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.     

Hydrogen-bonded complexes of serotonin with methanol and ethanol: a DFT study

Density functional theoretical studies on hydrogen-bonded complexes of serotonin with methanol/ethanol have been carried out in a systematic way. The conformational analysis led to ten stable conformers that can be either gauche or anti depending on the dihedral angle values taken by ethylamine side chain and the 5-hydroxyl group. Serotonin-molecules strongly bind with ethanol than methanol. Ethylamine side chain is the most reactive site in both methanol/ethanol complexes and it is responsible for the stability order. The topological parameters, electron density, and Laplacian of electron density show excellent correlation with the hydrogen bond length. Natural bond orbital analysis confirms C–H···O hydrogen bond formed between the serotonin–alcohol complexes to be red shift in nature except for Gph(out)anti complex both with methanol and ethanol to be blue shifted. The energy decomposition analysis reveals that strong interactions between serotonin and ethanol/methanol are due to the attractive contributions from the electrostatic component.     

Nature of MoH···I bonds in Cp2Mo(L)H···I‐C≡C‐R Complexes (L=H,CN, PPh2, C(CH3)3; R=NO2, Cl,Br, H,OH, CH3, NH2)

The nature of the MoH···I bond in Cp₂Mo(L)H···I‐C≡C‐R (L= H, CN, PPh₂, C(CH₃)₃; R=NO₂, Cl, Br, H, OH, CH₃, NH₂) was investigated using electrostatic potential analysis, topological analysis of the electron density, energy decomposition analysis and natural bond orbital analysis. The calculated results show that MoH···I interactions in the title complexes belong to halogen‐hydride bond, which is similar to halogen bonds, not hydrogen bonds. Different to the classical halogen bonds, the directionality of MoH···I bond is low; Although electrostatic interaction is dorminant, the orbital interactions also play important roles in this kind of halogen bond, and steric interactions are weak; the strength of H···I bond can tuned by the most positive electrostatic potential of the I atom. As the electron‐withdrawing ability of the R substituent in the alkyne increases, the electrostatic potential maximum of the I atom increases, which enhances the strength of the H···I halogen bond, as well as the electron transfer.     

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.     

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     

On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

It is demonstrated that in all types of hydrogen bonds (X—H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X--H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X—H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C—H bond lengths with proton donor-acceptor distance in F3C—H…OH2 and F3C—H…Cl^- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X—H…π complexes and the blue-shifted lithium bonds in the X—Li…Y complexes.     

The effect of methyl group on the cooperativity between three types of hydrogen bond: O?H···O,C?H···O,and O?H···π

The effect of the methyl group on the cooperativity between three types of hydrogen bond (O H···O, C H···O, and O H···π) in cyclic complex involving an acetylene and two waters has been studied on the basis of high-level ab initio calculations. The total interaction energy of three hydrogen bonds increases as the number of methyl group in the complex increases. The binding distances of O H···π and O H···O hydrogen bonds shorten, while that of C H···O hydrogen bond elongates with increasing methyl group. This indicates that addition of methyl group leads to enhancement of O H···π and O H···O hydrogen bonds, and weakening of C H···O hydrogen bond, as also shown in frequency shift, chemical shifts, charge populations, and stabilization energies of orbital interactions. Although the presence of methyl group has a complicated effect on different type of hydrogen bond, the cooperativity of three hydrogen bonds increases in general with the addition of methyl group. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Synthesis,crystal structure and other properties of the complexes of Er(III), Yb(III) and Lu(III) with 4,4′-bipyridine and dichloroacetates

A novel mixed-ligand complexes of Er(III), Yb(III) and Lu(III) with title ligands were prepared and characterized by chemical and elemental analysis and IR spectroscopy, conductivity (in methanol, dimethyloformamide and dimethylsulphoxide). The thermal properties of complexes in the solid state were studied. The mode of metal–ligand coordination was discussed. The title compounds are isomorphic and isostructural in solid state. All atoms in studied compounds lie in general positions but occurrence of inversion on the midpoint of the bond linking two pyridine rings leads to existence in asymmetric unit one complex molecule and half of outer coordination sphere 4-bpy molecule. All chelating carboxylate groups are symmetrically bonded to the metal cations. The molecules of studied compounds are connected to the three dimensional network via O–H···O and O–H···N intermolecular hydrogen bonds. In the structures also exist C–H···O, C–H···Cl weak hydrogen bonds and π····π stacking interactions.     

