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Dinitrogen pentoxide (N2O5) is an important intermediate in the atmospheric chemistry of nitrogen oxides. Although there has been much research, the processes that govern the physical interactions between N2O5 and water are still not fully understood at a molecular level. Gaining a quantitative insight from computer simulations requires going beyond the accuracy of classical force fields while accessing length scales and time scales that are out of reach for high-level quantum-chemical approaches. To this end, we present the development of MB-nrg many-body potential energy functions for nonreactive simulations of N2O5 in water. This MB-nrg model is based on electronic structure calculations at the coupled cluster level of theory and is compatible with the successful MB-pol model for water. It provides a physically correct description of long-range many-body interactions in combination with an explicit representation of up to three-body short-range interactions in terms of multidimensional permutationally invariant polynomials. In order to further investigate the importance of the underlying interactions in the model, a TTM-nrg model was also devised. TTM-nrg is a more simplistic representation that contains only two-body short-range interactions represented through Born-Mayer functions. In this work, an active learning approach was employed to efficiently build representative training sets of monomer, dimer, and trimer structures, and benchmarks are presented to determine the accuracy of our new models in comparison to a range of density functional theory methods. By assessing the binding curves, distortion energies of N2O5, and interaction energies in clusters of N2O5 and water, we evaluate the importance of two-body and three-body short-range potentials. The results demonstrate that our MB-nrg model has high accuracy with respect to the coupled cluster reference, outperforms current density functional theory models, and thus enables highly accurate simulations of N2O5 in aqueous environments.

The quantum mechanics/molecular mechanics (QM/MM) approach is an essential and well-established tool in computational chemistry that has been widely applied in a myriad of biomolecular problems in the literature. In this publication, we report the integration of the QUantum Interaction Computational Kernel (QUICK) program as an engine to perform electronic structure calculations in QM/MM simulations with AMBER. This integration is available through either a file-based interface (FBI) or an application programming interface (API). Since QUICK is an open-source GPU-accelerated code with multi-GPU parallelization, users can take advantage of "free of charge" GPU-acceleration in their QM/MM simulations. In this work, we discuss implementation details and give usage examples. We also investigate energy conservation in typical QM/MM simulations performed at the microcanonical ensemble. Finally, benchmark results for two representative systems in bulk water, the N-methylacetamide (NMA) molecule and the photoactive yellow protein (PYP), show the performance of QM/MM simulations with QUICK and AMBER using a varying number of CPU cores and GPUs. Our results highlight the acceleration obtained from a single or multiple GPUs; we observed speedups of up to 53× between a single GPU vs a single CPU core and of up to 2.6× when comparing four GPUs to a single GPU. Results also reveal speedups of up to 3.5× when the API is used instead of FBI.

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.

Mössbauer isomer shift and quadrupole splitting properties have been calculated using the OLYP-D3(BJ) density functional method on previously obtained (W.-G. Han Du, et al., Inorg Chem. 2020, 59, 8906-8915) geometry optimized Fe

The reactive uptake of N

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.

Quantum chemistry enables to study systems with chemical accuracy (1 kcal/mol from experiment) but is restricted to a handful of atoms due to its computational expense. This has led to ongoing interest to optimize and simplify these methods while retaining accuracy. Implementing quantum mechanical (QM) methods on modern hardware such as multiple-GPUs is one example of how the field is optimizing performance. Multiscale approaches like the so-called QM/molecular mechanical method are gaining popularity in drug discovery because they focus the application of QM methods on the region of choice (e.g., the binding site), while using efficient MM models to represent less relevant areas. The creation of simplified QM methods is another example, including the use of machine learning to create ultra-fast and accurate QM models. Herein, we summarize recent advancements in the development of optimized QM methods that enhance our ability to use these methods in computer aided drug discovery.

