Quantum chemical prediction for complex organic molecules

Numerous types of quantum chemical calculations and protocols have been successfully applied to computing of small, uncomplicated organic molecules. Here, we argue for the need to shift attention to more challenging molecules that are marked by an interplay of complicating factors such as conformational, tautomeric, steric, and other effects. The challenge is not in choosing the right quantum chemical method and solvation model but in combining the existing methods to simultaneously and accurately describe the breadth of chemical and physical phenomena that give rise to the experimentally observed . The complexity of the phenomena that must be considered begs for the need for a greater automation of prediction workflows. We review our experience with these challenges and outline paths for future progress in the direction of tackling prediction of complex organic molecules.     

Theoretical analysis of electron transport through organic molecules

We present a theoretical study of electron transport through a variety of organic molecules. The analysis uses the Landauer formalism in combination with complex bandstructure and projected densities of states calculations to reveal the main aspects of coherent electronic transport through alkanes, benzene-dithiol, and phenylene-ethynylene oligomers. We examine the dependence of the current on molecule length, the effects of molecule-molecule interactions from film packing, differences in contact geometry, and the influence of phenyl ring rotation on the conductances of phenylene-ethynylene oligomers such as 1,4-bis-phenylethynyl-benzene.     

Ab Initio prediction of possible crystal structures for general organic molecules

The performance of a new crystal packing procedure for the ab initio prediction of possible molecular crystal structures is presented. The method is based upon only molecular information, i.e., no unit cell parameters are assumed to be known. The search for the global crystal energy minimum and all local minima inside an energy window is derived from Monte Carlo simulated annealing methods and has been applied to various organic molecules containing heteroatoms and polar groups. A systematic evaluation of the search method and of the quality of the potential energy function has been established. It is demonstrated that the packing of general organic molecules is possible even with standard force fields like CHARMM provided that the charges defining the electrostatic interactions are based upon physical models rather than transferable empirical parameters. Concepts of crystal packing that were based till now upon assumptions and speculations could be proved or disproved by solving directly the extended global optimization problem related to crystal packing. Crystal structures of molecules as complex as those treated in this article have not been, till now, predicted by a computational approach. In one case, a disagreement between the predicted and experimental structure was evident and, based upon the computations, we suspect that the published structure is the wrong one. © 1992 by John Wiley & Sons, Inc.     

Efficient computational methods for accurately predicting reduction potentials of organic molecules

A simple computational approach for predicting ground-state reduction potentials based upon gas phase geometry optimizations at a moderate level of density functional theory followed by single-point energy calculations at higher levels of theory in the gas phase or with polarizable continuum solvent models is described. Energies of the gas phase optimized geometries of the S0 and one-electron-reduced D0 states of 35 planar aromatic organic molecules spanning three distinct families of organic photooxidants are computed in the gas phase as well as well in implicit solvent with IPCM and CPCM solvent models. Correlation of the D0 - S0 energy difference (essentially an electron affinity) with experimental reduction potentials from the literature (in acetonitrile vs SCE) within a single family, or across families when solvent models are used, yield correlations with r(2) values in excess of 0.97 and residuals of about 100 mV or less, without resorting to computationally expensive vibrational calculations or thermodynamic cycles.     

On the potential dependence of electrosorption of neutral organic molecules

The theories of Frumkin and of Bockris et al. for the interpretation of the potential dependence of electrosorption of neutral molecules, are compared. They give rise to different forms of the function describing the potential or charge dependence of the adsorption equilibrium constant because they are based on different models of the interphase. Neither theory is at variance with thermodynamics, as recently claimed by Damaskin.     

Theoretical methods of investigation of excited states of organic molecules

A brief review of quantum-chemical methods applied to describe excited states of organic molecules is presented. The main emphasis is put on advantages and disadvantages of widely used computational techniques. A brief summary of the performance of such methods and practical recommendations on their use is included.     

