A theoretical study of substitution effects on halogen–π interactions

Ab initio calculations are performed to analyse the existence of intermolecular halogen···π interactions in NCX complexes with YC≡CY, where X = Cl, Br and Y = H, CN, F, Cl, OH, NH₂, and CH₃. Molecular geometries and interaction energies of the complexes are investigated at the MP2/aug-cc-pVTZ level of theory. Our results indicate that the interaction energies for the NCX···YC≡CY complexes lie in the range between ?0.5 and ?5.9 kcal/mol. The physical nature of the interactions is studied using symmetry-adapted perturbation theory (SAPT). The stability of the X···π interactions is predicted to be attributable mainly to electrostatic and dispersion effects.     

Density-functional study of CO adsorbed on RhN （N = 2-19） clusters

We investigate the structural, electronic and adsorption properties of one single CO molecule adsorbed on Rh_N (N = 2-19) clusters, using the density-functional theory in the spin-polarized generalized gradient approximation. It is found that the structural growth model of the Rh_N clusters transforms from double layers (N = 12-16) to three layers (N = 17-19). Three different adsorption types are the atop site adsorption for N = 6, 8, 9, 11, 12, the bridge site adsorption for N = 2-5, 7, 10, 13-15, 17 and the face adsorption for N = 16, 18, 19. The adsorption abilities of Rh_N clusters are related to C-O bond length, vibrational frequency, adsorption energy and the charge transfer between CO and Rh clusters as well as the electronic density of state. With the increase of Rh cluster size, the adsorption energy of CO adsorbed on Rh_N clusters tends to be 2.2 eV-2.3 eV, which is 0.2 eV-0.3 eV larger than the theoretical value (about 2.0 eV) of CO molecule adsorption on clean Rh (111) surface.     

The role of surface hydroxils of Al2O3·xH2O in the luminescence of adsorbed fluorescein molecules

Acta physica Academiae Scientiarum Hungaricae - Producing various surface hydroxil concentrations on Al2O3 films by surface reactions it was found that there is a distinct relation between the...     

A first-principles study of π-conjugated thiol phenothiazine derivatives adsorbed on Au(111) surface

We present an extensive theoretical study of a series of phenothiazine derivatives adsorbed on Au(111). A series of experimentally accessible quantities are calculated (ultra-violet photoemission spectra, scanning tunneling microscopy images). All simulations were performed by using DFT techniques and LCAO expansion of the molecular orbitals. The microscopic picture established in this work provides a deeper understanding of the interfacial processes that govern the working principle of single-molecule electronics and organic electronic devices.      

A study of the influence of surface layers’ disordering on the spectrum of energy losses of electrons passed through copper thin single crystal films

Results of the experimental investigation of energy losses of electron passed through thin films Cu (100) with a thickness of d ≈ 420 ? at E _p = 3 keV are presented. It is revealed that the surface plasmon peak disappears at a primary electron energy of ≥6 keV. For the first time, the degree of surface amorphization and area of the disordered layer are estimated by the change of elastic peak intensity during the passage of electrons through thin films of Cu (100). There is an additional energy loss of electrons peak caused by bulk plasmon, its intensity depending on the irradiation dose under ionic bombardment.     

HREELS study of C70 molecules adsorbed on a Si(1 1 1)-(7×7) surface

We have measured the coverage dependence of vibrational excitation spectra of C₇₀ molecules adsorbed on a Si(1 1 1)-(7×7) surface using high-resolution electron-energy-loss spectroscopy. At the monolayer coverage, the intensity of the 57 meV peak increases, and those of the 83 and 178 meV peaks decrease. Taking into account the dipole selection rule, the change in intensity of the 57 meV peak indicates that the average angle between the long axes of C₇₀ molecules and surface normal is about 40°. The decreases in intensities of the 83 and 178 meV peaks suggest that the rotational motion of molecules is quenched upon adsorption. We will discuss the Coriolis interaction between the accidentally degenerate A₂″ and E₁′ modes.     

