Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Difluoroamine Complex

Introduction　　ApplicationsofabinitiocalculationstointermolecularinteractionsincludingeitherweakvanderWaalsorstrongerhydrogenbondinghavedrawnmuchattentioninthepastdecadesbecausetheyareimportantinawiderangeofphysical,chemicalandbiologicalfields .1 5Inre centyears ,wehaveappliedtheintermolecularinteractionstoenergeticsystemsandobtainedsomemeaningfulinfor mationthatisvaluableforthestudyofenergeticmateri als .6 14 Thebehaviorofmolecularcomplexesisusuallybe tweentwoextremes :thegasphaseandthecrys…     

Studies in hydrogen bonding: Association within small clusters of water,methanol, and ammonia molecules using Jorgensen's intermolecular pair potentials

The geometries of the dimer, trimer, and tetramer hydrogen-bonded clusters of water, methanol, and ammonia molecules have been derived using previously published intermolecular pair potentials containing constants optimized from ab initio calculations. The lowest energy forms for the dimers of all three types of molecules have an open structure, while the trimers and tetramers have cyclic structures. The results are compared with those previously described using another empirical potential, EPEN .     

An HF and DFT ab initio Study on the Mechanism of ortho‐Directed Lithiation of Hydric and Nonhydric Aromatic Compounds Incorporating Aggregation and Discrete Solvation: The Role of N,N,N′,N′‐Tetramethylethane‐1,2‐diamine (TMEDA) in Lithiation Reactions

An HF and DFT ab initio study was set up to decipher the roles of aggregation and solvation in the ortho‐directed lithiation of aromatics (hydric and nonhydric), as well as to shed light on the much debated question of precomplexation in the mechanism of lithiation. Ab initio (HF/6‐31‐G*) calculations on the lithiation of non‐hydric aromatics have uncovered several competitive routes operating as a function of the aggregation state of the organolithium base used. Specifically, two competitive routes were found for the lithiation of the anisole model 2 by organolithium dimers 1‐dim , namely the so‐called cyclic‐dimer and open‐dimer routes, whereas, for organolithium tetramers 1‐tet , the corresponding cyclic route is the only one operative, and, for monomers 1‐mon , several optional routes seem to be available. Precomplexation is, in all cases, a requirement. According to the computational data presented, the mysterious rate acceleration experimentally observed for lithiations carried out in TMEDA can be assigned to an aggregation effect on the intermediate open‐dimer species, which subsidiarily give rise to several so‐called s‐monomer routes, of which the dimerization‐driven s‐monomer route s‐m_3b is the one having the lowest energy barrier. The relevant species characteristic of both the open‐dimer and s‐monomer routes are the so‐called open dimers, i.e., high‐energy intermediates (actually, spiro dimeric aggregates), resulting from cleavage‐induced associative complexation of the aromatic substrate upon the fully solvated organolithium dimer. DFT calculations (B3LYP/6‐31+G*) also revealed that the peri‐lithiation (i.e., Li at C(8)) of 1‐naphthol model 3 is a slow process taking place preferentially through the open‐dimer route.     

Differently coloured polymorphs of 4‐[(2‐nitrophenyl)azo]phenol

The crystal structures of the brown–yellow and orange polymorphs of the title compound, 4‐[(2‐nitro­phenyl)­diazenyl]­phenol, C₁₂H₉N₃O₃, have been determined and their visible reflection spectra recorded. Both structures adopt a stacking arrangement with interstack hydrogen bonds. Ab initio and semi‐empirical (AM1 and INDO‐CISD) calculations were performed in order to rationalize the difference in colour. It can be attributed neither to the subtle distinctions in molecular geometry nor to the effect of intermolecular electrostatic interactions. The most probable origin of this difference is the mixing of intramolecular n π* and intermolecular charge‐transfer excitations.     

