Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water

Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel

The self-consistent charge density functional tight binding (SCC-DFTB) method has been increasingly applied to study proton transport (PT) in biological environments. However, recent studies revealing some significant limitations of SCC-DFTB for proton and hydroxide solvation and transport in bulk aqueous systems call into question its accuracy for simulating PT in biological systems. The current work benchmarks the SCC-DFTB/MM method against more accurate DFT/MM by simulating PT in a synthetic leucine-serine channel (LS2), which emulates the structure and function of biomolecular proton channels. It is observed that SCC-DFTB/MM produces over-coordinated and less structured pore water, an over-coordinated excess proton, weak hydrogen bonds around the excess proton charge defect and qualitatively different PT dynamics. Similar issues are demonstrated for PT in a carbon nanotube, indicating that the inaccuracies found for SCC-DFTB are not due to the point charge based QM/MM electrostatic coupling scheme, but rather to the approximations of the semiempirical method itself. The results presented in this work highlight the limitations of the present form of the SCC-DFTB/MM approach for simulating PT processes in biological protein or channel-like environments, while providing benchmark results that may lead to an improvement of the underlying method.

Quantum mechanical force field for water with explicit electronic polarization

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

Anomalous stability of graphene containing defects covered by a water layer

Defects are inevitably present in graphene and can alter its properties and thus its applications. Interestingly, we find that commonly observed Stone-Wales and double vacancy defects do not affect graphene's hydrophilic and hydrophobic properties and that an adsorbed single water layer does not noticeably affect the defect-containing graphene's electronic properties. Our findings are based on calculations using a density functional tight-binding theory. Specifically, we observe negligible alteration in the interaction strength (less than 0.1 kcal mol(-1)) between a single water layer and graphene upon the incorporation of the various types of defects, which indicates that graphene has relatively stable hydrophilic and hydrophobic properties. The presence of a single water layer causes only negligible changes in the energy gap and a small charge transfer to the aqueous layer (less than 0.1 e). The results indicate that the electronic properties of graphene are determined mainly by its own structural characteristics and are not considerably affected by the adsorbed water layer. Further electronic structure analysis reveals that the two commonly observed defects do not change the sp(2) hybridization characteristics of the C atoms of graphene even in the water environment. Our results are significant for graphene studies and applications in areas such as life sciences and materials science where hydrophilic and hydrophobic properties and electronic properties are important.

Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models

The semiempirical MNDO-based AM1 and PM3 methods and the orthogonalization-corrected OM1, OM2, and OM3 models were reparameterized to improve their description of bulk water and of proton transfer in water. Reference data included the gas-phase geometries and energies of the water molecule, small water clusters, the hydronium ion, and small hydronium ion-water clusters, as well as the gas-phase potential energy surface for proton transfer between the two water molecules in a Zundel ion, all calculated at the MP2/aug-cc-pVTZ level of theory. Combined QM/MM molecular dynamics simulations were carried out for bulk water and for a proton solvated in water using large cluster models. Both the authentic and reparameterized semiempirical models were employed in the simulations. The reparameterization led to significantly better results in all cases. The new set of OM3 parameters gave the best overall results for the structural and dynamic properties of water and the hydrated proton, with a small but finite barrier of 0.1-0.2 kcal/mol in the potential of mean force for proton transfer, in agreement with ab initio path-integral molecular dynamics simulations. The reparameterized OM3 model is expected to be useful for efficient modeling of proton transfer in aqueous solution.

Assessing the Accuracy of Density Functional and Semiempirical Wave Function Methods for Water Nanoparticles: Comparing Binding and Relative Energies of (H2O)16 and (H2O)17 to CCSD(T) Results

