A theoretical study of the interactions between N,N-dimethylformamide and xylenes

The ab initio and density functional (DFT) methods were performed on binary systems of N,N-dimethylformamide (DMF) with xylenes (o-, or m-, or p-xylene), and seven stable configurations were obtained with no imaginary frequencies. To obtain the interaction energies of these complexes, single-point energy calculations with basis set superposition error (BSSE) correction were carried out at B3LYP/6-31G* and MP2/6-31G* levels. The structures, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution and bond characteristics of the mentioned complexes were calculated. The results indicated the presence of double C–H···O hydrogen bonds between DMF and xylenes in these complexes and the interaction energies of hydrogen bonding between DMF and xylene systems decreased in the following sequence: DMF–o-xylene: a1 > DMF–m-xylene: b1 > DMF–p-xylene: c1.     

Conformational analysis of 2-methyl-1,3,2-oxaza- and 2-methyl-1,3,2-oxathiaborinane associates with water molecule

The structure and conformational behavior of 1: 1 molecular assotsiates of 2-methyl-1,3,2-oxazaand 2-methyl-1,3,2-oxathiaborinanes with water were studied ab initio in terms of HF/6-31G(d) and PBE/3z quantum-chemical approximations. The most stable complexes are formed via hydrogen bonding with the heteroatoms (oxygen and nitrogen or sulfur). Their conformational behavior implies equilibrium between sofa and half-chair conformers, and intermolecular hydrogen bond is retained in the course of ring interconversion. No associate with a dative O→B bond is formed.     

Searching blue-shifted O–H···Y hydrogen bond in CH<Subscript>3</Subscript>OH complexes with CF<Subscript>4</Subscript>, C<Subscript>2</Subscript>F<Subscript>2</Subscript>, OC,Ne, and He: a theoretical study

The hydrogen-bonded structures of the CH₃OH complexes with CF₄, C₂F₂, OC, Ne, and He are designated as the starting points for geometry optimizations without and with counterpoise (CP) correction at MP2 level of theory with the basis sets 6-31+G*, 6-31++G**, and 6-311++G**, respectively. Tight convergence criteria are applied throughout all geometry optimizations in order to reduce the computational errors. According to the optimizations without CP correction, a blue-shifted O–H···Y (where Y = F, O, Ne, or He) hydrogen bond exists in all these five complexes. The magnitudes of blue shifts of ν(O–H) of the former four complexes with respect to that of CH₃OH are reduced greatly when the polarization and diffuse functions of the hydrogen atoms are added (results from 6-31+G* versus those from 6-31++G**). However, for the complexes CH₃OH–CF₄ and CH₃OH–C₂F₂, our optimizations using the CP corrections did not find the hydrogen-bonded structure to be a stationary point. The energy minimum of both the complexes corresponds to a non-hydrogen-bonded structure.     

[C5Li5]Mgn[C5Li5] (n?=?2–8): novel sandwich complexes containing –Mg–Mg– chain

A density functional theory (DFT) investigation on novel sandwich-type D ₅ [C₅Li₅]Mg _n [C₅Li₅] (n = 2–8) complexes containing –Mg–Mg– chain has been performed in this work. The equilibrium geometries, electronic structures, vibrational frequencies, and stabilities of these complexes are researched by B3LYP and BP86 methods at 6-311+G(d) levels of theory. The Mg _n ²⁺ sandwich complexes with D ₅ symmetry are all true minima on the potential energy surface. NBO analyses for the series of complexes reveal that the Mg–Mg bond is a weak σ covalent bond. There are mainly electrostatic interactions between C₅Li₅ ⁻ ligands and Mg _n ²⁺(n = 2–8) nuclear in these complexes. The NICS and NICS_zz computed with GIAO-B3LYP/6-311+G(d) indicates that the C₅Li₅ ⁻ rings in the series of complexes are aromatic. These novel complexes turn out to be strongly thermodynamically favored in the gas phases and may be targeted in future experiments to expand the structural domain of sandwich-type complexes.     

Effects of substituents and n-donors on the energies of Si←N,Si←O,and Si=C bonds in hypervalent silenes

The effect of the nature of substituents at sp²-hybridized silicon atom in the R₂Si=CH₂ (R = SiH₃, H, Me, OH, Cl, F) molecules on the structure and energy characteristics of complexes of these molecules with ammonia, trimethylamine, and tetrahydrofuran was studied by the ab initio (MP4/6-311G(d)//MP2/6-31G(d)+ZPE) method. As the electronegativity, χ, of the substituent R increases, the coordination bond energies, D(Si← N(O)), increase from 4.7 to 25.9 kcal mol⁻¹ for the complexes of R₂Si=CH₂ with NH₃, from 10.6 to 37.1 kcal mol⁻¹ for the complexes with Me₃N, and from 5.0 to 22.2 kcal mol⁻¹ for the complexes with THF. The n-donor ability changes as follows: THF ≤ NH₃ < Me₃N. The calculated barrier to hindered internal rotation about the silicon—carbon double bond was used as a measure of the Si=C π-bond energy. As χ increases, the rotational barriers decrease from 18.9 to 5.2 kcal mol⁻¹ for the complexes with NH₃ and from 16.9 to 5.7 kcal mol⁻¹ for the complexes with Me₃N. The lowering of rotational barriers occurs in parallel to the decrease in D _π(Si=C) we have established earlier for free silenes. On the average, the D _π(Si=C) energy decreases by ∼25 kcal mol⁻¹ for NH₃· R₂Si=CH₂ and Me₃N·R₂Si=CH₂. The D(Si←N) values for the R₂Si=CH₂· 2Me₃N complexes are 11.4 (R = H) and 24.3 kcal mol⁻¹ (R = F). sp²-Hybridized silicon atom can form transannular coordination bonds in 1,1-bis[N-(dimethylamino)acetimidato]silene (6). The open form (I) of molecule 6 is 35.1 and 43.5 kcal mol⁻¹ less stable than the cyclic (II, one transannular Si←N bond) and bicyclic (III, two transannular Si←N bonds) forms of this molecule, respectively. The D(Si←N) energy for structure III was estimated at 21.8 kcal mol⁻¹. Dedicated to Academician N. S. Zefirov on the occasion of his 70th birthday. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1952–1961, September, 2005.     

Molecular Structure of Complexes with Bifurcated Hydrogen Bond: I. N-(4-Methyl-2-nitrophenyl)acetamide

According to the results of HF/6-31G* and B3LYP/6-31G* nonempirical calculations, N-(4-methyl- 2-nitrophenyl)acetamide in the synperiplanar and antiperiplanar conformations gives stable complexes with protophilic solvents, which are stabilized by bifurcated (three-center) hydrogen bond. The complexes are characterized by (1) opposite variations of the interatomic distances and angles corresponding to intra- and intermolecular components of the bifurcated hydrogen bond, (2) extension of the intramolecular component and a more pronounced shortening of the intermolecular component with increase in the strength of the three-center H-complex, and (3) nonlinear and nonmonotonic relation between the NH stretching vibration frequency and the energy of complex formation.     

Orientation of hydrogen bond in H-complexes of sulfones and sulfonamides

According to the data of quantum chemical calculations using the DFT method (B3LYP/6-311G*), dimethylsulfone (I), N,N-dimethylmethanesulfonamide (II) and N,N-dimethyltrifluoromethanesulfonamide (III) form with methanol and phenol H-complexes of two types: (1) having nonlinear structure and (2) bidentate complexes with participation of both oxygen atom lone pairs in the formation of the H-bond. The angle determining the directionality of the hydrogen bond with respect to the axis of the nearest lone electron pair of the SO₂ group oxygen atom in the conformational isomers of these complexes falls within the range 3°–100°. Variation of the calculated values of Δν(OH) in the H-complexes is parallel to that observed in their IR spectra and reflects the decrease of basicity of the sulfonyl group in the order I > II > III.     

