Excited-State Dynamics and Nonlinear Optical Properties of Hyperpolarizable Chromophores Based on Conjugated Bis(terpyridyl)Ru(II) and Palladium and Platinum Porphyrinic Components: Impact of Heavy Metals upon Supermolecular Electro-Optic Properties.

A new series of strongly coupled oscillators based upon (porphinato)Pd, (porphinato)Pt, and bis(terpyridyl)ruthenium(II) building blocks is described. These RuPPd, RuPPt, RuPPdRu, and RuPPtRu chromophores feature bis(terpyridyl)Ru(II) moieties connected to the (porphinato)metal unit via an ethyne linker that bridges the 4'-terpyridyl and porphyrin macrocycle meso-carbon positions. Pump-probe transient optical data demonstrate sub-picosecond excited singlet-to-triplet-state relaxation. The relaxed lowest-energy triplet (T1) excited states of these chromophores feature absorption manifolds that span the 800-1200 nm spectral region, microsecond triplet-state lifetimes, and large absorptive extinction coefficients [ε(T1 → Tn) > 4 × 104 M-1 cm-1]. Dynamic hyperpolarizability (ßλ) values were determined from hyper-Rayleigh light scattering (HRS) measurements carried out at several incident irradiation wavelengths over the 800-1500 nm spectral region. Relative to benchmark RuPZn and RuPZnRu chromophores which showed large ßHRS values over the 1200-1600 nm range, RuPPd, RuPPt, RuPPdRu, and RuPPtRu displayed large ßHRS values over the 850-1200 nm region. Generalized Thomas-Kuhn sum (TKS) rules and experimental hyperpolarizability values were utilized to determine excited state-to-excited state transition dipole terms from experimental electronic absorption data and thus assessed frequency-dependent ßλ values, including two- and three-level contributions for both ßzzz and ßxzx tensor components to the RuPPd, RuPPt, RuPPdRu, and RuPPtRu hyperpolarizability spectra. These analyses qualitatively rationalize how the ßzzz and ßxzx tensor elements influence the observed irradiation wavelength-dependent hyperpolarizability magnitudes. The TKS analysis suggests that supermolecules related to RuPPd, RuPPt, RuPPdRu, and RuPPtRu will likely feature intricate dependences of experimentally determined ßHRS values as a function of irradiation wavelength that derive from substantial singlet-triplet mixing, and complex interactions among multiple different ß tensor components that modulate the long wavelength regime of the nonlinear optical response.

Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants.

Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.

Large Hyperpolarizabilities at Telecommunication-Relevant Wavelengths in Donor-Acceptor-Donor Nonlinear Optical Chromophores.

Octopolar D2-symmetric chromophores, based on the MPZnM supermolecular motif in which (porphinato)zinc(II) (PZn) and ruthenium(II) polypyridyl (M) structural units are connected via ethyne linkages, were synthesized. These structures take advantage of electron-rich meso-arylporphyrin or electron-poor meso-(perfluoroalkyl)porphyrin macrocycles, unsubstituted terpyridyl and 4'-pyrrolidinyl-2,2';6',2″-terpyridyl ligands, and modulation of metal(II) polypyridyl-to-(porphinato)zinc connectivity, to probe how electronic and geometric factors impact the measured hyperpolarizability. Transient absorption spectra obtained at early time delays (tdelay < 400 fs) demonstrate fast excited-state relaxation, and formation of a highly polarized T1 excited state; the T1 states of these chromophores display expansive, intense T1 → T n absorption manifolds that dominate the 800-1200 nm region of the NIR, long (µs) triplet-state lifetimes, and unusually large NIR excited absorptive extinction coefficients [ε(T1 → T n ) ∼ 105 M-1 cm-1]. Dynamic hyperpolarizability (ßλ) values were determined from hyper-Rayleigh light scattering (HRS) measurements, carried out at multiple incident irradiation wavelengths spanning the 800-1500 nm spectral domain. The measured ßHRS value (4600 ± 1200 × 10-30 esu) for one of these complexes, RuPZnRu, is the largest yet reported for any chromophore at a 1500 nm irradiation wavelength, highlighting that appropriate engineering of strong electronic coupling between multiple charge-transfer oscillators provides a critical design strategy to realize octopolar NLO chromophores exhibiting large ßHRS values at telecom-relevant wavelengths. Generalized Thomas-Kuhn sum (TKS) rules were utilized to compute the effective excited-state-to-excited-state transition dipole moments from experimental linear-absorption spectra; these data were then utilized to compute hyperpolarizabilities as a function of frequency, that include two- and three-state contributions for both ß zzz and ß xzx tensor components to the RuPZnRu hyperpolarizability spectrum. This analysis predicts that the ß zzz and ß xzx tensor contributions to the RuPZnRu hyperpolarizability spectrum maximize near 1550 nm, in agreement with experimental data. The TKS analysis suggests that relative to analogous dipolar chromophores, octopolar supermolecules will be likely characterized by more intricate dependences of the measured hyperpolarizability upon irradiation wavelength due to the interactions among multiple different ß tensor components.