The binding energies and relative conformational energies of five configurations of the water 16-mer are computed using 61 levels of density functional (DF) theory, 12 methods combining DF theory with molecular mechanics damped dispersion (DF-MM), seven semiempirical-wave function (SWF) methods, and five methods combining SWF theory with molecular mechanics damped dispersion (SWF-MM). The accuracies of the computed energies are assessed by comparing them to recent high-level ab initio results; this assessment is more relevant to bulk water than previous tests on small clusters because a 16-mer is large enough to have water molecules that participate in more than three hydrogen bonds. We find that for water 16-mer binding energies the best DF, DF-MM, SWF, and SWF-MM methods (and their mean unsigned errors in kcal/mol) are respectively M06-2X (1.6), ωB97X-D (2.3), SCC-DFTB-γ(h) (35.2), and PM3-D (3.2). We also mention the good performance of CAM-B3LYP (1.8), M05-2X (1.9), and TPSSLYP (3.0). In contrast, for relative energies of various water nanoparticle 16-mer structures, the best methods (and mean unsigned errors in kcal/mol), in the same order of classes of methods, are SOGGA11-X (0.3), ωB97X-D (0.2), PM6 (0.4), and PMOv1 (0.6). We also mention the good performance of LC-ωPBE-D3 (0.3) and ωB97X (0.4). When both relative and binding energies are taken into consideration, the best methods overall (out of the 85 tested) are M05-2X without molecular mechanics and ωB97X-D when molecular mechanics corrections are included; with considerably higher average errors and considerably lower cost, the best SWF or SWF-MM method is PMOv1. We use six of the best methods for binding energies of the water 16-mers to calculate the binding energies of water hexamers and water 17-mers to test whether these methods are also reliable for binding energy calculations on other types of water clusters.

Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms

Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.

A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries

We present benchmark calculations of nine selected points on potential energy surfaces describing proton transfer process in three model systems, H(5)O(2) (+), CH(3)OH…H(+)…OH(2), and CH(3)COOH…OH(2). The calculated relative energies of these geometries are compared to those calculated by various wave function and density functional methods, including the polarized molecular orbital (PMO) model recently developed in our research group and other semiempirical molecular orbital methods. We found that the SCC-DFTB and PMO methods (the latter available so far only for molecules consisting of only O and H and therefore only for the first of the three model systems) give results that are, on average, within 2 kcal/mol of the benchmark results. Other semiempirical molecular orbital methods have mean unsigned errors (MUEs) of 3 to 8 kcal/mol, local density functionals have MUEs in the range 0.7 to 3.7 kcal/mol, and hybrid density functionals have MUEs of only 0.3 to 1.0 kcal/mol, with the best density functional performance obtained by hybrid meta-GGAs, especially M06 and PW6B95.

Insights into the mechanism of proton transport in cytochrome c oxidase

Cytochrome c oxidase (CcO), known as complex IV of the electron transport chain, plays several important roles in aerobic cellular respiration. Electrons transferred from cytochrome c to CcO's catalytic site reduce molecular oxygen and produce a water molecule. These electron transfers also drive active proton pumping from the matrix (N-side) to intermembrane region (P-side) in mitochondria; the resultant proton gradient activates ATP synthase to produce ATP from ADP. Although the existence of the coupling between the electron transfer and the proton transport (PT) is established experimentally, its mechanism is not yet fully understood at the molecular level. In this work, it is shown why the reduction of heme a is essential for proton pumping. This is demonstrated via novel reactive molecular dynamics (MD) simulations that can describe the Grotthuss shuttling associated with the PT as well as the dynamic delocalization of the excess proton electronic charge defect. Moreover, the "valve" role of the Glu242 residue (bovine CcO notation) and the gate role of d-propionate of heme a(3) (PRDa3) in the explicit PT are explicitly demonstrated for the first time. These results provide conclusive evidence for the CcO proton transporting mechanism inferred from experiments, while deepening the molecular level understanding of the CcO proton switch.

Glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome C oxidase

One of the key unresolved issues regarding proton pumping in cytochrome c oxidase (CcO) is the identity of the gating element that prevents the backflow of protons. In this study, we analyze two popular proposals for this element: isomerization of the key branching residue (Glu-286) and (re)orientation of water molecules in the hydrophobic cavity. Using a multifaceted set of computational analyses that involve CcO embedded in either an implicit or explicit treatment of lipid membrane, we show that neither Glu-286 nor active-site water likely constitutes the gating element. Detailed energetic and structural analyses of the simulation results indicate that the gating-relevant properties of these structural motifs observed in previous work are likely a result of the simplified computational models employed in those studies.