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.     

Undergraduate women empowering women in computational chemistry: Three perspectives

The undergraduate computational chemistry research group headed by Mauricio Cafiero at Rhodes College has a history of including, promoting, and supporting women in this predominantly male field. Alums of this research group from 2004 to 2019 include nine M.Ds, two science researchers, two Ph.D.s, one secondary teacher, two pharmacists, a physical therapist, two nurses, six current medical school students, and five current science graduate students. They have produced 18 peer-reviewed publications with female undergraduate first authors and over 100 conference presentations, including 9 international conference presentations. While Professor Cafiero does all he can to support these students, he attributes the continuous success of the group in recruiting, retaining, and supporting these women to the students themselves. The students' success and visibility on campus helps to recruit new students. The heavy presence of women in this group provides a strong support system for women who may otherwise feel isolated in a male-dominated field; and these support groups provide models and support for women to overcome common obstacles that women in science face. We will profile three recent graduates who will discuss how the above points affected them during their time in the research group and discuss their experience in the context of some literature on women in Science, Technology, Engineering and Mathematics.     

Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry (MERCURY)

The molecular education and research consortium in undergraduate computational chemistry (MERCURY) consortium, established in 2000, has contributed greatly to the scientific development of faculty and undergraduates. The MERCURY faculty peer-reviewed publication rate from 2001 to 2019 of 1.7 papers/faculty/year is 3.4 times the rate of the physical science faculty at primarily undergraduate institutions. We have worked with over 1000 students on research projects since 2001, and 75% of our undergraduate research students have been under-represented in chemistry, either female or students of color. Approximately half of our alumni attend graduate school for the purpose of obtaining advanced degrees in STEM fields, and two-thirds are female and/or students of color. We have had more than 1600 attendees at 18 MERCURY conferences, including 111 invited speakers, 61 of whom have been female and/or faculty of color. In this paper, the research accomplishments, transformational outcomes, and scientific productivity of the MERCURY faculty are highlighted.     

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     

Using a lab wiki for longevity and knowledge transfer in undergraduate research

Continuity in research group collective knowledge is critical for running a successful research program, but in an undergraduate research lab, this can be particularly challenging. A wiki site dedicated to the research laboratory, a lab wiki, can bridge gaps in student-to-student knowledge transfer and contribute to the longevity of a research program. A lab wiki is an organized, easily accessible, collaborative resource that can contain tutorials, group-specific directions, links to resources, and guides to writing papers or proposals. The wiki language is easy for students to pick up and contributes to their participation in preserving group knowledge. This tutorial introduces the concept of a lab wiki, the advantages of it, example content, and practical implementation advice.     

Recent developments in computer vision-based analytical chemistry: A tutorial review

Chemical analysis based on colour changes recorded with imaging devices is gaining increasing interest. This is due to its several significant advantages, such as simplicity of use, and the fact that it is easily combinable with portable and widely distributed imaging devices, resulting in friendly analytical procedures in many areas that demand out-of-lab applications for in situ and real-time monitoring. This tutorial review covers computer vision-based analytical (CVAC) procedures and systems from 2005 to 2015, a period of time when 87.5% of the papers on this topic were published. The background regarding colour spaces and recent analytical system architectures of interest in analytical chemistry is presented in the form of a tutorial. Moreover, issues regarding images, such as the influence of illuminants, and the most relevant techniques for processing and analysing digital images are addressed. Some of the most relevant applications are then detailed, highlighting their main characteristics. Finally, our opinion about future perspectives is discussed.     

Reaction of bromine with 4,5-dimethyl-1,4-cyclohexadiene-1,2-dicarboxylic acid: a green chemistry puzzle for organic chemistry students

Abstract

Bromination of an alkene is a typical addition reaction covered in an introductory organic chemistry course and laboratory. In this undergraduate organic chemistry laboratory exercise, students studied the bromination of a 4,5-dimethyl-1,4-cyclohexadiene-1,2-dicarboxylic acid. The reaction has an unexpected outcome as bromination yields the aromatic product, 4,5-dimethylphthalic acid. Green chemistry modification involves application of a “bromide/peroxide reaction” with NaBr/H₂O₂ in an acidic medium as an in situ source of bromine. The experiment was carried out as a two-day exercise and the students integrated molecular modeling, interpretation of mass spectra, knowledge of stability of organic compounds, and knowledge of the reaction mechanisms of addition and elimination to explain the experimental outcome.     