Density Functional Theory Study of Hydrogen Bonds of Bipyridine with 1,3,5-Benzenetricarboxylic Acid

The hydrogen‐bonded dimer and trimer formed between 1,3,5‐benzenetricarboxylic acid and bipyridine have been investigated using a density functional theory (DFT) method and 6‐31++G** basis set. The interaction energies are ?45.783 and ?89.998 kJ·mol^?1 for the most stable dimer and trimer, respectively, after the basis set superposition error and zero‐point corrections. The formation of O–H...N hydrogen bonds makes O–H symmetric stretching modes in the dimer and trimer red‐shifted relative to those of the 1,3,5‐benzenetricarboxylic acid monomer. The natural bond orbit analysis shows that the inter‐molecular charge transfers are 0.60475e and 1.20225e for the dimer and trimer, respectively. Thermodynamic analysis indicates that the formation of trimer is an exothermic and spontaneous process at low and room temperature. A supramolecule can be constructed through the strong N···H–O intermolecular hydrogen bonds between bipyridine and 1,3,5‐benzenetricarboxylic acid, which is in good agreement with the experimental results.     

Quinazolines and 1,4-benzodiazepines. XLVI. Photochemistry of nitrones and oxaziridines

The cyclic nitrones 7-chloro-1,3-dihydro-5-phenyl-2H-1,4-benzodiazepin-2-one 4-oxide ( 5a ) and 1,3-dihydro-7-methylthio-5-phenyl-2H-1,4-benzodiazepin-2-one 4-oxide ( 5b ) are photoisomerized to readily isolable oxaziridines, 7-chloro-4,5-epoxy-5-phenyl-1,3,4–5-tetrahydro-2H-1,4-benzodiazepin-2-one ( 6a ) and 4,5-epoxy-5-phenyl-1,3,4,5-tetrahydro-7-methylthio-2H-1,4-benzo-diazepin-2-one ( 6b ). Oxaziridine 6b upon further irradiation gave ring expansion and ring contraction products, 4,6-dihydro-2-phenyl-9-methylthio-5H-1,3,6-benzoxadiazocin-5-one ( 7b ) and 4-benzoyl-3,4-dihydro-6-methylthioquinoxalin-2(1H)-one ( 8b ) respectively. The ring contraction product, 4-benzoyl-6-chloro-3,4-dihydroquinoxalin-2(1H)-one ( 8a ), was obtained from irradiation of oxaziridine 6a .     

C≡H ⋅<Emphasis Type="Italic">s</Emphasis> O Hydrogen Bonds in Small Ring Carbonyl Compounds: Vibrational Spectroscopy and <Emphasis Type="Italic">Ab initio</Emphasis> Calculations

The effect of the molecular structure on the properties of C-H⋅s O bonds was investigated in a set of small cyclic carbonyl compounds, using vibrational spectroscopy and ab initio calculations. Two main effects were studied: the size of the ring and the inclusion of oxygen atoms in the ring. The analysis of the band profile of the carbonyl stretching mode reveals the presence of single dimerization equilibria in the series cyclobutanone-cyclopentanone-cyclohexanone. The smallest cyclobutanone was found to have the lowest dimerization energy, with an experimental ΔH value of 3.7± 0.6 kJ mol⁻¹. The systems with oxygen atoms in the ring, γ-butyrolactone and ethylene carbonate were found to present more complex equilibria. Ab initio calculations suggest that this complexity is due to the presence of additional dimer structures and higher oligomers.     

Topological investigations of the molecular species and molecular interactions that characterize pyrrolidin-2-one + lower alkanol mixtures

Molar excess volumes, V^E, molar excess enthalpies, H^E, and speeds of sound data, u, of pyrrolidin-2-one (i) + ethanol or propan-1-ol or propan-2-ol or butan-1-ol (j) binary mixtures have been determined over entire composition range at 308.15 K. The observed speeds of sound data have been utilized to predict excess isentropic compressibilities, of the investigated binary mixtures. The observed excess thermodynamic properties V^E, H^E and have been analyzed in terms of Graph theory. The analysis of V^E data by the Graph theory suggests that pyrrolidin-2-one exists mainly as a mixture of cyclic and open dimer; ethanol as a mixture of dimer and trimer; butan-1-ol and propan-2-ol as mixture of monomer and dimer and propan-1-ol as a dimer in the pure state, and their mixtures contain 1:1 molecular complex. The IR studies lend additional credence to the nature and extent of interactions for the proposed molecular entities in the mixtures. Also, it has been observed that V^E, H^E and values predicted by the Graph theory compare well to with their corresponding experimental values.     

