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.     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Hydrogen‐bonded complexes of nicotine with simple alcohols

Ab initio and density functional theory studies have been performed on the hydrogen‐bonded complexes of neutral and protonated nicotine with ethanol, methanol, and trifluromethanol to explore their relative stability in a systematic way. Among all the hydrogen‐bonded nicotine complexes considered here, protonated forms in nicotine–ethanol and nicotine–methanol, and neutral form in nicotine–trifluromethanol complexes have been found to be the most stable. In the former two complexes, the proton attached to the pyrrolidine nitrogen acts as a strong hydrogen bond donor, whereas the pyrrolidine nitrogen atom acts as a hydrogen bond acceptor in the latter case. Neutral complex of nicotine with trifluromethanol has been found to possess a very short hydrogen bond (1.57 Å) and basis set superposition error corrected hydrogen bond energy value of 19 kcal/mol. The nature of the various hydrogen bonds formed has been investigated through topological aspects using Bader's atoms in molecules theory. From the calculated topological results, excellent linear correlation is shown to exist among the hydrogen bond length, electron density, and its Laplacian at the bond critical points for all the complexes considered. The natural bond orbital analysis has been carried out to investigate the charge transfer in the nicotine alcohol complexes. In contrast to the blue shifting behavior that is generally exhibited by other C? H···O hydrogen bonds involving sp³ carbon atom, the C? H···O hydrogen bond in the protonated nicotine–ethanol and methanol complexes has been found to be proper with red shifting in nature. © 2011 Wiley Periodicals, Inc.     

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

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

A simple method for the characterization of OHO-hydrogen bonds by H-solid state NMR spectroscopy

A set of OHO hydrogen bonded systems with known neutron diffraction structure has been studied by fast ¹H-MAS echo spectroscopy. It is shown that the application of a simple rotor synchronized echo sequence combined with fast MAS allows a faithful determination of the chemical shift of the proton in the hydrogen bond. Employing the empirical valence bond order model, the experimental ¹H chemical shifts of the hydrogen bonded protons are correlated to the hydrogen bond geometries. The resulting correlation between the proton chemical shift and the deviation of the proton from the center of the hydrogen bond covers a broad range of substances. Deviations from the correlation curve, which are observed in certain systems with strong hydrogen bonds, are explained in terms of proton tautomerism or delocalization in low-barrier hydrogen bonds. These deviations are a highly diagnostic tool to select potential candidates for further experimental and theoretical studies. Thus, the combination of the ¹H-MAS echo sequence with the correlation curve yields a simple and versatile tool for the structural analysis of OHO hydrogen bonds.     

NCO/NCS自由基与XY（X=H,Cl;Y=F,Cl,Br）间σ-型弱作用的理论研究

NCO和NCS是大气化学中非常引人关注的自由基,它们均有三个原子并且两个端基原子均可作为电子给体形成σ-型氢/卤键.本文在MP2/aug-cc-pVDZ水平上研究了NCO/NCS...XY（X=H,Cl;Y=F,Cl,Br）体系中的弱化学键.计算结果表明,氢/卤原子与N原子相连形成的复合物比与O/S原子相连形成的复合物稳定;氢/卤键的稳定性由分子静电势决定,而非原子电负性;对相同的电子给体B（B=N,O/S）和相同的卤原子来说,化学键的强度按Y=F,Cl,Br的顺序逐渐减弱.在氢/卤键形成过程中,自旋电子密度在电子给体和电子受体间的转移较少,但它在自由基内部发生重排,就本文研究的所有复合物而言,自旋电子密度均转移向XY分子的相反位置.     

Computational studies of σ-type weak interactions between NCO/NCS radicals and XY(X = H,Cl;Y = F,Cl,and Br)

The triatomic radicals NCO and NCS are of interest in atmospheric chemistry,and both the ends of these radicals can potentially serve as electron donors during the formation of σ-type hydrogen/halogen bonds with electron acceptors XY(X = H,Cl;Y = F,Cl,and Br).The geometries of the weakly bonded systems NCO/NCS···XY were determined at the MP2/aug-cc-pVDZ level of calculation.The results obtained indicate that the geometries in which the hydrogen/halogen atom is bonded at the N atom are more stable than those where it is bonded at the O/S atom,and that it is the molecular electrostatic potential(MEP)-not the electronegativity-that determines the stability of the hydrogen/halogen bond.For the same electron donor(N or O/S) in the triatomic radical and the same X atom in XY,the bond strength decreases in the order Y = F > Cl > Br.In the hydrogen/halogen bond formation process for all of the complexes studied in this work,transfer of spin electron density from the electron donor to the electron acceptor is negligible,but spin density rearranges within the triatomic radicals,being transferred to the terminal atom not interacting with XY.     