We report a new multi-GPU capable ab initio Hartree-Fock/density functional theory implementation integrated into the open source QUantum Interaction Computational Kernel (QUICK) program. Details on the load balancing algorithms for electron repulsion integrals and exchange correlation quadrature across multiple GPUs are described. Benchmarking studies carried out on up to four GPU nodes, each containing four NVIDIA V100-SXM2 type GPUs demonstrate that our implementation is capable of achieving excellent load balancing and high parallel efficiency. For representative medium to large size protein/organic molecular systems, the observed parallel efficiencies remained above 82% for the Kohn-Sham matrix formation and above 90% for nuclear gradient calculations. The accelerations on NVIDIA A100, P100, and K80 platforms also have realized parallel efficiencies higher than 68% in all tested cases, paving the way for large-scale ab initio electronic structure calculations with QUICK.

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.

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 ba(3) type CcO, also with comparisons/contrasts to aa(3) type CcOs. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a(3) Fe center and a near lying Cu center (called Cu(B)) where by successive reduction and protonation, molecular O(2) is transformed to two H(2)O, 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 ba(3) 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 P(R) → F → O(H) (ferryl-oxo → ferric-hydroxo) pathway to proton pumping by a water shift mechanism. Through this arc of the catalytic cycle, major shifts in pK(a)’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 Cu(B)(+) (cuprous state) in controlling access to the dinuclear reaction site is proposed.

Combined quantum mechanical/molecular mechanical (QM/MM) models using semiempirical and ab initio methods have been extensively reported on over the past few decades. These methods have been shown to be capable of providing unique insights into a range of problems, but they are still limited to relatively short time scales, especially QM/MM models using ab initio methods. An intermediate approach between a QM based model and classical mechanics could help fill this time-scale gap and facilitate the study of a range of interesting problems. Reactive force fields represent the intermediate approach explored in this paper. A widely used reactive model is ReaxFF, which has largely been applied to materials science problems and is generally used as a stand-alone (i.e., the full system is modeled using ReaxFF). We report a hybrid ReaxFF/AMBER molecular dynamics (MD) tool, which introduces ReaxFF capabilities to capture bond breaking and formation within the AMBER MD software package. This tool enables us to study local reactive events in large systems at a fraction of the computational costs of QM/MM models. We describe the implementation of ReaxFF/AMBER, validate this implementation using a benzene molecule solvated in water, and compare its performance against a range of similar approaches. To illustrate the predictive capabilities of ReaxFF/AMBER, we carried out a Claisen rearrangement study in aqueous solution. In a first for ReaxFF, we were able to use AMBER's potential of mean force (PMF) capabilities to perform a PMF study on this organic reaction. The ability to capture local reaction events in large systems using combined ReaxFF/AMBER opens up a range of problems that can be tackled using this model to address both chemical and biological processes.

International audience; Modeling adsorption at metal/water interfaces is a cornerstone toward an improved understanding in a variety of fields from heterogeneous catalysis to corrosion. We propose and validate a hybrid scheme that combines the adsorption free energies obtained in the gas phase at the density functional theory level with the variation in solvation from the bulk phase to the interface evaluated using a MM-based alchemical transformation, denoted MMsolv. Using the GAL17 force field for the platinum/water interaction, we retrieve a qualitatively correct interaction energy of the water solvent at the interface. This interaction is of near chemisorption character and thus challenging, both for the alchemical transformation and also for the fixed point-charge electrostatics. Our scheme passes through a state characterized by a well-behaved physisorption potential for the Pt(111)/H2O interaction to converge the free energy difference. The workflow is implemented in the freely available SolvHybrid package. We first assess the adsorption of a water molecule at the Pt/water interface, which turns out to be a stringent test. The intrinsic error of our quantum-mechanical/molecular mechanics (QM/MM) hybrid scheme is limited to 6 kcal mol–1 through the introduction of a correction term to attenuate the electrostatic interaction between near-chemisorbed water molecules and the underlying Pt atoms. Next, we show that the MMsolv solvation free energy of Pt (−0.46 J m–2) is in good agreement with the experimental estimate (−0.32 J m–2). Furthermore, we show that the entropy contribution at room temperature is roughly of equal magnitude as the free energy but with an opposite sign. Finally, we compute the adsorption energy of benzene and phenol at the Pt(111)/water interface, one of the rare systems for which experimental data are available. In qualitative agreement with the experiment, but in stark contrast with a standard implicit solvent model, the adsorption of these aromatic molecules is strongly reduced (i.e., less exothermic by ∼30 and 40 kcal mol–1 for our QM/MM hybrid scheme and experiment, respectively, but ∼0 with the implicit solvent) at the solid/liquid interface compared to the solid/gas interface. This reduction occurs mainly because of the competition between the organic adsorbate and the solvent for adsorption on the metallic surface. The semiquantitative agreement with experimental estimates for the adsorption energy of aromatic molecules thus validates the soundness of our hybrid QM/MM scheme.