IR Spectra of Paracetamol and Phenacetin. 1. Theoretical and Experimental Studies

IR spectra of paracetamol and phenacetin have been measured for powder crystals of these compounds and for their solutions in chloroform and dimethylsulfoxide. Ab initio calculations of their equilibrium geometry and vibrational spectra were carried out for spectrum interpretation. Differences between the experimental IR spectra of solutions and crystalline samples have been analyzed. Variations of molecular structure from the isolated state to molecular crystal were estimated based on the difference between the optimized molecular parameters of free molecules and the experimental bond lengths and angles evaluated for the crystal forms of the title compounds. The role of hydrogen bonds in the structure of molecular crystals of paracetamol and phenacetin is investigated, and spectral ranges with maximal intermolecular interactions are determined.     

Molecular calculations with the nonempirical ab initioMODPOT,VRDDO, and MODPOT/VRDDO procedures. XI. Theoretical study of the [C6H5OH ⃛OC6H5]− molecular complex: Ab initioMODPOT/VRDDO calculations and electrostatic molecular potential contour maps

The transport of C₆H₅O^? (or similarly charged moieties) through a lipoidal membrane may possibly be facilitated by forming complexes with the neutral compound. Thus, theoretical studies were performed on the model [C₆H₅OH ?OC₆H₅]^? molecular complex to obtain some information concerning the possible molecular and electronic structure of such complexes. Ab initio MODPOT /VRDDO SCF calculations were carried out on the neutral-anion dimer [C₆H₅OH ?OC₆H₅] to optimize the equilibrium geometry. Electrostatic molecular potential contour maps have been generated from the ab initio MODPOT /VRDDO results in the molecular plane and in the plane perpendicular to the molecular plane and intersecting the hydrogen bond O ?H? O. Difference maps have also been generated showing the change of potential on complex formation. There is a decrease of electrostatic interactions of the phenoxide anion upon complex formation with the neutral phenol. Counterpoise corrections for basis set size could not be made since calculation of the phenoxide anions in the basis set of the phenol plus the phenoxide anion led to an excited state for the phenoxide anion. This behavior is somewhat similar to that occurring in the stabilization method for excited states of negative ions as the size of the basis set is increased.     

5β,6β‐Epoxy‐17‐oxoandrostan‐3β‐yl acetate and 5β,6β‐epoxy‐20‐oxopregnan‐3β‐yl acetate

In the title compounds, C₂₁H₃₀O₄, (I), and C₂₃H₃₄O₄, (II), respectively, which are valuable intermediates in the synthesis of important steroid derivatives, rings A and B are cis‐(5β,10β)‐fused. The two molecules have similar conformations of rings A, B and C. The presence of the 5β,6β‐epoxide group induces a significant twist of the steroid nucleus and a strong flattening of the B ring. The different C17 substituents result in different conformations for ring D. Cohesion of the molecular packing is achieved in both compounds only by weak intermolecular interactions. The geometries of the molecules in the crystalline environment are compared with those of the free molecules as given by ab initio Roothan Hartree–Fock calculations. We show in this work that quantum mechanical ab initio methods reproduce well the details of the conformation of these molecules, including a large twist of the steroid nucleus. The calculated twist values are comparable, but are larger than the observed values, indicating a possible small effect of the crystal packing on the twist angles.     

A theoretical study on the protonation of cycloalkanes CnH2n (n = 3 to 6)

Ab initio self-consistent-field molecular orbital calculations have been carried out for the C_nH_2n (n = 3 to 6) cycloalkanes and various conformers of their protonated forms. The calculated protonation energies for the sequence of conformers of the protonated forms follow the experimentally observed trend. Correlations between optimum C? C? C bond angles at the protonation site and the calculated protonation energies have been observed, and these correlations may be of some use in estimating protonation energy-bond angle relations in other (strained) cyclic compounds when the central carbon atom of a C? C? C moiety is protonated.     

