Control of electron transport using redox‐active core dendrimers

We are constructing a model system to elucidate the molecular structure‐property relationships for attenuation of electron transfer (e.g. electron encapsulation). This information is relevant in bio‐electron transfer schemes and in emerging molecular electronics schemes such as storage of information using individual molecules. Our system consists of an inorganic cluster surrounded by dendritic ligands which act as an organic coating. Although the electrochemical and photophysical properties of a variety of metal clusters have been established, very little has been described on the chemistry on metal clusters.     

Photoluminescence Intensity Fluctuations and Electric‐Field‐Induced Photoluminescence Quenching in Individual Nanoclusters of Poly(phenylenevinylene)

Substantial fluctuations of the fluorescence intensity have been detected for single clusters of poly(phenylenevinylene) containing more than 75 polymer chains or 30 000 monomer units. To the best of our knowledge, this is the first time such fluctuations (which resemble the “blinking” effect in single‐molecule fluorescence) have been reported for such a large molecular ensemble containing several macromolecules. Together with the distinct jumps, smooth fluctuations of the fluorescence intensity, with characteristic times from milliseconds to seconds, were observed. This fact distinguishes the fluorescence behaviour of the polymer clusters from that of other multichromophoric systems such as the single chains of conjugated polymers reported in the literature. The consecutive or simultaneous switching of one or several emitting sites from the “on” to “off” state does not explain the character of the fluctuations observed. We suggest that the quenching of the light‐emitting exciton by a long‐lived species, such as, for example, polarons, plays an important role in these unusual fluctuations. Electric field induced fluorescence quenching differs significantly for different clusters. It is proposed that this fluorescence was mainly quenched by polarons injected from the electrodes in the presence of an electric field. The specific behaviour of each cluster is explained by suggesting a different position of the clusters with respect to the electrodes.     

Density functional studies on hydrogen‐bonded clusters of hydrogen halides and the interaction on halide anions

Density functional theory (DFT) calculations have been performed to study the structures and stability of X^?·(HX)_n=2–5 clusters where X = F, Cl, Br at B3LYP/6‐311++G** level of theory. The presence of halide ions in these clusters disintegrates the hydrogen halide clusters. All the hydrogen halides are then hydrogen bonded to the centrally placed halide ions, thereby forming multiple hydrogen bonds. The interaction energies have been corrected for the basis set superposition error (BSSE) using Boy's counterpoise correction method. Evidence for the destruction of hydrogen bonds in hydrogen halide clusters due to the presence of halide ions is further obtained from topological analysis and natural bond orbital analysis. The chemical hardness and chemical potential have been calculated for all the anion clusters. The above analysis reveals that hydrogen bonding in these systems is not an essentially electrostatic interaction. The nature of the stabilization interactions operative in these multiple hydrogen‐bonded clusters has been explained in terms of many‐body contribution to interaction energies. From these studies, an attempt has been made to understand the nature of the molecular properties resulting from different electronegativities of the halogens. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Essential dynamics for the study of microstructures in liquids

Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic‐molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen‐bonded clusters. © 2014 Wiley Periodicals, Inc.     

PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear d‐ and f‐block complexes

A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc.     

The Role of Interface on the Properties of Cluster Assemblies

Atomic clusters characterized by finite size, low dimensionality, and reduced coordination number exhibit many novel properties that are very different from their bulk. As these clusters are assembled, their properties can be significantly altered due to the interaction of these clusters with each other as well as with their support. This paper provides a brief review of the cluster properties that are affected when clusters are deposited on metallic or organic substrates, isolated in matrices or in zeolite cages, coated with acetate ligands, or simply allowed to self-assemble without the presence of any reactive species. It is shown that the interface between the clusters and their support can play an important role on the properties of clusters as their unique characteristics do.     

Density Functional Theory Investigations on Vibrational Spectra,Molecular Structure,and Properties of the L‐Serine,L‐Cysteine,and L‐Aspartic Acid Molecules

In this paper, we present a thorough investigation of the conformational space to characterize all possible gas‐phase structures of the neutral L‐serine, L‐cysteine, and L‐aspartic acid molecules. A total of 120 trial structures were generated for L‐aspartic acid and 96 trial structures for L‐serine and L‐cysteine by combining all internal single‐bond rotamers. Various combinations of the Hartree–Fock and density functional theory/B3LYP methods with different bases were used to optimize all possible trial structures. The theoretical studies on the structure, harmonic vibrational spectra, and molecular properties of these amino acids are presented. The assignments of the calculated wave numbers resulting from potential energy distributions were performed using the VEDA 4 program to allow a good interpretation of the theoretical vibrational spectra of the title compounds. The fundamental harmonic frequencies were found to be in good agreement with data in the literature. A natural bond orbital analysis was performed to investigate the charge delocalization throughout the molecules for the three test compounds. Moreover, an extensive discussion of the highest occupied molecular orbital–lowest unoccupied molecular orbital energy gap as well as other related molecular properties are reported.     

Theoretical Characterization of Charge Transport in One‐Dimensional Collinear Arrays of Organic Conjugated Molecules

A great deal of interest has recently focused on host–guest systems consisting of one‐dimensional collinear arrays of conjugated molecules encapsulated in the channels of organic or inorganic matrices. Such architectures allow for controlled charge and energy migration processes between the interacting guest molecules and are thus attractive in the field of organic electronics. In this context, we characterize here at a quantum‐chemical level the molecular parameters governing charge transport in the hopping regime in 1D arrays built with different types of molecules. We investigate the influence of several parameters (such as the symmetry of the molecule, the presence of terminal substituents, and the molecular size) and define on that basis the molecular features required to maximize the charge carrier mobility within the channels. In particular, we demonstrate that a strong localization of the molecular orbitals in push–pull compounds is generally detrimental to the charge transport properties.     

