Molecular interactions and crystal packing in nematogen: Computational thermodynamic approach

A computational thermodynamic approach of molecular interactions in a nematogen p-n-alkyl benzoic acid (nBAC) molecule with an alkyl group butyl (4BAC) has been carried out with respect to translational and orientational motion. The atomic net charge and dipole moment at each atomic center were evaluated using the complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrödinger perturbation theory along with multicentered-multipole expansion method were employed to evaluate long-range intermolecular interactions, while a 6-exp potential function was assumed for short-range interactions. Various possible geometrical arrangements of molecular pairs with regard to different energy components were considered, and the energetically favorable configuration was found to understand the crystal packing picture. Furthermore, these interaction energy values are taken as input to calculate the configurational entropy at room temperature (300 K), nematic-isotropic transition temperature (386 K) and above transition temperature (450 K) during different modes of interactions. An attempt has been made to describe interactions in a nematogen at molecular level, through which one can simplify the system to make the model computationally feasible in understanding the delicate interplay between energy and entropy, that accounts for mesomorphism and there by to analyze the molecular structure of a nematogen.     

The dynamics of nonadiabatic transitions in collisions between the I<Subscript>2</Subscript>(<Emphasis Type="Italic">E</Emphasis>) and I<Subscript>2</Subscript>(<Emphasis Type="Italic">X</Emphasis>) molecules

The paper presents the results of a theoretical study of the dynamics of nonadiabatic transitions between the ion-pair states E0 _g ⁺ and D0 _u ⁺ of the I₂ molecule induced by collisions with the I₂ molecule in the ground electronic state X0 _g ⁺ . The potential energy surfaces and diabatic coupling matrix elements of electronic states were obtained using a model based on the diatomics-in-molecule approximation. Special perturbation theory for intermolecular interaction was used to show that the large transition dipole moment between the E0 _g ⁺ and D0 _u ⁺ states caused the appearance of additional long-range corrections, an electrostatic dipole-quadrupole correction to the diabatic coupling matrix elements and induction dipole-dipole correction to the potential energy surface. The influence of these corrections on nonadiabatic dynamics was studied at the level of the semiclassical approximation. The electrostatic correction was found to sharply increase the contribution of resonance (accompanied by minimum kinetic energy changes) vibronic transitions at large distances between the colliding molecules. The induction correction had the opposite effect because of the high transition probability at short distances. The results obtained were in qualitative agreement with experimental data. The conclusion was drawn that obtaining quantitative agreement required a more balanced inclusion of interactions at short and long distances.     

Experimental and theoretical investigation of topological and energy characteristics of electron density in crystals of SbVo-amidophenolate complexes

Experimental and theoretical investigations of electron density in the complexes [4,6-ditert-butyl-N-(2,6-diisopropylphenyl)-1,2-amidophenolato]tricyclohexylantimony(V) (1) and [4,6-di-tert-butyl-N-(2,6-dimethylphenyl)-1,2-amidophenolato]tri-4-fluorophenylantimony(V) (2) were performed based on high-resolution X-ray diffraction data and density functional theory calculations (B3LYP/DGDZVP). The nature of chemical bonding, the energy of intraand intermolecular interactions in the crystals, and the atomic charge distribution were studied.     

A quantum chemical study of the Fe@<Emphasis Type="Italic">C</Emphasis><Subscript>60</Subscript> endocomplex

At the DFT (U)PBE0/cc-pVDZ level the structural parameters of a hypothetical Fe@C ₆₀ endocomplex are determined. The (A ₁//C _3v )–Fe@C ₆₀ state characterized by the electron spin square of 3.07 au, the free valence of 4.15, the dipole moment of 1.15 D, and the 172 pm Fe nuclear shift relative to the center of inertia of С₆₀ corresponds to the energy minimum. The Stone–Wales rearrangement in the quasi-triplet state increases the endocomplex energy by 1.56 eV and by 0.79 eV in the quasi-quintet state.     

Variation of the Intersection Point of the Potential Surface Crossing Induced by the Laser Phase Along the Reaction Path in Ion-Molecule Reactions: Application To Li<Superscript>+</Superscript> + CH<Subscript>4</Subscript>

A laser ion-molecule reaction interaction through both polarizability and dipole moment contribution leads to variation in the intersection point in potential energy surface crossings along the reaction path; the polarizability is maximum and the dipole changes its sign at s = 4 a.u., defining a virtual transition state. Using the gauge representation (electric field gauge) for a wave length λ = 20.6 μm, intensity I = 5×10¹² W/cm², I = 1×10¹³ W/cm², I = 3×10¹³ W/cm², we show here that we can create a laser-induced potential energy surface crossing along the reaction path (s = 7-8 a.u.). We illustrate such effects for the Li H + CH ₃ ⁺ ? Li⁺ + CH₄ reaction which takes the form of inverted Morse (without a barrier) using ab initio methods for calculating the reaction path and electric properties of the ion-molecule reaction.     

