A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions

A new grid-cell algorithm is presented that permits the fast construction of cutoff-based nonbonded pairlists in molecular simulations under periodic boundary conditions based on an arbitrary box shape. The key features of the method are (1) the use of a one-dimensional mask array (to determine which grid cells contain interacting atoms) that incorporates the effect of periodicity, and (2) the grouping of adjacent interacting cells of the mask array into stripes, which permits the handling of empty cells with a very low computational overhead. Testing of the algorithm on water systems of different sizes (containing about 2000 to 11,000 molecules) shows that the method (1) is about an order of magnitude more efficient compared to a standard (double-loop) algorithm, (2) achieves quasi-linear scaling in the number of atoms, (3) is weakly sensitive in terms of efficiency to the chosen number of grid cells, and (4) can be easily parallelized.     

Probing interfacial characteristics of rubrene/pentacene and pentacene/rubrene bilayers with soft X-ray spectroscopy

The electronic structure of rubrene/pentacene and pentacene/rubrene bilayers has been investigated using soft X-ray absorption spectroscopy, resonant X-ray emission spectroscopy, and density-functional theory calculations. X-ray absorption and emission measurements reveal that it has been possible to alter the lowest unoccupied and the highest occupied molecular orbital states of rubrene in rubrene/pentacene bilayer. In the reverse case, one gets p* molecular orbital states originating from the pentacene layer. Resonant X-ray emission spectra suggest a reduction in the hole-transition probabilities for the pentacene/rubrene bilayer in comparison to reference pentacene layer. For the rubrenepentacene structure, the hole-transition probability shows an increase in comparison to the rubrene reference. We also determined the energy level alignment of the pentacene-rubrene interface by using X-ray and ultraviolet photoelectron spectroscopy. From these comparisons, it is found that the electronic structure of the pentacene-rubrene interface has a strong dependence on interface characteristics which depends on the order of the layers used.     

Computationally derived rules for persistence of C60 nanowires on recumbent pentacene bilayers

The tendency for C(60) nanowires to persist on two monolayers of recumbent pentacene is studied using molecular dynamics (MD) simulations. A review of existing experimental literature for the tilt angle adopted by pentacene on noble metal surfaces shows that studies cover a limited range from 55° to 90°, motivating simulation studies of essentially the entire range of tilt angles (10°-90°) to predict the optimum surface tilt angle for C(60) nanowire formation. The persistence of a 1D nanowire depends sensitively on this tilt angle, the amount of initial tensile strain, and the presence of surface step edges. At room temperature, C(60) nanowires oriented along the pentacene short axes persist for several nanoseconds and are more likely to occur if they reside between, or within, pentacene rows for ? ≤ ～60°. The likelihood of this persistence increases the smaller the tilt angle. Nanowires oriented along the long axes of pentacene molecules are unlikely to form. The limit of stability of nanowires was tested by raising the temperature to 400 K. Nanowires located between pentacene rows survived this temperature rise, but those located initially within pentacene rows are only stable in the range ?(1) = 30°-50°. Flatter pentacene surfaces, that is, tilt angles above about 60°, are subject to disorder caused by C(60) molecules "burrowing" into the pentacene surface. An initial strain of 5% applied to the C(60) nanowires significantly decreases the likelihood of nanowire persistence. In contrast, any appreciable surface roughness, even by half a monolayer in height of a third pentacene monolayer, strongly enhances the likelihood of nanowire formation due to the strong binding energy of C(60) molecules to step edges.     

固相转晶合成含硼CF-2沸石过程中甲胺分子的状态变化

以¹³C MAS NMR与TG-DTG为主要手段,研究了多孔玻璃粉于蒸汽相中转变为含硼CF-2沸石过程中模板剂甲胺分子的状态变化.结果表明甲胺分子经历了三种状态变化:在反应初期,甲胺分子与多孔玻璃表面羟基形成弱相互作用;随着反应进行,一部分弱相互作用的甲胺分子转变为强相互作用的甲胺分子;强相互作用的甲胺分子与硅羟基、铝羟基、硼羟基共同形成CF-2沸石晶核,晶核长大成晶体,甲胺分子进入沸石孔道内,此时存在与多孔玻璃粉表面羟基弱相互作用、强相互作用以及处于沸石孔道内的三种甲胺分子.随着结晶度进一步升高,多孔玻璃表面弱相互作用与强相互作用的甲胺分子依次逐渐消失,最终全部进入CF-2沸石孔道内.孔道内有自由状态和质子化的甲胺分子.SEM照片从形貌上直观地表征了多孔玻璃向CF-2沸石的转变过程.     