PSI3: an open-source Ab Initio electronic structure package

PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis‐set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file‐system‐sizes), especially multi‐index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree‐Fock, multiconfigurational self‐consistent‐field, second‐order Møller‐Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second‐order perturbation theory; coupled cluster frequency‐dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born‐Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open‐source, GNU General Public License. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007     

A program for automatically predicting supramolecular aggregates and its application to urea and porphin

Not only the molecular structure but also the presence or absence of aggregates determines many properties of organic materials. Theoretical investigation of such aggregates requires the prediction of a suitable set of diverse structures. Here, we present the open‐source program EnergyScan for the unbiased prediction of geometrically diverse sets of small aggregates. Its bottom‐up approach is complementary to existing ones by performing a detailed scan of an aggregate's potential energy surface, from which diverse local energy minima are selected. We crossvalidate this approach by predicting both literature‐known and heretofore unreported geometries of the urea dimer. We also predict a diverse set of dimers of the less intensely studied case of porphin, which we investigate further using quantum chemistry. For several dimers, we find strong deviations from a reference absorption spectrum, which we explain using computed transition densities. This proof of principle clearly shows that EnergyScan successfully predicts aggregates exhibiting large structural and spectral diversity. © 2018 Wiley Periodicals, Inc.     

Grcarma: A fully automated task‐oriented interface for the analysis of molecular dynamics trajectories

We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross‐platform, Perl/Tk‐based front‐end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user‐friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root‐mean‐square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free‐open source software available immediately for download. © 2013 Wiley Periodicals, Inc.     

Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase

Collisions between O³⁺ ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum–chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non‐negligible amount of the radical cation monomer is observed. New fragment‐ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.     

Tight binding molecular dynamics studies of GamAsn and AlmAsn clusters

The parametrized tight binding molecular dynamics method is used to study the structures and properties of small GaAs and AlAs clusters. Relative stabilities and ground state properties of GaAs clusters consisting of up to 4 atoms agree with those obtained in previous studies. Similar properties are found for small AlAs clusters. The present study of microclusters of both GaAs and AlAs revealed that the icosahedral structure is unstable for the binary clusters. Stability of such clusters increases monatomically as a function of As to Ga or As to Al ratio.     

The role of protein “Stability patches” in molecular recognition: A case study of the human growth hormone‐receptor complex

Dynamic characteristics of protein surfaces are among the factors determining their functional properties, including their potential participation in protein‐protein interactions. The presence of clusters of static residues—“stability patches” (SPs)—is a characteristic of protein surfaces involved in intermolecular recognition. The mechanism, by with SPs facilitate molecular recognition, however, remains unclear. Analyzing the surface dynamic properties of the growth hormone and of its high‐affinity variant we demonstrated that reshaping of the SPs landscape may be among the factors accountable for the improved affinity of this variant to the receptor. We hypothesized that SPs facilitate molecular recognition by moderating the conformational entropy of the unbound state, diminishing enthalpy–entropy compensation upon binding, and by augmenting the favorable entropy of desolvation. SPs mapping emerges as a valuable tool for investigating the structural basis of the stability of protein complexes and for rationalizing experimental approaches, such as affinity maturation, aimed at improving it. © 2015 Wiley Periodicals, Inc.     

Aggregation‐Induced Emission Properties of Copper Iodide Clusters

The aggregation‐induced emission (AIE) properties of two different copper iodide clusters have been studied. These two [Cu₄I₄L₄] clusters differ by their coordinated phosphine ligand and the luminescent mechanochromic properties are only displayed by one of them. The two clusters are AIE‐active luminophors that exhibit an intense emission in the visible region upon aggregation. The formed particles present luminescent thermochromism comparable to that of the bulk compounds. The observed AIE properties can be attributed to suppression of nonradiative relaxation of the excited states in a more rigid state, in relation to the large structural relaxation of the excited triplet state. The differences observed in the AIE properties of the two clusters can be related to the different ligands. A correlation between the luminescence mechanochromic properties and the AIE effect is not straightforward, but the formation of “soft” molecular solids is a common characteristic that can explain the photoactive properties of these compounds.     

Boosting Size‐Selective Hydrogen Combustion in the Presence of Propene Using Controllable Metal Clusters Encapsulated in Zeolite

A strategy is presented for making metal clusters encapsulated inside microporous solids selectively accessible to reactant molecules by manipulating molecular sieve size and affinity for adsorbed molecules. This expands the catalytic capabilities of these materials to reactions demanding high selectivity and stability. Selective hydrogen combustion was achieved over Pt clusters encapsulated in LTA zeolite (KA, NaA, CaA) in a propene‐rich mixture obtained from propane dehydrogenation, showing pore‐size dependent selectivity and coking rate. Propene tended to adsorb at channels or external surfaces of zeolite, interfering the diffusion of hydrogen and oxygen. Tailoring the surface of LTA zeolite with additional alkali or alkaline earth oxides contributed to narrowing zeolite pore size and their affinity for propene. The thus‐modified Pt@KA catalyst displayed excellent hydrogen combustion selectivity (98.5 %) with high activity and superior anti‐coking and anti‐sintering properties.     

多元多金属含氧簇合物在催化化学中的应用*

多金属含氧簇合物在催化化学中的重要性与日俱增,在原子经济反应和环境友好催化方面有着诱人的实用前景。这类物种的催化活性、理化性质、分子结构和固态体相结构以及制备方法均能在分子水平上给出详细信息,因而被视为混合金属氧化物催化剂的分子设计材料。本文拟对能够直观反映出这种信息的多元多金属含氧簇合物催化的研究作一评述。