基于氢键作用结合的超分子聚合物

非共价键结合的超分子聚合物由于其特殊的结构及性能引起了广泛的关注。本文在介绍超分子化学、氢键及超分子聚合物的基础上,主要综述了以氢键为结合力的多重氢键作用、羧基（D）与吡啶基（A）作用以及氢键与其它非共价键协同作用形成的超分子聚合物体系,并对超分子聚合物的研究现状及前景进行了评述。     

Solvent effects on glycine II. Water-assisted tautomerization

The water-assisted tautomerization of glycine has been investigated at the B3LYP/6-31+G** level using supermolecules containing up to six water molecules as well as considering a 1:1 glycine-water complex embedded in a continuum. The conformations of the tautomers in this mechanism do not display an intramolecular H bond, instead the functional groups are bridged by a water molecule. The replacement of the intramolecular H bond by the bridging water reduces the polarity of the N-H bond in the zwitterion and increases that of the O-H bond in the neutral, stabilizing the zwitterion. Both the charge transfer effects and electrostatic interactions stabilize the nonintramolecularly H-bonded zwitterion conformer over the intramolecularly hydrogen bonded one. The nonintramolecularly H-bonded neutral is favored only by charge transfer effects. Although there is no strong evidence whether the intramolecularly hydrogen bonded or non hydrogen bonded structures are favored in the bulk solution represented as a dielectric continuum, it is likely that the latter species are more stable. The free energy of activation of the water-assisted mechanism is higher than the intramolecular proton transfer channel. However, when the presumably higher conformational energy of the zwitterion reacting in the intramolecular mechanism is taken into account, both mechanisms are observed to compete. The various conformers of the neutral glycine may form via multiple proton transfer reactions through several water molecules instead of a conformational rearrangement.     

A simple model of hydrogen bonding with particular application to trends in hydrogen‐bonded dimers

A simple model has been proposed to explain trends in the computed interaction energy, bond length changes, frequency shifts and infrared intensities for the chlorofluoromethanes CF_nCl_mH, FH and FArH on complexation with the isoelectronic diatomics BF, CO, N₂ and the rare gas atoms Kr, Ar, Ne to form a series of linear or nearly linear hydrogen‐bonded complexes. The dipole moment derivative of the proton donor (with respect to the stretching coordinate) and the chemical hardness of the hydrogen‐bonded atom of the proton acceptor are identified as two useful parameters for rationalizing the changes in some of the molecular properties of the proton donor when the hydrogen bond is formed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Excited‐State Hydrogen Bonding Strengthening and Weakening with Intramolecular Charge Transfer in Resorufin‐Water Complexes: A TD‐DFT Study

The geometric structures, infrared spectra and hydrogen bond binding energies of the various hydrogen‐bonded Res^?‐water complexes in states S0 and S1 have been calculated using the density functional theory (DFT) and time‐dependent density functional theory (TD‐DFT) methods, respectively. Based on the changes of the hydrogen bond lengths and binding energies as well as the spectral shifts of the vibrational mode of the hydroxyl groups, it is demonstrated that hydrogen bonds HB‐II, HB‐III and HB‐IV are strengthened while hydrogen bond HB‐I is weakened in the four singly hydrogen‐bonded Res^?‐Water complexes upon photoexcitation. When the four hydrogen bonds are formed simultaneously between one resorufin anion and four water molecules in the Res^?‐4Water complex, all the hydrogen bonds are weakened in both the ground and excited states compared with those in the corresponding singly hydrogen‐bonded Res^?‐Water complexes. Furthermore, in complex Res^?‐4Water, hydrogen bonds HB‐II and HB‐IV are strengthened while hydrogen bonds HB‐I and HB‐III are weakened after the electronic excitation. The hydrogen bond strengthening and weakening in the various hydrogen‐bonded Res^?‐water complexes should be due to the redistribution of the charges among the four heteroatoms (O_1‐3 and N₁) within the resorufin molecule upon the optical excitation.     