Shifting Electronic Structure by Inherent Tension in Molecular Bottlebrushes with Polythiophene Backbones.

Bottlebrush macromolecules can be regarded as molecular tensile machines, where tension is self-generated along the backbone due to steric repulsion between densely grafted side chains. This intrinsic tension is amplified upon adsorption of bottlebrush molecules onto a substrate and increases with grafting density, side chain length, and strength of adhesion to the substrate. To investigate the effects of tension on the electronic structure of polythiophene (PT), bottlebrush macromolecules were prepared by grafting poly(n-butyl acrylate) (PBA) side chains from PT macroinitiators by atom transfer radical polymerization (ATRP). The fluorescence spectra of submonolayers of PT bottlebrushes were measured on a Langmuir-Blodgett (LB) trough with the backbone tension adjusted by controlling the side-chain length, surface pressure, and chemical composition of a substrate. The wavelength of maximum emission has initially red-shifted, followed by a blue-shift as the backbone tension increases from 0 to 2.5 nN, which agrees with DFT calculations. The red-shift is ascribed to an increase in the conjugation length due to the extension of the PT backbone at lower force regime (0-1.0 nN), while the blue-shift is attributed to deformations of bond lengths and angles in the backbone at higher force regime (1.0-2.5 nN).

Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods.

Conventional combined quantum mechanical/molecular mechanical (QM/MM) methods lack explicit treatment of Pauli repulsions between the quantum-mechanical and molecular-mechanical subsystems. Instead, classical Lennard-Jones (LJ) potentials between QM and MM nuclei are used to model electronic Pauli repulsion and long-range London dispersion, despite the fact that the latter two are inherently of quantum nature. Use of the simple LJ potential in QM/MM methods can reproduce minimal geometries and energies of many molecular clusters reasonably well, as compared to full QM calculations. However, we show here that the LJ potential cannot correctly describe subtle details of the electron density of the QM subsystem because of the neglect of Pauli repulsions between the QM and MM subsystems. The inaccurate electron density subsequently affects the calculation of electronic and magnetic properties of the QM subsystem. To explicitly consider Pauli interactions with QM/MM methods, we propose a method to use empirical effective potentials on the MM atoms. The test case of the binding energy and magnetic properties of a water dimer shows promising results for the general application of effective potentials to mimic Pauli repulsions in QM/MM calculations.

Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies.

