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Although the dinuclear center (DNC) of the resting oxidized "as-isolated" cytochrome c oxidase (CcO) is not a catalytically active state, its detailed structure, especially the nature of the bridging species between the Fea33+ and CuB2+ metal sites, is still both relevant and unsolved. Recent crystallographic work has shown an extended electron density for a peroxide type dioxygen species (O1-O2) bridging the Fea3 and CuB centers. In this paper, our density functional theory (DFT) calculations show that the observed peroxide type electron density between the two metal centers is most likely a mistaken analysis due to overlap of the electron density of a water molecule located at different positions between apparent O1 and O2 sites in DNCs of different CcO molecules with almost the same energy. Because the diffraction pattern and the resulting electron density map represent the effective long-range order averaged over many molecules and unit cells in the X-ray structure, this averaging can lead to an apparent observed superposition of different water positions between the Fea33+ and CuB2+ metal sites.

After a general introduction to the features and mechanisms of cytochrome c oxidases (CcOs) in mitochondria and aerobic bacteria, we present DFT calculated physical and spectroscopic properties for the catalytic reaction cycle compared with experimental observations in bacterial ba3 type CcO, also with comparisons/contrasts to aa3 type CcOs. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a3 Fe center and a near lying Cu center (called CuB) where by successive reduction and protonation, molecular O2 is transformed to two H2O molecules, and protons are pumped from an inner region across the membrane to an outer region by transit through the CcO integral membrane protein. Structures, energies and vibrational frequencies for Fe-O and O-O modes are calculated by DFT over the catalytic cycle. The calculated DFT frequencies in the DNC of CcO are compared with measured frequencies from Resonance Raman spectroscopy to clarify the composition, geometry, and electronic structures of different intermediates through the reaction cycle, and to trace reaction pathways. X-ray structures of the resting oxidized state are analyzed with reference to the known experimental reaction chemistry and using DFT calculated structures in fitting observed electron density maps. Our calculations lead to a new proposed reaction pathway for coupling the PR → F → OH (ferryl-oxo → ferric-hydroxo) pathway to proton pumping by a water shift mechanism. Through this arc of the catalytic cycle, major shifts in pKa's of the special tyrosine and a histidine near the upper water pool activate proton transfer. Additional mechanisms for proton pumping are explored, and the role of the CuB+ (cuprous state) in controlling access to the dinuclear reaction site is proposed.

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.

The topology of the molecular electron density of benzene dithiol gold cluster complex Au4 -S-C6 H4 -S'-Au'4 changed when relativistic corrections were made and the structure was close to a minimum of the Born-Oppenheimer energy surface. Specifically, new bond paths between hydrogen atoms on the benzene ring and gold atoms appeared, indicating that there is a favorable interaction between these atoms at the relativistic level. This is consistent with the observation that gold becomes a better electron acceptor when relativistic corrections are applied. In addition to relativistic effects, here, we establish the sensitivity of molecular topology to basis sets and convergence thresholds for geometry optimization.

Organic photovoltaic (OPV) cells have attracted considerable attention as renewable energy source with potential for large scale deployment. Among the most efficient OPVs are so-called bulk-heterojunction (BHJ) cells in which the active material consists of an electron donor and electron acceptor material. In this chapter we review how density functional theory (DFT) methods can be employed to characterize interfacial properties, UV-Vis absoprtion spectra, and photoinduced charge separation in BHJ-OPV donor-acceptor complexes based on semiconducting polymers as donor and fullerene derivatives as acceptor. The methods presented here are transferable also to other donor acceptor materials.

Broken-symmetry density functional calculations have been performed on the [Fea34+,CuB2+] state of the dinuclear center (DNC) for the PR → F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+, which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea34+,CuB2+] state (state F) is of the form Fea34+═O2–···CuB2+, in which the H2O ligand that resulted from protonation of the OH– ligand in the PR state is dissociated from the CuB2+ site. The calculated Fea34+═O2– distance in F (1.68 A) is 0.03 A longer than that in PR (1.65 A), which can explain the different Fea34+═O2– stretching modes in P (804 cm–1) and F (785 cm–1) identified by resonance Raman experiments. In this F state, the CuB2+···O2– (ferryl–oxygen) distance is only...