Synthesis and reactions of halo-, nitro-, and arylazo-substituted 3-cinnamoyltropolones. Formation of styryl-substituted heterocycle-fused troponoid compounds

3-Cinnamoyltropolone ( 1 ) reacted with bromine to afford 7-bromo- ( 2 ), 5,7-dibromo-3-cinnamoyltropolone ( 3 ), and 6,8-dibromo-4,9-dihydrocyclohepta[b]pyrane-4,9-dione ( 4 ) according to amount of the reagent. Iodination and nitration of 1 gave respectively 7-iodo- ( 5 ) and 5-nitro-3-cinnamoyltropolone ( 6 ). Azo-coupling reactions gave 5-arylazo-3-cinnamoyltropolones 7a-f . Compounds 1, 2, 3 and 5 reacted with hydroxylamine to give 3-styryl-8H-cyclohept[d]isoxazol-8-ones 10-13 , while 6 and 7a gave 5-nitro-3-styryl-8H-cyclohept[d]-isoxazol-8-one oxime ( 14 ) and 2-cinnamoyl-7-methoxy-4-phenylazotropone ( 15 ), respectively. The reactions of 1,3 , and 5 with phenylhydrazine gave 3-styryl-1,8-dihydrocycloheptapyrazol-8-ones 16-19 .     

Theoretical study of the H 5 + system

Ab initio calculations have been carried out for the ground state of H ₅ ⁺ in order to predict its equilibrium geometry, binding energy, enthalpy of formation, and the features of the H₂ · H ₃ ⁺ interaction at large and intermediate intermolecular distances. The extended basis set of Gaussian functions was carefully optimized to describe the various kinds of intermolecular interactions. Electron correlation was accounted for by means of CI calculations. Different from previous studies we find a D _2d equilibrium geometry with D _e = 7.4 kcal/mol and H ₃₀₀ ⁰ –8.7 kcal/mol. The potential surface turns out to be extremely shallow in the vicinity of the D _2d structure which results in a great mobility of the central nucleus at room temperature.     

Molecular orbital treatments of hydrogen bonded systems. 2. Dimers of water and HCN

Calculations were performed to investigate the reliabilities of the CNDO/2, PRDDO, and MNDO approximate molecular orbital methods. Systems selected for study included the linear, cyclic, and bifurcated dimers of water as well as the linear and cyclic dimers of HCN. The PRDDO method was found to provide the most consistently accurate reproduction of ab initio and experimental data. CNDO/2 performed fairly well in a number of cases but yielded extremely poor results for the cyclic dimers of both H₂O and HCN. Hydrogen bond strengths were consistently underestimated by MNDO which also furnished erroneously large intermolecular separations. In addition, MNDO calculations indicate the bifurcated water dimer to be most stable in contrast to other quantum mechanical and experimental information.See Ref. [1] for Paper 1 of this series.     

Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Dimethylnitroamine Clusters

Ab initio SCF and Mφller-Plesset correlation correction methods in combination with counterpose procedure for BSSE correction have been applied to the theroetical studying of dimethylnitroamine and its dimers and trimers.Three optimized stable dimers and two trimers have been obtained.The corrected binding energies of the most stable dimer and trimer were predicted to be -24.68kJ/mol and -47.27kJ/mol,respectively at the MP2/6-31G^*//HF/6-31G^* level.The proportion of correlated interation energies to their total interaction energies for all clusters was at least 29.3 percent,and the BSSE of ΔE(MP2) was at least 10.0kJ/mol.Dispersion and/or electrostatic force were dominant in all clusters.There exist cooperative effects in both the chain and the cyclic trimers.The vibrational frequencies associated with N-O stretches or wags exhibit slight red shifts,but the modes associated with the motion of hydrogen atoms of the methyl group show somewhat blue shifts with respect to those of monomer.Thermodynamic properties of dimethylnitroamine and its clusters at different temperatures have been calculated on the basis of vibrational analyses.The changes of the Gibbs free energies for the aggregation from monomer to the most stable dimer and trimer were predicted to be 14.37kJ/mol and 30.40kJ/mol,respectively,at 1 atm and 298.15K.     

