Chemical Physics Letters (v.598, #C)

Contents (iii-viii).

Display OmittedA computational study of anionic complexes of general formula [F―X⋯CH3⋯Y―F] (X, Y = Cl, Br) predicted minimum energy structures with unusual bonding features. The two F atoms, the halogens X and Y and the central C atom all lie on the same straight line, with the three H atoms forming covalent C―H bonds perpendicular to this straight line. The bonding analysis suggests that the extra negative charge is localized on the central C atom and interacts favourably with the sigma-holes originating from the adjacent F―X and Y―F molecular subunits. This unusual cooperative bonding results in energetically stable complexes.

Oxidized forms of polyene antibiotic amphotericin B by Mariusz Gagoś; Grzegorz Czernel (5-9).
Display OmittedAmphotericin B (AmB) is one of the most important drug for the medical treatment of internal fungal infections. In this work we study electronic absorption and fluorescence properties of AmB in aqueous solution upon adding strong oxidizing agent. Particularly, we focus on the origin of the emission band ∼470 nm, which has been previously assigned to either formation of AmB dimers or to tetraene and pentaenes impurities. We find clear correlation between appearance of this band and oxidation of AmB, therefore, we conclude that the emission with maximum ∼470 nm is mainly related to the oxidation of AmB chromophore.

Display OmittedWe investigate the noncovalent functionalization of metallic single-walled carbon nanotubes (SWCNT) (6,0) by 4,4′-methylene diphenyl diisocyanate (MDI) and toluene-2,4-diisocyanate (TDI) molecules using the density functional theory (DFT) method with van der Waals dispersion correction. The obtained local minima show the dependence between the molecular arrangement of the adsorbates on SWCNT surface and their binding energies. We analyze the interplay between the π–π stacking interactions and isocyanate functional groups. For the analysis of the changes in the electronic structure we calculate the density of states (DOS) and charge density plots.

Display OmittedNon-coherent upconversion, realized by homomolecular triplet–triplet annihilation of a zinc metalloporphyrin absorber, has been measured for the metalloporphyrin adsorbed on metal oxide films (ZrO2, TiO2 and ZrO2/TiO2 mixed oxides) in which the semiconductor conduction band energy lies between the metalloporphyrin’s upconverted and prompt S1 excited states. Upconverted emission was observed for pure and mixed metal oxide films, regardless of the relative energies of the states, indicating electron transfer from upconverted states to the semiconductor was not competitive. Upconversion was attributed to aggregation of the absorber, likely in defects on the films, leading to efficient homomolecular triplet–triplet annihilation.

The OH radical products from unimolecular decay of energized CH2OO and CH3CHOO Criegee intermediates are detected by laser-induced fluorescence shortly after they are formed utilizing 248 nm photolysis of diiodo precursors and subsequent reaction with O2. The OH radicals from both CH2OO and CH3CHOO are produced with average rotational energies of ∼1–2 kcal mol−1. A different mechanism for unimolecular decay of CH3CHOO is evident from noticeably broader OH A-X (1,0) line profiles, which is attributed to Doppler broadening. Modeling of the Doppler profiles suggests that most of the available energy is channeled into translational excitation of the products.

Display OmittedStacking interactions between aromatic molecules (benzene, p-cymene, biphenyl, and di- and tetra-hydrogen anthracene) and G.C and A.T canonical Watson–Crick (WC) base pairs are explored. Two functionals with dispersion corrections: ω-B97XD and B3LYP-D3 are used. For a comparison also the MP2 and B3LYP-D3/PCM methods were used for the most stable p-cymene…WC geometries. It was found that the stacking interaction increases with the size of π-conjugation system. Its extent is in agreement with experimental finding on anticancer activity of Ru(II) piano-stool complexes where intercalation of these aromatic molecules should play an important role. The explored structures are considered as ternary system so that decomposition of the interaction energy to pairwise and non-additivity contributions is also examined.

Effect of isotope substitution in binary liquids with Thermal-Lens spectroscopy by Indrajit Bhattacharyya; Pardeep Kumar; Debabrata Goswami (35-38).
Display OmittedEffect of isotope substitution from the modulation of Thermal-Lens (TL) signals in binary liquid mixtures is explored using femtosecond pump–probe mode-mismatched Z-scan TL spectroscopy. Binary solutions of water and heavy water with pure methanol at various concentrations are used for the study, where pure methanol acts as the TL marker across the different samples. The TL signal is found to be effectively modulated by isotope substitution under the experimental conditions, indicating that TL signal depends on hydrogen bonding.