Microwave spectrum,centrifugal perturbation,dipole moment,and conformation of 4-methyl-1,3-dioxane

The microwave spectrum of 4-methyl-1,3-dioxane is studied in a frequency range from 16 GHz to 40 GHz. The rotational transitions of a-, b-, and c-types with J ≤ 57 are identified. The rotational constants (MHz) A = 4802.335(2), B = 2376.163(1), C = 1738.852(1) and the quartic constants of the centrifugal distortion are found for the ground vibrational state of the molecule. The components of the dipole moment (D) μ _a = 0.73(1), μ_b = 1.32(1), μ_c = 1.36(1) and the total dipole moment μ = 2.03(1) are determined. The experimental data obtained correspond to the chair conformation of the molecule with the equatorial orientation of the methyl group.     

Synthesis and structure of novel substituted <Emphasis Type="Italic">N</Emphasis>-sulfinylanilines

N-Sulfinylanilines derived from 4-bromoaniline, 3-nitroaniline, and 4,4′-di(ethane-1,2-diyl)dianiline were synthesized. X-ray diffraction analysis of 4-bromo-N-sulfinylaniline, 3-nitro-N-sulfinylaniline, and 4,4′-(ethane-1,2-diyl)di-N-sulfinylaniline was performed. The sulfinyl function in the planar conformation of the Ar-NSO fragment was found to have Z configuration. The nature of intra- and intermolecular structure-forming interactions was established.     

Factors determining the reactivity of the bromine atom toward haloalkanes

Experimental data concerning reactions of the bromine atoms with haloalkanes and carbonyl compounds (25 reactions) have been analyzed within the intersecting parabolas model. The following factors have an effect on the activation energy of these reactions: enthalpy of reaction, triplet repulsion, electronegativity of reaction center atoms, dipole–dipole and multidipole interactions of the reaction center with polar groups, and the interaction of π electrons with electrons of the reaction center. The increments characterizing the contribution from each factor to the activation energy of the reaction have been calculated. The increment ΔEμ, which characterizes the dipole–dipole interaction in the transition state, and the dipole moment of the polar group (μ) are correlated by the following empirical equation: ln(ΔE _μ/Σμ) = ?0.14 + 0.47(ΔE _μ/Σμ) ? 0.024(ΔE _μ/Σμ)².     

<Emphasis Type="Italic">Ab initio</Emphasis> prediction of plausible conformers of a flexible N-(3-chloro-4-fluorophenyl)thiourea (CFT) molecule: A validation study

The current aim of the ab initio crystal structure prediction is to find the possible conformers of the flexible N-(3-chloro-4-fluorophenyl)thiourea (CFT) molecule using gas phase optimization with an MP2/6-31G(d,p) basis set, and the lattice energy minimization in the presence of a repulsion-dispersion electrostatic potential. If the molecule deviates from the gas phase conformation, suitable intermolecular interactions are added, and the molecule favours stable packing. The crystal structure is said to be feasible if the intermolecular lattice energy compensates the intermolecular energy penalty associated with the suboptimal gas phase conformers. The idea of the current research is to find the least energy hydrogen bonded crystal structure from a set of rigid conformers in a conformation region, with a significant similarity of packing, which may lead to the prediction of polymorphs associated with the considered CFT molecule.     

Microwave spectrum,centrifugal perturbation,dipole moment,and conformation of 5-methyl-1,3-dioxane

The microwave spectrum of 5-methyl-1,3-dioxane was studied in the frequency range 12–35 GHz. The a and c type rotation transitions with J≤30 were identified. The rotational constants A = 4658.5244(33) MHz, B = 2383.3930(12) MHz, and C = 1724.28907(88) MHz and the quartic constants of the centrifugal distortion of the molecule in the ground vibrational state were determined. The components of the dipole moment were found, μ _a = 1.76 ± 0.01 D and μ _c = 1.10 ± 0.01 D; the net dipole moment of the molecule is μ = 2.08 ± 0.01 D. 5-Methyl-1,3-dioxane was calculated by the B3PW91/aug-cc-pVDZ density functional theory method. The calculated data are compared with the experimental data. The most stable conformation is the chair conformation with an equatorial orientation of the methyl group.     