We present a theoretical study on the role of van der Waals (vdW) interactions on the structure and, as a consequence, the photoinduced charge separation (CS) of a series of dimer complexes formed by the polymer P3HT and the fullerene derivative PCBM. CS rate constants for P3HT/PCBM dimer structures in which vdW interactions are taken into account agree well with experimental data. Without proper treatment of vdW interactions during geometry optimizations, the predicted CS rates can be too low by up to 3 orders of magnitude. These variations in computed CS rates are not due to changes in the Gibbs energy for CS. Instead, the electronic coupling increases by up to 2 orders of magnitude for structures obtained with dispersion-corrected density functionals that lead to deformations in the P3HT oligomer with pronounced π–π stacking interactions with PCBM.

Characterizing structural and phase transformations of water at the molecular level is key to understanding a variety of multiphase processes ranging from ice nucleation in the atmosphere to hydration of biomolecules and wetting of solid surfaces. In this study, state-of-the-art quantum simulations with a many-body water potential energy surface, which exhibits chemical and spectroscopic accuracy, are carried out to monitor the microscopic melting of the water hexamer through the analysis of vibrational spectra and appropriate structural order parameters as a function of temperature. The water hexamer is specifically chosen as a case study due to the central role of this cluster in the molecular-level understanding of hydrogen bonding in water. Besides being in agreement with the experimental data available for selected isomers at very low temperature, the present results provide quantitative insights into the interplay between energetic, entropic, and nuclear quantum effects on the evolution of water clusters from "solid-like" to "liquid-like" structures. This study thus demonstrates that computer simulations can now bridge the gap between measurements currently possible for individual isomers at very low temperature and observations of isomer mixtures at ambient conditions.

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.

Two-body and three-body energies, modulated by higher-body terms and nuclear quantum effects, determine the structure of liquid water and require sub-chemical accuracy that is achieved by the MB-pol model but not by existing DFT functionals., Despite its apparent simplicity, water displays unique behavior across the phase diagram which is strictly related to the ability of the water molecules to form dense, yet dynamic, hydrogen-bond networks that continually fluctuate in time and space. The competition between different local hydrogen-bonding environments has been hypothesized as a possible origin of the anomalous properties of liquid water. Through a systematic application of the many-body expansion of the total energy, we demonstrate that the local structure of liquid water at room temperature is determined by a delicate balance between two-body and three-body energies, which is further modulated by higher-order many-body effects. Besides providing fundamental insights into the structure of liquid water, this analysis also emphasizes that a correct representation of two-body and three-body energies requires sub-chemical accuracy that is nowadays only achieved by many-body models rigorously derived from the many-body expansion of the total energy, which thus hold great promise for shedding light on the molecular origin of the anomalous behavior of liquid water.

Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F), we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.

In order to cast some light onto the nature of the chemical bonding between a 8-unit oligomer of the poly(3-hexylthiophene) (P3HT) and the fullerene derivative [6,6]-phenyl-C 61 -butyric acid methyl ester (PCBM) in the two stables isomers reported recently [I. Gutierrez-Gonzalez, B. Molina-Brito, A.W. Gotz, F.L. Castillo-Alvarado, J.I. Rodriguez, Chem. Phys. Lett. 612, 234 (2014)], we have performed a Bader's quantum theory of atoms in molecules (QTAIM) analysis. According to QTAIM, no covalent bonds are formed between P3HT and PCBM, and hydrogen and stacking interactions account for about 90% and 10% of the total number of bonds between P3HT and PCBM, respectively.

Cisplatin (cDDP) is known to bind to the CXXC motif of proteins containing a ferrodoxin-like fold but little is known about its ability to interact with other Cu-binding proteins. MEK1/2 has recently been identified as a Cu-dependent enzyme that does not contain a CXXC motif. We found that cDDP bound to and inhibited the activity of recombinant MEK1 with an IC50 of 0.28 μM and MEK1/2 in whole cells with an IC50 of 37.4 μM. The inhibition of MEK1/2 was relieved by both Cu+1 and Cu+2 in a concentration-dependent manner. cDDP did not inhibit the upstream pathways responsible for activating MEK1/2, and did not cause an acute depletion of cellular Cu that could account for the reduction in MEK1/2 activity. cDDP was found to bind MEK1/2 in whole cells and the extent of binding was augmented by supplementary Cu and reduced by Cu chelation. Molecular modeling predicts 3 Cu and cDDP binding sites and quantum chemistry calculations indicate that cDDP would be expected to displace Cu from each of these sites. We conclude that, at clinically relevant concentrations, cDDP binds to and inhibits MEK1/2 and that both the binding and inhibitory activity are related to its interaction with Cu bound to MEK1/2. This may provide the basis for useful interactions of cDDP with other drugs that inhibit MAPK pathway signaling.

