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.     

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.     

Gabedit—A graphical user interface for computational chemistry softwares

Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, converting, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabedit. Some molecular properties of interest are processed directly from the output of the computational chemistry programs; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential, nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can display electronic circular dichroism, UV–visible, infrared, and Raman‐computed spectra after a convolution. Gabedit can generate a Povray file for geometry, surfaces, contours, and color‐coded planes. Output can be exported to a selection of popular image and vector graphics file formats; the program can also generate a series of pictures for animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated. Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at http://gabedit.sourceforge.net/ . © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

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.     

Open Chemistry,JupyterLab, REST,and quantum chemistry

Quantum chemistry must evolve if it wants to fully leverage the benefits of the internet age, where the worldwide web offers a vast tapestry of tools that enable users to communicate and interact with complex data at the speed and convenience of a button press. The Open Chemistry project has developed an open‐source framework that offers an end‐to‐end solution for producing, sharing, and visualizing quantum chemical data interactively on the web using an array of modern tools and approaches. These tools build on some of the best open‐source community projects such as Jupyter for interactive online notebooks, coupled with 3D accelerated visualization, state‐of‐the‐art computational chemistry codes including NWChem and Psi4, and emerging machine learning and data mining tools such as ChemML and ANI. They offer flexible formats to import and export data, along with approaches to compare computational and experimental data.     

Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach

Peptides bound to MHC molecules on the surface of cells convey critical information about the cellular milieu to immune system T cells. Predicting which peptides can bind an MHC molecule, and understanding their modes of binding, are important in order to design better diagnostic and therapeutic agents for infectious and autoimmune diseases. Due to the difficulty of obtaining sufficient experimental binding data for each human MHC molecule, computational modeling of MHC peptide-binding properties is necessary. This paper describes a computational combinatorial design approach to the prediction of peptides that bind an MHC molecule of known X-ray crystallographic or NMR-determined structure. The procedure uses chemical fragments as models for amino acid residues and produces a set of sequences for peptides predicted to bind in the MHC peptide-binding groove. The probabilities for specific amino acids occurring at each position of the peptide are calculated based on these sequences, and these probabilities show a good agreement with amino acid distributions derived from a MHC-binding peptide database. The method also enables prediction of the three-dimensional structure of MHC-peptide complexes. Docking, linking, and optimization procedures were performed with the XPLOR program [1].     

Origin of diastereocontrol in the oxy-Michael reactions of delta-lactol anions: a computational and experimental study

The diastereoselectivity in the alkylation and Michael addition of "naked" 6-substituted delta-lactolates has been studied by density functional (B3LYP) calculations with ab initio (MP2) energy refinements. The resulting proposed model for the origins of stereocontrol in this reaction has been tested by experiment. The reactions lead to a high cis diastereoselectivity across the THP ring due to the preference for both the alkoxide and the 6-substituent to sit equatorial in the alkylation transition structure. In the oxy-Michael addition of these lactolates to beta-substituted nitroolefins, we propose that the high diastereoselectivity beta- to the nitro group is a result of a combination of steric, stereoelectronic and solvation factors.     

Novel nonperipheral octa-3-hydroxypropylthio substituted metallo-phthalocyanines: synthesis,characterization, and investigation of their electrochemical,photochemical and computational properties

The current study describes the synthesis, electrochemical, computational, and photochemical properties of octa (3-hydroxypropylthio) substituted cobalt (II) ( 4 ), copper (II) ( 5 ), nickel (II) ( 6 ) and zinc(II) ( 7 ) phthalocyanine derivatives. These novel compounds were characterized by elemental analysis,¹H,¹³C NMR, FT-IR, UV-Vis, and MS. The redox behaviors of these metallo-phthalocyanines were investigated by the cyclic voltammetric method. The optimized molecular structure and gauge-including atomic orbital (GIAO)¹H and¹³C NMR chemical shift values of these phthalocyanines in the ground state had been calculated by using B3LYP/6–31G(d,p) basis set. The outcomes of the optimized molecular structure were given and compared with the experimental NMR values. The photochemical properties including photodegradation and singlet oxygen generation of zinc(II) phthalocyanine were studied in DMSO solution for the determination of its photosensitizer behaviors.     

