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
A semiclassical phase-space perspective of band- and topological-insulator regimes of 2D Dirac materials, and normal- and superradiant-phases of atom-field interacting models is given in terms of delocalization, entropies, and quantum correlation measures. From this point of view, the low-energy limit of tight-binding models describing the electronic band structure of topological 2D Dirac materials like phosphorene and silicene with tunable band gaps, share similarities with Rabi-Dicke and Jaynes-Cummings atom-field interaction models, respectively. In particular, the edge state of 2D Dirac materials in the topological insulator phase exhibits a Schr\”odinger cat structure similar to the ground state of two-level atoms in a cavity interacting with a one-mode radiation field in the superradiant phase. Delocalization seems to be a common feature of topological insulator and superradiant phases.
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.
The influences of the initial states of HCl on the stereodynamics properties of the Ca+HCl reaction are investigated by utilizing the method based on the quasi-classical trajectory (QCT) theory and the analytical potential energy surface (APES). The orientation and alignment behaviors for the rotational angular momentum of the product, along with the generalized differential cross-section (PDDCS) dependent polarization, are employed to explore the stereodynamics properties. The initial rotational states of the HCl molecule impose a remarkable affection on the vector correlation distributions, regardless of the orientation, alignment, or PDDCS. The obvious forward or backward scattering, as well as the weak sideway scattering phenomena, are found for the different initial rotational states of the HCl molecule. The initial higher rotational-excited state of j=3 results in more obvious stereodynamics effects.
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.
The field of molecular magnetism has benefited from the fluid synergy between experimentalists and theoreticians for decades This has led to fundamental understanding of the processes that govern Single Molecule Magnets, allowing for the establishment of clear design criteria to control properties and the development of new synthetic methodologies, sophisticated magnetic measurements and innovative computational techniques. Herein we give an overview on the experimental and theoretical collaborative work we carried out as part of the synthesis group led by David Mills and the computational/theoretical team led by Nicholas Chilton at the University of Manchester. Together with this, we provide a perspective on collaborative work in molecular magnetism and how such collaborations are essential for advancing the field further.
We studied the ring opening of propylene oxide (PO) by salen-M coordinated OH- group [M = Al(Ⅲ), Sc(Ⅲ), Cr(Ⅲ), Mn(Ⅲ), Fe(Ⅲ), Co(Ⅱ), Co(Ⅲ), Ni(Ⅱ), Cu(Ⅱ), Zn(Ⅱ), Ru(Ⅲ) and Rh(Ⅲ)]. The results show that the ring opening energy barriers for M(II) complexes are much lower than those with M(III) complexes in the gas phase, and the barriers correlate linearly with the negative charges on the OH- group, the Fukui function condensed on the OH- group. The nucleophilicity ordering in gas phase can be rationalized by the ratio of formal positive charges/radius of M cations. Solvent effect greatly increases the barriers of M(II) complexes, but slightly changes the results of M(III) ones, making the barriers similar. Analysis indicates that the reaction heats are linearly proportional to the reverse reaction barriers. The relationships established here can be used to estimate the ring opening barriers and to screen epoxide ring opening catalysts.
We calculate the concerted pathway of 1, 2-bromochloroethane monocation to C2H4+ and BrCl using the Minnesota density functional M06-2X and the def2-TZVP basis set. We also calculate the elimination channel of 1, 2-bromochloroethane monocation to C2H4 and BrCl+ for the reason that positive charge can be assigned to either moiety in the fragmentation process of 1,2-C2H4BrCl+. Our results demonstrate that the elimination channel of 1, 2-bromochloroethane monocation to C2H4+ and BrCl is preferred, and the singly charged 1,2-bromochloroethane ions surpass two energy barriers and then separate into C2H4+ + BrCl by an asynchronous concerted process. Experimentally, we confirm that this elimination channel is from the dissociative ionization process of 1,2-bromochloroethane monocation by dc-slice imaging technique. Besides, we can see in laser-induced time-of-flight mass spectra of 1,2-bromochloroethane that fragment ion C2H4+ occur at the laser intensity of 6.0×1013 W/cm2 while BrCl+ occur at a higher laser intensity, which is consistent with the theoretical results that appearance energy of ion C2H4+ should be lower than that of BrCl+, and this is the reason why the low-velocity component of ion BrCl+ is absent from our sliced images.
Abstract: Searching for energetic materials with balanced detonation performance and sensitivity is the enduring ambition in the evolution of high energy density materials (HEDMs). The coplanar molecular structure of energetic compound has a powerful impact on performance. Herein, the novel compounds of bis(nitrotriazoles) tetrazine (BNTT) was designed and investigated by density functional theory(DFT) method. However, the coplanar BNTT’s oxides would a highlight of molecular design with good balance between superior performance with acceptable sensitivities. Results show that all these designed compounds possess high densities, positive heats of formation, remarkable detonation performance, and acceptable impact sensitivity. In particular, B1-3 possess higher density (ρ=1.97g·cm-3) and exhibits the better balance between detonation performance (Q=1779.83 cal·g-1, D=9.48km·s-1, P=42.01GPa) and sensitivity (h50%=28cm) than RDX. The theoretical study offer that all novel compounds possess acceptable sensitivity. It may be seen as the potential candidates of HEDMs.
Mechanism of the oxidative nonpolar inversion reaction catalyzed by N-heterocyclic carbenes (NHCs) to achieve benzoxazoles was investigated in very details. The reaction was revealed to occur through five processes, and for oxidation in the second process, two successive tautomerizations followed by oxidation were demonstrated to be more energetically favorable than the other two pathways. The rate-determining step was disclosed to be the oxidation by 3,3’-5,5’-tetra-tert-butyl-4,4’-diphenoquinone (DQ). Afterwards, mechanism calculations to the non-catalyzed reaction was conducted and it was revealed that the excessive exothermic property of the initial step should be the main reason for the extremely high barrier in the following step. While with participation of NHC, this unfavorable transformation can be deftly prevented according to the specific sequence and amount of reagents addition, and therefore to enable the reaction to occur under mild conditions.
Multi-reference configuration interaction, MR-CI (including extensivity corrections, named +Q) calculations have been performed on S0 to S3 states of cyclohexa-2,4-diene-1-thione (thione 24) and cyclohexa-2,5-diene-1-thione (thione 25), which are thione isomers of thiophenol. Several types of uncontracted MR-CIS and MR-CISD wavefunctions have been employed, comprising MR-CI expansions as large as ~ 374 x 106 configuration state functions. The nature of the studied excited states has been characterized. Vertical excitation energies (ΔE) and oscillator strengths (f) have been computed. The most intense transitions (S0→S2 for 24 and S0→S3 for 25) do not change with the wavefunction, although a variation as large as ~ 1 eV has been obtained for the S3 state of 24. On the other hand, ΔE changes at most ~ 0.15 eV for 25, as the wavefunction changes. The S1 state of both thiones has nπ* character and is in the visible region. For 24 S2 and S3 are ππ* and nπ* states, respectively, while for 25 the reverse order has been obtained. S2 and S3 are in the range from ~ 3.5 to 5.2 eV, at the highest level (MR-CI+Q). It is the first time that the excited states of the title molecules are studied. The computed results agree with the experimental onsets of photoreactions of thiones 24 and 25 found by Reva et. al. (Phys. Chem. Chem. Phys. 2015, 17, 4888).