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     

Synthesis and Crystal Structures of Hydrogen Monofluorophosphates with N‐containing Organic Cations. The Influence of Fluorine on their Hydrogen Bond Systems

The synthesis and crystal structures of guanidinium monofluorophosphate and hydrogen monofluorophosphates with the following cations: piperazinium, di‐ and triethylammonium, guanidinium, and dimethyluronium, are described and discussed. The structures of the acid salts consist of hydrogen‐bonded HPO₃F tetrahedra, which form infinite chains or cyclic dimers. The organic cations link these units together. All of the hydrogen bond systems observed consist of short O—H···O and longer N—H···O bonds. No O—H···F or N—H···F bonds were found. The F atom avoids hydrogen acceptor positions in the structures. The thermal behavior of [NHEt₃]HPO₃F was also studied.     

Studies of two different types of intramolecular C–H···F–C interactions from polyfluorinated diiodometal(II) diimine complexes

The X‐ray crystal structures of the polyfluorinated complexes [5,5′‐bis(HCF₂CF₂CF₂CF₂CH₂OCH₂)‐2,2′‐bpy]MI₂ ( 55‐8F‐PtI ₂ and 55‐8F‐PdI ₂ where M = Pt and Pd, respectively) were obtained. These two structures are found to show not only two different types of intramolecular, six‐membered cyclic C–H···F–C interactions (F₂C–H···F–C and HC–H···F–C) as important structural features but also alternating fluorinated and non‐fluorinated layers. The F₂C–H···F–C interactions, which are close to the metal core, are much better structurally characterized in this type of complexes with fluorous ponytails at the 5,5′ positions than those previously reported at the 4,4′ positions. The molecular planes of (bpy)MI₂ are extended by self‐matching, using two C–H···I hydrogen bonds and one C–H···F–C blue‐shifting hydrogen bond. The F₂C–H···F–C hydrogen bonds interact at the supramolecular level such that one polyfluorinated ponytail of the title compounds is transoid without an intramolecular C–H···F–C interaction, while the other polyfluorinated ponytail is cisoid with an intramolecular C–H···F–C interaction. Why one ponytail is cisoidal while the other is transoidal will be explained. Furthermore, the second type of C–H···F–C interactions involving the methylene H atom has been identified for the first time. In addition, these two metal structures are studied by density functional theory (DFT).     

Cooperative effect between pnicogen bond and hydrogen bond interactions in typical X…AsH2F…HF complexes (X = NR3, PR3 and OR2; R = CH3, H,F)

Abstract

Ab initio MP2/aug-cc-pVDZ calculations have been carried out to study the effect of F???H···F hydrogen bonds on the As···X pnicogen bond in X…AsH₂F…HF complexes (X?=?NR₃, PR₃ and OR₂; R?=?CH₃, H, F). The formation of F???H···F hydrogen bonds leads to shortening of the As···X distances and strengthening of the As···X interactions. The decrease of the pnicogen bond distance in the complexes is cost of electron-giving of X molecule that increased in the order R?=?CH₃?>?H?>?F for R substituents on X molecule. These effects are studied in the relationships of the structural characteristics, energetic, charge-transfer and electron density assets of the complexes. A satisfactory cooperative effect, with values that ranged between ?0.10 and ?3.98?kcal/mole, is found in the complexes.     

Theoretical Studies on the Halogen Bond between Propargyl Radical and Dihalogen Molecules

MP2/aug‐cc‐pVDZ calculations are carried out on the geometries, vibrational frequencies, interaction energies and topological properties for the π‐type halogen‐bonded complexes between propargyl radical and dihalogen molecules ClF, BrF and BrCl. There are two kinds of geometries: complex ( a ) involves the interaction between the X (X=Cl, Br) atom and the midpoint of C(1) –C(2) bond, complex ( b ) involves the interaction between the X atom and C(3) atom. The lengths of the halogen bond, the frequencies of the halogen bond, the elongation extent of the X–Y (XY=ClF, BrF, BrCl) bond, topological parameters at the BCPs of the halogen bond and X–Y bond are all well consistent with the interaction energies. The interaction of complex ( a ) is stronger than that of complex ( b ); the interaction of propargyl···BrF is stronger than that of propargyl···ClF and propargyl···BrCl. For the complexes ( a ) and ( b ), the charge transfer is observed from propargyl radical to XY, the atomic energy, the dipolar polarization, and the volume of the halogen atom X decrease upon complex formation.     

