An extended computational approach has been utilized to explore the reactions of acids with carbonyl oxide, also known as Criegee intermediate (CI). The reactions were explored inside water cluster containing 50 water molecules. All possibilities of product formation were considered. Among the considered acids, the rate of 1,4-insertion follows the order - HCOO < HCl < HNO3. The most stable products of the reactions between the considered acids and CI have been identified.
Predicting the energetics of chemical transformations requires localizing stationary points on a potential energy surface. Whereas educts and products of a chemical reaction may be known, transition state optimization is challenging, as good guesses may be unavailable. Extending stationary point searches to excited states leads to additional difficulties as several states may be close in energy, requiring efficient state-tracking. Herein we report the implementation of pysisyphus, an external optimizer, that allows not only the localization of stationary points in the ground state, but also for excited states by providing several state-tracking algorithms. Pysisyphus offers all necessary tools for calculating reaction paths starting from the optimization of the reactants, running chain-of-states methods like the nudged elastic band or the growing string method with subsequent transition state optimization and a concluding intrinsic reaction coordinate calculation.
We have explored the structural and energetic properties of a series of RMX3–NH3 (M=Si, Ge; X=F, Cl; R=CH3, C6H5) complexes using density functional theory and low-temperature infrared spectroscopy. In the minimum-energy structures, the NH3 binds axially to a halogen, while the organic group resides in equatorial site about the metal. Remarkably, the primary mode of interaction in several of these systems seems to be hydrogen bonding (C-H–N), rather than a tetrel N-M interaction. This is particularly clear for the RMCl3–NH3 complexes, and analyses of the charge distributions of the acid fragment corroborate this assessment. We also identified a set of metastable geometries in which the ammonia binds axial to the organic substituent. Acid fragment charge analysis also provide a clear rationale as to why these configurations are less stable than their R-equatorial counterparts. In matrix-IR experiments, we see clear evidence of the minimum-energy form of CH3SiCl3–NH3, but analogous results for CH3GeCl3–NH3 are less conclusive. Computational scans of the M-N distance potentials for CH3SiCl3–NH3 and CH3GeCl3–NH3, both in the gas phase and bulk dielectric media reveal a great deal of anharmonicity, and a propensity for condensed-phase structural change.
Single atom catalysts with iron ions in the active site, known as FeNC catalysts, show high activity for the oxygen reduction reaction and hence hold promise for access to low cost fuel cells. Due to the amorphous, multi-phase structure of the FeNC catalysts, the iron environment and its electronic structure are poorly understood. While it is widely accepted that the catalytically active site contains an iron ion ligated by several nitrogen donors embedded in a graphene-like plane, the exact structural details such as the presence or nature of axial ligands are unknown. Computational chemistry in combination with Mössbauer spectroscopy can help to unravel the geometric and electronic structures of the active sites. As a first step towards this goal, we present a calibration of computational Mössbauer spectroscopy for FeN4-like environments. The uncertainty of both the isomer shift and the quadrupole splitting prediction is determined, from which trust regions for the Mössbauer parameter predictions of computational FeNC models are derived. We find that TPSSh, B3LYP, and PBE0 perform equally well; the trust regions with B3LYP are 0.13 mm s−1 for the isomer shift and 0.45 mm s−1 for the quadrupole splitting. The calibration data is made publicly available in an interactive notebook that provides predicted Mössbauer parameters with individual uncertainty estimates from computed contact densities and quadrupole splitting values. We show that a differentiation of common FeNC Mössbauer signals by a separate analysis of isomer shift and quadrupole splitting will most likely be insufficient, whereas their simultaneous evaluation will allow the assignment to adequate computational FeNC models.
The possible effect of plastic nanoparticles of waste origin on biological systems is still unclear, and could pose a severe threat. Model studies on the molecular level are urgently needed in order to help revealing interplay between these particles biological systems, and thereby to indicate the direction further research. In the present study, simulated annealing molecular dynamics was adjusted and applied to generate an array of conformations for a sample peptide oligoalanine possibly binding to polyethylene and nylon 6,6 nanoplastics. The resulting structures, with a diameter up to 5 nm, were investigated with the aid of static quantum chemical calculations. The obtained data unequivocally show that both plastic nanoparticles influence the relative stability of α-helix, β-hairpin and other conformations strongly. The polyethylene nanoparticle increases the stability of the helical foldamer. The nylon 6,6 nanoplastic offers strong plastic-peptide interactions at its surface, which make the unfolding of the peptide thermodynamically highly favorable. These results further underscore that nanoplastics can do significant, molecular level damage to living organisms via facilitating the misfolding and denaturation of proteins. Furthermore, it is apparent that plastics can have very different effects on living matter depending on their composition, hence experiments with any single kind of plastics (e.g. polystyrene) should not be considered generally valid for all nanoplastics.