Charge recombination rate constants vary no more than 3-fold for interprotein ET in the Zn-substituted wild type (WT) cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and in complexes with four mutants of the Cc protein (i.e., F82S, F82W, F82Y, and F82I), despite large differences in the ET distance. Theoretical analysis indicates that charge recombination for all complexes involves a combination of tunneling and hopping via Trp191. For three of the five structures (WT and F82S(W)), the protein favors hopping more than that in the other two structures that have longer heme → ZnP distances (F82Y(I)). Experimentally observed biexponential ET kinetics is explained by the complex locking in alternative coupling pathways, where the acceptor hole state is either primarily localized on ZnP (slow phase) or on Trp191 (fast phase). The large conformational differences between the CcP:Cc interface for the F82Y(I) mutants compared to that the WT and F82S(W) complexes are predicted to change the reorganization energies for the CcP:Cc ET reactions because of changes in solvent exposure and interprotein ET distances. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy compensates the decreased role for hopping recombination (and the longer transfer distance) in the F82Y(I) mutants. Taken together, coupling pathway and reorganization energy effects for the five protein complexes explain the observed insensitivity of recombination kinetics to donor-acceptor distance and docking pose and also reveals how hopping through aromatic residues can accelerate long-range ET.

Noncovalent Interaction Analysis in Fluctuating Environments.

Noncovalent interactions play a central role in many chemical and biological systems. In a previous study, Johnson et al developed a NonCovalent Interaction (NCI) index to characterize and visualize different types of weak interactions. To apply the NCI analysis to fluctuating environments as in solution phase, we here develop a new Averaged NonCovalent Interaction (i.e., aNCI) index along with a fluctuation index to characterize magnitude of interactions and fluctuations. We applied aNCI for various systems including solute-solvent and ligand-protein noncovalent interactions. For water and benzene molecules in aqueous solution, solvation structures and the specific hydrogen bond patterns were visualized clearly. For the Cl-+CH3Cl SN2 reaction in aqueous solution, charge reorganization influences over solvation structure along SN2 reaction were revealed. For ligand-protein systems, aNCI can recover several key fluctuating hydrogen bond patterns that have potential applications for drug design. Therefore, aNCI, as a complementary approach to the original NCI method, can extract and visualize noncovalent interactions from thermal noise in fluctuating environments.

Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.

Variational fractional-spin density-functional theory for diradicals.

Accurate computation of singlet-triplet energy gaps of diradicals remains a challenging problem in density-functional theory (DFT). In this work, we propose a variational extension of our previous work [D. H. Ess, E. R. Johnson, X. Q. Hu, and W. T. Yang, J. Phys. Chem. A 115, 76 (2011)], which applied fractional-spin density-functional theory (FS-DFT) to diradicals. The original FS-DFT approach assumed equal spin-orbital occupancies of 0.5 α-spin and 0.5 ß-spin for the two degenerate, or nearly degenerate, frontier orbitals. In contrast, the variational approach (VFS-DFT) optimizes the total energy of a singlet diradical with respect to the frontier-orbital occupation numbers, based on a full configuration-interaction picture. It is found that the optimal occupation numbers are exactly 0.5 α-spin and 0.5 ß-spin for diradicals such as O(2), where the frontier orbitals belong to the same multidimensional irreducible representation, and VFS-DFT reduces to FS-DFT for these cases. However, for diradicals where the frontier orbitals do not belong to the same irreducible representation, the optimal occupation numbers can vary between 0 and 1. Furthermore, analysis of CH(2) by VFS-DFT and FS-DFT captures the (1)A(1) and (1)B(1) states, respectively. Finally, because of the static correlation error in commonly used density functional approximations, both VFS-DFT and FS-DFT calculations significantly overestimate the singlet-triplet energy gaps for disjoint diradicals, such as cyclobutadiene, in which the frontier orbitals are confined to separate atomic centers.

Tension trapping of carbonyl ylides facilitated by a change in polymer backbone.

Epoxidized polybutadiene and epoxidized polynorbornene were subjected to pulsed ultrasound in the presence of small molecules capable of being trapped by carbonyl ylides. When epoxidized polybutadiene was sonicated, there was no observable small molecule addition to the polymer. Concurrently, no appreciable isomerization (cis to trans epoxide) was observed, indicating that the epoxide rings along the backbone are not mechanically active under the experimental conditions employed. In contrast, when epoxidized polynorbornene was subjected to the same conditions, both addition of ylide trapping reagents and net isomerization of cis to trans epoxide were observed. The results demonstrate the mechanical activity of epoxides, show that mechanophore activity is determined not only by the functional group but also the polymer backbone in which it is embedded, and facilitate a characterization of the reactivity of the ring-opened dialkyl epoxide.