Amination with Pd-NHC complexes: rate and computational studies involving substituted aniline substrates

The amination of aryl chlorides with various aniline derivatives using the N-heterocyclic carbene-based Pd complexes Pd-PEPPSI-IPr and Pd-PEPPSI-IPent (PEPPSI=pyridine, enhanced precatalyst, preparation, stabilization, and initiation; IPr=diisopropylphenylimidazolium derivative; IPent= diisopentylphenylimidazolium derivative) has been studied. Rate studies have shown a reliance on the aryl chloride to be electron poor, although oxidative addition is not rate limiting. Anilines couple best when they are electron rich, which would seem to discount deprotonation of the intermediate metal ammonium complex as being rate limiting in favour of reductive elimination. In previous studies with secondary amines using PEPPSI complexes, deprotonation was proposed to be the slow step in the cycle. These experimental findings relating to mechanism were corroborated by computation. Pd-PEPPSI-IPr and the more hindered Pd-PEPPSI-IPent catalysts were used to couple deactivated aryl chlorides with electron poor anilines; while the IPr catalysis was sluggish, the IPent catalyst performed extremely well, again showing the high reactivity of this broadly useful catalyst.     

Engaging undergraduate students in computational chemistry research: A tutorial for new assistant professors

In this article, we provide advice and insights, based on our own experiences, for computational chemists who are beginning new tenure-track positions at primarily undergraduate institutions. Each of us followed different routes to obtain our tenure-track positions, but we all experienced similar challenges when getting started in our new position. In this article, we discuss our approaches to seven areas that we all found important for engaging undergraduate students in our computational chemistry research, including setting up computational resources, recruiting research students, training research students, designing student projects, managing the lab, mentoring students, and student conference participation.     

Latrunculin analogues with improved biological profiles by "diverted total synthesis": preparation, evaluation, and computational analysis

Deliberate digression from the blueprint of the total syntheses of latrunculin A (1) and latrunculin B (2) reported in the accompanying paper allowed for the preparation of a focused library of "latrunculin-like" compounds, in which all characteristic structural elements of these macrolides were subject to pertinent molecular editing. Although all previously reported derivatives of 1 and 2 were essentially devoid of any actin-binding capacity, the synthetic compounds presented herein remain fully functional. One of the designer molecules with a relaxed macrocyclic backbone, that is compound 44, even surpasses latrunculin B in its effect on actin while being much easier to prepare. This favorable result highlights the power of "diverted total synthesis" as compared to the much more widely practiced chemical modification of a given lead compound by conventional functional group interconversion. A computational study was carried out to rationalize the observed effects. The analysis of the structure of the binding site occupied by the individual ligands on the G-actin host shows that latrunculin A and 44 both have similar hydrogen-bond network strengths and present similar ligand distortion. In contrast, the H-bond network is weaker for latrunculin B and the distortion of the ligand from its optimum geometry is larger. From this, one may expect that the binding ability follows the order 1 >/= 44 > 2, which is in accord with the experimental data. Furthermore, the biological results provide detailed insights into structure/activity relationships characteristic for the latrunculin family. Thus, it is demonstrated that the highly conserved thiazolidinone ring of the natural products can be replaced by an oxazolidinone moiety, and that inversion of the configuration at C16 (latrunculin B numbering) is also well accommodated. From a purely chemical perspective, this study attests to the maturity of ring-closing alkyne metathesis (RCAM) catalyzed by a molybdenum alkylidyne complex generated in situ, which constitutes a valuable tool for advanced organic synthesis and natural product chemistry.     

Enantioselective and diastereoselective Tsuji-Trost allylic alkylation of lactones: an experimental and computational study

The Tsuji-Trost protocol has been successfully employed for the allylic alkylation of preformed lactone enolates. It has been demonstrated that this Pd-catalyzed reaction can be carried out in an enantio- and diastereoselective manner. The use of additives, such as LiCl, was found to be crucial for reaching high levels of product selectivity. For one particular pair of reactants, density functional theory was used to investigate the mechanism of the nucleophilic addition. Among the five pathways considered, the reaction between an (allyl)Pd(BINAP) complex and a LiCl-lithium enolate adduct is predicted to be the most likely route for C-C bond formation. LiCl plays a key role as the connecting link between the noble metal and the enolate in the kinetically favored transition state. The computed diastereoselectivity ratio is in good agreement with the experimentally observed value.     

