Influence of Intermolecular Vibrations on the Electronic Coupling in Organic Semiconductors: The Case of Anthracene and Perfluoropentacene

We have performed classical molecular dynamics simulations and quantum‐chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room‐temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian‐like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry. The calculated distributions have been plugged into Monte‐Carlo simulations of hopping transport, which show that lattice vibrations impact charge transport properties to various degrees depending on the actual crystal structure.     

Structure and electronic properties of deformed single-walled carbon nanotubes: quantum calculations

The electronic properties of single-walled carbon nanotubes (SWCNTs) can be modified by deforming their structure under high pressure. The aim of this study was to use quantum calculations to investigate one such property, the energy band gap, in relation to molecular structures of armchair and zigzag SWCNTs of various sizes and shapes deformed by applied forces. To model the increase in pressure, the degree of flatness (η) of the SWCNTs was adjusted as the primary parameter. The calculations gave accurate C-C bond lengths of the SWCNTs in their distorted states; these distortions significantly affected the electronic properties, especially the energy band gap of the SWCNTs. These results may contribute to a more refined design of new nano-electronic devices.     

Using Molecular Quantum Similarity Measures as Descriptors in Quantitative Structure-Toxicity Relationships

Abstract

In this paper molecular quantum similarity measures (MQSM) are used to describe molecular toxicity and to construct Quantitative Structure-Toxicity Relationships (QSTR) models. This study continues the recently described relationships between MQSM and log P values, which permits to use the theoretical MQSM as an alternative to the empirical hydrophobic parameter in QSPR studies. In addition a new type of MQSM is presented in this work: it is based on the expectation value of electron–electron repulsion energy. The molecular properties studied here, as application examples are aquatic toxicity, toxicology on Bacteria and inhibition of a macromolecule employing four different molecular sets.     

Probing interatomic potentials by ion translational energy spectrometry: A new crossed molecular beams apparatus

This report presents details of the development of a new crossed molecular beams apparatus designed and fabricated to carry out high sensitivity ion translational energy spectrometric investigations of the potential energy surfaces of small molecular species. The translational energy spectrometer is used to carry out experimental studies of ion-neutral reactions resulting in charge stripping of CS⁺ radicals and dissociation of metastable CO²⁺ dications. These results are interpreted in the light of high-levelab initia molecular orbital calculations of the pertinent molecular potential energy functions. New results for the double ionisation energy of CS and the kinetic energy released upon dissociation of specific electronic states of CO²⁺ are presented.     

The effect of confinement on the electronic energy and polarizability of a hydrogen molecular ion

The electronic energy and the polarizability of a confined hydrogen molecular ion in the ground state and the first excited state, for cavities of different volumes, are calculated using the variational method. In the treatment adopted an alternative molecular wave function is introduced with only one variational parameter and based on wave functions used for confined atoms. © 2016 Wiley Periodicals, Inc.     

Molecular electronic virial theorem

The partitioning of the molecular electronic energy into true one-electron quantities defined by a molecular electronic virial theorem (MEVT) is studied for a number of molecules. Since the theorem is derived for exact wavefunctions, its applicability to various ab initio wavefunctions at difierent levels of accuracy is examined. The average percentage deviations of the theorem for near Hartree-Fock, double zeta, STO-6G and STO-3G type wave functions are 0.4, 1.7, 2.3 and 3.3, respectively.     

Indo-Mo Model with s·p Separation

A newly developed self-consistent-field molecular orbital theory is described and tested. The intermediate neglect of differential overlap (INDO) approximation is used, and all interaction integrals are differentiated according to their dependence upon 2s and 2p AO's. The bonding parameter β_l is reformulated so that the model is calibrated to only one specific molecular property, namely, the ionization energy of Hi. We expect that this model will not be biased toward any special families of molecules.     

ESCAPE: A novel approach for a fast estimation of dynamic correlation energies: Application to large organic molecules