Theoretical study of catalytic mechanism for single-site water oxidation process.

Water oxidation is a linchpin in solar fuels formation, and catalysis by single-site ruthenium complexes has generated significant interest in this area. Combining several theoretical tools, we have studied the entire catalytic cycle of water oxidation for a single-site catalyst starting with [Ru(II)(tpy)(bpm)(OH(2))](2+) (i.e., [Ru(II)-OH(2)](2+); tpy is 2,2':6',2''-terpyridine and bpm is 2,2'-bypyrimidine) as a representative example of a new class of single-site catalysts. The redox potentials and pK(a) calculations for the first two proton-coupled electron transfers (PCETs) from [Ru(II)-OH(2)](2+) to [Ru(IV) = O](2+) and the following electron-transfer process to [Ru(V) = O](3+) suggest that these processes can proceed readily in acidic or weakly basic conditions. The subsequent water splitting process involves two water molecules, [Ru(V) = O](3+) to generate [Ru(III)-OOH](2+), and H(3)O(+) with a low activation barrier (~10 kcal/mol). After the key O-O bond forming step in the single-site Ru catalysis, another PECT process oxidizes [Ru(III)-OOH](2+) to [Ru(IV)-OO](2+) when the pH is lower than 3.7. Two possible forms of [Ru(IV)-OO](2+), open and closed, can exist and interconvert with a low activation barrier (< 7 kcal/mol) due to strong spin-orbital coupling effects. In Pathway 1 at pH = 1.0, oxygen release is rate-limiting with an activation barrier ~12 kcal/mol while the electron-transfer step from [Ru(IV)-OO](2+) to [Ru(V)-OO](3+) becomes rate-determining at pH = 0 (Pathway 2) with Ce(IV) as oxidant. The results of these theoretical studies with atomistic details have revealed subtle details of reaction mechanisms at several stages during the catalytic cycle. This understanding is helpful in the design of new catalysts for water oxidation.

Liquid water simulations with the density fragment interaction approach.

We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129, 054102.] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve the efficiency of the DFI approach and thus enable the calculations for large molecules: the electrostatic interactions between fragments are computed efficiently by means of polarizable electrostatic-potential-fitted atomic charges; and frozen fragment pseudopotentials, similar to the effective fragment potentials that can be fitted from interactions between small molecules, are employed to take into account the Pauli repulsion effect among fragments. Our reformulated and parallelized DFI method demonstrates excellent parallel performance based on the benchmarks for the system of 256 water molecules. Molecular dynamics simulations for the structural properties of liquid water also show a qualitatively good agreement with experimental measurements including the heat capacity, binding energy per water molecule, and the radial distribution functions of atomic pairs of O-O, O-H, and H-H. With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible.

Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways.

4-Oxalocrotonate tautomerase (4-OT), a member of tautomerase superfamily, is an essential enzyme in the degradative metabolism pathway occurring in the Krebs cycle. The proton transfer process catalyzed by 4-OT has been explored previously using both experimental and theoretical methods; however, the elaborate catalytic mechanism of 4-OT still remains unsettled. By combining classical molecular mechanics with quantum mechanics, our results demonstrate that the native hexametric 4-OT enzyme, including six protein monomers, must be employed to simulate the proton transfer process in 4-OT due to protein-protein steric and electrostatic interactions. As a consequence, only three out of the six active sites in the 4-OT hexamer are observed to be occupied by three 2-oxo-4-hexenedioates (2o4hex), i.e., half-of-the-sites occupation. This agrees with experimental observations on negative cooperative effect between two adjacent substrates. Two sequential proton transfers occur: one proton from the C3 position of 2o4hex is initially transferred to the nitrogen atom of the general base, Pro1. Subsequently, the same proton is shuttled back to the position C5 of 2o4hex to complete the proton transfer process in 4-OT. During the catalytic reaction, conformational changes (i.e., 1-carboxyl group rotation) of 2o4hex may occur in the 4-OT dimer model but cannot proceed in the hexametric structure. We further explained that the docking process of 2o4hex can influence the specific reactant conformations and an alternative substrate (2-hydroxymuconate) may serve as reactant under a different reaction mechanism than 2o4hex.

Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.

We describe the new Pathways plugin for the molecular visualization program visual molecular dynamics. The plugin identifies and visualizes tunneling pathways and pathway families in biomolecules, and calculates relative electronic couplings. The plugin includes unique features to estimate the importance of individual atoms for mediating the coupling, to analyze the coupling sensitivity to thermal motion, and to visualize pathway fluctuations. The Pathways plugin is open source software distributed under the terms of the GNU's Not Unix (GNU) public license.

Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru2+-Ru3+ Self-Exchange Electron Transfer.

A fragment-based fractional number of electron (FNE) approach, is developed to study entire electron transfer (ET) processes from the electron donor region to the acceptor region in condensed phase. Both regions are described by the density-fragment interaction (DFI) method while FNE as an efficient ET order parameter is applied to simulate the electron transfer process. In association with the QM/MM energy expression, the DFI-FNE method is demonstrated to describe ET processes robustly with the Ru2+-Ru3+ self-exchange ET as a proof-of-concept example. This method allows for systematic calculations of redox free energies, reorganization energies, and electronic couplings, and the absolute ET rate constants within the Marcus regime.

Improving band gap prediction in density functional theory from molecules to solids.

A novel nonempirical scaling correction method is developed to tackle the challenge of band gap prediction in density functional theory. For finite systems the scaling correction largely restores the straight-line behavior of electronic energy at fractional electron numbers. The scaling correction can be generally applied to a variety of mainstream density functional approximations, leading to significant improvement in the band gap prediction. In particular, the scaled version of a modified local density approximation predicts band gaps with an accuracy consistent for systems of all sizes, ranging from atoms and molecules to solids. The scaled modified local density approximation thus provides a useful tool to quantitatively characterize the size-dependent effect on the energy gaps of nanostructures.

λ-Meta Dynamics Approach To Compute Absolute Solvation Free Energy.

We present a new approach to combine λ dynamics with meta-dynamics (named λ-meta dynamics) to compute free energy surface with respect to λ. Particularly, the λ-meta dynamics method extends meta-dynamics to a single virtual variable λ, i.e., the coupling parameter between solute and solvent, to compute absolute solvation free energy as an exemplary application. We demonstrate that λ-meta dynamics simulations can recover the accurate potential of mean force surface with respect to λ compared to the benchmark results from traditional λ-dynamics with umbrella sampling. The solvation free energy results for five small organic molecules from λ-meta dynamics simulations using the same filling scheme show that the statistical errors are within ±0.5 kcal/mol. The new λ-meta dynamics method is general and other variables such as order parameters to describe conformational changes can be easily combined with λ-meta dynamics. This should allow for efficient samplings on high-dimension free energy landscapes.

Singlet-triplet energy gaps for diradicals from fractional-spin density-functional theory.

Open-shell singlet diradicals are difficult to model accurately within conventional Kohn-Sham (KS) density-functional theory (DFT). These methods are hampered by spin contamination because the KS determinant wave function is neither a pure spin state nor an eigenfunction of the S(2) operator. Here we present a theoretical foray for using single-reference closed-shell ground states to describe diradicals by fractional-spin DFT (FS-DFT). This approach allows direct, self-consistent calculation of electronic properties using the electron density corresponding to the proper spin eigenfunction. The resulting FS-DFT approach is benchmarked against diradical singlet-triplet gaps for atoms and small molecules. We have also applied FS-DFT to the singlet-triplet gaps of hydrocarbon polyacenes.

Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation.

Many gram-positive pathogens possess external pili or fimbriae with which they adhere to host cells during the infection process. Unusual dual intramolecular isopeptide bonds between Asn and Lys side chains within the N-terminal and C-terminal domains of the pilus subunits have been observed initially in the Streptococcus pyogenes pilin subunit Spy0128 and subsequently in GBS52 from Streptococcus agalactiae, in the BcpA major pilin of Bacillus cereus and in the RrgB pilin of Streptococcus pneumoniae, among others. Within each pilin subunit, intramolecular isopeptide bonds serve to stabilize the protein. These bonds provide a means to withstand large external mechanical forces, as well as possibly assisting in supporting a conformation favored for pilin subunit polymerization via sortase transpeptidases. Genome-wide analyses of pili-containing gram-positive bacteria are known or suspected to contain isopeptide bonds in pilin subunits. For the autocatalytic formation of isopeptide cross-links, a conservation of three amino acids including Asn, Lys, and a catalytically important acidic Glu (or Asp) residue are responsible. However, the chemical mechanism of how isopeptide bonds form within pilin remains poorly understood. Although it is possible that several mechanistic paths could lead to isopeptide bond formation in pili, the requirement of a conserved glutamate and highly organized positioning of residues within the hydrophobic environment of the active site were found in numerous pilin crystal structures such as Spy0128 and RrgB. This suggests a mechanism involving direct coupling of lysine side chain amine to the asparagine carboxamide mediated by critical acid/base or hydrogen bonding interactions with the catalytic glutamate residue. From this mechanistic perspective, we used the QM/MM minimum free-energy path method to examine the reaction details of forming the isopeptide bonds with Spy0128 as a model pilin, specifically focusing on the role of the glutamate in catalysis. It was determined that the reaction mechanism likely consists of two major steps: the nucleophilic attack on Cγ by nitrogen in the unprotonated Lys ε-amino group and, then two concerted proton transfers occur during the formation of the intramolecular isopeptide bond to subsequently release ammonia. More importantly, within the dual active sites of Spy0128, Glu(117), and Glu(258) residues function as crucial catalysts for each isopeptide bond formation, respectively, by relaying two proton transfers. This work also suggests that domain-domain interactions within Spy0128 may modulate the reactivity of residues within each active site. Our results may hopefully shed light on the molecular mechanisms of pilin biogenesis in gram-positive bacteria.

Concerted O atom-proton transfer in the O-O bond forming step in water oxidation.

As the terminal step in photosystem II, and a potential half-reaction for artificial photosynthesis, water oxidation (2H(2)O --> O(2) + 4e(-) + 4H(+)) is key, but it imposes a significant mechanistic challenge with requirements for both 4e(-)/4H(+) loss and O-O bond formation. Significant progress in water oxidation catalysis has been achieved recently by use of single-site Ru metal complex catalysts such as [Ru(Mebimpy)(bpy)(OH(2))](2+) [Mebimpy = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine; bpy = 2,2'-bipyridine]. When oxidized from to Ru(V) = O(3+), these complexes undergo O-O bond formation by O-atom attack on a H(2)O molecule, which is often the rate-limiting step. Microscopic details of O-O bond formation have been explored by quantum mechanical/molecular mechanical (QM/MM) simulations the results of which provide detailed insight into mechanism and a strategy for enhancing catalytic rates. It utilizes added bases as proton acceptors and concerted atom-proton transfer (APT) with O-atom transfer to the O atom of a water molecule in concert with proton transfer to the base (B). Base catalyzed APT reactivity in water oxidation is observed both in solution and on the surfaces of oxide electrodes derivatized by attached phosphonated metal complex catalysts. These results have important implications for catalytic, electrocatalytic, and photoelectrocatalytic water oxidation.