First-principles study on the doping effects of Al in α-MnO2

In this paper, first-principles calculations have been implemented to study the structural relaxation, formation energies and electronic structure of Al doped α-MnO₂. Both Al insertion and Al substitution reactions in the α-MnO₂ were considered. Calculated formation energies indicate that Mn atom is easier to be displaced by Al atom under the O-rich growth condition compared with Al insertion reaction. Besides, it can be found that Al doping can afford acceptor impurity level which can accommodate electrons, thus contributing to the improvement of conductivity of α-MnO₂. The conductivity of α-MnO₂ is gradually improved with the increasing doping concentration of Al, and Al_0.0417Mn_0.9583O₂ exhibits the best conductivity. Lastly, the electronic structure of Al_0.0417Mn_0.9583O₂ was further investigated by analysis of total charge density and Bader charge. It is clear that Al doping can afford more electrons for α-MnO₂, which also contributes to improvement of its conductivity.     

A photoelectron spectroscopic study of the second ionisation of the CF(X2Π) radical

The CF(X²Π) radical has been re-investigated with vacuum ultraviolet photoelectron spectroscopy. Two bands were observed and assigned to the ionisations CF⁺(X¹Σ⁺)←CF(X²Π) and CF⁺(a³Π)← CF(X²Π). The first band, which has been observed previously, has an adiabatic ionisation energy of (9.11±0.02) eV and a vertical ionisation energy of (9.55±0.02) eV. For the second band, three vibrational components were observed with the first, the most intense, at an ionisation energy of (13.94±0.02) eV. Analysis of the vibrational structure in the two observed bands allowed ω_e and r_e to be determined as 1810±30 cm⁻¹ and 1.154±0.005 Å, respectively for the first ionic state, CF⁺(X¹Σ⁺), and 1614±30 cm⁻¹ and 1.213±0.005 Å, respectively for the second ionic state, CF⁺(a³Π). Comparison of the ionisation energies and spectroscopic constants obtained has been made with values obtained from recent multi-reference configuration interaction calculations.     

A theoretical study of rotational-vibrational levels of the lower two 2Σ+ states of the CaH molecule

Computation of the rotational vibrational levels of the X²Σ⁺ and B²Σ⁺ states of the CaH molecule is carried out by using the adiabatic potential curves obtained by an ab initio SCF-CI calculation (N. Honjou, M. Takagi, M. Makita, and K. Ohno, J. Phys. Soc. Japan 50, 2095–2100 (1981)). Due to two minima in the adiabatic potential curve of the B²Σ⁺ state, an irregularity is found in the rotational-vibrational levels.     

A theoretical study of the stereodynamics on the abstraction reactions H/D ＋ HS/DS

The quasi-classical trajectory(QCT) method is employed to calculate the stereodynamics of the abstraction reactions H/D+HS/DS based on an accurate potential energy surface [L S J,Zhang P Y,Han K L and He G Z 2012 J.Chem.Phys.136 094308].The reaction cross sections of the title reaction are computed,and the vector correlations for different collision energies and different initial vibrational states are presented.The influences of the collision energy and reagent vibration on the product polarization are studied,and the product polarizations of the title reactions are found to be distinctly different,which arises from the different mass factors,collision energies,and reagent vibrational states.     

A theoretical study of FeNC in the Δ electronic ground state

We report an ab initio calculation, at the MR-SDCI + Q + E_rel/[Roos ANO (Fe), aug-cc-pVQZ (C, N)] level of theory, of the potential energy surface for ⁶Δ_i FeNC. From the ab initio results, we have computed values for the standard spectroscopic parameters of FeN¹²C and FeN¹³C. Analytical representations of the potential energy surfaces have been fitted through the ab initio points, and the resulting functions have been used for directly solving the rotation-vibration Schrödinger equation by means of the MORBID program and by means of an adiabatic-separation method. For ⁶Δ_i FeNC, our ab initio calculations show that the equilibrium structure is linear with r_e (Fe-N) = 1.9354 Å and r_e (N-C) = 1.1823 Å. We find that the bending potential is very shallow, and the MORBID calculations show that the zero-point averaged structure is bent with the expectation values 〈r (Fe-N)〉 = 1.9672 Å, 〈r(N-C)〉 = 1.1866 Å, and . The experimentally derived bond length r₀ (N-C) = 1.03(8) Å reported for ⁶Δ_i FeNC by Lie and Dagdigian [J. Chem. Phys. 114 (2001) 2137-2143] is much shorter than the corresponding ab initio r_e-value and the averaged value from MORBID. Our calculations suggest that this discrepancy is caused by the inadequate treatment of the large-amplitude bending motion of ⁶Δ_i FeNC. It would appear that for floppy triatomic molecules such as FeNC, r₀-values have little physical meaning, at least when they are determined with the effects of the large-amplitude bending motion being ignored, i.e., under the assumption that the r₀ structure is linear.     