Advanced wave function-based quantum chemical ab initio methods, such as CCSD(T), are able to calculate the energies of small- to medium-sized molecules with chemical accuracy. Unfortunately, these methods scale quite unfavorably with the size of the system and are getting too time consuming—and too expensive—for larger molecules. In order to be able to treat larger organic molecules, we propose a novel scheme for a quick and reliable estimate of molecular correlation energies, which we call ESCAPE (ES timation of C orrelA tion energies by P air E nergies). It is based on the pair correlation energies for localized molecular orbitals that have been generated by CCSD[T] and fitted to suitable functional forms. All fit parameters are stored in a large parameter file. Aiming at chemical accuracy (±1 kcal/mol), we have first limited our approach to aliphatic hydrocarbons. The total molecular CCSD[T] correlation energies of a training set of 41 aliphatic hydrocarbons could be reproduced with a mean absolute error (MAE) of 0.56 kcal/mol or 0.11%. A similar accuracy could be obtained for a test set of 11 additional hydrocarbons with up to eight carbon atoms (MAE of 0.65 kcal/mol or 0.09%). In a more critical test, we checked the small energy differences for a set of 13 isomerization reactions. The comparison with experimental data showed that we could reach chemical accuracy as well. Our estimate (MAE of 0.55 kcal/mol) is slightly inferior to the CCSD[T] result (MAE of 0.17 kcal/mol), but superior to SCF, DFT/B3LYP, and DFT/B3LYP + D3. Moreover, in all cases, we obtained the correct sign, that is, the correct equilibrium structure. A similar accuracy could be reached in an application to the three lowest isomers of the C₆₀ molecule. Using the example of a set of eight alcohols, we were able to proof the method's ability for molecules including heteroatoms. Three fast steps are necessary for the application to any aliphatic hydrocarbon or alcohol: (1) An SCF calculation at the selected molecular geometry; it can be fast since a medium size basis set is generally sufficient. (2) The localization of the occupied molecular orbitals and determination of their properties (center of charge and spatial extent). (3) Estimate of the correlation energy using the existing parameter file. © 2019 Wiley Periodicals, Inc.     

分子基逻辑材料*

在适当的条件下分子开关将输入的信息转换为输出信号,利用这一特点,可在分子体系根据二进位布尔逻辑规则实现信号转换。目前,用化学体系进行基本的布尔逻辑功能执行 (PASS、YES、NOT、AND、NAND、OR、NOR、XNOR和INH)都已成为可能。在此基础上,逻辑门的整合与编程,以及更进一步的复杂分子运算开始受到人们的关注。迄今为止,以高灵敏性的荧光输出信号为主,人们在分子水平上设计实现了多种复杂的逻辑电路,包括组合逻辑电路和时序逻辑电路等,并开始涉及信息处理的安全平台设计。本文主要介绍了近年来利用分子荧光开关体系模拟数字逻辑电路过程中所取得的最新进展,对分子逻辑电路研究的热点和问题进行了展望。     

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

Substituent Effect Parameters: Extending the Applications to Organometallic Chemistry

Typically, metal complexes are constituted of an acceptor metal ion and one or more Iigands containing the donor atoms. Accordingly, the properties of a metal complex are equally dependent on the nature of the metal ion and the ligands. Minute structural variations in the ligand will may result in linear changes in the respective energetic parameters and such linear relationships have paramount importance in organometallic chemistry. The variation in ligands is virtually limitless and substantial because of the extent of organic chemistry available for the modelling of desirable ligands, apart from the variation in metal ions. Anyhow, there is still a need for new parameters for the design and quantification of new ligands which in turn leads to the synthesis of metal complexes with possibly predictable chemical properties. Previous studies have demonstrated that quantum chemically derived molecular electrostatic potential (MESP) parameters can be listed as one of the superior quantifiers in this regard, which can act as an effective ligand electronic parameter. The interaction between the ligand part and metal-containing part will be crucial in assessing the reactivity of organometallic complexes. Here we are applying MESP based substituent constants derived from substituted benzenes to forecast the interaction energies in (pyr^*)W(CO)₅, (NHC^*)Mo(CO)₅ and (η⁶-arene^*)Cr(CO)₃ complexes. Ligands and metal ions are varied in each case for better understanding and transparency.     

功能分子体系的设计与构建

功能分子在外界刺激(酸、碱、光等)的诱导下能发生分子构型、构象变化,并引起相应的物理化学性质变化,或能实现特定的功能,例如具有方向性的电子、能量转移,对分子/离子的识别能力的调控,以及光/电开关功能.功能分子的设计是分子材料科学研究的基础.作者将就我们在分子机器,化学传感器等功能分子的设计合成与性质研究领域取得的进展作一总结,并对未来的发展进行了描述.     

Building photoactive molecular-scale wires

Polyalkynylene groups are known to function as excellent electronic conductors at the molecular level. Such moieties have now been used to interconnect redox and photoactive transition metal oligopyridine complexes so that the efficiency of light-induced energy or electron transfer along the molecular axis can be monitored. The important issues that control the effectiveness of electronic coupling through the alkyne are discussed. In particular, attention is given to separating the effects of electron delocalization within the triplet manifold from the more general decoupling of metal-centered and charge-transfer excited states that occurs upon lowering the triplet energy. The role of the auxiliary ligands is considered, as is the effect of nuclearity. Similarly, the size of the nuclear reorganization energy has to be taken into account in a proper discussion of the photophysical properties of such systems. A second issue of importance to the design of photoelectronic devices concerns the use of interspersed groups to modulate the electronic coupling properties of the alkyne spacer. Such electron relays may be aryl hydrocarbons or platinum bis-acetylides, both groups being able to curtail electron flow along the molecular axis.     