4-羟甲基吡啶－水红移氢键的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-311++G**基函数对4-羟甲基吡啶与水形成的1:1和1:2（摩尔比）氢键复合物进行了理论计算研究,分别得到稳定的4-羟甲基吡啶－H₂O和4-羟甲基吡啶－(H₂O)₂氢键复合物3个和8个。经基组重叠误差和零点振动能校正后,最稳定的1:1和1:2氢键复合物的相互作用能分别为-20.536和-44.246 kJ/mol。振动分析显示O-H···N(O)氢键的形成使复合物中O-H键对称伸缩振动频率红移(减小)。自然键轨道分析表明,4-羟甲基吡啶与水形成最稳定的1:1和1:2氢键复合物时,分子间电荷转移分别为0.02642 e 和0.03813 e 。含时密度泛函理论TD-B3LYP/ 6-311++G**计算显示,相对于4-羟甲基吡啶单体分子,氢键H-OH···N和H-OH···OH的形成分别使最大吸收光谱波长兰移8~16纳米和红移4~11纳米。     

Cooperative enhancement of water binding to antiparallel β‐sheet models: Analysis by ab initio calculations

The cooperative enhancement of water binding to the antiparallel β‐sheet models has been studied by quantum chemical calculations at the MP2/6‐311++G**//MP2/6‐31G* level. The binding energies of the two antiparallel β‐sheet models consisting of two strands of diglypeptide are calculated by supermolecular approach. Then water molecules are gradually bonded to the diglypeptide by N? H···OH₂ and C?O···HOH hydrogen bonds. Our calculation results indicated that the hydrogen bond length and the atom charge distribution are affected by the addition of H₂O molecules. The binding energy of antiparallel diglypeptide β‐sheet models has a great improvement by the increasing of the hydrogen bond cooperativity and the more H₂O molecules added the more cooperativity enhancement can be found. The orbital interactions are calculated by natural bond orbital analysis, and the results indicate that the cooperative enhancement is closely related to the orbital interaction. © 2012 Wiley Periodicals, Inc.     

Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin

The interaction of phenylalanine diamide (Ac‐Phe‐NHMe) with egg yolk lecithin (EYL) in chloroform was studied by ¹H and ¹³C NMR. Six complexes EYL–Ac‐Phe‐NHMe, stabilized by N–H···O or/and C–H···O hydrogen bonds, were optimized at M06‐2X/6‐31G(d,p) level. The assignment of EYL and Ac‐Phe‐NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO‐3G_mag basis set. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar ‘head’ of the lecithin. Additionally, the most probable lecithin site of H‐bond interaction with Ac‐Phe‐NHMe is the negatively charged oxygen in phosphate group that acts as proton acceptor. Copyright © 2014 John Wiley & Sons, Ltd.     

Time‐dependent density functional theory study on the electronic excited‐state hydrogen‐bonding dynamics of 4‐aminophthalimide (4AP) in aqueous solution: 4AP and 4AP–(H2O)1,2 clusters

The time‐dependent density functional theory (TDDFT) method has been carried out to investigate the excited‐state hydrogen‐bonding dynamics of 4‐aminophthalimide (4AP) in hydrogen‐donating water solvent. The infrared spectra of the hydrogen‐bonded solute?solvent complexes in electronically excited state have been calculated using the TDDFT method. We have demonstrated that the intermolecular hydrogen bond C? O···H? O and N? H···O? H in the hydrogen‐bonded 4AP?(H₂O)₂ trimer are significantly strengthened in the electronically excited state by theoretically monitoring the changes of the bond lengths of hydrogen bonds and hydrogen‐bonding groups in different electronic states. The hydrogen bonds strengthening in the electronically excited state are confirmed because the calculated stretching vibrational modes of the hydrogen bonding C?O, amino N? H, and H? O groups are markedly red‐shifted upon photoexcitation. The calculated results are consistent with the mechanism of the hydrogen bond strengthening in the electronically excited state, while contrast with mechanism of hydrogen bond cleavage. Furthermore, we believe that the transient hydrogen bond strengthening behavior in electroniclly excited state of chromophores in hydrogen‐donating solvents exists in many other systems in solution. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O–H···N bond to O–H···π bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and π-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O–H···N/O–H···π bond representing new type of H bonds.     

Molecular dynamics of 6‐methyl‐2‐phenyl‐2,3‐dihydro‐4H‐chromen‐4‐one and 6‐methyl‐2‐(4‐nitrophenyl)‐2,3‐dihydro‐4H‐chromen‐4‐one (flavanone) derivatives in a solution studied by NMR spectroscopy

Molecular dynamics of benzoxazepin, oxime, pyrazole, and thiosemicarbazone derivatives of some flavanones have been investigated in a solution using NMR. The results confirm the formation of different O–H···O, O–H···N, N···H–N type intramolecular hydrogen bonds in the pyrazole and oxime molecules. The rotational barrier energy and energy of intramolecular hydrogen bonds have been determined. Copyright © 2013 John Wiley & Sons, Ltd.