The safer chemical design game. Gamification of green chemistry and safer chemical design concepts for high school and undergraduate students

Green chemistry can strongly attract students to chemistry. We, therefore, developed a green chemistry educational game that motivates students at the undergraduate and advanced high school levels to consider green chemistry and sustainability concerns as they design a hypothetical, chemical product. The game is intended for incorporation into any chemistry course for majors and non-majors that teaches sustainability and/or the Principles of Green Chemistry at the undergraduate level. The game is free of charge and encourages students to think like professional chemical designers and to develop a chemical product with respect to function and improved human and environmental health. This computer simulation has been assessed by educators and can be seamlessly integrated into an existing curriculum.     

Understanding the defect chemistry of oxide nanoparticles for creating new functionalities:A critical review

This work presents a critical review on the studies of defect chemistry of oxide nanoparticles for creating new functionalities pertinent to energy applications including dilute-magnetic semiconductors,giant-dielectrics,or white light generation.Emphasis is placed on the relationships between the internal structure and defective surfaces of oxide nanoparticles and their synergy in tailoring the materials properties.This review is arranged in a sequence:(1) structural fundamentals of bulk oxides,using TiO2 a...     

A computational investigation of HCN2+ isomeric structures: implications for the chemistry of Titan's atmosphere.

The structure and stability of various HCN2+ isomeric structures have been investigated at the complete active space SCF (CASSCF) and multireference-configuration interaction [MR-Cl-SD(Q)] levels of theory with the 6-31G(d) and 6-311G(d,p) basis sets. The investigated species include the singlet (S) and triplet (T) open-chain H-N-C-N+ ions 1S, 1S', and 1T, the open-chain H-C-N-N+ ions 2S, 2S', and 2T, the HC-N2+ cyclic structures 3S and 3T, and the HN-CN+ cyclic structures 4S and 4T. All these species have been identified as true energy minima on the CASSCF(8,7)/6-31G(d) potential energy surface, and their optimised geometries, refined at the CASSCF(8,8)/6-31G(d) level of theory, have been used to perform single point calculations at the [MR-Cl-SD(Q]/6-311G(d,p) computational level. The most stable structure was the H-N-C-N+ ion 1T, whose absolute enthalpy of formation at 298.15 K has been estimated as 333.9 +/- 2 kcalmol(-1) using the Gaussian-3 (G3) procedure. The two species closest in energy to 1T are the triplet H-C-N-N+ ion 2T and the singlet diazirinyl cation 3S, whose G3 enthalpies of formation at 298.15 K are 343.5 +/- 2 and 340.6 +/- 2 kcalmol(-1), respectively. Finally, we have discussed the implications of our calculations for the detailed structure of the HCN2+ ions formed in the reaction between N3+ and HCN, experimentally observed by flowing after-glow-selected ion flow/drift tube mass spectrometry and possibly occurring in Titan's atmosphere.     

High oxidation state organometallic chemistry in aqueous media: new opportunities for catalysis and electrocatalysis

Molybdenum has been used as a case study for the rational development of a new domain of organometallic chemistry, combining oxo-stabilized high oxidation state metals and aqueous media. The pH-dependent conversion of oxo, hydroxo, and aqua ligands allows the opening of free coordination sites, while the use of a redox active metal opens possible pathways for coupled proton and electron transfer to and from activated substrates. While our work has so far only concentrated on synthesis and analytical investigations, the development of catalytic and electrocatalytic processes in water or aqueous media is a promising application of this new research area.     

A Computational Study of Vicinal Fluorination in 2,3‐Difluorobutane: Implications for Conformational Control in Alkane Chains

A comprehensive conformational analysis of both 2,3‐difluorobutane diastereomers is presented based on density functional theory calculations in vacuum and in solution, as well as NMR experiments in solution. While for 1,2‐difluoroethane the fluorine gauche effect is clearly the dominant effect determining its conformation, it was found that for 2,3‐difluorobutane there is a complex interplay of several effects, which are of similar magnitude but often of opposite sign. As a result, unexpected deviations in dihedral angles, relative conformational energies and populations are observed which cannot be rationalised only by chemical intuition. Furthermore, it was found that it is important to consider the free energies of the various conformers, as these lead to qualitatively different results both in vacuum and in solvent, when compared to calculations based only on the electronic energies. In contrast to expectations, it was found that vicinal syn‐difluoride introduction in the butane and by extension, longer hydrocarbon chains, is not expected to lead to an effective stabilisation of the linear conformation. Our findings have implications for the use of the vicinal difluoride motif for conformational control.     