A. Otero-de-la-Roza acknowledges support from the Spanish government for a Ramón y Cajal fellowship (No. RyC-2016-20301) and for financial support (Project Nos. PGC2018-097520-A-100 and RED2018-102612-T)., Aprà, E., Bylaska, E.J., De Jong, W.A., Govind, N., Kowalski, K., Straatsma, T.P., Valiev, M., Van Dam, H.J.J., Alexeev, Y., Anchell, J., Anisimov, V., Aquino, F.W., Atta-Fynn, R., Autschbach, J., Bauman, N.P., Becca, J.C., Bernholdt, D.E., Bhaskaran-Nair, K., Bogatko, S., Borowski, P., Boschen, J., Brabec, J., Bruner, A., Cauët, E., Chen, Y., Chuev, G.N., Cramer, C.J., Daily, J., Deegan, M.J.O., Dunning, T.H., Jr., Dupuis, M., Dyall, K.G., Fann, G.I., Fischer, S.A., Fonari, A., Früchtl, H., Gagliardi, L., Garza, J., Gawande, N., Ghosh, S., Glaesemann, K., Götz, A.W., Hammond, J., Helms, V., Hermes, E.D., Hirao, K., Hirata, S., Jacquelin, M., Jensen, L., Johnson, B.G., Jónsson, H., Kendall, R.A., Klemm, M., Kobayashi, R., Konkov, V., Krishnamoorthy, S., Krishnan, M., Lin, Z., Lins, R.D., Littlefield, R.J., Logsdail, A.J., Lopata, K., Ma, W., Marenich, A.V., Martin Del Campo, J., Mejia-Rodriguez, D., Moore, J.E., Mullin, J.M., Nakajima, T., Nascimento, D.R., Nichols, J.A., Nichols, P.J., Nieplocha, J., Otero-De-La-Roza, A., Palmer, B., Panyala, A., Pirojsirikul, T., Peng, B., Peverati, R., Pittner, J., Pollack, L., Richard, R.M., Sadayappan, P., Schatz, G.C., Shelton, W.A., Silverstein, D.W., Smith, D.M.A., Soares, T.A., Song, D., Swart, M., Taylor, H.L., Thomas, G.S., Tipparaju, V., Truhlar, D.G., Tsemekhman, K., Van Voorhis, T., Vázquez-Mayagoitia, A., Verma, P., Villa, O., Vishnu, A., Vogiatzis, K.D., Wang, D., Weare, J.H., Williamson, M.J., Windus, T.L., Woliński, K., Wong, A.T., Wu, Q., Yang, C., Yu, Q., Zacharias, M., Zhang, Z., Zhao, Y., Harrison, R.J.

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...

Interactions of N2O5 with water media are of great importance in atmospheric chemistry and have been the topic of extensive research for over two decades. Nevertheless, many physical and chemical properties of N2O5 at the surface or in bulk water are unknown or not microscopically understood. This study presents extensive new results on the physical properties of N2O5 in water and at the surface of water, with a focus on their microscopic basis. The main results are obtained using ab initio molecular dynamics and calculations of a potential of mean force. These include: (1) collisions of N2O5 with water at 300 K lead to trapping at the surface for at least 20 ps and with 95% probability. (2) During that time, there is no N2O5 hydrolysis, evaporation, or entry into the bulk. (3) Charge separation between the NO2 and NO3 groups of N2O5, fluctuates significantly with time. (4) Energy accommodation of the colliding N2O5 at the surface takes place within picoseconds. (5) The binding energy of N2O5 to a nanosize amorphous ice particle at 0 K is on the order of 15 kcal mol−1 for the main surface site. N2O5 binding to the cluster is due to one weak hydrogen bond and to interactions between partial charges on the N2O5 and on water. (6) The free-energy profile was calculated for transporting N2O5 from the gas phase through the interface and into bulk water. The corresponding concentration profile exhibits a propensity for N2O5 at the aqueous surface. The free energy barrier for entry from the surface into the bulk was determined to be 1.8 kcal mol−1. These findings are used to interpret recent experiments. We conclude with implications of this study for atmospheric chemistry.