The aromaticity of boron-nitrogen clusters has been revisited through a systematic analysis using magnetic criteria. The results obtained through Ring Current Strength (RCS) measurements indicate that B2N2 has a strongly antiaromatic character, even the bond pattern analysis reveals that this system is doubly antiaromatic presenting two σ- and two π-orbitals of 4c-2e, according to the Adaptive Natural Density Partitioning bond pattern analysis (AdNDP) and z-component of the dissected Nucleus Independent Chemical Shift (NICSzz) isolines. B4N4 and B6N6 are marginally antiaromatic according to RCS and the bond pattern suggest four and six 8c-2e and 12c-2e delocalized π-orbitals respectively. B3N3 and B5N5 are slightly aromatic, with a bond pattern of three and five 6c-2e and 10c-2e π-orbitals respectively. All rest of the systems (x = 7 – 11) are non-aromatic. The results show some discrepancies with results based on the classical nucleus independent chemical shift, which can be attributed to tensor in-plane and core electron contributions. Finally, presented results reveal the need to be careful with the interpretations given by this index, so it will be necessary the use of 1D, 2D or 3D derived methodologies for a complete and correct analysis of (anti)aromaticity.
We report implementation of a hierarchical equations of motion (HEOM) module within the open-source Libra software. It includes the standard and scaled HEOM algorithms for computing the dynamics of open quantum systems interacting with a harmonic bath. The module allows computing evolution of the reduced density matrix as well as spectral lineshapes. The truncation, filtering, and “update list” schemes as well as OpenMP parallelization allow for further computational saving. The package is written in a mix of C++ and Python languages, delivering the best compromise between user friendliness and efficiency. The Python layer of the package takes advantage of standard Python libraries, such as h5py which allows efficient storage and retrieval of the generated results. The package can be seamlessly used within Jupyter notebooks; its careful design shall provide the maximal convenience and intuitiveness to its users.
Theoretical elucidation of the turn-off mechanism of the luminescence of a chemosensor based on a metal-organic framework (MOF) [Zn2(OBA)4(BYP)2] (BYP: 4,4’-bipyridine; H2OBA: 4,4’-oxybis(benzoic acid)), selective to nitrobenzene via quantum chemical computations is presented. The electronic structure and optical properties of Zn-MOF were investigated through the combination of density functional theory (DFT) and time-dependent-DFT methods. Our results indicate that the fluorescence emission is governed by a linker (BPY) to linker (OBA) charge transfer (LLCT) involving orbitals π-type. Next, interaction with the analyte was analyzed, where very interesting results were obtained, i.e. the LUMO is now composed by orbitals from nitrobenzene, which changes the emissive state of the Zn-MOF. This fact suggests that the LLCT process is blocked, inducing then the fluorescence quenching. Otherwise, the Morokuma-Ziegler energy decomposition and NOCV (Natural Orbitals for Chemical Valence) on the Zn-MOF-nitrobenzene interactions were studied in detail, which illustrate the possible channels of charge transfer between Zn-MOF and nitrobenzene. Finally, we believe that this proposed methodology can be applied to different chemosensor-analyte systems to evidence the molecular and electronic factors that govern the sensing mechanisms.
Density functional theory, or DFT, has become ubiquitous for chemical applications in research and in education. The exact functional at the foundation of DFT is unfortunately unknown, and issues arise when choosing an approximation for a specific application. With this tutorial review, we tackle the selection problem and many related ones, such as the choices of a basis set and of an integration grid, that are often overlooked by occasional practitioners and by more experienced users as well. We offer a practical approach in the form of a commented notebook containing 12 experiments that can be run on a simple computer in just a few hours. We propose this review as a primary source for those who are willing to include DFT in their everyday research or teaching activities in a way that reflects the research advances of the field in the last couple of decades
The MERCURY consortium, established in 2000, has contributed greatly to the scientific development of faculty and undergraduates. The MERCURY faculty peer review publication rate from 2001-2019 of 1.7 papers/faculty/year is 3.4 times the rate of 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 underrepresented 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 2/3 are female and/or students of color. We have had more than 1600 attendees at the 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.