Vibrational dynamics of hydrogen‐bonded HCN complexes with OH and NH acids: Computational DFT systematic study

Vibrational properties (band position, infrared [IR], and Raman intensities) of C?N stretching mode were studied in 65 gas phase hydrogen‐bonded 1:1 complexes of HCN with OH acids and NH acids using density functional theory (DFT) calculations at the B3LYP‐6‐311++G(d,p) level. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in acids OH/NH stretching bands were also considered. Experimentally observed blue shift of the C?N stretching band promoted by hydrogen bonding, which shortens the triple bond length, is very well reproduced and quantitatively depends on the hydrogen bond length. Both IR and Raman ν(C?N) band intensities are enhanced, also in good agreement with the experimental results. IR intensity increase is a direct function of the hydrogen bond energy. However, the predicted Raman intensity raise is a more complex function, depending simultaneously on characteristics of both the hydrogen bond (C?N bond length) and the H‐donating acid (polarizability). With these two parameters, ν (C?N) Raman intensities of the complexes are explained with a mean error of ±2.4%. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

A Theoretical Study on Hydrogen‐Bonded Complex of Proflavine Cation and Water: The Site‐dependent Feature of Hydrogen Bond Strengthening and Weakening

The intermolecular hydrogen‐bonds between proflavine cation (PC) and water molecules are investigated by density functional theory (DFT) and time‐dependent density functional theory (TDDFT) methods. The ground‐state geometry optimizations, electronic excitation energies and corresponding oscillation strengths of the low‐lying electronically excited states for the isolated proflavine cation, the hydrogen‐bonded PC–H2O dimer and PC–(H2O)2 trimer are calculated. Intermolecular hydrogen bonds at the central site of proflavine molecule are found to be stronger than the peripheral site. The hydrogen bond N–H???O for the hydrogen‐bonded dimer are indicated to be weakened in the excited states, since the excitation energy is increased slightly comparing to the monomer. Hydrogen bonds of PC–(H2O)2 trimer with the same type as the dimer are strengthened in the excited state, which is demonstrated by the decrease of the excited energies. Thus, hydrogen bond strengthening and weakening are observed to reveal site dependent feature in proflavine molecule. Furthermore, the hydrogen bond at central site induces the blue‐shift of the absorption spectrum, while the ones at peripheral site induce red‐shift. Hydrogen bonds with the same type at peripheral and central sites of proflavine molecule provide different effects on the photochemical and photophysical properties of proflavine.     

A DFT-based study of the hydrogen-bonding interactions between epicatechin and methanol/water

Tea polyphenols are essential components that give tea its medicinal properties. Methanol and water are frequently used as solvents in the extraction of polyphenols. Hydrogen-bonding interactions are significant in the extraction reaction. Density functional theory (DFT) techniques were used to conduct a theoretical investigation on the hydrogen-bonding interactions between methanol or water and epicatechin, an abundant polyphenol found in tea. After first analyzing the epicatechin monomer's molecular geometry and charge characteristics, nine stable epicatechin (EC) H₂O/CH₂OH complex geometries were discovered. The presence of hydrogen bonding in these improved structures has been proven. The calculated hydrogen bond structures are very stable, among which the hydrogen bond bonded with a hydroxyl group has higher stability. The nine complex structures’ hydrogen bonds were thought to represent closed-shell-type interactions. The interaction energy with 30O-31H on the epicatechin benzene ring is the strongest in the hydrogen bond structure. While the other hydrogen bonds were weak in strength and mostly had an electrostatic nature, the hydrogen bonds between the oxygen atoms in H₂O or CH₂OH and the hydrogen atoms of the hydroxyl groups in epicatechin were of moderate strength and had a covalent character. Comparing the changes in the hydrogen bond structure vibration peak, the main change in concentration peak is the hydrogen bond vibration peak in the complex. Improved the study on the hydrogen bond properties of CH₂OH and H₂O of EC.     