Protonated silanoic acid HSi(OH)2+ and its neutral counterpart: a tandem mass spectrometric and CBS-QB3 computational study

Protonated silanoic acid, HSi(OH)₂⁺, 1a ⁺, is cleanly generated by the dissociative electron ionization of triethoxysilane, HSi(OC₂H₅)₃, and tetraethoxysilane, Si(OC₂H₅)₄. This follows from tandem mass spectrometric experiments and CBS-QB3 model chemistry calculations. The calculations predict that 1a ⁺ (ΔH_f(298 K) = 205 kJ mol⁻¹) is separated by high barriers from its isomers HOSiOH₂⁺, 1b ⁺ and HSi(O)OH₂⁺, 1c ⁺. Low-energy (metastable) ions 1a ⁺ dissociate by loss of H₂O via the pathway 1a ⁺ → 1b ⁺ → SiOH⁺ + H₂O. Analysis of the metastable peak for this process confirms that the isomerization step 1a ⁺ → 1b ⁺ is rate determining. The calculations further predict that the incipient ions 1b ⁺ communicate via a low barrier with the proton-bound dimer SiO···H···OH₂⁺, 1d ⁺. This dimer ion is much lower in energy than its counterpart OSi···H···OH₂⁺, 1e ⁺, which is calculated to be only marginally stable. A comparison of the potential energy diagram for the silicon-containing ions 1a ⁺– 1e ⁺ with that of their carbon analogues reveals that the dissociation chemistries of HSi(OH)₂⁺ and HC(OH)₂⁺ are only superficially similar. Neutralization–reionization experiments confirm the theoretical prediction that the HSi(OH)₂^• radical (ΔH_f(298 K) = −455 kJ mol⁻¹) is a stable species in the rarefied gas phase. However, owing to a mismatch of Franck–Condon factors a large fraction of the neutralized ions dissociates by loss of H^• yielding Si(OH)₂. Copyright © 2004 John Wiley & Sons, Ltd.     

Integrating social and environmental justice into the chemistry classroom: a chemist’s toolbox

ABSTRACT

Although the chemical enterprise has provided numerous contributions to humanity, unintended consequences contribute to a disproportionate exposure of hazardous chemicals to certain populations based on race and socioeconomic status. Integrating concepts of social and environmental justice within chemistry curriculum provides an educational framework to help mitigate these impacts by training the next generation of chemists with justice-centered and green chemistry principles to guide their future work. Green and sustainable chemistry technologies can contribute to social equity and environmental justice. However, equity and social justice have only recently become a significant part of the green chemistry conversation. This article summarizes how the authors have explored issues of equity and environmental justice with the green and sustainable chemistry community. It offers a toolbox for college and university instructors containing foundational language, research, and idea-generation that can be used to strengthen the transition of a traditional chemistry curriculum toward a justice-centered one.     

Selective Modification for Red-Shifted Excitability: A Small Change in Structure,a Huge Change in Photochemistry

We developed three bathochromic, green-light activatable, photolabile protecting groups based on a nitrodibenzofuran (NDBF) core with D-π-A push–pull structures. Variation of donor substituents (D) at the favored ring position enabled us to observe their impact on the photolysis quantum yields. Comparing our new azetidinyl-NDBF (Az-NDBF) photolabile protecting group with our earlier published DMA-NDBF, we obtained insight into its excitation-specific photochemistry. While the “two-photon-only” cage DMA-NDBF was inert against one-photon excitation (1PE) in the visible spectral range, we were able to efficiently release glutamic acid from azetidinyl-NDBF with irradiation at 420 and 530 nm. Thus, a minimal change (a cyclization adding only one carbon atom) resulted in a drastically changed photochemical behavior, which enables photolysis in the green part of the spectrum.