Through Bridge Spin Coupling in Homo- and Heterobimetallic Porphyrin Dimers upon Stepwise Oxidations: A Spectroscopic and Theoretical Investigation

We have described copper(II)-iron(III) and copper(II)-manganese(III) heterobimetallic porphyrin dimers and compared them with the corresponding homobimetallic analogs. UV-visible spectra are very distinct in the heterometallic species while electrochemical studies demonstrate that these species, as compared to the homobimetallic analog, are much easier to oxidize. Combined Mössbauer, EPR, NMR, magnetic and UV-visible spectroscopic studies show that upon 2e-oxidation of the heterobimetallic complexes only ring-centered oxidation occurs. The energy differences between HOMO and LUMO are linearly dependent with the low-energy NIR band obtained for the 2e-oxidized complexes. Also, strong electronic communication between two porphyrin rings through the bridge facilitates coupling between various unpaired spins present while the coupling model depends on the nature of metal ions used. While unpaired spins of Fe(III) and the porphyrin π-cation radical are strongly antiferromagnetically coupled, such coupling is rather weak between Mn(III) and a porphyrin π-cation radical. Moreover, the coupling between two π-cation radicals are much stronger in the 2e-oxidized complexes of dimanganese(III) and copper(II)-manganese(III) porphyrin dimers as compared to their diiron(III) and copper(II)-iron(III) analogs. Furthermore, coupling between the unpaired spins of a π-cation radical and copper(II) is much stronger in the 2e-oxidized complex of copper(II)-iron(III) porphyrin dimer as compared to its copper(II)-manganese(III) analog. The Mulliken spin density distributions in 2e-oxidized homo- and heterobimetallic complexes show symmetric and asymmetric spread between the two macrocycles, respectively. In both the 2e-oxidized heterobimetallic complexes, the Cu(II) porphyrin center acts as a charge donor while Fe(III)/Mn(III) porphyrin center act as a charge acceptor. The experimental observations are also strongly supported by DFT calculations.     

Interaction energy and surface reconstruction between sheets of layered silicates

Interactions between two layered silicate sheets, as found in various nanoscale materials, are investigated as a function of sheet separation using molecular dynamics simulation. The model systems are periodic in the xy plane, open in the z direction, and subjected to stepwise separation of the two silicate sheets starting at equilibrium. Computed cleavage energies are 383 mJ /m(2) for K-mica, 133 mJ /m(2) for K-montmorillonite (cation exchange capacity=91), 45 mJ /m(2) for octadecylammonium (C(18))-mica, and 40 mJ /m(2) for C(18)-montmorillonite. These values are in quantitative agreement with experimental data and aid in the molecular-level interpretation. When alkali ions are present at the interface between the silicate sheets, partitioning of the cations between the surfaces is observed at 0.25 nm separation (mica) and 0.30 nm separation (montmorillonite). Originally strong electrostatic attraction between the two silicate sheets is then reduced to 5% (mica) and 15% (montmorillonite). Weaker van der Waals interactions decay within 1.0 nm separation. The total interaction energy between sheets of alkali clay is less than 1 mJ /m(2) after 1.5 nm separation. When C(18) surfactants are present on the surfaces, the organic layer (>0.8 nm) acts as a spacer between the silicate sheets so that positively charged ammonium head groups remain essentially in the same position on the surfaces of the two sheets at any separation. As a result, electrostatic interactions are efficiently shielded and dispersive interactions account for the interfacial energy. The flexibility of the hydrocarbon chains leads to stretching, disorder, and occasional rearrangements of ammonium head groups to neighbor cavities on the silicate surface at medium separation (1.0-2.0 nm). The total interaction energy amounts to less than 1 mJ /m(2) after 3 nm separation.     

Simple Landau model of the R(IV)-R(III)-R(V) rotator phases of alkanes

Simple Landau-type free energy function is presented to describe the R(IV)-R(III)-R(V) rotator phase sequence and the transitions between them. The order parameters necessary to describe the above rotator phase transitions are identified. Varying the coupling between the order parameters, the R(IV)-R(III) and R(III)-R(V) transitions occur. Available experimental results are consistent with our model.     

