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Cytochrome bd-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the Mycobacterium tuberculosis (Mtb) bacterium that causes tuberculosis (TB) in humans, the Vibrio cholerae bacterium that causes cholera, the Pseudomonas aeruginosa bacterium that contributes to antibiotic resistance and sepsis, and the Campylobacter jejuni bacterium that causes food poisoning. Escherichia coli (E. coli) is another organism exhibiting the cytochrome bd oxidase. Since it has the highest sequence identity to Mtb (36 %) and we are ultimately interested in finding drug targets for TB, we have built parameters for the E. coli bd oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome bd-type oxidases (heme b558, heme b595, and heme d) along with their axial ligands. This data report includes the parameter files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions.

Density functional vibrational frequency calculations have been performed on eight geometry optimized cytochrome c oxidase (CcO) dinuclear center (DNC) reaction cycle intermediates and on the oxymyoglobin (oxyMb) active site. The calculated Fe-O and O-O stretching modes and their frequency shifts along the reaction cycle have been compared with the available resonance Raman (rR) measurements. The calculations support the proposal that in state A[Fe(a3)(3+)-O(2)(−•)⋯Cu(B)(+)] of CcO, O(2) binds with Fe(a3)(2+) in a similar bent end-on geometry to that in oxyMb. The calculations show that the observed 20 cm(−1) shift of the Fe(a3)-O stretching mode from state P(R) to F is caused by the protonation of the OH(−) ligand on Cu(B)(2+) (P(R)[Fe(a3)(4+)=O(2−)⋯HO(−)-Cu(B)(2+)] → F[Fe(a3)(4+)=O(2−)⋯H(2)O-Cu(B)(2+)]), and that the H(2)O ligand is still on the Cu(B)(2+) site in the rR identified F[Fe(a3)(4+)=O(2−)⋯H(2)O-Cu(B)(2+)] state. Further, the observed rR band at 356 cm(−1) between states P(R) and F is likely an O-Fe(a3)-porphyrin bending mode. The observed 450 cm(−1) low Fe(a3)-O frequency mode for the O(H) active oxidized state has been reproduced by our calculations on a nearly symmetrically bridged Fe(a3)(3+)-OH-Cu(B)(2+) structure with a relatively long Fe(a3)-O distance near 2 Å. Based on Badger’s rule, the calculated Fe(a3)-O distances correlate well with the calculated ν(Fe-O)(−2/3) (ν(Fe-O) is the Fe(a3)-O stretching frequency) with correlation coefficient R = 0.973.

Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches that have not been validated against extensive first-principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from icelike layers, and an MD simulation of an interface between a c(4 × 6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.

The diamagnetic compounds Cp'2Ni2E2 (1: E = S, 2: E = Se, 3: E = Te; Cp'\n= 1,2,3,4,-tetraisopropylcyclopentadienyl), first reported by Sitzmann\nand co-workers in 2001 {[}Sitzmann, H.; Saurenz, D.; Wolmershauser, G.;\nKlein, A.; Boese, R. Organometallics 2001, 20, 700], have unusual E\ncenter dot center dot center dot E distances, leading to ambiguities in\nhow to best describe their electronic structure. Three limiting\npossibilities are considered: case A, in which the compounds contain\nsingly bonded E-2(2)- units; case B, in which a three-electron E-E\nhalf-bond exists in a formal E-2(3-) unit; case C, in which two E-2(-)\nions exist with no formal E-E bond. One-electron reduction of 1 and 2\nyields the new compounds {[}Cp{*}Co-2]{[}Cp'2Ni2E2] (1red: E = S, 2red:\nE = Se; Cp{*} = 1,2,3,4,5-pentamethylcyclopentadieyl). Evidence from\nX-ray crystallography, X-ray absorption spectroscopy, and X-ray\nphotoelectron spectroscopy suggest that reduction of 1 and 2 is\nNi-centered. Density functional theory (DFT) and ab initio\nmultireference methods (CASSCF) have been used to investigate the\nelectronic structures of 1-3 and indicate covalent bonding of an E23-\nligand with a mixed-valent Ni-2(II,III) species. Thus, reduction of 1\nand 2 yields Ni2(II,II) species 1red and 2red that bear unchanged\nE-2(3-) ligands. We provide strong computational and experimental\nevidence, including results from a large survey of data from the\nCambridge Structural Database, indicating that M2E2 compounds occur in\nquantized E-2 oxidation states of (2 x E2-), E-2(3-), and E-2(2-),\nrather than displaying a continuum of variable E-E bonding interactions.

We re-investigate the image charge model of Iori and Corni (Iori and Corni, J. Comput. Chem. 2008, 29, 1656). We find that a simple symmetrization of their model allows to obtain quantitatively correct results for the electrostatic interaction of a water molecule with a metallic surface. This symmetrization reduces the magnitude of the electrostatic interaction to less than 10% of the total interaction energy. © 2017 Wiley Periodicals, Inc.

We present a new implementation of analytical gradients for subsystem density-functional theory (sDFT) and frozen-density embedding (FDE) into the Amsterdam Density Functional program (ADF). The underlying theory and necessary expressions for the implementation are derived and discussed in detail for various FDE and sDFT setups. The parallel implementation is numerically verified and geometry optimizations with different functional combinations (LDA/TF and PW91/PW91K) are conducted and compared to reference data. Our results confirm that sDFT-LDA/TF yields good equilibrium distances for the systems studied here (mean absolute deviation: 0.09 A) compared to reference wave-function theory results. However, sDFT-PW91/PW91k quite consistently yields smaller equilibrium distances (mean absolute deviation: 0.23 A). The flexibility of our new implementation is demonstrated for an HCN-trimer test system, for which several different setups are applied. © 2016 Wiley Periodicals, Inc.

