogen bond strength and with increasing overtone and furthermore that these changes are in part responsible for the lack of observed overtone spectra for complexes.     

Red and blue shifted hydridic bonds

By performing MP2/aug‐cc‐pVTZ ab initio calculations for a large set of dimer systems possessing a R? H hydridic bond involved in diverse types of intermolecular interactions (dihydrogen bonds, hydride halogen bonds, hydride hydrogen bonds, and charge‐assisted hydride hydrogen bonds), we show that this is rather an elongation than a shortening that a hydride bond undergoes on interaction. Contrary to what might have been expected on the basis of studies in uniform electric field, this elongation is accompanied by a blue instead of red shift of the R? H stretching vibration frequency. We propose that the “additional” elongation of the R? H hydridic bond results from the significant charge outflow from the sigma bonding orbital of R? H that weakens this bond. The more standard red shift obtained for stronger complexes is explained by means of the Hermansson's formula and the particularly strong electric field produced by the H‐acceptor molecule. © 2014 Wiley Periodicals, Inc.     

HCN(HNC)与NH3, H2O和HF分子间相互作用的理论研究

在MP2/aug-cc-pVTZ水平上, 对HCN(HNC)与NH3, H2O和HF分子间可能存在的氢键型复合物进行了全自由度能量梯度优化, 通过在相同水平上的频率验证分析发现了稳定的分子间相互作用形式是HCN(HNC)作为质子供体或作为质子受体形成的复合物. 基组重叠误差对总相互作用能的影响均小于3.34 kJ/mol. 通过自然键轨道(NBO)分析, 研究了单体和复合物中的原子电荷和电荷转移对分子间相互作用的影响. 对称性匹配微扰理论(SAPT, Symmetry Adapted Perturbation Theory)能量分解结果表明, 在分子间相互作用中, 静电作用与诱导作用占主导地位, 而诱导作用与复合物的电荷转移之间具有良好的正相关性.     

Vibrational spectroscopic properties of hydrogen bonded acetonitrile studied by DFT

Vibrational properties (band position, Infrared and Raman intensities) of the acetonitrile C[triple bond]N stretching mode were studied in 27 gas-phase medium intensity (length range: = 1.71-2.05 angstroms; -deltaE range = 13-48 kJ/mol) hydrogen-bonded 1:1 complexes of CH3CN with organic and inorganic acids using density functional theory (DFT) calculations [B3LYP-6-31++G(2d,2p)]. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in the OH stretching band of the acids were also considered. Experimentally observed blue-shifts of the C[triple bond]N stretching band promoted by the hydrogen bonding, which shortens the triple bond length, are very well reproduced and quantitatively depend on the hydrogen bond length. Both predicted enhancement of the infrared and Raman nu(C[triple bond]N) band intensities are in good agreement with the experimental results. Infrared band intensity increase is a direct function of the hydrogen bond energy. However, the predicted increase in the Raman band intensity increase is a more complex function, depending simultaneously on the characteristics of both the hydrogen bond (C[triple bond]N bond length) and the H-donating acid polarizability. Accounting for these two parameters, the calculated nu(C[triple bond]N) Raman intensities of the complexes are explained with a mean error of +/- 2.4%.     

碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

正确理解核酸碱基和蛋白质多肽间的作用机制有助于人们利用这些生物分子有效地进行分子设计,进而制备具有特殊纳米结构和功能的生物分子材料.本文优化得到了碱基腺嘌呤与N-甲基乙酰胺、甘氨酸二肽、丙氨酸二肽形成的20个氢键复合物的结构并计算了结合能,探讨了腺嘌呤与多肽酰胺间氢键作用的最佳位点.研究发现:腺嘌呤可以使用两个不同位点(A1位点和A2位点)与N-甲基乙酰胺形成N―H…N型或者N―H…O=C型氢键复合物,腺嘌呤使用A1位点与N-甲基乙酰胺形成的N―H…N型氢键复合物更稳定;二肽分子可以使用主链上两个不同位点(丙氨酸的Ala7位点和Ala5位点或者甘氨酸的Gly7位点和Gly5位点)与腺嘌呤形成含有N―H…N和N―H…O=C两条氢键的复合物,二肽分子使用Ala7或Gly7位点与腺嘌呤形成的氢键复合物更稳定;腺嘌呤与多肽间的氢键作用强于其与N-甲基乙酰胺的作用.基于分子中的原子理论与自然键轨道计算结果分析了氢键作用的本质.     