A theoretical study of N–H ··· π H-bond interaction of pyrrole: from clusters to the liquid

The N–H?···?π H-bond interactions of clusters and liquid formed by pyrrole molecules were investigated by Quantum Mechanics (QM) and classical Molecular Dynamics (MD), respectively. Based on the optimized geometry at the B97-D/aug-cc-pVTZ level of theory including dispersion correction, the nature and the origin of N–H?···?π H-bond interactions were unveiled by atoms in molecules (AIM), natural bond orbital (NBO), and energy decomposition analysis (EDA). Among them, the AIM analysis gives evidence to the presence of N–H?···?π H-bond interactions, the NBO examination reveals that π?→?σ* donor-acceptor orbital interaction is of great importance. EDA study indicates that N–H?···?π interactions are governed by the electrostatic and dispersion term. Meanwhile, MD simulation with OPLS-AA (optimized potentials for liquid simulations all-atom) was applied to study the pure liquid pyrrole at different temperature. The results confirm the existence of the N–H?···?π H-bond in the pure liquid pyrrole, and further characterized the structures of this H-bond which is somewhat different to the clusters.     

A density functional theory study on the adsorption of CO and O2 on Cu-terminated Cu2O （111） surface

The adsorptions of CO and 02 molecules individually on the stoichiometric Cu-terminatcd Cu20 （111） surface are investigated by first-principles calculations on the basis of the density functional theory. The calculated results indicate that the CO molecule preferably coordinates to the Cu2 site through its C atom with an adsorption energy of-1.69 eV, whereas the 02 molecule is most stably adsorbed in a tilt type with one O atom coordinating to the Cu2 site and the other O atom coordinating to the Cul site, and has an adsorption energy of -1.97 eV. From the analysis of density of states, it is observed that Cu 3d transfers electrons to 2π orbital of the CO molecule and the highest occupied 5σ orbital of the CO molecule transfers electrons to the substrate. The sharp band of Cu 4s is delocalized when compared to that before the CO molecule adsorption, and overlaps substantially with bands of the adsorbed CO molecule. There is a broadening of the 2π orbital of the 02 molecule because of its overlapping with the Cu 3d orbital, indicating that strong 3d-2π interactions are involved in the chemisorption of the 02 molecule on the surface.     

Surface corrugation effects on the adsorption dynamics of xenon on Pt(110)−(1 × 2)

The adsorption probability of xenon on Pt(110)(1 × 2) shows a strong dependence on both the polar (θ_i) and aximuthal angles of incidence. For atoms incident along the (11̄0) direction the adsorption probability increases slowly with increasing angle of incidence, scaling as E_i, cos^0.5θ, whereas along the (100) azimuth it decreases with increasing angle of incidence, exhibiting “negative” energy scaling. The hard cube washboard model does not account quantitatively for these differences with a single consistent set of parameters.     