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.

Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes—NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.

After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3–CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185–190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment., From density functional theory calculations on the dinuclear Fe-a3−CuB complex (DNC) in a type B bacterial cytochrome c oxidase, we construct a catalytic reaction wheel diagram for the full redox, O2 binding, and proton-transfer cycle. A new low-energy pathway is found. Strong shifts in the dipole moment direction/magnitude over the cycle and associated energy differences indicate that the DNC plays a major role not only in the chemical reaction cycle but also in proton pumping.

Glycoside hydrolases (GHs) cleave glycosidic linkages in carbohydrates, typically via inverting or retaining mechanisms, the latter of which proceeds via a two-step mechanism that includes formation of a glycosyl-enzyme intermediate. We present two new structures of the catalytic domain of Hypocrea jecorina GH Family 7 cellobiohydrolase Cel7A, namely a Michaelis complex with a full cellononaose ligand and a glycosyl-enzyme intermediate, that reveal details of the 'static' reaction coordinate. We also employ transition path sampling to determine the 'dynamic' reaction coordinate for the catalytic cycle. The glycosylation reaction coordinate contains components of forming and breaking bonds and a conformational change in the nucleophile. Deglycosylation proceeds via a product-assisted mechanism wherein the glycosylation product, cellobiose, positions a water molecule for nucleophilic attack on the anomeric carbon of the glycosyl-enzyme intermediate. In concert with previous structures, the present results reveal the complete hydrolytic reaction coordinate for this naturally and industrially important enzyme family.

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.

A new set of i-TTM potential energy functions describing the interactions between alkali metal ions and water molecules is reported. Following our previous study on halide ion–water interactions [J. Phys. Chem. B, 2016, 120, 1822], the new i-TTM potentials are derived from fits to CCSD(T) reference energies and, by construction, are compatible with the MB-pol many-body potential, which has been shown to accurately predict the properties of water from the gas to the condensed phase. Within the i-TTM formalism, two-body repulsion, electrostatic, and dispersion energies are treated explicitly, while many-body effects are represented by classical induction. The accuracy of the new i-TTM potentials is assessed through extensive comparisons with results obtained from different ab initio methods, including CCSD(T), CCSD(T)-F12b, DF-MP2, and several DFT models, as well as from polarizable force fields for M+(H2O)n clusters with M+ = Li+, Na+, K+, Rb+, and Cs+, and n = 1–4.

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.

Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.

We describe a new interface of the GPU parallelized Terachem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.

The difference-based adaptive solvation quantum mechanics/molecular mechanics (adQM/MM) method (J. Chem. Theory Comput.2009, 5, 2212) as implemented in the Amber software was applied to the study of several chemical processes in solution. The adQM/MM method is based on an efficient selection scheme that enables quantum-mechanical treatment of the active region of a molecular system in solution taking explicitly into account diffusion of solvent molecules between the QM and the MM regions. Specifically, adQM/MM molecular dynamics simulations are carried out to characterize (1) the free energy profiles of halide exchange SN2 reactions in water, (2) the hydration structure of the Cl(-) ion, and (3) the solvation structure of the zwitterionic form of glycine in water. A comparison is made with the results obtained using standard MM and QM/MM methods as well as with the available fully QM and experimental data. In all cases, it is shown that the adaptive QM/MM simulations provide a physically realistic description of the system of interest.

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.