The effect of hydrogen bonding on structural parameters ii. an ab initio study of the monohydrated formamide molecule

Four hydrogen-bonded formamide-water complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is an acceptor. The results indicate that the effect on the conjugated NCO fragment depends on both the type and the energy of the hydrogen bond formed. Although, in all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond, there is a significant difference in the effect of the two types of hydrogen bonds. This difference may be explained by changes in the electron populations. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond, and analytical expressions have been found for the variations of the CO and CN bond lengths with changes in the hydrogen bond length. Potential functions for the N-H β O and O-H β O hydrogen bonds have also been derived.     

Time-dependent density functional theory study on hydrogen-bonded intramolecular charge-transfer excited state of 4-dimethylamino-benzonitrile in methanol

The time-dependent density functional theory (TDDFT) method was carried out to investigate the hydrogen-bonded intramolecular charge-transfer (ICT) excited state of 4-dimethylaminobenzonitrile (DMABN) in methanol (MeOH) solvent. We demonstrated that the intermolecular hydrogen bond C[triple bond]N...H-O formed between DMABN and MeOH can induce the C[triple bond]N stretching mode shift to the blue in both the ground state and the twisted intramolecular charge-transfer (TICT) state of DMABN. Therefore, the two components at 2091 and 2109 cm(-1) observed in the time-resolved infrared (TRIR) absorption spectra of DMABN in MeOH solvent were reassigned in this work. The hydrogen-bonded TICT state should correspond to the blue-side component at 2109 cm(-1), whereas not the red-side component at 2091 cm(-1) designated in the previous study. It was also demonstrated that the intermolecular hydrogen bond C[triple bond]N...H-O is significantly strengthened in the TICT state. The intermolecular hydrogen bond strengthening in the TICT state can facilitate the deactivation of the excited state via internal conversion (IC), and thus account for the fluorescence quenching of DMABN in protic solvents. Furthermore, the dynamic equilibrium of these electronically excited states is explained by the hydrogen bond strengthening in the TICT state.     

Cooperativity in ionic liquids

Cooperativity in ionic liquids is investigated by means of static quantum chemical calculations. Larger clusters of the dimethylimidazolium cation paired with a chloride anion are calculated within density functional theory combined with gradient corrected functionals. Tests of the monomer unit show that density functional theory performs reasonably well. Linear chain and ring aggregates have been considered and geometries are found to be comparable with liquid phase structures. Cooperative effects occur when the total energy of the oligomer differs from a simple sum of monomer energies. Cooperative effects have been found in the structural motifs examined. A systematic study of linear chains of increasing length (up to nine monomer units) has shown that cooperativity plays a more important role than expected and is stronger than in water. The Cl...H distance of the chloride to the most acidic proton increases with an increasing number of monomer units. The average bond distance approaches 218.9 pm asymptotically. The dipole moment grows almost linearly and the dipole moment per monomer unit reaches the asymptotic value of 16.3 D. The charge on the chloride atoms decreases with an increasing chain length. In order to detect local hydrogen bonding in the clusters a new parametrization of the shared-electron number method is introduced. We find decreasing hydrogen bond energies with an increasing cluster size for both the first hydrogen bond to the most acidic proton and the average hydrogen bond.     

Triangular Halogen Bond and Hydrogen Bond Supramolecular Complex Consisting of Carbon Tetrabromide,Halide, and Solvent Molecule： A Theoretical and Spectroscopic Study

The theoretical calculation and spectroscopic experiments indicate a kind of triangular three bonding supramolecular complexes CBr4…X^-…-H-C, which consist of carbon tetrabromide, halide, and protic solvent molecule （referring to dichloromethane, chloroform and acetonitrile）, can be formed in solution. The strength of halogen and hydrogen bonds in the triangular complexes using halide as common acceptor obeys the order of iodide〉bromide〉chloride. The halogen and hydrogen bonds work weak-cooperatively. Charge transfer bands of halogen bonding complexes between CBra and halide are observed in UV-Vis absorption spectroscopy in three solvents, and then the stoichiometry of 1：1, formation constants K and molar extinction coefficients ε of the halogen bonding complexes are obtained by Benesi-Hildebrand method. The K and ε show a dependence on the solvent dielectric constant and, on the whole, obey an order of iodide〉bromide〉chloride in the same solvents. Furthermore, the C-H vibrational frequencies of solvent molecules vary obviously with the addition of halide, which indicates the C-H…X- interaction. The experimental data indicate that the halogen bond and hydrogen bond coexist by sharing a common halide acceptor as predicted by calculation.