Two-dimensional pentacene:3,4,9,10-perylenetetracarboxylic dianhydride supramolecular chiral networks on Ag(111)

Self-assembly of the binary molecular system of pentacene and 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) on Ag(111) has been investigated by low-temperature scanning tunneling microscopy, molecular dynamics (MD), and density functional theory (DFT) calculations. Well-ordered two-dimensional (2D) pentacene:PTCDA supramolecular chiral networks are observed to form on Ag(111). The 2D chiral network formation is controlled by the strong interfacial interaction between adsorbed molecules and the underlying Ag(111), as revealed by MD and DFT calculations. The registry effect locks the adsorbed pentacene and PTCDA molecules into specific adsorption sites due to the corrugation of the potential energy surface. The 2D supramolecular networks are further constrained through the directional CO...H-C multiple intermolecular hydrogen bonding between the anhydride groups of PTCDA and the peripheral aromatic hydrogen atoms of the neighboring pentacene molecules.     

Epitaxial growth of pentacene films on Cu110

The molecular structure of thin pentacene (C(22)H(14)) films grown on a Cu(110) surface has been studied by means of He atom scattering, low energy electron diffraction, thermal desorption spectroscopy, x-ray photoelectron spectroscopy, and x-ray absorption spectroscopy. Depending on the actual film thickness three different crystalline phases have been identified which reveal a characteristic reorientation of the molecular plane relative to the substrate surface. In the monolayer regime the molecules form a highly ordered commensurate (6.5x2) structure with a planar adsorption geometry. For thin multilayers (thickness <2 nm) a second phase is observed which is characterized by a lateral ((-0.65 5.69) ( 1.90 1.37)) structure and a tilting of the molecular plane of about 28 degrees around their long axis which remains parallel to the surface. Finally, when exceeding a thickness of about 2 nm subsequent growth proceeds with an upright molecular orientation and leads to the formation of crystalline films which are epitaxially oriented with respect to the substrate. The present study thus demonstrates that also on metal substrates highly ordered pentacene films with an upright orientation of the molecular planes can be grown. Photoelectron spectroscopy data indicate further that thick films do not grow in a layer-by-layer mode but reveal a significant degree of roughness.     

Pentacene nanorails on Au(110)

We studied the molecular orientation of pentacene monolayer phases on the Au(110) surface by means of near-edge X-ray absorption spectroscopy at the carbon K-shell and scanning tunneling microscopy. The highest coverage phase, displaying a (6 x 8) symmetry, is found to be formed by two types of differently oriented molecules mimicking regular arrays of nanorails. Flat-lying molecules, aligned side-by-side with the long molecular axis along the [001] direction, form long crosstie chains extending in the [110] direction. In between the adjacent flat chains, additional molecules, tilted by 90 degrees around their molecular axis, line up head-to-tail into rails extending along [110]. These molecules are very weakly hybridized with the substrate, as indicated by their lowest unoccupied molecular orbitals, which closely resemble those of the free molecule. The nanorail structure is found to be stable up to 420 K in vacuum and to also remain in place after exposure to air, thus being a template well suited for further self-assembly of organic heterostructures. The tilted quasi-free molecules open the possibility for an optimal lateral pi-coupling to other molecules or molecular assemblies.     

