cclib: a library for package-independent computational chemistry algorithms

There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum.     

Cuby: An integrative framework for computational chemistry

Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows. For users, Cuby provides a unified and userfriendly way to automate their work, seamlessly integrating calculations carried out in different computational chemistry programs. For example, the QM/MM module allows combining methods across the interfaced programs and the builtin molecular dynamics engine makes it possible to run a simulation on the resulting potential. For programmers, it provides high‐level, object‐oriented environment that allows rapid development and testing of new methods and computational protocols. The Cuby framework is available for download at http://cuby4.molecular.cz . © 2016 Wiley Periodicals, Inc.     

JACOB: An enterprise framework for computational chemistry

Here, we present just a collection of beans (JACOB): an integrated batch‐based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user‐specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application‐programming interface provides a set of generic tools for processing large‐scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob . © 2013 Wiley Periodicals, Inc.     

The unimolecular chemistry of protonated glycine and the proton affinity of glycine: a computational model

The potential energy hypersurface of protonated glycine, GH⁺, has been investigated. The calculated G2(MP2) value for the proton affinity (PA) of glycine, PA _calc=895kJ mol⁻¹, is in good agreement with the experimental value which has been estimated to lie in the range 864kJ mol⁻¹ < PA _exp <891kJ mol⁻¹. Ab initio quantum chemical calculations of relevant parts of the potential energy surface of GH⁺ give a reaction model which is consistent with the observed mass spectrometric fragmentation pattern. The lowest energy unimolecular reactions of GH⁺ are two distinct processes: (1) loss of CO, which has a substantial barrier for the reverse reaction, and (2) loss of CO plus H₂O, which has no barrier for the reverse reaction. Received: 15 November 1996 / Accepted: 6 May 1997     

Excitation energy calculation of conjugated hydrocarbons: a new Pariser-Parr-Pople model parameterization approaching CASPT2 accuracy

A new parameterization for the Pariser-Parr-Pople (PPP) model for conjugated hydrocarbons is proposed in this work. The distance-dependence of PPP parameters are obtained from CASPT2 ground state and low-lying excited state energies of ethylene and its cation at various C-C single bond lengths and are fitted to a set of carefully chosen mathematical functions. Our new PPP model is applied to the calculation of vertical singlet-triplet energy gaps and the excitation energies for low-lying π→π(*) valence excitations in various π-conjugated molecules. Results with the new PPP model are consistently better than the standard PPP model in use. It often surpasses density functional theory and single-reference excited state methods such as configuration interaction singles or time-dependent density functional theory in terms of its accuracy and agrees reasonably well with high-level theories or experiments.     

A hybrid ab initio/free electron computational model for conjugated dye molecules: Simple cyanines and oxonols

Justifications developed for the application the free electron model to the π‐orbitals of conjugated molecules suggest that the optical properties of these molecules would be well described by a one‐dimensional free electron model with a potential chosen to reproduce the energy level spacing of the ground state occupied π‐orbitals. Such a hybrid ab initio/free electron modeling approach, where the free electron potential parameters are optimized on a molecule‐by‐molecule basis, is developed, and applied to a series of simple cyanine and oxonol dyes. The ensuing predictions for λ_max, oscillator strengths, and redox properties compare well to available experimental information. Two important strengths of this approach are that no explicit calculations of the excited electronic state are required, and that the ab initio determination of the occupied π‐orbital level spacing considers all the electrons (π and σ) of the entire molecule in a specified geometry, environment, etc. This second characteristic gives the ability to efficiently model modifications of the optical properties of conjugated molecules resulting from chemical and/or physical modifications occuring within and remote to the conjugated region of the molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 943–953, 2000     

Interstellar chemistry: a strategy for detecting polycyclic aromatic hydrocarbons in space

Polycyclic aromatic hydrocarbons (PAHs) have long been postulated as constituents of the interstellar gas and circumstellar disks. Observational infrared emission spectra have been plausibly interpreted in support of this hypothesis, but the small (or zero) dipole moments of planar, unsubstituted PAHs preclude their definitive radio astronomical identification. Polar PAHs, such as corannulene, thus represent important targets for radio astronomy because they offer the possibilities of confirming the existence of PAHs in space and revealing new insight into the chemistry of the interstellar medium. Toward this objective, the high-resolution rotational spectrum of corannulene has been obtained by Fourier transform microwave spectroscopy, and the dipole moment (2.07 D) of this exceptionally polar PAH has been measured by exploiting the Stark effect.     

Network visualization system for computational chemistry

Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are: Network support due to built-in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems. The possibility of working with output files in real time mode. The possibility of animation from an output file during all steps of optimization. The quick processing of huge volumes of data. The development of custom interfaces.     

Array files for computational chemistry: MP2 energies

A simple message‐passing implementation for distributed disk storage, called array files (AF), is described. It is designed primarily for parallelizing computational chemistry applications but it should be useful for any application that handles large amounts of data stored on disk. AF allows transparent distributed storage and access of large data files. An AF consists of a set of logically related records, i.e., blocks of data. It is assumed that the records have the typical dimension of matrices in quantum chemical calculations, i.e., they range from 0.1 to ～32 MB in size. The individual records are not striped over nodes; each record is stored on a single node. As a simple application, second‐order Møller‐Plesset (MP2) energies have been implemented using AF. The AF implementation approaches the efficiency of the hand‐coded program. MP2 is relatively simple to parallelize but for more complex applications, such as Coupled Cluster energies, the AF system greatly simplifies the programming effort. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007.     