Ab initio study on the ground and low-lying excited states of cesium iodide (CsI)

Potential energy curves (PECs) for the ground and low-lying excited states of the cesium iodide (CsI) molecule have been calculated using the internally contracted multireference configuration interaction calculation with single and double excitation method with the relativistic pseudopotentials. PECs for seven Lambda-S states, X 1Sigma+, 2 1Sigma+, 3Sigma+, 1Pi, and 3Pi are first calculated and then those for 13 Omega states are obtained by diagonalizing the matrix of the electronic Hamiltonian H(el) plus the effective one-electron spin-orbit (SO) Hamiltonian H(SO). Spectroscopic constants for the calculated ground X 0+-state PEC with the Davidson correction are found to agree well with the experiment. Transition dipole moments (TDMs) between X 0 and the other Omega states are also obtained and the TDM between X 0+ and A 0+ is predicted to be the largest and that between X 0+ and B 0+ is the second largest around the equilibrium internuclear distance. The TDMs between X 0+ and the Omega=1 states are estimated to be nonzero, but they are notably small as compared with those between the 0+ states. Finally, vibrational levels of the X 0+ PEC for the two isotopic analogs, (133)CsI and (135)CsI, are numerically obtained to investigate the isotope effect on the vibrational-level shift. It has been found that the maximized available isotope shift is approximately 30 cm(-1) around nu=136.     

A study on the antipicornavirus activity of flavonoid compounds (flavones) by using quantum chemical and chemometric methods

The AM1 semiempirical method is employed to calculate a set of molecular properties (variables) of 45 flavone compounds with antipicornavirus activity, and 9 new flavone molecules are used for an activity prediction study. Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA), Stepwise Discriminant Analysis (SDA), and K-Nearest Neighbor (KNN) are employed in order to reduce dimensionality and investigate which subset of variables should be more effective for classifying the flavone compounds according to their degree of antipicornavirus activity. The PCA, HCA, SDA, and KNN methods showed that the variables MR (molar refractivity), B(9) (bond order between C(9) and C(10) atoms), and B(25) (bond order between C(11) and R(7) atoms) are important properties for the separation between active and inactive flavone compounds, and this fact reveals that electronic and steric effects are relevant when one is trying to understand the interaction between flavone compounds with antipicornavirus activity and the biological receptor. In the activity prediction study, using the PCA, HCA, SDA, and KNN methodologies, three of the 9 new flavone compounds studied were classified as potentially active against picornaviruses.     

High resolution electron energy loss spectroscopy of clean and hydrogen covered Si(001) surfaces: First principles calculations

Surface phonons, conductivities, and loss functions are calculated for reconstructed (2×1), p(2×2) and c(4×2) clean Si(001) surfaces, and (2×1) H and D covered Si(001) surfaces. Surface conductivities perpendicular to the surface are significantly smaller than conductivities parallel to the surface. The surface loss function is compared to high resolution electron energy loss measurements. There is good agreement between calculated loss functions and experiment for H and D covered surfaces. However, agreement between experimental data from different groups and between theory and experiment is poor for clean Si(001) surfaces. Formalisms for calculating electron energy loss spectra are reviewed and the mechanism of electron energy losses to surface vibrations is discussed.     

Dissociative electron attachment to CH2Cl2, CHCH3Cl2, and C(CH3)2Cl2

We perform theoretical studies of dissociative electron attachment (DEA) for the compounds CH(2-n)(CH(3))(n)Cl(2), n = 0, 1, 2, by combining the finite-element discrete model with the resonance R-matrix theory. An unexpectedly low DEA cross section for CH(2)Cl(2) is likely due to the relatively large resonance width for this compound that confirms experimental observations. However, there are some quantitative discrepancies with the experimental results. Since DEA cross sections are very sensitive to the resonance width, a slight adjustment of its value can significantly improve agreement between theory and experiment. Our calculation of the thermal rate coefficients show that there are some inconsistencies between beam and swarm measurements and between different swarm measurements of the rate coefficients for DEA to CH(2)Cl(2). Further experimental and theoretical studies are warranted.     

Theoretical investigation of structural and electronic propertyies of [PW12O40]3- on graphene layer

The structural and electronic properties of [PW(12)O(40)](3-) (PW(12)) anion deposited on a graphene layer are investigated by using periodic density functional theory. The equilibrium geometries of graphene-PW(12) (G-PW(12)) are examined based on six different configurations. The adsorption energy and charge transfer between PW(12) and graphene are calculated and analyzed. We found that the interaction between PW(12) and graphene are noncovalent. The formation of G-PW(12) complex is theoretically predicted to be feasible from an energetic perspective with electron transfer from the PW(12) to graphene.     