Broken-symmetry density functional calculations have been performed on the [Fea3, CuB] dinuclear center (DNC) of ba3 cytochrome c oxidase from Thermus thermophilus in the states of [Fea3(3+)-(HO2)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], using both PW91-D3 and OLYP-D3 functionals. Tyr237 is a special tyrosine cross-linked to His233, a ligand of CuB. The calculations have shown that the DNC in these states strongly favors the protonation of His376, which is above propionate-A, but not of the carboxylate group of propionate-A. The energies of the structures obtained by constrained geometry optimizations along the O-O bond cleavage pathway between [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] have also been calculated. The transition of [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] → [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] shows a very small barrier, which is less than 3.0/2.0 kcal mol(-1) in PW91-D3/OLYP-D3 calculations. The protonation state of His376 does not affect this O-O cleavage barrier. The rate limiting step of the transition from state A (in which O2 binds to Fea3(2+)) to state PM ([Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], where the O-O bond is cleaved) in the catalytic cycle is, therefore, the proton transfer originating from Tyr237 to O-O to form the hydroperoxo [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] state. The importance of His376 in proton uptake and the function of propionate-A/neutral-Asp372 as a gate to prevent the proton from back-flowing to the DNC are also shown.

Isoflavones are known to show fluorescence with intensities that depend strongly on the solvent properties and exhibit Stokes' shifts as large as 1.4 eV. While some of this behavior can be explained by (excited state) deprotonation, this mechanism does not apply for all isoflavones. The aim of this study is to computationally and experimentally investigate the reasons for this anomalous behavior of neutral isoflavones, taking the daidzein molecule as a model compound. We find that the absence in fluorescence in aprotic solvents and the weak fluorescence in protic solvents can be explained by a change of order of the lowest singlet states in which a fluorescent charge-transfer state lies below the nonfluorescent locally excited state in water but not in acetonitrile. The large Stokes' shift is partly due to a significant rotation among the chromone-phenyl bond in the excited state. © 2011 American Chemical Society.

Recent work has shown that the many-body expansion of the interaction energy can effectively be used to develop analytical representations of global potential energy surfaces (PESs) for water. In this study, the role of short- and long-range contri- butions at different orders is investigated by analyzing water potentials that treat the leading terms of the many-body expansion through implicit (i.e., TTM3-F and TTM4-F PESs) and explicit (i.e., WHBB and MB-pol PESs) representations. It is found that explicit short-range representations of 2-body and 3-body interactions along with a physically correct integration of short- and long-range contributions are necessary for an accurate representation of the water interactions from the gas to the condensed phase. Similarly, a complete many-body representation of the dipole moment surface is found to be crucial to reproducing the correct intensities of the infrared spectrum of liquid water.

We have assessed the accuracy of a representative set of currently available approximate kinetic-energy functionals used within the frozen-density embedding scheme for the NgAuF (Ng=Ar, Kr, Xe) molecules, which we partitioned into a Ng and a AuF subsystem. Although it is weak, there is a covalent interaction between these subsystems which represents a challenge for this subsystem density functional theory approach. We analyzed the effective-embedding potentials and resulting electron density distributions and provide a quantitative analysis of the latter from dipole moment differences and root-mean-square errors in the density with respect to the supermolecular Kohn-Sham density functional theory reference calculation. Our results lead to the conclusion that none of the tested approximate kinetic-energy functionals performs well enough to describe the bond between the noble gas and gold adequately. This observation contributes to the growing evidence that the current procedure to obtain approximate kinetic-energy functionals by reparametrizing functionals obtained via the "conjointness" hypothesis of Lee, Lee, and Parr [Phys. Rev. A 44, 768 (1991)] is insufficient to treat metal-ligand interactions with covalent character. © 2010 American Institute of Physics.

An improved version of our method for computing QTAIM [J.I. Rodríguez, A.M. Köster, P.W. Ayers, A. Santos-Valle, A. Vela, G. Merino, J. Comput. Chem. (2009), in press, doi:10.1002/jcc.21134] is presented. Vectorization and parallelization of the previous algorithm, together with molecular symmetry, make the present algorithm as much as two orders of magnitude faster than our original method. The present method scales linearly with both system size and the number of processors. The performance of the method is demonstrated by computing the QTAIM atomic properties of a series of carbon nanotubes. Our results show that the CPU time for a QTAIM property calculation is comparable to that of a SCF-single point calculation. The accuracy of the original method is also improved. © 2009 Elsevier B.V. All rights reserved.

Commonly used exchange-correlations functionals are known to produce inaccurate electric field gradient (EFG) values at the nuclei of transition metals and heavy atoms in molecular calculations. This makes density functional theory (DFT) essentially inapplicable for the determination of nuclear quadrupole moments (NQM) from absolute EFG estimates. However, in a recently proposed indirect approach, the NQM is determined from the changes in the EFG along a series of molecules. We investigate this indirect approach within four-component relativistic DFT, showing that, at least in a series of chemically strictly related molecules, EFG variations can be computed quite accurately. This leads to surprisingly stable and reliable estimates of the NQM, even in notoriously ‘difficult’ cases such as 197 Au.

Applications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PYADF, a scripting framework for quantum chemistry. PYADF handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object-oriented implementation in the Python programming language. We give an overview of the capabilities of PYADF and illustrate its usefulness in quantum-chemical multiscale simulations with a number of examples taken from recent applications. © 2011 Wiley Periodicals, Inc.

A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol.