Theoretical study of molecular interactions of phosphorus ylide with HF, HCN, and HN3

The molecular interactions between phosphorous ylide (PY) and HX molecules (X?=?F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond H···C, X···P interaction and classical hydrogen bond H···X were found for complex formation between PY and HX molecules. From the predicted models, stability of the H···C type complexes are greater than other types. Quantum theories of atoms in molecules and natural bond orbitals methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾, and the charge transfer qCT in the studied systems.     

Ab initio study of water clustering in the presence of a methyl radical

The geometrical structure and binding energy of small clusters of methyl radical and water molecules (up to five water molecules) in gas phase and water media have been investigated at the MP2 level of theory using 6-311++G(2df,2p) basis set. The complexes characterized contain OH···O, CH···O, and OH···C attractive interactions with stabilization energies in the range 6–143 kJ mol^?1. The solvent has an enhancing influence on the stabilities of studied clusters. The atoms in molecules theory were also applied to explain the nature of the complexes. The interaction energies have been partitioned with the natural energy decomposition analysis showing that the most important attractive term corresponds to the charge transfer one.     

Theoretical study of molecular interactions of sulfur ylide with HF, HCN, and HN3

The molecular interactions between sulfur ylide (SY) and HX molecules (X = F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond (HB) H···C and classical HB H···X were found for complex formation between SY and HX molecules. Stability of the H···C type complexes are greater than H···X complexes. Quantum theories of atoms in molecules, natural bond orbitals, and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾ and the charge transfer qCT in the studied systems.     

A Hybrid statistical mechanics—quantum chemical model for proton transfer in 5‐azauracil and 6‐azauracil in water solution

A hybrid statistical physics—quantum‐chemical methodology was implemented to study the water‐assisted intramolecular proton‐transfer processes in 5‐ and 6‐azauracils in aqueous solutions. The solvent effects were included in the model by explicit inclusion of two pairs of water molecules, which model the relevant part of the first hydration shell around the solute. The position of these water molecules was initially estimated by carrying out a classical Metropolis of dilute water solutions of the title compounds and subsequently analyzing solute–solvent intermolecular interactions in the Monte Carlo‐generated configurations. Sequentially to the statistical physics simulation, ab initio quantum mechanical (QM) level of theory was implemented. The effects of the water as solvent (at ab initio QM level) were introduced at two different levels—using solute–solvent clusters (four‐water molecules) and using the same clusters embedded in an external continuum. Full geometry optimizations of these complexes were carried out at MP2/6–31 + G(d, p) and conductor‐polarizable continuum model (C‐PCM)/MP2/6–31 + G(d, p). Single point calculations were performed at CCSD(T)/6–31 + G(d, p)//MP2/6–31 + G(d, p) computational level to obtain more accurate energies. According to our calculations hydrated azauracils should exist in three forms: mainly dioxo form and two hydroxy forms. The calculated proton transfer activation energies for tautomeric reactions of 5‐azauracil and 6‐azauracil show different pictures for these two compounds. According to C‐PCM/MP2/6–31 +G(d, p) data, water‐assisted proton transfer in 5‐azauracil realizes through two parallel reactions: 1,3,5‐triazine‐2,4(1H,3H)‐dione → 6‐hydroxy‐1,3,5‐triazin‐2(1H)‐one and 1,3,5‐triazine‐2,4(1H,3H)‐dione → 4‐hydroxy‐1,3,5‐triazin‐2(1H)‐one. Tautomeric equilibrium in 6‐azauracil in water could occur by two contiguous reactions: 1,2,4‐triazine‐3,5(2H,4H)‐dione → 5‐hydroxy‐1,2,4‐triazin‐3(2H)‐one and 5‐hydroxy‐1,2,4‐triazin‐3(2H)‐one → 3‐hydroxy‐1,2,4‐triazin‐5(2H)‐one. The proton transfer investigated reactions in 5‐ and 6‐azauracils involve concerted atomic movement. © 2015 Wiley Periodicals, Inc.     

Crystallographic and theoretical studies of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid (1/1) with intermolecular O–H···N hydrogen bonds and S···O heteroatom interactions

Abstract  The molecular and crystal structure of a 1:1 co-crystal of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid, (1), has been determined by X-ray diffraction at the monoclinic space group P2₁/c with cell parameters of a = 8.422(6), b = 7.343(4), c = 16.112(7) ?, β = 104.988(8)°, V = 962.5(10) ?³ and Z = 2. In the crystal structure, two components connect via the intermolecular O–H···N hydrogen bonds [2.804(4) ?] and S···O heteroatom interaction [2.945(3) ?] with R ₂ ²(7) couplings to form a unique and infinite one-dimensional supramolecular tape structure. The calculations of (1) at the HF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels can almost reproduce X-ray geometry. In addition, the distances of the intermolecular O–H···N and S···O interactions by MP2/6-31G(d) and B3LYP/6-31G(d) levels agree well with those in the crystal. The calculated binding energies corrected BSSE and ZPE are −4.487 (HF), −7.473 (MP2), and −5.640 (B3LYP) kcal/mol. The results suggest that the complex (1) is very stable and the dispersion interaction is significantly important for the attractive intermolecular interaction in (1). The NBO analysis has revealed that the n(N) → σ*(O–H) interaction gives the strongest stabilization to the system and the major interaction for the intermolecular S···O contact is n(O) → σ*(S–N). Index Abstract  In the crystal structure of the title compound, the molecules are linked by intermolecular O–H···N hydrogen bonds and short S···O heteroatom interactions with R ₂ ²(7) couplings to construct a unique and infinite one-dimensional supramolecular tape structure.      

Chiral discrimination in hydrogen‐bonded complexes of hydrogen peroxide with methyl hydroperoxide: Theoretical study

For the first time, the discrimination of different chiral forms of 1:1 complexes with hydrogen peroxide and methyl hydroperoxide have been investigated using density functional theory (DFT) and Møller–Plesset type 2 (MP2) methods at varied basis set levels from 6‐31+G(d,p) to 6‐31++G(2d,2p). Three pairs of chiral enantiomers were considered. The optimized geometric parameters, interaction energies, and chirodiastatic energies for various isomers at different levels are estimated. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the ΔG_solv. The gas phase results show that the heterochiral six‐membered ring complex (structure I) and homochiral five‐membered ring complexes (structures IV and V) are preferred configurations for the three pairs of chiral enantiomers. The solvation effect on six‐membered ring complexes (structures I and II) shows nonsignificant changes in the configurations preferred, but on five‐membered ring complexes, the homo‐/heterochiral preference is found to be inverse in the polar solvent. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Complexation of Phenol and Thiophenol by Amine N‐Oxides: Isothermal Titration Calorimetry and ab Initio Calculations

To develop a new solvent‐impregnated resin (SIR) system for removal of phenols from water, the complex formation of dimethyldodecylamine N‐oxide (DMDAO), trioctylamine N‐oxide (TOAO), and tris(2‐ethylhexyl)amine N‐oxide (TEHAO) with phenol (PhOH) and thiophenol (PhSH) is studied. To this end we use isothermal titration calorimetry (ITC) and quantum chemical modeling (on B3LYP/6‐311G(d,p)‐optimized geometries: B3LYP/6‐311+G(d,p), B3LYP/6‐311++G(2d,2p), MP2/6‐311+G(d,p), and spin component scaled (SCS) MP2/6‐311+G(d,p); M06‐2X/6‐311+G(d,p)//M06‐2X/6‐311G(d,p), MP2 with an extrapolation to the complete basis set limit (MP2/CBS), as well as CBS‐Q). The complexes are analyzed in terms of structural (e.g., bond lengths) and electronic elements (e.g., charges). Furthermore, complexation and solvent effects (in benzene, toluene, and mesitylene) are investigated by ITC measurements, yielding binding constants K, enthalpies ΔH⁰, Gibbs fre energies ΔG⁰, and entropies ΔS⁰ of complex formation, and stoichiometry N. The ITC measurements revealed strong 1:1 complex formation between both DMDAO–PhOH and TOAO–PhOH. The binding constant (K=1.7–5.7×10⁴ M ^?1) drops markedly when water‐saturated toluene was used (K=5.8×10³ M ^?1), and π–π interaction with the solvent is shown to be relevant. Quantum mechanical modeling confirms formation of stable 1:1 complexes with linear hydrogen bonds that weaken on attachment of electron‐withdrawing groups to the amine N‐oxide moiety. Modeling also showed that complexes with PhSH are much weaker than those with PhOH, and in fact too weak for ITC determination. CBS‐Q incorrectly predicts equal or even higher binding enthalpies for PhSH than for PhOH, which invalidates it as a benchmark for other calculations. Data from the straightforward SCS‐MP2 method without counterpoise correction show very good agreement with the MP2/CBS values.     

A theoretical study of the neutral and the double-charged cation of cyclo[8]pyrrole and its interaction with inorganic anions

A theoretical study of the complexation of cyclo[8]pyrrole dication, 2, and the corresponding system in neutral form, 3, with six anionic molecules has been carried out up to the B3LYP/6–311++G(2d,2p) computational level. The effect of the water solvation has been taken into account by means of the PCM method. The gas phase results correspond to the very large interaction energies expected for the interaction of molecules of opposite charge. In all the complexes, the analysis of the electron density by means of the Atoms In Molecules (AIM) methodology shows the presence of eight intermolecular interactions between the individual molecules. The results, using the water solvent model, indicate that the 2:SO₄ ²⁻ complex is more stable than the 2:NO₃ ⁻, in agreement with experimental results.      

Kinetic and thermodynamic inclusion complexes of symmetric teramethyl-substituted cucurbit[6]uril with HCl salts of N,N′-bis(pyridylmethyl)-1,6-hexanediamine

The host–guest interaction of symmetrical α,α′,δ,δ′-tetramethyl-cucurbit[6]uril (TMeQ[6]) with the hydrochloride salts of N,N′-bis(4-pyridylmethyl)-1,6-hexanediamine (P6), N,N′-bis(3-pyridyl-methyl)-1,6-hexanediamine (M6) and N,N′-bis(2-pyridylmethyl)-1,6-hexanediamine (O6) was investigated via single crystal X-ray diffraction, ¹H NMR spectroscopy, electronic absorption spectroscopy and fluorescence spectroscopy. Single crystal X-ray diffraction showed that the hexyl moiety of P6 or M6 was incorporated in the cavity of TMeQ[6], while the two pyridylmethyl moieties of O6 were incorporated in the TMeQ[6] cavity in the solid state. The ¹H NMR results in aqueous solution revealed that the TMeQ[6]-P6 and TMeQ[6]-M6 host–guest interaction systems produce a kinetic dumbbell-shaped inclusion complex at the initial stage and then an equilibrium pseudorotaxane-shaped inclusion complex as the only product after heating. However, only the pseudorotaxane-shaped inclusion complex was observed for the TMeQ[6]-O6 host–guest interaction system. Aqueous absorption spectrophotometric analysis showed that the dumbbell-shaped inclusion complexes were stable at pH 5.6, had a host–guest ratio of 2:1 and formed quantitatively at ～10¹¹ l²/mol² for the TMeQ[6]-M6 and TMeQ[6]-O6 systems. The transformation from dumbbell to pseudorotaxane-shaped inclusion complexes for the TMeQ[6]-P6 and TMeQ[6]-M6 host–guest systems yielded activation energies of 59.35 ± 1.55 and 78.7 ± 3.45 kJ/mol, respectively. The pseudorotaxane-shaped inclusion complexes were stable at pH 5.6, had a host–guest ratio of 1:1 and formed quantitatively at ～10⁷ l/mol for the TMeQ[6]-M6 and TMeQ[6]-P6 systems.     

Theoretical study of [Hg3(o-C6F4)3]n · {benzene} (n = 1, 2) complexes

The electronic structure and spectroscopic properties of [Hg₃(o-C₆F₄)₃]_n · {benzene} (n = 1, 2) were studied at the HF, MP2 and PBE levels. The interaction between [Hg₃(o-C₆F₄)₃] and benzene at the HF and MP2 levels was analyzed. Secondary π-interactions (Hg–benzene) were found to be the main contribution short-range stability in the [Hg₃(o-C₆F₄)₃] · {benzene} complex. At the MP2 and PBE levels equilibrium Hg–C distances of 338.4 and 361.4 pm; and interaction energies of 46.6 and 29.2 kJ/mol were found, respectively. The absorption spectra of these complexes were calculated by the single excitation time-dependent method at PBE level.     

Theoretical study on coordination of methanol clusters to 3-methyl-4-pyrimidone

Density functional theory (DFT), MP2, and couple cluster ab initio methods were employed to investigate the microsolvation of 3-methyl-4-pyrimidone (3M4P) surrounded by methanol (MeOH) molecules. Structures are analyzed based on hydrogen bonds with a focus on relative energies, interaction energies, hydrogen bond cooperativity, hydrogen bonding geometries, and redshifts in the frequencies of O–H and C=O stretching modes. Our results show that there is no preferential orientation of MeOH attacks on the carbonyle site of 3M4P; both trans and cis 3M4P-MeOH complexes have same chance to be observed. cis 3M4P-MeOH and 3M4P-MeOH complex in which MeOH is located on N lie 0.56 and 3.11 kJ/mol at CCSD(T)/6-31+G(d,p) (0.63 and 1.67 kJ/mol at MP2/6-311++G(d,p)) above trans 3M4P-MeOH. MeOH dimers form more stable 3M4P-(MeOH)₂ complexes compare to 3M4P-(MeOH)₂ complexes in which individual MeOH molecules bind to carbonyl and N. Relative energies of 3M4P-(MeOH)₃ computed using various DFT methods point out the complex formed by linear MeOH trimer along methyl group of 3M4P (cis 3M4P-(MeOH)₃) as lowest. Carbonyl group is predicted as preferential site for hydrogen bond interaction. Besides O–H…O and O–H…N hydrogen bonds, 3M4P-(MeOH)₂ and 3M4P-(MeOH)₃ complexes are also stabilized by H–O…H–C weak interactions.     

Synthesis and spectral studies of nickel(II) complexes derived from disalicylaldehyde oxaloyldihydrazone

The mononuclear nickel(II) complex [Ni(H₂slox)(H₂O)₃] (1) and polymeric dinuclear complexes [Ni₂(slox)(A₄)] {A = H₂O (2), py (3), 2-pic (4), 3-pic (5) and 4-pic (6)} and the discrete binuclear complexes [Ni₂(slox)(NN)₃] {NN = bpy (7) and phen (8)} have been synthesized from disalicylaldehyde oxaloyldihydrazone (H₄slox) in methanol. All of the complexes are nonelectrolytes. Complexes 1, 7, and 8 are paramagnetic while binuclear 2–6 possess anomalously low μ _eff value, indicating considerable metal–metal interaction. Discrete binuclear 7 and 8 have no interaction between the two nickel(II) ions. The anomalously low magnetic moment values in 2–6 are explained as metal–metal interaction via phenoxide bridge. Such metal–metal interactions are less in 7 and 8 due to coordination of bipyridine and phenanthroline molecules which do not allow phenoxide bridging. The dihydrazone coordinates to the metal center as a dibasic tridentate ligand in keto-enol form in staggered configuration in 1, while in the remaining complexes the dihydrazone is tetrabasic hexadentate in enol form in anticis configuration. The metal center has a tetragonally distorted octahedral stereochemistry.     

Nonclassical B-Hb⋯π interaction in diborane⋯localized-π sandwiches: A DFT-D3 study

The study presents a quantitative estimation of B-H_b⋯π interaction in diborane-localized-π half sandwiches and sandwiches. DFT-D3 method is used for geometry optimization and estimating the stability of the complexes (in terms of stabilization energies). The diborane molecule is the source of bridging hydrogen and O₂, C₂H₄, and C₂H₂ molecules are considered as the localized π-systems. MP2 and CCSD(T) calculations are also performed to measure the stability of the chosen complexes. Results indicate that the complexes are feebly stable in gas phase with stabilization energies <5.0 kcal mol⁻¹. Compared to DFT-D3 functionals, MP2 calculations are found to be more suitable in predicting the stability of the complexes. Dispersive interaction is the primary mode of interaction in stabilizing the complexes. Presence of substituents either on diborane or on the considered π-systems play key role in stabilizing the complexes. Thermochemical analysis demonstrates the exothermic nature of complexation. ¹H and ¹³B NMR analysis are also performed.     

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,structures and luminescence properties of two gallium(III) complexes with 5,7-dimethyl-8-hydroxyquinoline

Luminescent gallium(III) complexes featuring 5,7-dimethyl-8-hydroxyquinoline (DimOx) are systematically compared and their structural features are correlated with their photophysical properties. The two complexes are chemically identical; however, contain various number of solvent molecules in the crystalline lattice which is representative of the bulk material confirmed by both nuclear magnetic resonance and elemental analysis. Detailed structural comparisons highlight the effect which the solvent molecules have on the intra- and intermolecular interactions. A distinct number of interactions are found for the gallium complex (1) containing more than one solvent molecule for unit cell. Variation in complex morphology is similarly observed via SEM micrographs. The distinct luminescent properties of the two gallium complexes appear directly related to octahedral coordination of the 8-hydroxyquinoline ligand as well as the number of identical coordinated solvent molecules.     

两个有机锡杂环羧酸酯配合物的合成、结构及抗癌活性

合成了2个有机锡杂环羧酸酯配合物：二（邻溴苄基）锡二（2-吡啶甲酸）酯（1）和三（2-甲基-2-苯基丙基）锡3-吲哚丁酸酯（2）。通过元素分析、红外光谱、核磁共振谱（¹H、¹³C和¹¹⁹Sn）、X射线衍射、热重分析进行了表征,用X射线单晶衍射方法测定了配合物的晶体结构,进行了配合物的结构量子化学从头计算和体外抗癌活性研究。结果显示：配合物均为单锡核分子,锡原子分别为六配位的畸变八面体构型和四配位的畸变四面体构型;配合物对人肝癌细胞（HUH7）、人肺癌细胞（A549）、人表皮癌细胞（A431）、人结肠癌细胞（HCT-116）和乳腺癌细胞（MDA-MB-231）的抑制活性均比临床使用的顺铂强。     

Ab initio investigation on stability and properties of XYCO... HZ complexes. II: Post hartree-fock studies on H2CO... HF

Ab initio MP2 level of theory in conjunction with three basis sets of a triple-zeta quality was applied to study the molecular geometry and stability of the H₂CO... HF complex. An interaction energy predicted for this system at the highest, MP4(SDTQ)/6-311 + +G(2df, 2pd)//MP2/6-311 + +G(2df, 2pd), level corrected for the BSSE and ZPE contributions amounts to -4.85 kcal/ mol. BSSE contributes significantly to the interaction energies at all applied levels. Reliable MP2/ 6-311 + +G(2df, 2pd) level harmonic vibrational frequencies, IR intensities, and the predicted isotopic shifts upon deuteration and¹⁸O substitution are presented in order to facilitate experimental studies on the IR spectrum of the title complex.     

Theoretical Study of Sticking Processes on Molecular Models of Silica Surfaces

The adsorption of small charged and neutral molecules on silica supports was modelled using perturbative post-Hartree–Fock quantum chemical methods (MP2 and MP4). The simplest spherosiloxane compound (H₄Si₄O₆) was used to mimic the surface while several molecules (namely CH₄, NH ₄ ⁺ , NH₃, OH ₃ ⁺ H ₃ ⁺ ) were considered as adsorbed species. Direct sticking of the molecules on one of the (Si–O)₃ ring leads to very different binding energies for cations (more than 11 kcal/mol) and neutral molecules (a few kcal/mol). These results indicate a dominant strong ion–multipole interaction for the first ones and a weak dispersion-type interaction for the latter. If the spherosiloxane cluster is screened by a mantle of accreted dust as it is the case in interstellar environment, the value of the binding energies, computed using the continuum dielectric theory, are predicted to be significantly reduced.     

Atom-atom potential analysis of the complexing characteristics of cyclodextrins (host) with benzene and p-dihalobenzenes (guest)

Abstract

Intermolecular interaction and modelling calculations on the complexes of α-, β- and γ-cyclodextrins (host) with benzene and p-dihalobenzenes (guest) were performed. The complex formation mechanism between the host and guest molecules was evaluated from three-dimensional potential maps generated by the atom-atom potential method, and the molecular packing of the complexed compounds was visualized by a space-fill representation. Stable inclusion complexes only form when both the host and guest molecules experience a significant decrease in the complexing potential. The host and guest molecules have a maximum molecular surface contact at the minimum potential, which depends on both the cavity size and the molecular volumes of the guest molecules. The calculated interaction energies can be correlated to the association constants of complex formation determined from experiment. The molecular dynamics of the guest molecules are also discussed.     

A post‐HF study on the halogen bonding interaction of pyrene with diatomic halogen molecules

We present a detailed SCS‐MP2 study on the potential energy curves (PEC) for interactions between diatomic halogen molecules and pyrene. BSSE corrected CCSD[T] energies at equilibrium distances are computed and compared to CCSD(T) energies. The most stable conformation of these weakly bound van der Waals complexes is almost linear in the perpendicular direction to the pyrene plane. The complexes of highly polarizable bromine and iodine molecules with pyrene are very stable and they carry rather large number of vibrational states. Despite its small size, F₂ also forms strong halogen bonding similar to Br₂ and I₂. The interaction between Cl₂ and pyrene is the weakest and it is attributed to the highest polarizability / molar mass ratio of chlorine among the others. I₂‐pyrene is found to be the most stable complex due to the strongest mutual polarization effects and is carrying more than 60 vibrational states. Due to the rather large number of electrons in some complexes, the relativistic corrections are also considered. © 2016 Wiley Periodicals, Inc.