Theoretical study of hydrogen-bonded formaldehyde complexes

The hydrogen-bonded complexes involving formaldehyde and a series of proton donors of varying strengths, have been investigated at different levels of ab initio MO theory. The structures of the studied complexes were SCF optimized at the 6-31G basis set level. The binding energy was estimated employing basis set superposition correction, zero-point vibrations and MP2 correlation contribution at the different basis set: STO-3G; 6-31G; MP2/6-31G; 6-31G**; MP2/6-31G**; 6-311G(2d, 2p) and MP2/6-311G(2d, 2p). Linear relationships were found of the calculated binding energy with: the calculated shift in the carbonyl stretching frequency, the changes in carbonyl bond length and the optimum value of hydrogen-bond distance; furthermore the calculations confirm a parallel trend between the proton-donor ability and the strength of the hydrogen bond.     

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine–propanoic acid (Cys–Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra- and inter-molecular H-bonds have been found in Cys–Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of Cys–Prop complexes. The strongest H-bonds (O2H^A···O1^B and O2H^A···O1^B) exist in the most stable Cys–Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (ρ) of BCP and H-bond length as well as the Fock matrix element (F _ij) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.     

Calculation of the hydrogen binding energies of complexes between formamide and adenine-thymine pair

The hydrogen bonding of complexes formed between formamide and adenine-thymine base pair has been completely investigated in the present study. In order to gain deeper insight into structure, charge distribution, and energies of complexes, we have investigated them using density functional theory at 6–311++G(d, p), 6–31G, 6–31+G(d), and 6–31++G(d, p) level. Seven stable cyclic structures (ATF1–ATF7) being involved in the interaction has been found on the potential energy surface. In addition, for further correction of interaction energies between adenine—thymine and formamide, the basis set superposition error associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported.     

Theoretical binding affinities and spectroscopy of complexes formed by cyclobis(paraquat-<Emphasis Type="Italic">p</Emphasis>-anthrancene) with some pharmaceutical molecules

Theoretical investigation on the stabilities and spectroscopic properties of the complexes formed by cyciobis(paraquat-p-anthracene) with pharmaceutical molecules were performed using the semi-empirical PM3 and B3LYP/3-21G methods. Based on the B3LYP/3-21G optimized geometries, the energies of the complexes were calculated at B3LYP/6-31G(d) level. The binding energies of the complexes were computed after the correction of basis set superposition error (BSSE). The energy gaps of the complexes are decreased due to the formation of the hydrogen bonds. The stretching vibrations of the C-H bonds adjacent to the hydrogen bonds in the IR spectra of the complexes calculated with PM3 method are red-shifted compared with those of the host. The chemical shifts of α-C and β-C atoms in the complexes calculated at B3LYP/3-21G level are shifted downfield due to the formation of the hydrogen bonds and the electron-withdrawing effect of the nitrogen atoms. The aromaticities of the complexes are improved because of the enlargement of the conjugation system and the overlap of electron cloud based on the nuclear independent chemical shifts (NICS) calculated at B3LYP/3-21G level.     

Matrix IR-spectroscopic and quantum-chemical study of difluorostannylene complexation with dinitrogen

Complexes of difluorostannylene with dinitrogen of composition 1∶1 and 1∶2 were stabilized in Ar matrix (12 K) and characterized by IR spectra. The bands at 588, 565, and 583, 557 cm⁻¹, respectively, were assigned to these complexes. Potential energy surfaces of the systems SnF₂+N₂ and SnF₂+2N₂ were studied by theab initio MP2/3-21G(d2)//HF/3-21G(d2) method using the basis set including polarization functions at Sn, F, and N atoms. Equilibrium structures of the complexes haveC _s andC _2v symmetry and correspond to coordination of lone electron pairs of nitrogen molecules with vacant p-AO of the carbenic center. The calculated complexation energies are equal to 4.6 and 8.9 kcal mol⁻¹, respectively. Based on results of quantum-chemical calculations an interpretation of the IR spectra of the complexes was given and it was shown that cycloaddition of SnF₂ to a triple N≡N bond with formation ofcyclo-SnF₂N₂ is energetically unfavorable. The absorption band belonging to SiF₄·N₂ complex in Ar matrix was detected and assigned. Dedicated to the memory of Academician M. E. Vol'pin timed to his 75th birthday. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1087–1093, June, 1998.     