Adsorption and structure of hydrocarbons in MCM-41: a computational study

The adsorption of linear, branched, and cyclic hydrocarbons in MCM-41 is studied using Configurational Bias Monte Carlo simulations. A new computational model for MCM-41 is proposed which, although simple, is able to predict adsorption isotherms which are in agreement with the scarce experimental data. The structure of the adsorbed phase is analyzed and found to be similar to that of studies using small, hard spheres trapped in pores. The adsorption of mixtures is investigated, and the adsorption hierarchy is discussed. The structure of the adsorbed mixture is revealed and shows that all components of the mixture exhibit structure, even if they are only adsorbed in small quantities. Finally, the model is modified to include surface roughness and the effect on the adsorption isotherms and structure of the adsorbed phase is discussed.     

Enumeration of conjugated hydrocarbons: Hollow hexagons revisited

The numbers of nonisomorphic hollow hexagons are expressed in terms of a generating function.     

Parametrization of the equations-of-motion method for conjugated hydrocarbons

The equations-of-motion (EOM ) method has been parametrized for the evaluation of the “π → π*” transition energies and moments of conjugated hydrocarbons. In this new semiempirical scheme, the effect of the dynamical screening by σ electrons is explicitly included.     

Photoactive donor-acceptor conjugated macrocycles: New opportunities for supramolecular chemistry

The design and synthesis of photoactive macrocyclic molecules continue to attract attention because such species play important roles in supramolecular chemistry as well as photoelectronic applications. Donor-acceptor (D-A) conjugated macrocycles are an emerging class of photoactive molecules due to their D-A conjugated structural characteristics and tunable optical properties. In addition, the well-defined cavities in such D-A macrocycles endow them with versatile host-guest properties. In this review, we provide a comprehensive summary of D-A conjugated macrocycle chemistry, detailing recent progress in the area of synthetic methods, optical properties, host-guest chemistry and applications of the underlying chemistry to chemical sensors, bioimaging and photoelectronic devices. Our objective is to provide not only a review of the fundamental findings, but also to outline future research directions where D-A conjugated macrocycles and their constructs may have a role to play.     

New photo- and electroluminescent conjugated copolyfluorenes with 7,8,10-triarylfluoranthene units in the backbone

A new monomer, the dibromo derivative of fluoranthene 1-[7,10-bis(4-bromophenyl)fluoranthen-8-yl]pyrene, is synthesized and used to prepare three new copolyfluorenes containing 3, 5, and 10 mol % 7,8,10-triarylfluoranthene groups via the Yamamoto reaction. The number-average molecular masses and polydispersities of the polymers vary in ranges 41900?C78900 and 2.7?C3.5, respectively. All polymers are soluble in common organic solvents, and their glass-transition temperatures are from 95 to 115°C. Temperatures corresponding to a 10% loss in weight during heating in argon and air are in the ranges 420?C435 and 405?C415°C, respectively. The photoluminescence spectra of the polymers exhibit strong blue emission with a maximum at 418 nm, whereas the absorption spectra show characteristic peaks at 351?C357 nm. All polymers possess reversible or partially reversible redox behavior owing to high electric activity and demonstrate redox pairs at 1.51 eV (oxidation) and ?2.09 eV (reduction).     

Switching of molecular insertion in a cyclic molecule via photo- and thermal isomerization

Two new cyclic ligands were synthesized: a ligand with two trans-azobenzene moieties and one bipyridine moiety, trans(2)-oAB-O13, and a ligand with two trans-azobenzene moieties and two bipyridine moieties, trans(2)-oAB-bpy. Both ligands underwent reversible trans-cis isomerization at the azobenzene moieties. The mole ratios of the trans(2) form:trans-cis form:cis(2) form, evaluated by (1)H NMR spectroscopy of the photostationary states prepared by 1 h illumination, were 0.13:0.27:0.60 (365 nm irradiation) and 0.41:0.47:0.12 (436 nm irradiation) for oAB-O13, and 0.18:0.12:0.70 (365 nm irradiation) and 0.36:0.43:0.21 (436 nm irradiation) for oAB-bpy. When trans(2)-oAB-O13 was mixed with Cu(I), both the bipyridine units and the polyether chains coordinated to the copper center. Addition of a noncyclic bipyridine ligand, trans(2)-oAB-2OH, afforded a bis(bipyridine)copper(I) complex, [Cu(trans(2)-oAB-O13)(trans(2)-oAB-2OH)]BF(4). The bis(bipyridine) ligand, trans(2)-oAB-bpy, formed a 1:1 complex with Cu(I), [Cu(trans(2)-oAB-bpy)]BF(4). [Cu(cis(2)-oAB-bpy)]BF(4) did not undergo the ligand substitution reaction with a noncyclic ligand with two azobenzene moieties and one bipyridine moiety, oAB, whereas its thermal isomerization in the presence of oAB caused the formation of [Cu(trans(2)-oAB-bpy)(trans(2)-oAB)]BF(4), indicating that the isomerization and ligand exchange reactions synchronized via a conformational change of the cyclic ligand.