The X<Superscript>−</Superscript>···benzohydrazide complexes: the interplay between anion-π and H-bond interactions

The compounds containing the benzohydrazide (BH) nucleus have a variety of biological activities because of various noncovalent intermolecular interactions. The interplay between anion-π and H-bond interactions, which can affect the activity of compounds, has been investigated in ten substituted BH exposed to the chloride ion using the quantum mechanical calculations. The total interaction energy is separated into the anion-π (ΔE _Aπ) and H-bond (ΔE _HB) contributions where both interactions are presented in the complexes. The electron-withdrawing substituents (EWSs) increase |ΔE _Aπ| and decrease |ΔE _HB|, while reversed changes are observed with the electron-donating substituents (EDSs). In addition, the total binding energy (ΔE) becomes more/less negative in the presence of EWSs/EDSs. The synergetic effects of mentioned interactions and substituent effects have also been investigated using the atoms in molecules (AIM), natural bond orbital (NBO) and molecular electrostatic potential (MEP) analyses. A good correlation is found between the energy data and the Hammett constants, the minimum of electrostatic potential (V _min) and the results of population analyses.     

Crystal and molecular structures of two modifications of a chelate compound of Pb[(<Emphasis Type="Italic">iso</Emphasis>-C<Subscript>4</Subscript>H<Subscript>9</Subscript>)<Subscript>2</Subscript>PS<Subscript>2</Subscript>]<Subscript>2</Subscript>

A chelate compound Pb[(iso-C₄H₉)₂PS₂]² is synthesized. Using X-ray diffraction data, the crystal structures of two modifications of this compound are determined (X8 APEX diffractometer, MoK _α radiation, 14169 F _hkl , R = 0.0480 for the low temperature α-form and 6261 F _hkl , R = 0.0387 for the β-form studied at ambient temperature). The crystals are triclinic: a = 11.047(2) Å, b = 14.486(3) Å, c = 32.048(6) Å; α = 91.30(3)°, β = 99.73(3)°, γ = 101.61(3)°, V = 4942.9(17) ų, Z = 8, ρ_calc = 1.682 g/cm³ (α-modification) and a = 11.2124(5) Å, b = 14.6989(7) Å, c = 17.1644(6) Å; α = 109.393(1)°, β = 94.989(2)°, γ = 101.649(1)°, V = 2576.83(19) ų, Z = 4, ρ_calc = 1.613 g/cm³ (β-modification), space group \(P\bar 1\) for both polymorphs. The structures are molecular, coordination cores of PbS₄ are tetragonal pyramids with Pb atoms in the vertices and S atoms in the base. In both structures intermolecular Pb...S contacts yield supramolecular ensembles comprising by four molecules, where PbS₄₊₂ cores form planar aggregates of edge-sharing octahedra. The ensembles are joined by weak intermolecular S...S interactions resulting in the development of polymeric chains along the a axis.     

Structural and vibrational investigation of 1, 2-<Emphasis Type="Italic">bis</Emphasis>(3, 4-dimethoxyphenyl) ethane-1, 2-dione (Veratril): experimental and theoretical studies

The molecular and crystal structures of 1,2-bis(3,4-dimethoxyphenyl)ethane-1,2-dione (TMBZ = tetramethoxybenzil) were determined by a single-crystal X-ray diffraction, ¹H NMR, and FT-IR spectroscopy. The compound TMBZ (C₁₈H₁₈O₆, M _r = 330.32) crystallized in the orthorhombic Fdd2 space group wherein: a = 39.145(4), b = 18.167(2), c = 4.3139(5) Å and β = 90°, Z = 8. The packing of the molecules in the crystal lattice is stabilized by intermolecular C–H?O contacts in the herringbone arrangement. The molecular geometry and harmonic frequencies of TMBZ in the ground state were calculated utilizing density functional (B3LYP) method with the 6-311++G(d, p)-basis set. The density functional theory optimized the geometric structure, and vibrational wave numbers of TMBZ in gas phase were compared with the experimental data. A complete assignment of the fundamentals was proposed based on the total energy distribution calculation.     