Synthesis,characterization and biological activities of 3-methylbenzyl 2-(6-methyl pyridin-2-ylmethylene)hydrazine carbodithioate and its transition metal complexes

A tridentate nitrogen-sulfur Schiff base, 3-methylbenzyl 2-(6-methylpyridin-2-ylmethylene)hydrazine carbodithioate (6mpyS3M), was synthesized by condensation of 6-methylpyridine-2-aldehyde with S-3-methylbenzyldithiocarbazate. It crystallized in space group P 2₁/n. It displayed intermolecular N–H···N hydrogen bonding between the α-nitrogen and the pyridyl nitrogen. The thione sulfur is in a trans position with respect to the 6-methylpyridine fragment across the C–N bond but adopts a cis position with the 3-methylbenzyl fragment through the C–S bond. Octahedral complexes containing two 6mpyS3M ligands were prepared with Cu(II), Ni(II), Zn(II) and Cd(II). 6mpyS3M and its metal complexes were assayed against selected microbes and two breast cancer cell lines. 6mpyS3M was strongly active against both cancer cell lines. Its metal complexes showed high selectivity with Cu(II), Ni(II) and Zn(II) complexes strongly active against only one of the cancer cell lines, whereas the Cd(II) complex was strongly active only against the other. Only Cu(II) and Cd(II) complexes were active against some of the bacteria.     

Self-assembly of DMF with chloromethane and their structures: a theoretical study

The stability of hydrogen-bonded complexes, DMF–H _n CCl_4−n (n = 1–3), has been investigated by several theoretical methods including the MP2 level of ab initio theory at various basis sets from 6-31+G* to 6-311++G**. Two stable configurations (respectively a and b) were obtained for each complex with no imaginary frequencies. The minimum energy structure of these complexes has also been analyzed by means of the atoms in molecule theory at MP2/6-311++G** level. It is found that C–H···O hydrogen bonding exists in these systems and that the intensity of HB interaction gradually increases with successive chlorination. Computed results indicate that these complexes automatically assemble into different stable configurations. For the complexes under consideration, their stabilities can be mainly ascribed to the intermolecular HB interaction. The present work is helpful to clearly understand the interaction mechanism of these complexes in theory.     

Synthesis,characterization, and quantum chemical calculational studies on 3-<Emphasis Type="Italic">p</Emphasis>-methylphenyl-4-amino- 1, 2, 4-triazole-5-thione

The title compound of 3-p-methylphenyl-4-amino-1, 2, 4-triazole-5-thione was synthesized and characterized by elemental analysis, IR, electronic spectra, and X-ray single crystal diffraction. Quantum chemical calculations of the structure, natural bond orbital, and thermodynamic functions of the title compound were performed by using B3LYP/6-311G** and HF-6-311G** methods. Both the methods can well simulate the molecular structure. Vibrational frequencies were predicted, assigned and compared with the experimental values, and B3LYP/6-311G** method is superior to HF/6-311G** method to predict the vibrational frequencies. Electronic absorption spectra calculated by B3LYP/6-311G** method have some red shifts compared with the experimental ones and natural bond orbitals analyses indicate that the two absorption bands are mainly derived from the contribution of n → π^* and π → π^* transitions. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between C ⁰ _p,m , S ⁰ _m , H ⁰ _m , and temperatures.     

Novel modified chiral NiII complexes with the Schiff bases of (E)-and (Z)-2-aminobut-2-enoic acids: Synthesis and study

Ni^II complexes with the Schiff bases of (E)-and (Z)-2-aminobut-2-enoic acids were obtained with (S)-N-(2-benzoylphenyl)-1-(2-chlorobenzyl)pyrrolidine-2-carboxamide and (S)-N-(2-benzoylphenyl)-1-(3,4-dimethylbenzyl)pyrrolidine-2-carboxamide as new chiral auxiliaries. Asymmetric addition of nucleophiles to the C=C bond of these complexes was studied. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 428–435, March, 2006.     