Synthesis of substituted N-phenylmaleimides and use in a Diels–Alder reaction: a green multi-step synthesis for an undergraduate organic chemistry laboratory

ABSTRACT

This paper describes the design and implementation of a minimally hazardous, environmentally friendly, and energy efficient sequential reaction sequence within a sophomore level Organic Chemistry lab course to efficiently synthesize N-phenylmaleimide precursors for a Diels–Alder reaction. Substituted N-phenylmaleimides are a class of very expensive precursors of considerable interest due to their biological properties and use as intermediates in synthesis. The synthesis described herein produces a substituted N-phenylmaleimide in two steps from maleic anhydride and a substituted aniline followed by its Diels–Alder reaction with 2,5-dimethylfuran. The experiment exposes students to the green chemistry principles of atom economy, use of safer chemicals, design for energy efficiency, waste reduction, and inherently safer chemistry for accident prevention and enables students to use ¹H NMR spectroscopy to characterize the products.     

The fundamentals behind solving for unknown molecular structures using computer‐assisted structure elucidation: a free software package at the undergraduate and graduate levels

The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer‐Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd.     

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.     

A computational methodology for accurate predictions of rate constants in solution: Application to the assessment of primary antioxidant activity

The accurate prediction of rate constants for chemical reactions in solution, using computational methods, is a challenging task. In this work, a computational protocol designed to be a reliable tool in the study of radical‐molecule reactions in solution is presented. It is referred to as quantum mechanics‐based test for overall free radical scavenging activity (QM‐ORSA) because it is mainly intended to provide a universal and quantitative way of evaluating the free radical scavenging activity of chemical compounds. That is, its primary antioxidant activity. However, it can also be successfully applied to obtain accurate kinetic data for other chemical reactions in solution. The QM‐ORSA protocol has been validated by comparison with experimental results, and its uncertainties have been proven to be no larger than those arising from experiments. Further applications of QM‐ORSA are expected to contribute increasing the kinetic data for free radical‐molecule reactions relevant to oxidative stress, which is currently rather scarce. © 2013 Wiley Periodicals, Inc.     

"Click chemistry" in zeolites: copper(I) zeolites as new heterogeneous and ligand-free catalysts for the Huisgen [3+2] cycloaddition

For the first time, copper(I)-exchanged zeolites were developed as catalysts in organic synthesis. These solid materials proved to be versatile and efficient heterogeneous, ligand-free catalytic systems for the Huisgen [3+2] cycloaddition. These cheap and easy-to-prepare catalysts exhibited a wide scope and compatibility with functional groups. They are very simple to use, easy to remove (by filtration), and are recyclable (up to three times without loss of activity). Investigations with deuterated alkynes and deuterated zeolites proved that this Cu(I)-zeolite-catalyzed "click" reaction exhibited a mechanism different from that reported for the Meldal-Sharpless version.     

A novel tubular hydrogen‐bond pattern in a new diazaphosphole oxide: a combination of X‐ray crystallography and theoretical study of hydrogen bonds

In the structure of 2‐(4‐chloroanilino)‐1,3,2λ⁴‐diazaphosphol‐2‐one, C₁₂H₁₁ClN₃OP, each molecule is connected with four neighbouring molecules through (N—H)₂…O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R ³₃(12) and R ₄³(14) hydrogen‐bond ring motifs, combined with a C (4) chain motif. The hole constructed in the tubular architecture includes a 12‐atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co‐operating in classical hydrogen bonding, takes part in an N—H…π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen‐bond pattern. The energies of the N—H…O and N—H…π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen‐bonded cluster of molecules as the input file for the chemical calculations. In the ¹H NMR experiment, the nitrogen‐bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the ²J _H–P coupling constant.     

Building capacity for undergraduate education and training in computational molecular science: A collaboration between the MERCURY consortium and the Molecular Sciences Software Institute

The Molecular Sciences Software Institute (MolSSI) is an National Science Foundation (NSF) funded institute that focuses on improving software, education, and training in the computational molecular sciences. Through a collaboration with the Molecular Education and Research Consortium in Undergraduate computational chemistRY (MERCURY), the MolSSI has developed resources for undergraduate and other early career students to lay an educational foundation for the next generation of computational molecular scientists. The resources focus on introducing best practices in software engineering to students from the very start to make their software more useable, maintainable, and reproducible.