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Since the form of the exact functional in density functional theory is unknown, we must rely on density functional approximations (DFAs). In the past, very promising results have been reported by combining semi-local DFAs with exact, i.e. Hartree–Fock, exchange. However, the spin-state energy ordering and the predictions of global minima structures are particularly sensitive to the choice of the hybrid functional and to the amount of exact exchange. This has been already qualitatively described for single conformations, reactions, and a limited number of conformations. Here, we have analyzed the mixing of exact exchange in exchange functionals for a set of several hundred isomers of the transition metal carbide, Mo4C2. The analysis of the calculated energies and charges using PBE0-type functional with varying amounts of exact exchange yields the following insights: (1) The sensitivity of spin-energy splitting is strongly correlated with the amount of exact exchange mixing. (2) Spin contamination is exacerbated when correlation is omitted from the exchange-correlation functional. (3) There is not one ideal value for the exact exchange mixing which can be used to parametrize or choose among the functionals. Calculated energies and electronic structures are influenced by exact exchange at a different magnitude within a given distribution; therefore, to extend the application range of hybrid functionals to the full periodic table the spin-energy splitting energies should be investigated. [ABSTRACT FROM AUTHOR]

The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes. [ABSTRACT FROM AUTHOR]

Ni‐CeO2 nanoparticles (NPs) are promising nanocatalysts for water splitting and water gas shift reactions due to the ability of ceria to temporarily donate oxygen to the catalytic reaction and accept oxygen after the reaction is completed. Therefore, elucidating how different properties of the Ni‐Ceria NPs relate to the activity and selectivity of the catalytic reaction, is of crucial importance for the development of novel catalysts. In this work the active learning (AL) method based on machine learning regression and its uncertainty is used for the global optimization of Ce(4‐x)NixO(8‐x) (x = 1, 2, 3) nanoparticles, employing density functional theory calculations. Additionally, further investigation of the NPs by mass‐scaled parallel‐tempering Born‐Oppenheimer molecular dynamics resulted in the same putative global minimum structures found by AL, demonstrating the robustness of our AL search to learn from small datasets and assist in the global optimization of complex electronic structure systems. [ABSTRACT FROM AUTHOR]

Heterogeneous reactions at the surfaces of mineral dusts represent a key process in the formation of atmospheric aerosols. To quantify the rate of aerosol formation in climate modeling as well as combat hazardous aerosols, a deep understanding of the mechanisms of these reactions is essential. In the present work, density functional theory calculations, including a Hubbard-like +U correction, were employed to elucidate the reaction between SO2 and the hematite(0001) surface. Three reaction conditions are considered: dry, wet, and aerobic. In the absence of water and oxygen, adsorption energies of SO2 on the clean Fe–O3–Fe-termination were found to be about −0.8 to −1.0 eV and resulted in the formation of an adsorbed SO3-like species. The addition of water leads to surface hydroxylation and has little effect on promoting the SO2 adsorption. Under such circumstances, an HSO3-like species was formed with a smaller adsorption energy of about −0.5 eV. By contrast, the presence of molecular oxygen enhances the SO2 adsorption significantly as the two species combine to form sulfate SO42−, with adsorption energies of −1.31 to −1.64 eV. The calculated vibrational frequencies of the adsorbate species provide insight into the surface bonding and a useful spectral fingerprinting for experimental measurements. These results elucidate the atomistic mechanism of the reaction between SO2 and hematite and highlight the important role of atmospheric O2 in the formation of sulfates. [ABSTRACT FROM AUTHOR]

We present a new local meta-GGA exchange-correlation density functional by combining the TPSS meta-GGA exchange and the τ1 meta-GGA correlation functionals. The TPSS meta-GGA exchange-correlation and the τ1 meta-GGA correlation functionals have been implemented in the deMon code. The parameters in the τ1 meta-GGA correlation model are reoptimized in a synchronized way to match the original TPSS meta-GGA exchange counterpart. This reparametrized meta-GGA functional is referred to as “TPSSτ3”. The TPSSτ3 and TPSSτ1 meta-GGAs are validated using a test set that consists of covalent molecules, hydrogen-bonded complexes, and van der Waals interactions. The calculated results from TPSSτ1 and TPSSτ3 are analyzed and compared with reliable experimental data and theoretical data, as well as with those from Bmτ1 and TPSS calculations. The τ1 correlation model describes the aromatic compounds better than TPSS. TPSSτ3 yields satisfactory results for the covalent molecules, the hydrogen-bonded complexes, and the van der Waals complexes in the test set compared with TPSS, Bmτ1 and TPSSτ1. [ABSTRACT FROM AUTHOR]

The study of materials in the nanoscale regime has important applications for catalytic reactions, the energy industry and medicine. We performed exploratory density functional theory calculations for molybdenum disulphide (MoS2) and calcium carbonate (CaCO3) nanoparticles (NPs), the former being developed as a hydrogenation and coke-prevention catalyst and the latter representing the catalytic support in some reservoirs. Utilizing Born–Oppenheimer Molecular Dynamics with reduced masses as a global optimization method, we found Mo8S16 and Mo16S32 NPs with lower-lying energies than those of locally optimized crystal geometries. Our results suggest that MoS2 NPs prefer a tetragonal lattice arrangement which is in agreement with previous studies of smaller MoS2 NPs. It remains to be seen how prenucleation MoS2 clusters of the hexagonal phase are formed. The CaCO3 NPs showed small energy differences between vastly different conformations. Therefore, in order to capture only their supporting effects in reservoirs, one should consider keeping a substantial part of the models fixed. [ABSTRACT FROM AUTHOR]

Abstract: Exemplars of the state of the art in modeling enzymes are reviewed through a selection of works from leading schools using QM‐only cluster models, QM/MM models and QM/MM/MD models. A computational protocol is proposed, intended to guide neophytes through the myriad of methodological choices that are necessary for the successful study of chemical reactions in the complex enzymatic environment. [ABSTRACT FROM AUTHOR]

The structures and stabilities of the glycerol (G) and glycerol 3-phosphate (G3P) isomers have been calculated in the gas phase, using an ab initio density functional theory (DFT) method. The different conformational structures are shown to be at the origin of the various phospholipid conformers, except, obviously, for the alkyl chain torsions. The G3P conformations have been examined taking into account the experimental structures of the complexation sites in the glycerol kinase (GK) and glycerol 3-phosphate acyl transferase (G3PAT) enzymes, which correspond to the first and second steps of the “de novo” phospholipid biogenesis, respectively. The conformational analysis of the glycerophosphate skeleton is shown to determine most of the structural characteristics of the phosphatidyl choline lipids, which differ by the length of their diacyl chains, i.e., dilauroyl (DL), dimyristoyl (DM), and dipalmitoyl (DP) phosphatidylcholines (PC). Higher energy conformers with kinks in the acyl chains have been found, in preparation for molecular dynamics studies of the chain melting phase transformation. [ABSTRACT FROM AUTHOR]

Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated—B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP—and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, sR, scaling globally the vdW radii. For good results, a basis set of at least triple-ζ quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 555–569, 2007 [ABSTRACT FROM AUTHOR]

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton. [ABSTRACT FROM AUTHOR]