The trinuclear complex [('S 2 '){Ni(PMe 3 )} 2 Fe(CO)('S 2 ') 2 ] (1) {'S 2 -' 2- = 1,2-benzenedithiolate(2-)} has been reported as a structural as well as functional model for [NiFe] hydro-genases since it contains key structural features of the [NiFe] hydrogenase active site, and is oxidized by protons to give [1] + and H 2 . Complex 1 formed as an unexpected product from the reaction of [Fe(CO) 2 ('S 3 ')] 2 {'S 3 '2- = bis(2-mercaptophenyl) sulfide(2-)} and [Ni(PMe 3 ) 2 ('S 2 ')]. Both the iron and nickel centers of 1 are chelated by 'S 2 ' donors, but not with any 'S 3 ' ligand. In order to understand this reaction, the new precursor [Fe(CO) 2 ( si S 3 )] 2 (2) { si S 3 2- = bis(2-mercapto-3-trimethylsilylphenyl) sulfide(2-)} was synthesized. Compound 2 readily loses its CO ligand to give [Fe(CO)( si S 3 )] 2 (3), which consists of two 16 valence electron fragments and could be isolated in the solid state. Conversion of 3 to 2 is feasible with gentle bubbling of CO gas for about 2 min. Treatment of 2 with [Ni(PMe 3 ) 2 ('S 2 ')] resulted exclusively in the formation of complex 1, which confirms that all three 'S 2 ' ligands in 1 originate from [Ni(PMe 3 ) 2 ('S 2 ')]. Therefore, an alternative synthesis of 1, which does not involve any 'S 3 ' ligand, has been developed. Density functional theory (DFT) calculations suggest that the oxidation states of the metal centers are Fe II and Ni II and do not change upon oxidation of 1 to [1] + . The unpaired electron in [1] + is located to a large extent on the nickel atoms and the adjacent thiolate donor functions. The charge, however, is distributed over the whole cluster, main parts residing on the 'S 2 ' ligands. Preliminary constant potential coulometric measurements indicate that 1 mediates the reduction of protons to dihydrogen at a mild potential (-0.48 V vs. NHE). Based upon these experimental and theoretical results, plausible mechanisms for this reduction are briefly discussed.

We have tested the performance of a large set of kinetic energy density functionals of the local density approximation (LDA), the gradient expansion approximation (GEA), and the generalized gradient approximation (GGA) for the calculation of interaction energies within a subsystem approach to density functional theory. Our results have been obtained with a new implementation of interaction energies for frozen-density embedding into the Amsterdam Density Functional program. We present data for a representative sample of 39 intermolecular complexes and 15 transition metal coordination compounds with interaction energies spanning the range from -1 to -783 kcal/mol. This is the first time that kinetic energy functionals have been tested for such strong interaction energies as the ligand-metal bonds in the investigated coordination compounds. We confirm earlier work that GGA functionals offer an improvement over the LDA and are particularly well suited for weak interactions like hydrogen bonds. We do, however, not find a particular reason to prefer any of the GGA functionals over another. Functionals derived from the GEA in general perform worse for all of the weaker interactions and cannot be recommended. An unexpectedly good performance is found for the coordination compounds, in particular with the GEA-derived functionals. However, the presently available kinetic energy functionals cannot be applied in cases in which a density redistribution between the subsystems leads to strongly overlapping subsystem electron densities. © 2009 American Chemical Society.

Enantiomerically pure cyclic (R,R)-sulfates have been transformed into novel enantiopure ligands of the general type (S,S)-2,4-R2-1-(3-phenylpropyl)phosphetane (7a−c; R = Cy, i-Pr, t-Bu). 7a−c spli...

Phthalic acid [C6H4-1,2-(COOH)2, H2PA] and terephthalic acid [C6H4-1,4-(COOH)2, H2TPA] have been reacted with aqueous solutions of the hydroxides [(η5-C5H5)2Co]+[OH]- and [(η6-C6H6)2Cr]+[OH]- produced insitu by oxidation of the parent neutral molecules. The acid–base reaction leads to self-assembly of the deprotonated acid anions into honeycomb superstructures held together by hydrogen-bonding interactions of the O–H···O and charged O–H···O- types. The superanions accommodate the [(η5-C5H5)2Co]+ and the paramagnetic [(η6-C6H6)2Cr]+ organometallic cations via charge-assisted C–Hδ+···Oδ- hydrogen bonds. Four novel organic–organometallic cocrystals, namely {[(η5-C5H5)2Co]+}4{[HPA]-}2[PA]2-·4H2O (1), [(η6-C6H6)2Cr]+-[HPA]-[H2PA] (2), {[(η5-C5H5)2Co]+}2[TPA]2-·6H2O (3) and {[(η6-C6H6)2Cr]+}2[TPA]2-·6H2O (4) have been isolated and structurally characterized by low-temperature X-ray diffraction measurements. It is shown that phthalic acid is a very versatile building block in the formation of hydrogen-bonded networks and unprecedented superanionic architectures. The role played by water molecules in the stabilization of the crystal structures in the absence of all or almost all acidic protons is discussed.

