Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH<Subscript>2</Subscript>···Y

Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y··· H₂CZ (Z = O, S, Se) and Y···H₂CZ₂ (Z = F, Cl, Br) (Y = Cl⁻, Br⁻) at the MP2/6-311++G(d,p) and MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent blue-shifted H-bonds Y···H-C, and that the interaction energies and blue shifts are large, the energy of each Y···H-C H-bond is 15–27 kJ/mol, and Δr(CH) = −0.1 − −0.5 pm and Δv(CH) = 30 − 80 cm⁻¹. The natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hyperconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of electron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.     

Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-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, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.     

Theoretical study of the N—H···O red-shifted andblue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO···HNO, HCOOH···HNO, HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F. The geomet- ric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO···HNO and HCOOH···HNO the N—H bond is strongly contracted and N—H···O blue-shifted hydrogen bonds are observed. While in complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F, the N—H bond is elongated and N—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 redistribu- tion, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X—H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO···HNO and HCOOH···HNO, the shortening effects dominate which lead to the blue shift of the N—H stretching frequencies. In complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F where elongating effects are dominant, the N—H···O hydrogen bonds are red-shifted.     

Isotopic effects in NH…N hydrogen bonds

The value of the isotopic ratio (ISR) v_s(NH)/v_s(ND) has been determined for a number of crystalline compounds containing homoconjugated [NHN]⁺ cations, including various salts of 1,8-bis(N,N-dimethylamino)naphthalene (DMAN). The results obtained, together with the literature data, enabled us to plot a correlation between the ISR and v_s(NH) which appears to be similar to that found by Novak for OHO systems. For DMAN · HPF₆ the highest ISR value known so far (2.05) is reported. An empirical analytical form of the correlation is proposed.     

Theoretical study of the bent U(��8-C8H8)2(CN)? complex

The ground-state electronic structure of the cyanido complex [U(??⁸-C₈H₈)₂(CN)]^? as well as the thermodynamic properties and infrared spectrum are investigated using density functional theory including scalar relativistic effects. The complex is compared with the well-known uranocene U(??⁸-C₈H₈)₂. Despite the broken symmetry, the gain in electrostatic interaction and a significant uranium-CN^? orbital interaction is sufficient to stabilize the bent CN^? complex with respect to uranocene. The formation of the CN^? complex is exothermic justifying the recently experimentally reported compound.     

Solid state self-assembly of triptycene-based catechol derivatives by multiple O-H…O hydrogen bonds

Single crystals of two triptycene-based catechol derivatives 1 and 2 were obtained,and their X-ray crystal structural studies showed that the two tecton molecules had different conformations in the solid state,and they could self-assemble into interesting 3D networks with solvent molecules included inside, in which multiple O-H…O hydrogen bonds played important roles.     

Theoretical study of the inner hydrogen migration in the β-substituted 5,10,15,20-tetraphenylporphyrins

In order to investigate the mechanism of the N-H migration in asymmetrical metal-free porphyrins, four porphyrins of electron-withdrawing or electron-donating substituent at the β-position were studied theoretically. For porphyrin 2 (R = OMe), 3 (R = Me), and 4 (R = NO(2)), four different asynchronous N-H migration pathways exist due to symmetry reasons. The corresponding trans-, cis-, and transition state geometries were analyzed using a normal structure decomposition method. Our data show that the hydrogen migration of porphyrin 2, 3, and 4 in clockwise (A, B) are much more preferred than counterclockwise (C, D) direction.     

Theoretical study of proton transfer in ammonia–hydrogen halides in the presence of methanol

In this work, the effect of solvent (methanol, CH₃OH) molecules on proton transfer (PT) between ammonia and hydrogen halides was studied. We performed MP2 and B3LYP calculations on HX–NH₃–(CH₃OH) _n clusters for three hydrogen halides, HF, HCl, and HBr, with the number of methanol molecules varying from none to three (n = 0–3). The results showed that stepwise association of methanol molecules with the gas-phase complex can eventually facilitate ionization within the complex, producing the $ {\text{NH}}_{4}^{ + } {\text{X}}^{ - } - \left( {{\text{CH}}_{ 3} {\text{OH}}} \right)_{\text{n}} $ cluster. We found that PT occurs on addition of from one (for HBr) to three (for HF) methanol molecules. The interaction energy $ E_{\text{int}} $ and $ \Updelta E_{\text{add}} $ for the complexes were calculated and basis set superposition error (BSSE) correction was also performed. Atoms-in-molecule and natural-bond-orbital analysis were used to study the properties of the hydrogen bonds in the complexes.     

Consequence of hydrogen atom abstraction from 5’-hydroxyl group of 2’-deoxyadenosine. Theoretical quantum mechanics study

Reactive oxygen species (ROS) may generate different nucleoside/nucleotide radicals in a cell environment. In this study, the possibility of cyclic-2’-deoxyadenosines formation by a rearrangement of their free radicals was investigated. It seems that for cyclic-nucleosides formation, adoption of an O4’-exo conformation by the sugar moiety is necessary. However, this is the energetically unfavoured form of the 2-deoxyribose ring. Moreover, the creation of a O5’, C8 bond in purine deoxy-nucleosides/nucleotides leads to the termination of the DNA elongation process.      