DFT study of small aluminum and boron hydrides: isomeric composition and physical properties

The structure, energetics, and physical properties, including rotational constants, characteristic vibrational temperatures, dipole moment, static polarizability, HOMO-LUMO gap, formation enthalpy and collision diameter of different isomeric forms of atomic Al _n H _m and B _n H _m clusters with n = 1..4 and all feasible m numbers are studied within the density functional theory framework. The search of isomer structures has been accomplished using multistep hierarchical algorithm. Temperature dependences of thermodynamic functions (enthalpy, entropy and specific heat capacity) have been calculated both for the individual isomers and for the ensemble of isomers with equilibrium composition for each class of clusters, taking into account the anharmonicity of cluster vibrations and the contribution of excited electronic states. The prospects of the application of small atomic Al _n H _m and B _n H _m clusters as the components of energetic and hydrogen storage materials are also discussed.     

Intermolecular interactions and binding mechanism of inclusion complexation between sulfonate calix[<Emphasis Type="Italic">n</Emphasis>]arenes and ethidium bromide

In this work, the interactions between ethidium bromide (ET) and water-soluble sulfonate calix[n]arenes (n: 4, 6, and 8) were investigated by NMR, FT-IR, and fluorescence spectroscopic methods. The aim was to evaluate both the stoichiometry and the mechanism of the possible complex structure between sulfonate calix[n]arenes and ET. The spectroscopic data revealed that a 1:1 binding mode between calixarene and ET was occurred. Furthermore, thermodynamic parameters and fluorescence titration experiments were studied at different temperatures to determine both the quenching mechanism and the type of intermolecular forces in complex formation. Host–guest complexation of sulfonate calix[n]arenes and ET could be used to overcome some adverse effects related to the using of ethidium bromide during biological applications as a DNA marker treatment.     

Reactivity of haloalkanes in their reactions with the chlorine atom

Experimental kinetic data on reactions of the chlorine atom with halogenated derivatives of methane and ethane (37 reactions) have been analyzed by the intersecting-parabolas method. The following five factors have an effect on the activation energy of these reactions: the enthalpy of reaction, triplet repulsion, the electronegativities of the reaction center atoms, the dipole–dipole and multidipole interactions between the reaction center and polar groups, and the effect of π electrons in the vicinity of the reaction center. The increments characterizing the contribution from each factor to the activation energy of the reaction have been calculated. The contribution from the polar interaction, ΔE _μ, to the activation energy depends on the dipole moment of the polar group and obeys the following empirical equation: ln(Δ_{E μ}/Σμ) = ?0.74 + 0.87(ΔE _μ/Σμ) ? 0.084(ΔE _μ/Σμ)².     

Surface properties and hydrogen bonds of mono-functional polybenzoxazines with different <Emphasis Type="Italic">N</Emphasis>-substituents

A series of mono-functional benzoxazine monomers with different N-substituents were synthesized from phenol, formaldehyde, and various amines (ammonia, methylamine, n-butylamine, dodecylamine), named P-am, P-m, P-b, and P-da, respectively. The surface properties of these polybenzoxazine films were proven by contact angle measurements. The hydrogen bond network of the polybenzoxazine systems was studied using the FTIR spectra. And the results showed that the surface free energy increased with increasing the fraction of intermolecular hydrogen bonding when the N-substituent was an alkyl chain. However, the rule was not suitable when the N-substituent was H. That was because there was one more kind of intramolecular hydrogen bond in the poly(P-am). Based on these findings, we proposed that both the N-substituent alkyl group and the fraction of intermolecular hydrogen bonding had effects on the surface free energy.     

Inter- and intramolecular interactions in 2,3-dihydroquinazolin-4(1<Emphasis Type="Italic">H</Emphasis>)-ones: molecular structure and conformational analysis

X-ray crystal structure analysis and quantum chemical calculations based on the density functional theory (DFT) were used for structural and electronic characterizations of three 2,3-dihydroquinazolin-4(1H)-ones (DHQZs). The occurrence of the C₂-stereocenter in the heterocyclic ring causes the formations of both R- and S-enantiomers. X-ray diffraction technique indicates that these compounds exist as a racemic mixture in the crystal structure, and the enantiomers are orientated to each other via hydrogen bonding between the potential hydrogen donor (N₃–H) and acceptor species (C₄ = O group) in each layer under the formation of an enantio-syndio packing. Additional intermolecular and intramolecular interactions affect the orientations of the molecules adopted in the crystal packing, especially the orientation of the ring substitution. Most computational data, including the bond lengths and angles, are well in agreement with the experimental data. Dihedral angle scanning elucidates the effect of the nature and the location of the additional substituent on the aryl group at C₂-position on the total energy content of the molecule.