Atomic forces for geometry‐dependent point multipole and Gaussian multipole models

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry‐dependent multipole models. In this study, atomic force expressions for geometry‐dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives . The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen‐bonded dimers are used to test the intermolecular electrostatic energies and atomic forces calculated by geometry‐dependent multipoles fit to the ab initio electrostatic potential. The electrostatic energies and forces are compared with their reference ab initio values. It is shown that both static and geometry‐dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, whereas geometry‐dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry‐dependent multipole models. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Competition between hydrogen bonding and dispersion interactions in the indole···pyridine dimer and (indole)2···pyridine trimer studied in a supersonic jet

Structures of the indole···pyridine dimer and (indole)2···pyridine trimer have been investigated in a supersonic jet using resonant two-photon ionization (R2PI) and IR-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. R2PI spectra of the dimer and the trimer recorded by electronic excitation of the indole moiety show that the red-shift in the band origin of the dimer with respect to the 0(0)(0) band of the monomer is larger compared to that of the trimer. The presence of only one conformer in the case of both the dimer and the trimer has been confirmed from IR-UV hole-burning spectroscopy. The structures of the dimer and the trimer have been determined from resonant ion dip infrared (RIDIR) spectra combined with ab initio as well as DFT/M05-2X and DFT/M06-2X calculations. It has been found that the dimer, observed in the experiment, has a V-shaped geometry stabilized by N–H···N and C–H···N hydrogen bonding interactions, as well as C–H···π and π···π dispersion interactions. The geometry of the trimer has been found to be a cyclic one stabilized by N–H···N, N–H···π, C–H···π, and C–H···N interactions. The most important finding of this current study is the observation of the mixed dimer and trimer, which are stabilized by hydrogen bonding as well as dispersion interactions.     

Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations

Ab initio MP2/6-31G* interaction energies were calculated for more than 80 geometries of stacked cytosine dimer. Diffuse polarization functions were used to properly cover the dispersion energy. The results of ab initio calculations were compared with those obtained from three electrostatic empirical potential models, constructed as the sum of a Lennard-Jones potential (covering dispersion and repulsion contributions) and the electrostatic term. Point charges and point multipoles of the electrostatic term were also obtained at the MP2/6-31G* level of theory. The point charge MEP model (atomic charges derived from molecular electrostatic potential) satisfactorily reproduced the ab initio data. Addition of π-charges localized below and above the cytosine plane did not affect the calculated energies. The model employing the distributed multipole analysis gave worse agreement with the ab initio data than the MEP approach. The MP2 MEP charges were also derived using larger sets of atomic orbitals: cc-pVDZ, 6-311 + G(2d, p), and aug-cc-pVDZ. Differences between interaction energies calculated using these three sets of point charges and the MP2/6-31G* charges were smaller than 0.8 kcal/mol. The correlated ab initio calculations were also compared with the density functional theory (DFT) method. DFT calculations well reproduced the electrostatic part of interaction energy. They also covered some nonelectrostatic short-range effects which were not reproduced by the empirical potentials. The DFT method does not include the dispersion energy. This energy, approximated by an empirical term, was therefore added to the DFT interaction energy. The resulting interaction energy exhibited an artifact secondary minimum for a 3.9-4.0 vertical separation of bases. This defect is inherent in the DFT functionals, because it is not observed for the Hartree-Fock + dispersion interaction energy.© 1996 John Wiley & Sons, Inc.     

Cationic oligomerization of anethole: Selective synthesis of dimers and trimers

A linear unsaturated dimer of anethole [II, (E)-1,3-bis(p-methoxyphenyl)-2-methylpentene-1], was prepared in 98% yield with an acetyl perchlorate (AcClO₄) catalyst in a nonpolar solvent (C₆H₆) at a high temperature (70°C). At 0°C a linear unsaturated trimer was formed in high yield with dimer II. The geometric structure of the linear unsaturated dimers was determined by analysis of the nuclear Overhauser effect (NOE) on their ¹H-NMR spectra. NOE analysis showed that at 0°C with AcClO₄, trans-anethole gives the (E)-form (II), whereas cis-anethole yields the (Z)-form. On the other hand, with a metal-halide catalyst (BF₃OEt₂) a cyclic dimer and a cyclic trimer were produced in high yields in a polar solvent [(CH₂Cl₂)] at 70°C; higher oligomers (≥ tetramer) were scarcely formed. The effect of catalysts on the structure of oligomers was explained in terms of the interaction between a growing carbocation and a counterion.