双接触弯曲蓝移氢键CH_2…Y的理论研究

用量子化学从头算方法在MP2/6-311 G(d,p)与MP2/6-311 G(2df,2p)两个理论级别上研究了双接触弯曲氢键Y…H2CZ(Z=O,S,Se)和Y…H2CZ2(Z=F,Cl,Br)(Y=Cl-,Br-).计算表明,在这些复合物中都存在两个等价的Y…H—C蓝移氢键;相互作用能和蓝移都比较大,每个Y…H—C氢键的能量为15～27kJ/mol,CH键长变化为-0.1～-0.5pm,CH伸缩振动频率位移为30～80cm-1.自然键轨道分析表明,3个因素导致了这些蓝移氢键的形成:(1)存在较大的重杂化;(2)弯曲的氢键构型使得分子间直接超共轭相互作用比较小,而存在相当的分子间间接超共轭相互作用;(3)质子给体的分子内超共轭相互作用较大地减小.电子密度拓扑性质的研究表明,在这些氢键复合物中都存在3个分子间临界点:在接受体原子Y与每个H原子之间存在一个键临界点,也存在相应的键径和原子间界面;在YHCH四边形内部存在一个环临界点.因此这些分子间相互作用可以严格地看作氢键.     

Theoretical study on the vibrational state distribution of product CO in the photolysis of acetone CH_3COCH_3-→2CH_3 CO

The photolysis of acetone has been studied at 6-311G basis set using unrestricted Hartree-Fock method. The results show that ground state acetone (S_0) cannot easily dissociate. The electrons of acetone undergo n→Ⅱ transition in laser, and excited acetone (T_1) can easily dissociate: and acetyl can further undergo thermolytic dissociation: CH_3CO→CH_3 CO(R_2). The dynamic information (ω_K, B_(KF), V_0(S)) of reaction R_2 is obtained and the vibrational state distributions of product CO are calculated. The calculated value consists with the experimental value.     

Theoretical study of the intermolecular hydrogen bond interaction for furan-HCl and furan-CHCl_3 complexes

The importance of intermolecular interactions in biology and material science has prompted chemists to explore the nature of the variety of such interactions. The strongest of these interac-tions are the hydrogen bonds, which play an important role in determining the molecular confor-mation, crystal packing, and the structure of biological systems such as nucleic acids. Extensive experimental and theoretical efforts[1—5] have been devoted to the studies of this type of interac-tions, such as …     

An ab initio SCF-MO study of the hydrogen bonded complexes CO2…HF,CO2…HCl,SCO…HF and SCO…HCl

Large scale gaussian orbital SCF-MO results are given for the title molecules, including geometry optimization. The calculated hydrogen bond lengths agree well with experiment where comparison is possible, as do the changes in electric dipole moment on complex formation. The changes in electron distribution on complex formation are discussed in terms of Mulliken population indices, and calculated hydrogen bond energies are given.     

Theoretical study of intramolecular proton transfer of perylenequinone

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Theoretical study on the reaction mechanism of(CH_3)_3CO+CO

The global environment pollution includes pho-tochemical smog, acid rain and stratospheric ozonedepletion. The short-lived species/radicals in atmos-phere are closely related to these phenomena. Theshort-lived species/radicals bring the photochemicalsmog,…     

The topology of π···H hydrogen bonds

Abstract  

Unsaturated hydrocarbons are routinely used as proton acceptors because their π clouds possess a capacity to interact with Lewis acids and cationic species. Thus, in order to understand the formation of π hydrogen-bonded complexes, which in many cases are considered as weakly bound systems, the topological quantification of the charge density ruled by quantum mechanic theorems is very useful. Although elaborated by Richard Bader 40 years ago, the Quantum Theory of Atoms in Molecules (QTAIM) has only recently become widely known, and it has been applied in several scientific fields, allowing great insights in chemical bonding studies of intermolecular systems, in particular those formed by π···H hydrogen bonds.     

Infrared study of hydrogen bonds involving 2,2′-bipyridine and 2,2′-bipyrimidine. Influence of equivalent nitrogen atoms on the hydrogen bond strength

Hydrogen bonding between proton donors (phenols and water) and 2,2′-bipyridine (BPR) or 2,2′-bipyrimidine (BPM) has been investigated by infrared and FT-infrared techniques. The thermodynamic parameters (K, - ΔH, - ΔS°) and the frequency shifts of the ν_OH stretching vibrations have been determined in carbon tetrachloride solution. The spectroscopic results suggest that the complexes formed between phenols covering a large pK_a range (10.3–3.50) and BPR or BPM are of the normal OH⋯N type. The thermodynamic and spectroscopic properties of the BPR and BPM complexes are compared with those previously reported for the interaction between the same proton donors and the model molecules pyridine and pyrimidine. The BPR and pyridine complexes belong to the same series. The behaviours of BPM and pyrimidine are in complete contrast, the thermodynamic parameters and the related proton affinity being much higher for BPM than for pyrimidine. The results are probably ascribable to the presence of two equivalent neighbouring nitrogen atoms, the approach of a hydroxylic proton donor being greatly favoured in this electron-rich region. This effect does not exist in BPR, owing to its transoid configuration in solvents of weak polarity.     

A new anion receptor utilising aromatic and aliphatic C…H hydrogen bonds

We have synthesised 2, which bound weakly basic halide ions only with C–H…anion hydrogen bonds. Compound 2 utilised one aromatic C–H hydrogen bond and one benzylic C–H hydrogen bond to bind weakly halide ions such as chloride, bromide and iodide in solution. Ab initio calculations of binding energy values for these anions are in good agreement with experimental data. Although the binding affinities of 2 for these anions were low, 2 could be a unique example of host, which utilised only C–H hydrogen bonds to bind anion.     

Theoretical ab initio study of the interplay between hydrogen bonding, cation–π and π–π interactions

The interplay among three important non-covalent interactions involving aromatic rings is studied by means of ab initio calculations (RI-MP2/aug-cc-pVTZ//RI-MP2/aug-cc-pVDZ, and RI-MP2/CBS levels of theory). They demonstrate that synergetic effects are present in complexes where hydrogen bonding interactions, cation–π, and π–π interactions coexist. These synergetic effects have been studied using the genuine non-additivity energies and the molecular interaction potential with polarization partition scheme.