Change of molecular structure in the excited states: A (CNDO/2) hole-potential study on phosphine

Molecular structure of phosphine in a number of excited electronic states is studied using the method of hole-potential within the basic framework of CNDO/2 theory. Effects of including 3d-functions of phosphorus in the basis set on computed molecular geometries, transition energies and inversion barriers in the excited states have been investigated. An attempt is made to rationalise qualitatively the structural changes in the excitedstate in terms of Walsh-type correlation diagram constructed with the eigenvalues of the Fock operator in theV _N-1 potential model. A simple orbital model for predicting the nature of structural changes in the excited states is proposed.     

Characterizing the excited states of large photoactive systems by exciton models

The theoretical investigation of excited state for large photoactive systems plays the fundamental role in understanding various optical processes in material and biological system. Frenkel exciton (FE) model describing the excitation of the whole system as a collective effect of quasi-particles of excitons, that is, bound electron–hole pairs, is well-known as a simple but powerful theoretical scheme to present a clear and insightful physical picture for complicated excited state problems. In this mini-review, we summarize our recent developments of quantum chemical methods based on exciton models and their related applications for large photoactive systems. It is shown that our developed ab initio renormalized exciton model (REM) and block interaction product state (BIPS) schemes provide new efficient and automatic low-scaling excited state methods for both localized and delocalized excited states in large systems. Illustrative examples including simulations of both absorption and emission spectrum in large sized molecular aggregates, indicate the exciton model based methods provide promising computational tools for unravel the mechanism of photophysical and photochemical processes in large photoactive systems.     

The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials

The Dynamo module library has been developed for the simulation of molecular systems using hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials. Dynamo is not a program package but is a library of Fortran 90 modules that can be employed by those interested in writing their own programs for performing molecular simulations. The library supports a range of different types of molecular calculation including geometry optimizations, reaction‐path determinations and molecular dynamics and Monte Carlo simulations. This article outlines the general structure and capabilities of the library and describes in detail Dynamo's semiempirical QM/MM hybrid potential. Results are presented to indicate three particular aspects of this implementation—the handling of long‐range nonbonding interactions, the nature of the boundary between the quantum mechanical and molecular mechanical atoms and how to perform path‐integral hybrid‐potential molecular dynamics simulations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1088–1100, 2000     

Numerical coupled Liouville approach: Application to second hyperpolarizability of molecular aggregate

In our previous study [Int. J. Quant. Chem., to appear], we have developed a novel numerical calculation scheme for a dynamics of quantum network for linear molecular aggregates under intense time‐dependent electric fields. In this approach, each molecule is assumed to be an electric dipole arranged linearly with an angle from the longitudinal axis, and the molecular interactions are taken into account by adding the radiations from these dipoles to the external electric fields. The effects of the radiations from all the dipoles involve the intermolecular distance, the speed of light, retarded polarization, and its first‐ and second‐order time derivatives at the position of each dipole. The quantum dynamics is performed by solving coupled Liouville equations composed of the Liouville equation for each dipole. In the present study, we develop a calculation approach of nonperturbative second hyperpolarizability γ in our novel approach and examine the γ of dimer models composed of two‐state molecules under the one‐photon near resonant intense laser fields. Similar phase transition‐like behavior in the field‐intensity dependence of the γ is observed. We also investigate the second hyperpolarizability spectra in the three‐photon resonant region for dimers composed of three‐state molecules, which mimic the electronic states of allyl cation. Contrary to the one‐photon resonant case, phase transition‐like behavior is not observed in the intensity dependence of γ in the three‐photon resonant region. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 295–306, 1999     

Pteros: Fast and easy to use open‐source C++ library for molecular analysis

An open‐source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open‐source Artistic License from http://sourceforge.net/projects/pteros/ . © 2012 Wiley Periodicals, Inc.     