Theoretical study of the influence of phosphorus containing substituents on organic molecules

An ab initio study of the importance of the phosphorus atom in PHY, PY₂, POY₂ (Y=–H, –CH₃, –NH₂, –OH and –F) functional groups is presented. Methods like HF, DFT, MP(2,4), QCISD(T), CCSD(T) are used to estimate structural and energetic behaviour and obtain charge distribution. The radicals and their positive and negative ions are considered as well as neutral and negatively charged organic compounds in order to compare these situations. By the use of different properties, the influence of the phosphorus containing groups and the importance of the phosphorus atom in these substituents is discussed and clarified.     

Hydrogen-bonded materials based on organic tautomeric molecules: Theoretical treatment

The crystalline Br, I and CH₃ derivatives of 9-hydroxyphenalenone (5X–9HPO) and their deuteroxy analogues (5X–9DPO) are treated by application of the Ising model approaches. The molecular field parameter (J₀) as well as the tunneling parameter (Ω) are evaluated for each material with the help of different quantum chemistry procedures. As our evaluations show both relations Ω(D)/J₀ and Ω(H)/J₀ are less than unity in the case of 5CH₃–9(H/D)PO derivatives that leads to an appearance of the low-temperature ordered (anti-ferroelectric) phase. A relatively small Ω(D)/J₀ (0.2–0.4) values derived in the case of 5Br– and 5I–9DPO imply the tendency to transition into the similar phase in these species. At the same time a rather large values of Ω(H)/J₀ (0.9–1.7) derived in the case of their hydroxy analogues speak in favor of their quantum paraelectric behavior. The obtained theoretical estimations and conclusions are compared with the available experimental data.     

Electrostatic potential for some non-spherical organic molecules: An oblate-spheroidal dipolar approximation

A spheroidal dipolar expansion is used for the determination of the electrostatic potential due to three non-spherical organic molecules: to-luene, phenol and cyclohexanone. The agreement of experimental facts with the prediction of the most probable reactive sites on each molecule deduced from calculated equipotential maps is discussed.     

Graphical prediction of quantum interference-induced transmission nodes in functionalized organic molecules

Quantum interference (QI) in molecular transport junctions can lead to dramatic reductions of the electron transmission at certain energies. In a recent work [Markussen et al., Nano Lett., 2010, 10, 4260] we showed how the presence of such transmission nodes near the Fermi energy can be predicted solely from the structure of a conjugated molecule when the energies of the atomic p(z) orbitals do not vary too much. Here we relax the assumption of equal on-site energies and generalize the graphical scheme to molecules containing different atomic species. We use this diagrammatic scheme together with tight-binding and density functional theory calculations to investigate QI in linear molecular chains and aromatic molecules with different side groups. For the molecular chains we find a linear relation between the position of the transmission nodes and the side group π orbital energy. In contrast, the transmission functions of functionalized aromatic molecules generally display a rather complex nodal structure due to the interplay between molecular topology and the energy of the side group orbital.     

Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.     

Ground state Pi-electron triplet molecules of potential use in the synthesis of organic ferromagnets

2,3,6,7,10,11-Tris(N,N′-diethylethylenediamino)triphenylene (HET) has been synthesized by a route involving hexabromination of triphenylene, reaction with ethylenediamine, hexa-acetylation, and reduction with diborane. Cyclic voltammetry shows that HET can be reversibly oxidized to a mono-cation HET⁺, a dication HET²⁺, a trication HET³⁺, and a tetraction HET⁴⁺. Beyond that the oxidation is irreversible. The dication HET²⁺ is a ground-state triplet species. This fact, and the low oxidation potential required to produce it, make it of interest in testing proposed mechanism for preparing organic ferromagnetic materials.     