Nickel(II) Bisporphyrin-Fused Pentacenes Exhibiting Abnormal High Stability

A series of largely π-extended multichromophoric molecules including cross-conjugated, half cross-conjugated, conjugation-interrupted and linearly conjugated systems were synthesized and characterized. These multichromophoric molecular systems revealed interesting structural-property relationships. Bisporphyrin-fused pentacenes Pen-1 b and Pen-2 a showed rich redox chemistry with 7 and 8 observable redox states, respectively. The linearly-conjugated bisporphyrin-fused pentacenes ( Pen-1 b and Pen-2 a ) possess much narrower HOMO–LUMO gaps (1.65 and 1.42 eV redox, respectively) and higher HOMO energy levels than those of their pentacene analogues (2.23 and 2.01 eV redox, respectively), similar to those of much less stable hexacenes and heptacenes. An estimated half-life of >945 h was obtained for bisporphyrin-fused pentacene Pen-2 a , which is much longer than that of its pentacene analogue ( BPE-P , half-life, 33 h).     

Orientation of pentacene molecules on SiO2: from a monolayer to the bulk

Near edge x-ray absorption fine structure (NEXAFS) spectroscopy is used to study the orientation of pentacene molecules within thin films on SiO2 for thicknesses ranging from monolayers to the bulk (150 nm). The spectra exhibit a strong polarization dependence of the pi* orbitals for all films, which indicates that the pentacene molecules are highly oriented. At all film thicknesses the orientation varies with the rate at which pentacene molecules are deposited, with faster rates favoring a thin film phase with different tilt angles and slower rates leading to a more bulklike orientation. Our NEXAFS results extend previous structural observations to the monolayer regime and to lower deposition rates. The NEXAFS results match crystallographic data if a finite distribution of the molecular orientations is included. Damage to the molecules by hot electrons from soft x-ray irradiation eliminates the splitting between nonequivalent pi* orbitals, indicating a breakup of the pentacene molecule.     

Solid state effects in the NEXAFS spectra of alkane-based van der Waals crystals: Breakdown of molecular model

Experimental data conclusively shows that the weak van der Waals interactions between alkane molecules, <1.5% the strength of covalent bonding on a per carbon atom basis, modify the carbon 1s near edge X-ray absorption fine structure (NEXAFS) spectrum significantly in ordered solids, both in intensity, spectral shape, peak position, and dichroic signature. This constitutes a further breakdown of the ‘building block’ model, or, more precisely, even a molecular model in interpreting NEXAFS spectra. These observations have significant implications for the interpretation and use of NEXAFS spectra from any crystalline or semi-crystalline macromolecules, small molecules, or other weakly interacting systems.     

Effect of molecule-substrate interaction on thin-film structures and molecular orientation of pentacene on silver and gold

Evaporated pentacene thin films with thicknesses from several nm to 150 nm on gold and silver substrates have been studied by ultraviolet photoelectron spectroscopy (UPS), near-edge X-ray absorption fine structure (NEXAFS), scanning tunneling microscopy (STM), and atomic force microscopy (AFM). It was found that pentacene thin-film structures, particularly their molecular orientations, are strongly influenced by the metal substrates. UPS measurements revealed a distinct change in the valence band structures of pentacene on Au compared to those on Ag, which is attributed to the different packing between adjacent molecules. Using NEXAFS, we observed 74+/-5 degrees and 46+/-5 degrees molecular tilt angles on Ag and Au, respectively, for all measured thicknesses. We propose that pentacene molecules stand up on the surface and form the "thin-film phase" structure on Ag. On Au, pentacene films grow in domains with molecules either lying flat or standing up on the substrate. Such a mixture of two crystalline phases leads to an average tilt angle of 46 degrees for the whole film and the change in valence band structures. STM and distance-voltage (z-V) spectroscopy studies confirm the existence of two crystalline phases on Au with different conducting properties. z-V spectra on the low conducting phase clearly indicate its nature as "thin-film phase".     

A high-resolution near-edge x-ray absorption fine structure investigation of the molecular orientation in the pentacene/poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) pentacene/system

We present x-ray photoemission spectroscopy and highly resolved near-edge x-ray absorption fine structure spectroscopy measurements taken on pentacene thin films of different thicknesses deposited on a spin coated poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) substrate. Thin films of pentacene were prepared by using organic molecular beam deposition in situ using strictly controlled evaporation conditions. Our investigations show that pentacene thin films on PEDOT:PSS are characterized by upright standing molecules. Due to the strong dichroic behavior, the calculated values of the molecular orientation give a clear indication not only of the real molecular arrangement in the films but also of a high orientational order. This high degree of molecular orientation order is a characteristic already of the first layer. The films show the tendency to grow on the PEDOT:PSS substrate following an island-fashion mode, with a relatively narrow intermixing zone at the interface between the pentacene and the polymer blend. The peculiarity of the growth of pentacene on PEDOT:PSS is due to the fact that the substrate does not offer any template for the nucleated films and thus exerts a lateral order toward the crystal structure arrangement. Under these conditions, the upright orientation of the molecules in the films minimizes the energy required for the system stability.     

Products and mechanism of acene dimerization. A computational study

The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso-carbon atoms of the central ring of acene blocks the reactivity of this ring but does not efficiently prevent dimerization through other rings.     

Molecular orientation and film morphology of pentacene on native silicon oxide surface

The growth morphology and mechanism of pentacene films on native Si oxide surface have been studied by using high-resolution electron energy loss spectroscopy (HREELS), X-ray diffraction (XRD), and atomic force microscopy (AFM). Despite the good agreement between our own and the reported XRD results, the previous XRD interpretation that the pentacene molecules are tilt-standing on the substrate cannot explain our HREELS data. The HREELS results show that a substantial portion of the first two layers of pentacene molecules are tilted-standing or randomly oriented, whereas the upper-layer molecules are mostly lying flat to the substrate. AFM reveals that the first two layers of molecules form a flat and smooth surface, but the upper layers show a rough terrace structure with a mean-square roughness equal to the average thickness (without counting the first two layers). This relationship is explained by a theoretical model which assumes the pentacene molecules to remain on a particular molecule layer after arrival. The observed film growth morphology may have significant implication on the performance of electronic devices based on pentacene thin films. A plausible explanation was proposed for the discrepancy between the HREELS-indicated and the XRD-derived molecular orientations.     

Weakly interacting molecular layer of spinning C60 molecules on TiO2 (110) surfaces

The adsorption of C(60), a typical acceptor organic molecule, on a TiO(2) (110) surface has been investigated by a multitechnique combination, including van der Waals density functional calculations. It is shown that the adsorbed molecules form a weakly interacting molecular layer, which sits on the fivefold-coordinated Ti that is confined between the prominent bridging oxygen rows (see figure).     

Molecular orientation of evaporated pentacene films on gold: alignment effect of self-assembled monolayer

Pentacene films deposited on self-assembled monolayers (SAMs) bearing different terminal functional groups have been studied by reflection-absorption IR, grazing angle XRD, NEXAFS, AFM, and SEM analyses. A film with pentacene molecules nearly perpendicularly oriented was observed on Au surfaces covered with an SAM of alkanethiol derivative of X-(CH2)(n)-SH, with X = -CH(3), -COOH, -OH, -CN, -NH(2), C(60), or an aromatic thiol p-terphenylmethanethiol. On the other hand, a film with the pentacene molecular plane nearly parallel to the substrate surface was found on bare Au surface. A similar molecular orientation was found in thinner ( approximately 5 nm) and thicker (100 nm) deposited films. Films deposited on different surfaces exhibit distinct morphologies: with apparently smaller and rod-shaped grains on clean bare Au surface but larger and islandlike crystals on SAM-modified surfaces. X-ray photoemission electron microscopy (X-PEEM) was used to analyze the orientation of pentacene molecules deposited on a SAM-patterned Au surface. With the micro-NEXAFS spectra and PEEM image analysis, the microarea-selective orientation control on Au was characterized. The ability to control the packing orientation in organic molecular crystals is of great interest in fabricating organic field effect transistors because of the anisotropic nature of charge transport in organic semiconducting materials.     

Photophysical properties of dioxolane-substituted pentacene derivatives dispersed in tris(quinolin-8-olato)aluminum(III)

Two novel dioxolane-substituted pentacene derivatives, namely, 6,14-bis-(triisopropylsilylethynyl)-1,3,9,11-tetraoxa-dicyclopenta[b,m]pentacene (TP-5) and 2,2,10,10-tetraethyl-6,14-bis-(triisopropylsilylethynyl)-1,3,9,11-tetraoxa-dicyclopenta[b,m]pentacene (EtTP-5), have been synthesized and spectroscopically characterized. Here, we examine the steady-state and time-resolved photoluminescence (PL) of solid-state composite films containing these pentacene derivatives dispersed in tris(quinolin-8-olato)aluminum(III) (Alq(3)). The films show narrow red emission and high absolute photoluminescence quantum yields (phi(PL) = 59% and 76% for films containing approximately 0.25 mol % TP-5 and EtTP-5, respectively). The F?rster transfer radius for both guest-host systems is estimated to be approximately 33 A. The TP-5/Alq(3) thin films show a marked decrease in phi(PL) with increasing guest molecule concentrations, accompanied by dramatic changes in the PL spectra, suggesting that intermolecular interactions between pentacene molecules result in the formation of weakly radiative aggregates. In contrast, a lesser degree of fluorescence quenching is observed for EtTP-5/Alq(3) films. The measured fluorescence lifetimes of TP-5 and EtTP-5 are similar (approximately 18 ns) at low concentrations but deviate at higher concentrations as aggregation begins to play a role in the TP-5/Alq(3) films. The onset of aggregation in EtTP-5/Alq(3) films occurs at higher guest molecule concentrations (>1.00 mol %). The addition of ethyl groups on the terminal dioxolane rings leads to an increase in the intermolecular spacing in the solid, thereby reducing the tendency for pi-pi molecular stacking and aggregation.     

High‐Yield Excited Triplet States in Pentacene Self‐Assembled Monolayers on Gold Nanoparticles through Singlet Exciton Fission

One of the major drawbacks of organic‐dye‐modified self‐assembled monolayers on metal nanoparticles when employed for efficient use of light energy is the fact that singlet excited states on dye molecules can be easily deactivated by means of energy transfer to the metal surface. In this study, a series of 6,13‐bis(triisopropylsilylethynyl)pentacene–alkanethiolate monolayer protected gold nanoparticles with different particle sizes and alkane chain lengths were successfully synthesized and were employed for the efficient generation of excited triplet states of the pentacene derivatives by singlet fission. Time‐resolved transient absorption measurements revealed the formation of excited triplet states in high yield (172±26 %) by suppressing energy transfer to the gold surface.     

Substituent effects on the electronic characteristics of pentacene derivatives for organic electronic devices: dioxolane-substituted pentacene derivatives with triisopropylsilylethynyl functional groups

The intramolecular electronic structures and intermolecular electronic interactions of 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS pentacene), 6,14-bis-(triisopropylsilylethynyl)-1,3,9,11-tetraoxa-dicyclopenta[b,m]-pentacene (TP-5 pentacene), and 2,2,10,10-tetraethyl-6,14-bis-(triisopropylsilylethynyl)-1,3,9,11-tetraoxa-dicyclopenta[b,m]pentacene (EtTP-5 pentacene) have been investigated by the combination of gas-phase and solid-phase photoelectron spectroscopy measurements. Further insight has been provided by electrochemical measurements in solution, and the principles that emerge are supported by electronic structure calculations. The measurements show that the energies of electron transfer such as the reorganization energies, ionization energies, charge-injection barriers, polarization energies, and HOMO-LUMO energy gaps are strongly dependent on the particular functionalization of the pentacene core. The ionization energy trends as a function of the substitution observed for molecules in the gas phase are not reproduced in measurements of the molecules in the condensed phase due to polarization effects in the solid. The electronic behavior of these materials is impacted less by the direct substituent electronic effects on the individual molecules than by the indirect consequences of substituent effects on the intermolecular interactions. The ionization energies as a function of film thickness give information on the relative electrical conductivity of the films, and all three molecules show different material behavior. The stronger intermolecular interactions in TP-5 pentacene films lead to better charge transfer properties versus those in TIPS pentacene films, and EtTP-5 pentacene films have very weak intermolecular interactions and the poorest charge transfer properties of these molecules.