Discrimination between peptide 3(10)- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra

Detailed spectral simulations based on ab initio density functional theory computations of the amide I and II infrared (IR) and vibrational circular dichroism (VCD) spectra for Ac-(Ala)(4)-NH(2), Ac-(Aib-Ala)(2)-NH(2), and Ac-(Aib)(4)-NH(2) constrained to 3(10)- and alpha-helical conformations are presented. Parameters from these ab initio calculations are transferred onto corresponding larger oligopeptides to simulate the spectra for dodecamers. The differences between conformations and for different Aib substitution patterns within a conformation are reflected in observable spectral patterns where data are available. Simulated IR spectra show small frequency shifts in the amide I maxima between 3(10)- and alpha-helices, but the same magnitude shifts occur within one conformation upon Aib substitution. Thus, from a computational basis, the frequency of the amide I maximum does not discriminate between the 3(10)- or alpha-helical conformations. Calculated VCD band shapes for 3(10)-helices showed more significant changes in amplitude, with change in the fraction of Aib, than those for alpha-helices. Generally, with increasing Aib content, the overall amide I VCD intensity becomes weaker and the amide I couplet becomes more conservative, while the amide II VCD is less affected. Although the detailed band shape is shown to be sensitive to alpha-Me substitution, the basic pattern of amide I and II relative VCD intensities still differs between alpha- and 3(10)-helices and, as a consequence, successfully discriminates between them. These predictions are all borne out in experimental spectra of Aib, mixed Aib-Ala, and Ala-based helical peptides, where available.     

Gamma-Fe2O3/II-VI sulfide nanocrystal heterojunctions

Heterostructure nanocrystals (NCs) of gamma-Fe(2)O(3) and MS (M = Zn, Cd, Hg) are synthesized. The large lattice mismatch between gamma-Fe(2)O(3) and MS NCs leads to noncentrosymmetric structures. Crystallographic planes at the heterojunctions are identified by high-resolution transmission electron microscopy. Preferential formation of trimers and higher oligomers for ZnS and dimers or isolated particles for CdS and HgS with gamma-Fe(2)O(3) NCs are observed and explained by changes in the effective mismatch between the coincidence lattices of the most commonly observed junction planes.     

Structures, energies, and spin-spin coupling constants of fluoro-substituted 1,3-diborata-2,4-diphosphoniocyclobutanes: four-member B-P-B-P rings B2P2F(n)H(8-n) with n = 0, 1, 2, 4

An ab initio study has been carried out to determine the structures, relative stabilities, and spin-spin coupling constants of a set of 15 fluoro-substituted 1,3-diborata-2,4-diphosphoniocyclobutanes B(2)P(2)F(n)H(8-n), for n = 0, 1, 2, 4, with four-member B-P-B-P rings. Except for B(2)P(2)F(4)H(4) with four fluorines bonded to two borons, these rings are puckered in a butterfly conformation. For a fixed number of fluorines, the isomers with B-F bonds are significantly more stable than those with P-F bonds. As the number of fluorines increases, the energy difference between the most stable isomer and the other isomers increases. Transition structures which interconvert axial and equatorial positions present relatively small inversion barriers. Coupling constants involving (31)P, namely, (1)J(B-P), (1)J(P-F), (2)J(P-P), (2)J(P-F), and (3)J(P-F) are large and are capable of providing structural information. They are sensitive to the number of fluorines present and can discriminate between axial, equatorial, and geminal B-F and P-F bonds, although not all do this to the same extent. (1)J(B-P) and (2)J(P-P) are similar in equilibrium and transition structures. Although transition structures no longer discriminate between axial and equatorial bonds, (1)J(P-F) and (3)J(P-F) remain sensitive to the number of fluorine atoms present.     

The effect of fluorination: a crystallographic and computational study of mesogenic alkyl 4-[2-(perfluorooctyl)ethoxy]benzoates

The series of alkyl 4-[2-(perfluorooctyl)ethoxy]benzoates (F8-n) shows a systematic change of crystal structures depending on the length of the alkyl chain: separate packing of perfluorooctyl (Rf) and alkyl (Rh) chains from each other for shorter (n=2) and longer (n=11) members, alternate packing of Rf and Rh chains for middle (n=6,7) members, and an intermediate type of packing for n=4. Semiempirical MO calculations show slightly repulsive interactions between the Rf chains, and attractive ones between Rf and Rh chains and between Rh and the core of a molecular pair. It is concluded that fluorination determines the molecular shape of the crystal structures by making the chain rigid. It is confirmed that the interactions between Rf chains are small compared with those between other moieties and that they are forced to aggregate owing to the exclusion from other moieties. Thus, the effect is dependent on the geometries and intermolecular interactions of the other moieties.     