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.

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.

The accurate representation of multidimensional potential energy surfaces is a necessary requirement for realistic computer simulations of molecular systems. The continued increase in computer power accompanied by advances in correlated electronic structure methods nowadays enables routine calculations of accurate interaction energies for small systems, which can then be used as references for the development of analytical potential energy functions (PEFs) rigorously derived from many-body (MB) expansions. Building on the accuracy of the MB-pol many-body PEF, we investigate here the performance of permutationally invariant polynomials (PIPs), neural networks, and Gaussian approximation potentials (GAPs) in representing water two-body and three-body interaction energies, denoting the resulting potentials PIP-MB-pol, Behler-Parrinello neural network-MB-pol, and GAP-MB-pol, respectively. Our analysis shows that all three analytical representations exhibit similar levels of accuracy in reproducing both two-body and three-body reference data as well as interaction energies of small water clusters obtained from calculations carried out at the coupled cluster level of theory, the current gold standard for chemical accuracy. These results demonstrate the synergy between interatomic potentials formulated in terms of a many-body expansion, such as MB-pol, that are physically sound and transferable, and machine-learning techniques that provide a flexible framework to approximate the short-range interaction energy terms., This work was supported by the National Science Foundation through Grant No. ACI-1642336 (to F.P. and A.W.G.). This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant No. ACI-1548562. J.B. is grateful for a Heisenberg professorship funded by the DFG (No. Be3264/11-2). E.Sz. would like to acknowledge the support of the Peterhouse Research Studentship and the support of BP International Centre for Advanced Materials (ICAM). M.C. was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 677013-HBMAP). G.I. acknowledges funding from the Fondazione Zegna

Interactions of N2O5 with water media are of great importance in atmospheric chemistry and have been the topic of extensive research for over two decades. Nevertheless, many physical and chemical properties of N2O5 at the surface or in bulk water are unknown or not microscopically understood. This study presents extensive new results on the physical properties of N2O5 in water and at the surface of water, with a focus on their microscopic basis. The main results are obtained using ab initio molecular dynamics and calculations of a potential of mean force. These include: (1) collisions of N2O5 with water at 300 K lead to trapping at the surface for at least 20 ps and with 95% probability. (2) During that time, there is no N2O5 hydrolysis, evaporation, or entry into the bulk. (3) Charge separation between the NO2 and NO3 groups of N2O5, fluctuates significantly with time. (4) Energy accommodation of the colliding N2O5 at the surface takes place within picoseconds. (5) The binding energy of N2O5 to a nanosize amorphous ice particle at 0 K is on the order of 15 kcal mol-1 for the main surface site. N2O5 binding to the cluster is due to one weak hydrogen bond and to interactions between partial charges on the N2O5 and on water. (6) The free-energy profile was calculated for transporting N2O5 from the gas phase through the interface and into bulk water. The corresponding concentration profile exhibits a propensity for N2O5 at the aqueous surface. The free energy barrier for entry from the surface into the bulk was determined to be 1.8 kcal mol-1. These findings are used to interpret recent experiments. We conclude with implications of this study for atmospheric chemistry.

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.

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 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 Å) is by 0.03 Å longer than that in PR (1.65 Å), 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 around 2.4 Å. Hence the subsequent OH state [Fea33+-OH−-CuB2+] with a μ-hydroxo bridge can be easily formed as shown by our calculations.

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.