Display OmittedThe temperature-dependent conductivity of polyaniline emeraldine salt (PAni-ES) was studied by terahertz (THz) time-domain spectroscopy from 80 to 290 K to investigate conduction properties in the THz region. The absorption coefficient and index of refraction increase with temperature. This reflects an increasing conductivity, which indicates a thermally assisted hopping transition. The frequency-dependent behavior of the conductivity is described by using the Mott–Davis model. The model fitting parameter, S, decreases with increasing temperature, indicating a possible correlated barrier hopping mechanism. Lastly, the activation energy at THz frequencies decreases with increasing frequency, suggesting intraband transitions.

Solvent effects on the first hyperpolarizability of retinal derivatives by L.A. Junior; G. Colherinhas; T.L. Fonseca; M.A. Castro (43-47).
Display OmittedMonte Carlo simulation (MC) and quantum mechanics (QM) calculations based on the MP2 method were used to study the first hyperpolarizability (β HRS) of retinal and retinoic acid isomers in protic and aprotic solvents. It is found that the first hyperpolarizability of the isomers can be considerably affected by the nature of solvent. For the all-trans retinal and retinoic acid isomers in methanol, the S-MC/MP2/6-31+G(d) approach predicts for β HRS static values of 56 × 10−30 and 36 × 10−30  esu, respectively, which are in good agreement with the available experimental results.

DFT study of the trioxotriangulene derivatives in bulk state by Luiza Buimaga-Iarinca; Calin G. Floare; Cristian Morari (48-52).
Display OmittedWe present density functional theory investigations on the electronic structure properties for three derivatives of trioxotriangulene that were recently used as electrode materials in Li–ion batteries. We compare the results obtained by standard GGA exchange–correlation functionals with those based on recently developed van der Waals exchange–correlation functionals for the free molecules and bulk structures. This allows us to point out the importance of van der Waals interaction for the stability of the structures as well as the main characteristics of the electronic structures.

Display OmittedThe photochromic behavior of spiropyran molecules is very sensitive to the property of surrounding media. Enhanced isomerization of spiropyran to merocyanine was observed after storing functionalized zeolites under ambient temperature and moisture for an extended period of time. Experimental results based on infrared spectroscopy suggest that the enhanced isomerization is due to an increase in the amount of surface-adsorbed water. The presence of more surface-adsorbed water likely altered the isomerization by stabilizing the merocyanine isomer. This observation was utilized to improve reversibility of the isomerization between spiropyran and merocyanine on NaY zeolite surfaces for potential optical applications.

Free radical pathways for the prebiotic formation of xanthine and isoguanine from formamide by Yassin A. Jeilani; Huyen Thi Nguyen; Beatriz H. Cardelino; Minh Tho Nguyen (58-64).
Free radical pathways for the synthesis of xanthine and isoguanine from formamide were studied using density functional theory (B3LYP/6-311G(d,p)). The proposed mechanisms are complex and appropriate for the non-aqueous scenario of prebiotic reactions. Formation of the carbonyl bond in the nucleobases proceeds through enol-keto tautomerization since the direct formation of the C=O bond is a highly endothermic step. The mechanisms show 2-amino-imidazole as a precursor for nucleobases and polyazaporphyrin. The proposed mechanisms contribute to a further understanding of the origin of biomolecules.

Display OmittedThe pH oscillations related to the protonation/deprotonation process in a room temperature ionic liquid (RTIL)–water system were observed at fixed temperatures. The RTIL was hydrophilic N, N-diethyl-N-methyl-N-2-methoxyethyl ammonium tetrafluoroborate ([DEME][BF4]). The rhythmic oscillations of pH were observed only at a water concentration of approximately 90 mol%, where the equilibrated pH value was approximately 3. In contrast, in the water-poor region from 6 to 10 mol% H2O, the pH was almost constant at approximately 8 within the investigated timeframe. The acid–base properties of the [DEME][BF4]–water mixture are related to particular aggregations in the liquid phase.

Pseudo Jahn–Teller origin of distortion in [6]cycloparaphenylene by Yuichiro Kameoka; Tohru Sato; Takahiko Koyama; Kazuyoshi Tanaka; Tatsuhisa Kato (69-74).
Display OmittedThe instability of the cylindrical D 6 h structure in [6]cycloparaphenylene, the non-zero dihedral angles between adjacent paraphenylene units, is investigated from the viewpoint of the pseudo Jahn–Teller effect, wherein the driving forces are orbital vibronic couplings of the deformation modes between occupied and unoccupied orbitals. We show that the overlap densities between the frontier orbitals including the highest occupied molecular orbital (HOMO) and a certain unoccupied/occupied molecular orbital mainly contribute to the instability. The results of vibronic coupling density analysis justify the strong coupling of the unoccupied orbital with the HOMO.