Quantum chemical and experimental studies on the structure and vibrational spectra of substituted 2-pyranones

A systematic study on the structural characteristics of the 2-pyranone ring containing molecules with bromine, nitrile, and amide substituents at the C-3 position in the ring is conducted in the electronic ground (S ₀) state by DFT calculations using the B3LYP/6-311++G** method. The geometrical structure of the bromine substituted compound, which shows potent hepatoprotective activity, is studied both in the ground (S ₀) and first excited singlet (S ₁) states using RHF/6-311++G** and CIS/6-311++G** methods respectively. The molecules are found to exist in two isomeric forms gauche and trans that have the enthalpy difference of less than 3.32 kcal/mol; the latter is the preferred orientation in the gaseous phase. The S ₁ state is a ¹(π,π*) state that arises π-electron transfer from the region of a double bond in the pyranone ring to the region of the internuclear bond connecting the 2-pyranone and benzene rings. A complete vibrational analysis is conducted for the 3-bromo-6-(4-chlorophenyl)-4-thiomethyl-2H-pyran-2-one molecule based on the experimental infrared spectra in the 50–4000 cm⁻¹ region and DFT/6- 311++G** computations of vibrational frequencies for the gauche and trans isomeric forms. Spectral assignments based on the potential energy distribution along the internal coordinates confirm the nonplanar structure of the molecule.     

Binding affinities and spectra of complexes formed by dehydrotetrapyrido[20]annulene and small molecules

Theoretical study on the binding affinities of dehydrotetrapyrido[20] annulene to the alkene and aromatic molecules was performed using the AM1 and DFT methods. It indicated that the host possesses the ability to bind the above molecules since the binding energies of the complexes were negative. The complexes were stabilized via the hydrogen bonding, static effect, and π — π stacking interaction between the host and guest molecules. Based on the B3LYP/3-21G optimized geometries, the electronic, IR, and NMR spectra were calculated using the INDO/CIS, AM1, and B3LYP/3-21G methods, respectively. Due to the hydrogen bonding, the first absorption maxima in the electronic spectra of studied complexes were blue-shifted, whereas the main IR frequencies for some of the complexes were red-shifted. At the same time, the chemical shifts of carbon atoms forming the bonds in the complexes were lower, compared to those of the host.     

CH3SH…HOO开壳型氢键复合物的结构及其电子密度拓扑性质

在DFT-B3LYP/6-311++G**水平下求得CH3SH…HOO复合物势能面上的稳定构型. 计算结果表明, 在HOO以其O8—H7作为质子供体与CH3SH分子中的S5原子为质子受体形成的氢键复合物1和2中, O8—H7明显被“拉长”, 且其伸缩振动频率发生显著的红移, 红移值分别为330.1和320.4 cm-1; 在CH3SH分子以其S5—H6作为质子供体与HOO的端基O9原子为质子受体形成的氢键复合物3和4中, 也存在类似的情况, 但S5—H6伸缩振动频率红移不大. 经MP2/6-311++G**水平计算的4种复合物含BSSE校正的相互作用能分别为-20.81, -20.10, -4.46和-4.52 kJ/mol. 自然键轨道理论(NBO)分析表明, 在CH3SH…HOO复合物1和2中, 引起H7—O8键长增加的因素包括两种电荷转移, 即孤对电子n1(S5)→σ*(H7—O8)和孤对电子n2(S5)→σ*(H7—O8), 其中后者为主要作用. 在复合物3和4中也有相似的电荷转移情况, 但轨道间的相互作用要弱一些. AIM理论分析结果表明, 4个复合物中的S5…H7间和O9…H6间都存在键鞍点, 且其Laplacian量▽2ρ(r)都是很小的正值, 说明这种相互作用介于共价键和离子键之间, 偏静电作用为主.     

Study of hydrogen bonding interactions relevant to biomolecular structure and function

Ab initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO-3G, 3-21G, 6-31G*, and MP2/6-31G* levels (geometries were fully optimized at each level). For anionic species, 6-31 + G* and MP2/6-31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for O? H-O and N? HO types of hydrogen bonds, but not for hydrogen bonds involving O-H? S and S-H? O, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate–water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.