Theoretical mechanistic studies on oxidation reactions of some saturated and unsaturated organic molecules

This account describes the results collected by our group during the last years on some themes of environmental/mechanistic interest. Theoretical quantum-mechanical investigations have been carried out to help clarifying the mechanism of some oxidation reactions, which involve mainly unsaturated but also saturated organics as substrates, and, as reactive oxidants, triplet or singlet dioxygen, hydroxyl, ozone, and nitrogen oxides. Depending on the problem, the calculations are either multi-configurational (as CAS-MCSCF, CAS-PT2, MC-QDPT2), or based on the Density Functional Theory for the heavier systems. Research work has thus been developed along the following lines: hydrocarbon oxidations under atmospheric or combustion conditions; definition of a model for soot particles and their interaction with species as HO, O₂, O₃, NO, NO₂, NO₃, etc.; investigation on the reaction mechanism of ¹Δ_g dioxygen with organic unsaturated systems (cycloaddition and ene reactions).     

Analysis of wave functions for open-shell molecules

During the past decade we have looked at several ways to track the distribution of unpaired electrons during chemical reactions and in different spin states. These methods were inspired by our previous work on singlet di-radicals where the spin density is zero yet there are clearly singly occupied orbitals. More recently we have been concerned with analysis of wave functions for single molecule magnets. This review discusses the mathematical framework by which open-shell systems can be described, in addition to methods that extract the effectively unpaired electron density, the spin state of atoms in a molecule, and other useful properties from a molecular wave function. Some of the difficulties associated with using broken spin Slater determinants to evaluate the exchange coupling parameters in the Heisenberg Hamiltonian are also mentioned.     

Semiempirical prediction of the hyperpolarizabilities for cyanovinyl-substituted donor-acceptor molecules

We present here a systematically theoretical study on the nonlinearities and their structure-property relationship of cyanovinyl-substituted donor-acceptor molecules by virtue of semiem-pirical PM3/AM1-FF approach.Good consistency between measured and calculated hyperpolarizabil-ities is obtained.Results show that conformation has a significant effect on hyperpolarizabilities.The torsion angle change between two conjugated parts of the molecular systems can substantially alter the nonlinearities.The total amount of charge transfer difference from donor to acceptor has been introduced to understand the microscopic nature of the nonlinear optical properties for the title molecules.General guidelines may be sought out in the search of molecules with large values of β Some molecules with large molecular hyperpolarizabilities can be predicted by the optimization for the longer π-electron systems with both acceptor and donor groups.     

Azulene-based organic functional molecules for optoelectronics

Design and synthesis of new organic functional materials with improved performance or novel properties are of great importance in the field of optoelectronics. Azulene, as a non-alternant aromatic hydrocarbon, has attracted rising attention in the last few years. Different from most common aromatic hydrocarbons, azulene has unique characteristics, including large dipole moment, small gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). However, the design and synthesis of azulene-based functional materials are still facing several challenges. This review focuses on the recent development of organic functional materials employing azulene unit. The synthesis of various functionalized azulene derivatives is summarized and their applications in optoelectronics are discussed, with particular attention to the fields including nonlinear optics (NLO), organic field-effect transistors (OFETs), solar cells, and molecular devices.     

One-electron reduction potential for oxygen- and sulfur-centered organic radicals in protic and aprotic solvents

We estimated one-electron reduction potentials of redox-active organic molecules for a spectrum of eight different functional groups (phenoxyl, p-benzoquinone, phenylthiyl, p-benzodithiyl, carboxyl, benzoyloxyl, carbthiyl, and benzoylthiyl) in protic (water) and aprotic (acetonitrile, N,N-dimethylacetamide) solvents. Electron affinities (EA) were evaluated in a vacuum with high level quantum chemical methods using Gaussian3-MP2 (G3MP2) and Becke 3 Lee, Yang, and Parr functional B3LYP with aug-cc-pVTZ basis set. To evaluate one-electron redox potentials, gas-phase free energies were combined with solvation energies obtained in a two-step computational approach. First, atomic partial charges were determined in a vacuum by the quantum chemical method B3LYP/6-31G(d,p). Second, solvation energies were determined, solving the Poisson equation with these atomic partial charges. Redox potentials computed this way, compared to experimental data for the 21 considered organic compounds in different solvents, yielded overall root-mean-square deviations of 0.058 and 0.131 V using G3MP2 or B3LYP to compute electronic energies, respectively, while B3LYP/6-31G(d,p) was used to compute solvation energies.