A molecular orbital explanation of bond distance variation caused by hydrogen bond formation

For hydrogen bond systems X–D–HA–Y, a simple molecular orbital model is proposed to understand the mechanism of the bond distance variations caused by the hydrogen bond formation. This model explains the bond distance variations for X–D and A–Y as follows. Electrostatic potential that the electrons in a molecule receive from other molecules causes the changes in atomic orbital energy differences between the bonded atoms. Then, the changes in the orbital energy differences make the bond orders larger or smaller and consequently the bond distances vary. The validity of this model has been confirmed by the effective fragment potential method, using the test systems of (HCOOH)₂, HCONH₂ (formamide) crystal and BF₃·2H₂O crystal.     

Reconsideration on hydrogen bond strengthening or cleavage of photoexcited coumarin 102 in aqueous solvent: a DFT/TDDFT study

In this work, the excited-state hydrogen bonding dynamics of photoexcited coumarin 102 in aqueous solvent is reconsidered. The electronically excited states of the hydrogen bonded complexes formed by coumarin 102 (C102) chromophore and the hydrogen donating water solvent have been investigated using the time-dependent density functional theory method. Two intermolecular hydrogen bonds between C102 and water molecules are considered. The previous works (Wells et al., J Phys Chem A 2008, 112, 2511) have proposed that one intermolecular hydrogen bond would be strengthened and the other one would be cleaved upon photoexcitation to the electronically excited states. However, our theoretical calculations have demonstrated that both the two intermolecular hydrogen bonds between C102 solute and H(2)O solvent molecules are significantly strengthened in electronically excited states by comparison with those in ground state. Hence, we have confirmed again that intermolecular hydrogen bonds between C102 chromophore and aqueous solvents are strengthened not cleaved upon electronic excitation, which is in accordance with Zhao's works.     

Ab initio and AIM studies on typical π‐type and pseudo‐π‐type halogen bonds: Comparison with hydrogen bonds

Series of typical π‐type and pseudo‐π‐type halogen‐bonded complexes B ··· ClY and B ··· BrY and hydrogen‐bonded complex B ··· HY (B = C₂H₄, C₂H₂, and C₃H₆; Y = F, Cl, and Br) have been investigated using the MP2/aug‐cc‐pVDZ method. A striking parallelism was found in the geometries, vibrational frequencies, binding energies, and topological properties between B ··· XY and B ··· HY (X = Cl and Br). It has been found that the lengths of the weak bond d(X ··· π)/d(H ··· π), the frequencies of the weak bond ν(X ··· π)/ν(H ··· π), the frequency shifts Δν(X? Y)/Δν(H? Y), the electron densities at the bond critical point of the weak bonds ρ_c(X ··· π)/ρ_c(H ··· π), and the electron density changes Δρ_c(X? Y)/Δρ_c(H? Y) could be used as measures of the strengths of typical π‐type and pseudo‐π‐type halogen/hydrogen bonds. The typical π‐type and pseudo‐π‐type halogen bond and hydrogen bond are noncovalent interactions. For the same Y, the halogen bond strengths are in the order B ··· ClY < B ··· BrY. For the same X, the halogen bond strength decreases according to the sequence F > Cl > Br that is in agreement with the hydrogen bond strengths B ··· HF > B ··· HCl > B ··· HBr. All of these typical π‐type and pseudo‐π‐type hydrogen‐bonded and halogen‐bonded complexes have the “conflict‐type” structure. Contour maps of the Laplacian of π electron density indicate that the formation of B ··· XY halogen‐bonded complex and B ··· HY hydrogen‐bonded complex is very similar. Charge transfer is observed from B to XY/HY and both the dipolar polarization and the volume of the halogen atom or hydrogen atom decrease on B ··· XY/B ··· HY complex formation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A novel tubular hydrogen‐bond pattern in a new diazaphosphole oxide: a combination of X‐ray crystallography and theoretical study of hydrogen bonds

In the structure of 2‐(4‐chloroanilino)‐1,3,2λ⁴‐diazaphosphol‐2‐one, C₁₂H₁₁ClN₃OP, each molecule is connected with four neighbouring molecules through (N—H)₂…O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R ³₃(12) and R ₄³(14) hydrogen‐bond ring motifs, combined with a C (4) chain motif. The hole constructed in the tubular architecture includes a 12‐atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co‐operating in classical hydrogen bonding, takes part in an N—H…π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen‐bond pattern. The energies of the N—H…O and N—H…π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen‐bonded cluster of molecules as the input file for the chemical calculations. In the ¹H NMR experiment, the nitrogen‐bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the ²J _H–P coupling constant.     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011