Doing things by halves: The dimeric compound (Cp'Ni)(2)(μ(2)-Se(2)) (Cp' = 1,2,3,4-tetraisopropylcyclopentadienyl), shown in the scheme, was investigated by using low temperature X-ray crystallography and X-ray absorption spectroscopy. The Se K-edge energy strongly indicates a Se physical oxidation state of -1.5, consistent with an unprecedented two-center/three-electron half-bonded Se(2)(3-) or "subselenide" ion.

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.

In the search for novel hydrogen storage media, the III-V hydridic material [NH4] [BH4] is a natural candidate. It can store a high wt% of hydrogen and has a favorable volumetric density. Unfortunately it was found to decompose slowly at room temperature. It is of interest to consider chemically related materials, such as the series of [X H4] [Y H4] ionic solids (X=B, Al,Ga and Y=N, P,As). Even if the wt% of hydrogen in the heavier congeners is necessarily lower, they might offer superior material properties, notably higher (but not too high) stability. We have therefore performed a first-principles investigation of the cohesive energies of the X H4 Y H4 solid-state materials. In addition we have analyzed the bond character and energy within the building blocks of these materials, the X H4- and Y H4+ molecular ions, including a comparison to the A H4 molecules (A=C,Si,Ge). The calculations have been performed within the density functional framework employing plane waves for the bulk materials and Slater-type functions for the molecules. A detailed study of the electronic structure reveals that the hydrides of the light (second period) elements, BH4-, CH4, and NH4+, exhibit the strongest and shortest X-H bonds. This is caused by Pauli repulsion effects of the hydrogen substituents with the larger cores of the heavier (third and fourth period) elements. The important consequence is that in the crystals, where the ionic hydrides retain their identity and charge, the distance between the negative and positive ions is larger in the heavier systems, hence less Madelung stabilization and a smaller cohesive energy. Moving from [NH4] [BH4] to heavier congeners thus does not seem to be a promising route to obtain more suitable materials for hydrogen storage. Other types of chemical variation (different substituents) on the [NH4] [BH4] building blocks may prove more advantageous. © 2009 The American Physical Society.

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.

Hydrazine nitrosation of [Ru(NO)(py(si)S4)]Br.THF (1) (py(si)S4(2-) = 2,6-bis(3-triphenylsilyl-2-sulfanylphenylthiomethyl)pyridine2-) in methanol/DMF led to the formation of mononuclear ammine complex [Ru(NH3)(py(si)S4)] (2) and N2O, whereas the reaction performed in THF/CH2Cl2/toluene afforded thioether-bridged dinuclear ammine complex [(NH3)Ru(mu-py(si)S4)Ru(py(si)S4)] (3). Compound 2 dimerizes in solution at room temperature to form 3 and is regenerated upon treatment of 3 with NH3. A plausible mechanism for the hydrazine nitrosation of 1 has been proposed. The reaction of 1 with NH3 or N3- does not lead to a nucleophilic attack at the NO+ ligand but to a deprotonation that yields neutral nitrosyl complex [Ru(NO){py(si)S4(H+)}] (4), which is supported by density functional theory calculations.

The potential-energy surfaces of 5,11-disubstituted 6,12-dimethoxychrysene and chrysene-6,12-dione derivatives were investigated by means of density functional calculations. We report relative energies of all conformers and an identification of the racemisation pathways of the chiral equilibrium structures. By analysis of homodesmotic reactions we were able to obtain an estimate for the strain energy of the substituted compounds. This strain energy can be used as a means of measuring the steric effects exerted by the substituents.

We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects in the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between (199)Hg and (13)C upon coordination of dimethylsulfoxide solvent molecules.

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.