The dissociation adiabaticity parameter and the strong field dissociation of HCl+

In earlier work on H2+, we showed how a dissociation adiabaticity parameter, gammaDv identical with (Dv/2Upm)(1/2) (Dv is the dissociation energy from vibrational state v and U(pm) is the molecular ion system's ponderomotive energy), proposed by Walsh et al., can be modified and be a useful indicator of the strong field dissociation regime for a homonuclear diatomic. In the case of H2+, the new adiabaticity parameter, gamma(mol), indicates when a dissociation process can be most easily described as multiphoton above-threshold dissociation (gamma(mol)>1) and when it is better described using barrier-suppressed dissociation (gamma(mol)<1). In the case of a heteronuclear diatomic like HCl+, different electronic states can lead to different dissociation product channels to which are ascribed different gamma(mol) values. We show for a wide range of laser wavelengths and intensities that this adiabaticity parameter successfully predicts the type of dissociation dynamics (multiphoton above-threshold dissociation versus barrier-suppressed dissociation) on each electronic potential curve. We also discover that the dynamics in one electronic state can influence the dynamics in another at the same laser wavelengths and intensities, overriding the predictive capability of an adiabaticity parameter defined for a particular electronic state. Reasonable physical explanations are provided for these overriding cases.     

Tuning of the electronic properties of H‐passivated armchair graphene nanoribbons by mild border oxidation: Theoretical study on periodic models

We report the results of a DFT study of the electronic properties, intended as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, of periodic models of H‐passivated armchair graphene nanoribbons (a‐GNRs) as that synthetized by bottom‐up technique, functionalized by vicinal dialdehydic groups. This material can be obtained by border oxidation in mild and easy to control conditions with ¹Δ_g O₂ as we reported in our previous paper (Ghigo et al., ChemPhysChem 2015, 16, 3030). The calculations show that the two models of border oxidized a‐GNRs (model A, 0.98 nm and model B, 1.35 nm wide) present LUMO and HOMO energies lowered by an extend roughly linearly dependent on the amount of oxygen chemically bound. The frontier orbital energy variations dependence on the % wt of oxygen bound are, for model A: ?0.12 eV for the LUMO and ?0.05 eV for the HOMO; for model B: ?0.15 eV (HOMO) and ?0.06 eV (LUMO). © 2016 Wiley Periodicals, Inc.     

New materials based on thiazolothiazole and thiophene candidates for optoelectronic device applications: theoretical investigations

We report theoretical analysis on the geometries and electronic properties of new conjugated compounds based on thiazolothiazole synthesized by Ando et al. (Synth. Met., 156:327 [13]). The theoretical ground-state geometry and electronic structure of the studied molecules were investigated by the density functional theory (DFT) method at Becke’s three-parameter functional and Lee–Yang–Parr functional (B3LYP) level with 6-31G(d,p) basis set. The effects of the ring structure and the substituents on the geometries and electronic properties of these materials are discussed to investigate the relationship between molecular structure and optoelectronic properties. This investigation was used to drive further syntheses towards compounds more useful as active optoelectronic materials. Theoretical knowledge of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels of the components is basic in studying organic solar cells, so the HOMO, LUMO, and gap energy V _oc (open-circuit voltage) of the studied compounds are calculated and discussed. These properties suggest these materials as good candidates for use in organic dye-sensitized solar cells.     

An extensible interface for QM/MM molecular dynamics simulations with AMBER

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface. © 2013 Wiley Periodicals, Inc.     

Theoretical study of AlC3+

A theoretical study of the AlC₃⁺ species has been carried out. Predictions have been made for some of the molecular properties (geometries, dipole moments, and harmonic vibrational frequencies) which could help in their possible experimental detection. In addition, a topological analysis of the electron density and its associated Laplacian has also been carried out. The global ground state is predicted to be a linear species with ¹Σ electronic state, but a rhombic four‐membered ring (¹A₁) lies close in energy. It seems that both isomers could be accessible to experimental detection. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Electronic reorganization triggered by electron transfer: The intervalence charge transfer of a Fe3+/Fe2+ bimetallic complex

The key role of the molecular orbitals in describing electron transfer processes is put in evidence for the intervalence charge transfer (IVCT) of a synthetic nonheme binuclear mixed‐valence Fe³⁺/Fe²⁺ compound. The electronic reorganization induced by the IVCT can be quantified by controlling the adaptation of the molecular orbitals to the charge transfer process. We evaluate the transition energy and its polarization effects on the molecular orbitals by means of ab initio calculations. The resulting energetic profile of the IVCT shows strong similarities to the Marcus' model, suggesting a response behaviour of the ensemble of electrons analogue to that of the solvent. We quantify the extent of the electronic reorganization induced by the IVCT process to be 11.74 eV, a very large effect that induces the crossing of states reducing the total energy of the transfer to 0.89 eV. © 2015 Wiley Periodicals, Inc.