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. We each 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. KEYWORDS — undergraduate research, computational chemistry, primarily undergraduate institution, tenure-track position, career pathways
Carbon dioxide has attracted considerable attention owing to its physics and abundant polymorphs. Despite decades of extensive experiments and theoretical simulations, the structure and properties of carbon dioxide under extreme pressures and temperatures are yet to be properly understood. Particularly, the intermediate phase IV of solid carbon dioxide, which separates the molecular phases at low pressures from the non-molecular phases at high pressures, has not been fully investigated, and its structure remains controversial. Here, based on the second-order Møller−Plesset perturbation (MP2) theory and the embedded fragment method, we study the crystal structure, equation of state, and Raman spectra of solid carbon dioxide phase IV at high pressures and temperatures. We demonstrate that the solid carbon dioxide phase IV is a molecular structure that remains in a molecular state rather than the bent state shown in other literatures, which is consistent with the experimental work by Datchi et al. and denies the observed results by Park et al. The proposed work is of great significance in determining the structure of the high-pressure phases of carbon dioxide and further exploring the new phase of molecular crystals.
The ab initio molecular dynamics simulations are performed to study the atomic structures of Co92-xBxTa8 (x = 30, 32.5, 35, 37.5, at.%) glassy alloys. The result shows that the local packing of B-centered clusters is more efficient than that for Co- and Ta-centered clusters. It is also found that B-centered clusters are the primary structure-forming clusters. The Kasper polyhedra with a Voronoi index of <0 3 6 0> and <0 2 8 0> are dominant in B-centered clusters. Specially, the <0 3 6 0> clusters can form a robust network structure, which plays a key role in mechanical properties. Such a network structure has a higher activation barrier for structural rearrangement and a better resist to plastic flow. Thus, the increase in the fraction of <0 3 6 0> with B content would result in an increase in yield strength as well as a sharp decrease in compression plasticity.
We seek to explain why the hydrogen bond possesses unusual strength in small water clusters that account for many of the complex behaviors of water. We have investigated and visualized the donation of covalent character from covalent (sigma) to hydrogen-bonds, by calculating the eigenvector coupling properties of QTAIM, stress tensor σ(r) and Ehrenfest Force F(r) on the F(r) molecular graph. The next generation 3-D bond-path framework sets are presented and only the F(r) bond-path framework sets reproduce the earlier finding on the coupling between covalent (sigma) and hydrogen-bonds that possess a degree of covalent character. The directional character of the covalent (sigma) and hydrogen-bonds 3-D bond-path framework sets for the F(r) explains differences found in the earlier results from QTAIM and the stress tensor σ(r).
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 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.
Detailed information on the H/D isotope effects for adsorption on the surface and absorption in the bulk is important for understanding the nuclear quantum effect. To achieve this purpose, we developed a new theoretical approach, namely, the combined plane wave and localized basis set (CPLB) method. By using the multi-component quantum chemical method, which takes into account the quantum effect of proton or deuteron, with localized part in CPLB method, direct analysis of H/D isotope effect about adsorption and absorption is achieved. In this study, we performed a theoretical investigation of the H/D isotope effects for adsorption on a Pd(111) surface and absorption in bulk Pd. We clearly showed H/D isotope effect on geometry during adsorption and absorption. Our developed CPLB approach is a powerful tool for analyzing the quantum nature of H/D in surface, bulk, and inhomogeneous systems.
GridMol is a “one-stop” platform for molecular modeling, scientific computing and molecular visualization aided by High Performance Computing Environment. GridMol version 2.0 emphatically introduces two unique features, the first is fragment-based linear scaling quantum chemistry methods, such as molecular fractionation with conjugate caps and fragment molecular orbital methods; the second is visualization of computational processes, such as structural optimization and intrinsic reaction coordinate calculation. Compared with version 1.0, fragment-based linear scaling quantum chemistry methods implemented in GridMol version 2.0 can be used as a useful tool for performing quantum calculations for large molecular systems to explore the mechanisms involved in protein–ligand or targeted-drug interactions.
The photocatalytic yield of the g-C3N4 for CO2 reduction was modified by phosphorus doping. The possible reaction pathways for CO2 reduction on the P-doped g-C3N4 (PCN) surface were investigated by DFT calculations for the first time. The experimental results showed that P doping improves the production of CH4 through the increase in the driving force of the electrons. The partial density of states of the PCN showed that the VBM and CBM are composed of px, py and s orbitals of the N atoms and pz states of carbon, nitrogen, and phosphorus, respectively and therefore, the P-doping increase carriers lifetime. Mechanism studies confirm that formic acid, formaldehyde, methanol and methane are the most probable products. The methane having positive adsorption energy can be easily desorbed from the PCN surface and the Gibbs activation energy of the final step is 1.98 eV. The formation of H2COOH is the rate-determining step.