Dimerization in the commensurate network of 4-n-octyl-4’-cyanobiphenyl (8CB) molecules adsorbed on MoS $_\mathsf{2}$ single crystal

By combining X-ray diffraction under grazing incidence (GIXD) and scanning tunneling microscopy (STM) measurements, we have determined the structure of 4-n-octyl-4-cyanobiphenyl (8CB) molecules adsorbed on MoS₂, under the thick organic film. The commensurability of the adsorbed network and the unit cell structure have been determined, revealing a complex 2D structure. This structure is characterized by straight ribbons with two types of ribbons, alternatively stacked. In one type, molecules are equally spaced, as they are paired in the other type. Considering the energetics of adsorption with a model of single ribbon, we recover the two observed ribbon structures. The alternate stacking of the ribbons appears as a consequence of the connection between the commensurabilities in the two main crystallographic directions. Moreover, we have found a particularly high value for the molecule-substrate potential corrugations, indicating that the dipole moment of 8CB molecules could play a fundamental role in the molecule-substrate interactions.Received: 1 April 2004, Published online: 29 June 2004PACS: 61.10.-i X-ray diffraction and scattering - 68.35.Bs Structure of clean surfaces (reconstruction) - 61.30.-v Liquid crystals - 68.35.Md Surface thermodynamics, surface energies     

Drug–DNA interaction: A theoretical study on the binding of thionine with DNAs of varying base composition

The recent studies carried out on the binding of small molecule to deoxyribonucleic acids suggested that the intercalation of a tricyclic heteroaromatic molecule, thionine, with natural DNAs provided thermal stabilization to the DNA complex. In the present study, we reported theoretical analysis of thionine binding with natural DNAs of varying base composition by using an amended Zimm and Bragg theory, to explain the melting behaviour and heat capacity of DNAs with and without thionine binding. We used experimental models of Paul et al. for implementing this study (Paul et al., 2010). The sharpness of transition has been examined in terms of half width and sensitivity parameter (ΔH/σ). The results of theoretical analysis concluded that the various parameters such as heat capacity curve, transition profile, half widths and sharpness of the transition are in good agreement with the experimental measurements for binding of thionine determined through DSC. The theoretical analysis proposed in this study, therefore, may be useful to understand interaction of small molecules with deoxyribonucleic acids. This approach may also be applied to design DNA binding therapeutic molecules and in the process of drug formulation and development.     

A comparative study on the effects of salt and filler on transport and structural properties of organic–inorganic hybrid electrolytes

Organic–inorganic hybrid electrolytes based on the reaction of tri-block copolymer poly(propylene glycol)-block-poly(ethylene glycol)-block-poly(propylene glycol) bis(2-aminopropyl ether), poly(ethylene glycol diglycidyl ether, and (3-glycidyloxypropyl)trimethoxysilane doped with LiClO₄ and SiO₂ nanoparticles were synthesized by a sol–gel process. The structural and dynamic properties of the materials thus obtained were systematically investigated by Fourier transform infrared spectroscopy, differential scanning calorimetry, thermogravimetric analysis, alternate current impedance, and ¹³C solid-state NMR measurements. A maximum ionic conductivity of 3.2?×?10^?5 S cm^?1 was obtained at 30 °C for the solid hybrid electrolyte with a [O]/[Li] ratio of 16 and 7 wt% of SiO₂ nanoparticles. A Vogel–Tamman–Fulcher-like temperature dependence of ionic conductivity was observed for the hybrid electrolytes, implying that the diffusion of charge carriers was assisted by the segmental motions of the polymer chains.     

Alignment of non-polar molecules—electric field effects in the 2H N.M.R. spectrum of perdeuterobenzene in solutions with nitrobenzene

Electric field experiments on the ²H N.M.R. spectrum of perdeuterobenzene, dissolved in nitrobenzene, are reported. The alignment of the polar molecules, induced by a strong electric field, is transferred to the non-polar ones and as a result their N.M.R. spectrum is modified.

Local field models, e.g. those of Lorentz and Onsager, treat the environment of a molecule as a continuum and are unable to explain the alignment of the non-polar molecules. Intermolecular interactions are essential. In an expression for the alignment these interactions are described in terms of correlation functions for the mixture.

N.M.R. and Kerr data of nitrobenzene-benzene solutions have been compared. The Kerr constant of a binary mixture is shown to depend on the alignments of both the polar and non-polar component. N.M.R. electric field experiments may be useful to separate these two contributions.