Dynamic behavior of highly excited molecular states in the strong monochromatic laser fields

The dynamic behavior of highly excited molecular states in an external monochromatic field has been investigated in order to establish the general trends in the Rydberg state manifestations in collisional and radiative processes. The effects of interference between direct (background) and resonant interactions and coupling between the continua on the fine structure of collision cross sections and near-threshold photoabsorption spectra are discussed. Analytical expressions for the widths and intensities of the Rydberg lines induced by mixing the field with other quasistationary states are derived and their dependence on the external field strength and frequency are analyzed. It was found that the appreciable stabilization of isolated Rydberg levels observed previously in superstrong fields is also possible in fields much weaker than atomic fields. The possibility of laser control for the energy averaged cross sections and reaction rate constants are considered. All effects are illustrated for thee ^– + H₂ ⁺ system.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 367–386, March, 1994.This work was supported by the Russian Foundation for Basic ReSearch (Grant No. 93-03-4700).     

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance‐critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix‐based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com . © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

Third‐order nonlinear optical properties of dendritic molecular aggregates: Effects of fractal architecture

We investigate the microscopic third‐order nonlinear optical properties, i.e., the second hyperpolarizabilities (γ), of two different sizes of molecular aggregates with a dendritic, i.e., Bethe‐lattice, structure. One possesses a nonfractal structure, while the other has a fractal structure. The aggregate is treated in a two‐exciton model composed of two‐state monomers coupled to each other by the dipole–dipole interaction. The off‐resonant γ of the aggregates are calculated by the numerical Liouville approach, including relaxation effects. The total γ value is partitioned into the contribution of virtual exciton generation, and its spatial contribution to γ is analyzed in relation to the virtual excitation processes in the perturbation theory. It is found that the intermolecular‐interaction effect enhances both one‐ and two‐exciton‐generation contributions, while the relaxation effect reduces those, although the one‐ and two‐exciton‐generation contributions have mutually opposite signs. From the comparison of spatial contributions to γ between the nonfractal and fractal aggregates, an enhancement of the contribution to γ from the periphery to the core is observed in the fractal structure, while such a feature is not observed in the nonfractal structure. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Ab initio study of molecular structures and excited states in anthocyanidins

The structural and electronic characters of four types of hydroxyl group-substituted anthocyanidins (pelargonidin, cyanidin, delphinidin, and aurantinidin) were examined using quantum chemical calculations. For these cationic molecules, both the planar and non-planar structures in the electronic ground state were determined at the B3LYP/D95 level of theory. We revealed that the planar structure is slightly more stable than the non-planar structure for each molecule. For the optimized planar structures, single excitation-configuration interaction (SE-CI) based on the restricted Hartree-Fock (RHF) wave function was evaluated and the electronic character in the low-excited states was discussed in terms of the MO theory. Symmetry adapted cluster (SAC)/SAC-CI calculations were also carried out to estimate the excitation energies precisely. The results showed that hydroxylation of the phenyl group causes a change in the excitation energies without taking the solvent effects into account. The results are in agreement with spectral experiments and previous MO calculations.     

PyFREC: Software for Förster electronic coupling evaluation in molecular fragments

Electronic couplings are crucial for understanding exciton dynamics and associated energy transfer in artificial and natural chromophores. The proposed PyFREC (Python FRagment Electronic Coupling) software enables evaluation of electronic couplings based on the Förster model. PyFREC features the decomposition of electronic couplings, obtained through quantum chemical calculations, into the orientation and dipole strength components. Furthermore, the variation method to evaluate energies of coupled electronic excited states and delocalization of electronic excitations is implemented in the software. PyFREC has been tested on the S22 benchmark dataset of non‐covalent complexes and water clusters. © 2016 Wiley Periodicals, Inc.     

The excited states of pyrazine: A basis set study

Summary Multiconfigurational second order perturbation theory (CASSCF/CASPT2) has been used to investigate the dependence of computed valence excitation energies and transition moments on the basis sets. Pyrazine has been selected as the test molecule. Atomic normal orbital (ANO) type basis sets are used throughout. Contractions of the structure (4s3p1d/2s) are found to be an optimal compromise between the quality and the size of the calculations and are capable of yielding results virtually identical to more extended basis sets.     

The calculation of ground and excited state molecular polarizabilities: A simple perturbation treatment

Second order perturbation theory has been coupled with the CNDO/S CI method of Del Bene and Jaffé to calculate the ground and excited state polarizabilities of various molecules. It is found that this treatment produces reasonably good polarizabilities with great computational ease.