Display OmittedInteractions of CO2 with CH3SZCHX2 (Z=O, S; X=H, CH3, F, Cl, Br) induce significantly stable complexes with interaction energies from −13.7 to −16.4 kJ mol−1 (MP2/aug-cc-pVTZ//MP2/6-311++G(2d,2p)). Remarkably, some stable shapes of CH3SZCH3⋯CO2 are revealed for the first time. Substitution of two H atoms in a CH3 of CH3SZCH3 by two X alike groups makes CH3SZCHX2⋯CO2 more stable than CH3SZCH3⋯CO2, and their stability increases in the order F < Cl < Br < CH3. The >S=O is stronger than the >S=S in interacting with CO2, and they both can be valuable candidates in the design of CO2-philic materials and in the findings of materials to adsorb CO2.

Display OmittedExciton diffusion length and charge mobility in donor and acceptor materials are important factors for the energy conversion efficiency of organic voltaics. Here, we theoretically analyze these quantities for tetrabenzoporphyrin (BP) and silylmethyl[60] fullerene (SIMEF) that have been exploited for the donor and acceptor of interpenetrating heterojunction organic solar cells. The exciton diffusion length and the charge mobility are calculated by means of density functional theory (DFT) and Fermi’s golden rule. The exciton diffusion length in the BP single crystal is found to be a few hundred nm. The charge mobility in the BP and SIMEF crystals exhibits a significant anisotropy.

Display OmittedDensity functional theory calculations for the structure and IR spectroscopy of deprotonated tyrosine and cysteine molecules in gas phase have been carried out to resolve the on-going debate about the global minimum of deprotonated amino acids. It is found that the global minimum of the deprotonated specie is not always directly produced from the most stable neutral conformer. Depending on the setup, the experimental IR spectroscopy of deprotonated amino acids could only give the information of the local minima of the deprotonated species.

On the stability of [Pb(Proline)]2+ complexes. Reconciling theory with experiment by Fernando Aguilar-Galindo; M. Merced Montero-Campillo; Manuel Yáñez; Otilia Mó (91-95).
Display OmittedSalt-bridge and canonical charge solvated complexes of neutral proline (Pro) and Pb(II), [Pb(Pro)] 2 +, are discussed for the first time. Although thermochemically stable with respect to their corresponding deprotonated forms [Pb(Pro-H)]+, the dicationic complexes are not observed experimentally. Indeed, for the deprotonated complexes a disagreement between IRMPD results and theoretical calculations was reported. We perform an exhaustive DFT assessment to correctly predict the experimental findings, and to rationalize why [Pb(Pro)] 2 + complexes are not observed. The deprotonation is likely to occur through a highly exergonic proton transfer between [Pb(Pro)] 2 + and a water molecule resulting in the observed [Pb(Pro-H)]+ singly charged ion.

Hexapole transmission spectrum of formaldehyde oxide by W.G. Roeterdink; J. Bulthuis; E.P.F. Lee; D. Ding; C.A. Taatjes (96-101).
Display OmittedIn this theoretical study we explore the feasibility to obtain molecular properties of the Criegee intermediate formaldehyde oxide (CH2OO) with hexapole state selection. Ab-initio calculations yielding the rotational constants and dipole moments of formaldehyde oxide are used as input for the simulations. Subsequently the hexapole focusing spectra are simulated for the low field seeking states. The focusing curves are sensitive to the details of the dipole moment, suggesting that the hexapole can be a useful tool to study the molecular properties of formaldehyde oxide, or potentially to select CH2OO for molecular beam scattering or photodissociation measurements.

Display OmittedClusters of tripeptides bound to alkali metal cations are generated through electrospray ionization, and collision-induced dissociation tandem mass spectrometry is carried out. Fragmentation products of peptides bound to small ions are b- and y-type fragments with the ion attached, whereas fragmentation of peptides bound to larger ions leads to complete dissociation of the ion. Density functional theory calculations suggest that the ion–peptide binding energy decreases with both the increasing ion radius and the average distance between the ion and the carbonyl O atoms. There is no apparent relation between the binding energy and the partial ion charge.

Exploring the limits: A low-pressure, low-temperature Haber–Bosch process by Aleksandra Vojvodic; Andrew James Medford; Felix Studt; Frank Abild-Pedersen; Tuhin Suvra Khan; T. Bligaard; J.K. Nørskov (108-112).
Display OmittedThe Haber–Bosch process for ammonia synthesis has been suggested to be the most important invention of the 20th century, and called the ‘Bellwether reaction in heterogeneous catalysis’. We examine the catalyst requirements for a new low-pressure, low-temperature synthesis process. We show that the absence of such a process for conventional transition metal catalysts can be understood as a consequence of a scaling relation between the activation energy for N2 dissociation and N adsorption energy found at the surface of these materials. A better catalyst cannot obey this scaling relation. We define the ideal scaling relation characterizing the most active catalyst possible, and show that it is theoretically possible to have a low pressure, low-temperature Haber–Bosch process. The challenge is to find new classes of catalyst materials with properties approaching the ideal, and we discuss the possibility that transition metal compounds have such properties.