Effect of clay aggregation on water diffusivity using low field NMR

Water diffusivity D measured by using NMR techniques in Na-smectite suspensions decreases with increasing smectite fraction (up to 50 wt%), but increases with increasing salinity (NaCl or CaCl(2) aqueous solutions) at a fixed clay fraction. The increase, larger for CaCl(2) solutions, is explained by aggregation of clay particles when high salinities are reached. Macroscopic organisation of dense mixtures of clay and aqueous solutions can be inferred by T(2) transverse NMR relaxation times which are sensitive to the volume to surface ratio. Dispersed suspensions exhibit mono-modal T(2) distributions, whereas bimodal T(2) distributions are observed for flocculated systems. The bimodal T(2) distributions are interpreted as a measurement of the spacing between clay particles within aggregates and between aggregates. Finally, the diffusion data can be gathered in an unique curve using the Debye length and the measured spacing between particles. When the thickness of the electro-diffuse layer (Debye length) is of the same order as the spacing between clay particles, the water diffusivity decreases. Otherwise it is constant at about 2.22+/-0.25x10(-9) m(2)/s. This last result illustrates clearly the effect of electro-chemical properties of smectite on water diffusivity.     

Excitation of analytes and enhancement of emission intensities in a d.c. plasma jet: a critical review leading to proposed mechanistic models

Experimental data and theoretical criteria are used to critically review existing models for analyte emission enhancement in the 3-electrode d.c. plasma (DCP). The analytical zone is characterized as a non-optically thin recombining plasma in partial thermodynamic equilibrium (PTE). Spectrochemical excitation the authors ascribe largely to: (1) argon resonance line radiative transport; (2) inversion of optically pumped argon states; (3) inversion of analyte populations by Franck-Condon collisions with argon; (4) energy cascading in analytes via a multitude of channels. Adding an easily ionized element (EIE): (1) induces additional resonance line radiative transfer; (2) raises electron densities in cooler, analyte-rich plasma margins; (3) locally increases argon optical absorption cross sections via Stark broadening; (4) redistributes ohmic heating. Coupling between the proposed mechanisms is non-linear. Relationships between radiative transfer and collisional redistribution and (1) background suppression by EIE and (2) analyte emission enhancement by helium are also examined. Similarities between DCP and inductively coupled plasma (ICP) excitation mechanisms are noted and practical implications are addressed.     

Electronic structures of WAlO(y) and WAlO(y) (-) (y = 2-4) determined by anion photoelectron spectroscopy and density functional theory calculations

The anion photoelectron spectra of WAlO(y) (-) (y = 2-4) are presented and assigned based on results of density functional theory calculations. The WAlO(2) (-) and WAlO(3) (-) spectra are both broad, with partially resolved vibrational structure. In contrast, the WAlO(4) (-) spectrum features well-resolved vibrational structure with contributions from three modes. There is reasonable agreement between experiment and theory for all oxides, and calculations are in particular validated by the near perfect agreement between the WAlO(4) (-) photoelectron spectrum and a Franck-Condon simulation based on computationally determined spectroscopic parameters. The structures determined from this study suggest strong preferential W-O bond formation, and ionic bonding between Al(+) and WO(y) (-2) for all anions. Neutral species are similarly ionic, with WAlO(2) and WAlO(3) having electronic structure that suggests Al(+) ionically bound to WO(y) (-) and WAlO(4) being described as Al(+2) ionically bound to WO(4) (-2). The doubly-occupied 3sp hybrid orbital localized on the Al center is energetically situated between the bonding O-local molecular orbitals and the anti- or non-bonding W-local molecular orbitals. The structures determined in this study are very similar to structures recently determined for the analogous MoAlO(y) (-)∕MoAlO(y) cluster series, with subtle differences found in the electronic structures [S. E. Waller, J. E. Mann, E. Hossain, M. Troyer, and C. C. Jarrold, J. Chem. Phys. 137, 024302 (2012)].     

Vibrational spectroscopy for glycine adsorbed on silicon clusters: Harmonic and anharmonic calculations for models of the Si(1 0 0)-2 × 1 surface

The vibrational spectroscopy of a glycine molecule adsorbed on a silicon surface is studied computationally, using different clusters as models for the surface. Harmonic frequencies are computed using density functional theory (DFT) with the B3LYP functional. Anharmonic frequency calculations are carried out using vibrational self-consistent field (VSCF) algorithms on an improved PM3 potential energy surface. The results are compared with experiments on Glycine@Si(1 0 0)-2 × 1.

The main findings are: (1) Agreement of the computed frequencies with experiment improves with cluster size. (2) The anharmonic calculations are generally in better agreement with experiment than the harmonic ones. The improvements due to anharmonicity are most significant for hydrogenic stretching. (3) An important part of the anharmonic effects is due to anharmonic coupling between different normal modes of the system. (4) The anharmonic coupling between glycine vibrational modes is much larger than the anharmonic coupling between glycine and “phonon” (cluster) modes.

Implications of the results for surface vibrational spectroscopy are discussed.     

A first-principles study of (R)- and (S)-PPA Molecules on Cu(111)

The adsorption of (R)- and (S)-2-phenylpropionamide (PPA, C(9)H(11)ON) molecules on a Cu(111) surface has been investigated using the density functional method with supercell models. The adsorption orientations of both (R)- and (S)-PPA molecules on the surface are the same: the phenyl rings are approximately parallel to the Cu(111) surface and positioned in the hollow sites, the amino and methyl groups occupy two-bridge sites, and the carbonyl occupies the top site. After the adsorption, the bond lengths in the two enantiomers are almost unchanged, but the changes for two dihedral angles show differences, especially for (R)-PPA molecule. The first angles between the (N,C9,C7) plane and the (C9,C7,C6) plane are 19.4 and 0.7 degrees for (R)- and (S)-PPA molecules, respectively, and the second angles between the (C8,C7,C6) plane and the (C7,C6,C5) plane are 74.8 and 0.4 degrees for (R)- and (S)-PPA molecules, respectively. The adsorption energies of (R)- and (S)-PPA molecules are calculated to be -34 and -26 kJ mol(-1), respectively. The simulated scanning tunneling microscopy (STM) images of (R)- and (S)-PPA molecules on the Cu(111) surface display different features and are coincident with the experimental ones. The interaction between the adsorption molecule and the metal surface is found to be responsible for the discrimination of (R)- and (S)-PPA molecules on the surface.     

Structural analysis of transition metal beta-X substituent interactions. Toward the use of soft computing methods for catalyst modeling

Fuzzy logic and neural network techniques are used to classify intramolecular interactions between transition metals (M) and beta-X substituents in the following structural motif (LnMC(alpha)(A1)(A2)-C(beta)(B1)(B2)X). These interactions are relevant to the direct polymerization of functionalized olefins by Ziegler-Natta (ZN) catalysis. The efficiency and effectiveness of different soft computing techniques are compared. These methods give not only encouraging results with respect to general data mining issues but also insight into the factors that effect interactions between transition metals and beta-X substituents.     

Freezing water in no-man's land

We report homogeneous ice nucleation rates between 202 K and 215 K, thereby reducing the measurement gap that previously existed between 203 K and 228 K. These temperatures are significantly below the homogenous freezing limit, T(H)≈ 235 K for bulk water, and well within no-man's land. The ice nucleation rates are determined by characterizing nanodroplets with radii between 3.2 and 5.8 nm produced in a supersonic nozzle using three techniques: (1) pressure trace measurements to determine the properties of the flow as well as the temperature and velocity of the droplets, (2) small angle X-ray scattering (SAXS) to measure the size and number density of the droplets, and (3) Fourier Transform Infrared (FTIR) spectroscopy to follow the liquid to solid phase transition. Assuming that nucleation occurs throughout the droplet volume, the measured ice nucleation rates J(ice,V) are on the order of 10(23) cm(-3) s(-1), and agree well with published values near 203 K.     

Density functional theory calculations of pressure effects on the vibrational structure of alpha-RDX

Pressure effects on the vibrational structure of alpha-RDX were examined using density functional theory (DFT) up to 4 GPa. The calculated vibrational frequencies at ambient conditions are in better agreement with experimental data than are previous single molecule calculations. The calculations showed the following pressure-induced changes: (i) larger shifts for lattice modes and for internal modes associated with the CH(2) and NO(2) groups as compared to the pressure shifts for modes associated with the triazine ring, (ii) enhancement of mixing between different vibrations, for example, between NN stretching and CH(2) scissor, wagging, twisting vibrations, and (iii) increase in mixing between translational lattice vibrations and the NO(2) wagging vibrations, reducing the distinction between internal and lattice modes. The calculated volume and lattice constants at ambient pressure are larger than the experimental values, due to the inability of the present density functional approach to correctly account for van der Waals forces. Consequently, the pressure-induced frequency shifts of many modes deviate substantially from experimental data for pressures below 1 GPa. With increasing pressure, both the lattice constants and the frequency shifts agree more closely with experimental values.