pDynamo3 Molecular Modeling and Simulation Program.

pDynamo3 is the first formal version of the Dynamo molecular modeling and simulation library that is written in Python 3. It follows from the previous pDynamo versions written in Python 2, the first of which was released in 2007. Both pDynamo and its predecessor, fDynamo, were designed with the aim of providing easy-to-use and flexible frameworks for performing molecular simulations at an atomistic level with a special emphasis on those employing hybrid quantum chemical and molecular mechanical potential methods. Although the use of pDynamo3 is quite similar to that of pDynamo2, it has added significant new capability and also undergone extensive restructuring that will make it much easier to extend with new functionality. The pDynamo3 code is issued under the GNU general public license at https://github.com/pdynamo/pDynamo3 with additional information on the pDynamo website https:www.pdynamo.org.

Density Fitting for QC/MM Interactions.

Density fitting is a standard technique in quantum chemistry as it helps to accelerate certain parts of a calculation, such as the computation of the electron repulsion energy, without significant loss of accuracy. This paper explores the effectiveness of this technique when it is extended to treat interactions with external electrostatic potentials, in particular those that arise from the environment in hybrid quantum chemical/molecular mechanical calculations. It is found that fitted densities are able to well reproduce the energies, forces, and properties obtained using unfitted densities, as long as a suitable operator is employed for the fitting. It is expected that this precision would be improved by the development of basis sets specifically designed to treat these types of interactions and that the use of this approximation could lead to substantial speed-ups in large hybrid potential simulations.

Electrocatalytic Hydrogen Evolution with a Cobalt Complex Bearing Pendant Proton Relays: Acid Strength and Applied Potential Govern Mechanism and Stability.

[Co(bapbpy)Cl]+ (bapbpy: 6,6'-bis(2-aminopyridyl)-2,2'-bipyridine) is a polypyridyl cobalt(II) complex bearing both a redox-active bipyridine ligand and pendant proton relays. This compound catalyzes electro-assisted H2 evolution in DMF with distinct mechanisms depending on the strength of the acid used as the proton source (pKa values ranging from 3.4 to 13.5 in DMF) and the applied potential. Electrochemical studies combining cyclic voltammetry and bulk electrolysis measurements enabled one to bring out four distinct catalytic processes. Where applicable, relevant kinetic information were obtained using either foot-of-the-wave analysis (FOWA) or analytical treatment of bulk electrolysis experiments. Among the different catalytic pathways identified in this study, a clear relationship between the catalyst performances and stability was evidenced. These results draw attention to a number of interesting considerations and may help in the development of future adequately designed catalysts.

Modeling the Hydrolysis of Iron-Sulfur Clusters.

Iron-sulfur (FeS) clusters are essential metal cofactors involved in a wide variety of biological functions. Their catalytic efficiency, biosynthesis, and regulation depend on FeS stability in aqueous solution. Here, molecular modeling is used to investigate the hydrolysis of an oxidized (ferric) mononuclear FeS cluster by bare dissociation and water substitution mechanisms in neutral and acidic solution. First, approximate electronic structure descriptions of FeS reactions by density functional theory are validated against high-level wave function CCSD(T) calculations. Solvation contributions are included by an all-atom model with hybrid quantum chemical/molecular mechanical (QM/MM) potentials and enhanced sampling molecular dynamics simulations. The free energy profile obtained for FeS cluster hydrolysis indicates that the hybrid functional M06 together with an implicit solvent correction capture the most important aspects of FeS cluster reactivity in aqueous solution. Then, 20 reaction channels leading to two consecutive Fe-S bond ruptures were explored with this calibrated model. For all protonation states, nucleophilic substitution with concerted bond breaking and forming to iron is the preferred mechanism, both kinetic and thermodynamically. In neutral solution, proton transfer from water to the sulfur leaving group is also concerted. Dissociative reactions show higher barriers and will not be relevant for FeS reactivity when exposed to solvent. These hydrolysis mechanisms may help to explain the stability and catalytic mechanisms of FeS clusters of multiple sizes and proteins.

Negative Impact of Carbapenem Methylation on the Reactivity of ß-Lactams for Cysteine Acylation as Revealed by Quantum Calculations and Kinetic Analyses.

The Enterococcus faecium l,d-transpeptidase (Ldtfm) mediates resistance to most ß-lactam antibiotics in this bacterium by replacing classical peptidoglycan polymerases. The catalytic Cys of Ldtfm is rapidly acylated by ß-lactams belonging to the carbapenem class but not by penams or cephems. We previously reported quantum calculations and kinetic analyses for Ldtfm and showed that the inactivation profile is not determined by differences in drug binding (KD [equilibrium dissociation constant] values in the 50 to 80 mM range). In this study, we analyzed the reaction of a Cys sulfhydryl with various ß-lactams in the absence of the enzyme environment in order to compare the intrinsic reactivity of drugs belonging to the penam, cephem, and carbapenem classes. For this purpose, we synthesized cyclic Cys-Asn (cCys-Asn) to generate a soluble molecule with a sulfhydryl closely mimicking a cysteine in a polypeptide chain, thereby avoiding free reactive amino and carboxyl groups. Computational studies identified a thermodynamically favored pathway involving a concerted rupture of the ß-lactam amide bond and formation of an amine anion. Energy barriers indicated that the drug reactivity was the highest for nonmethylated carbapenems, intermediate for methylated carbapenems and cephems, and the lowest for penams. Electron-withdrawing groups were key reactivity determinants by enabling delocalization of the negative charge of the amine anion. Acylation rates of cCys-Asn determined by spectrophotometry revealed the same order in the reactivity of ß-lactams. We concluded that the rate of Ldtfm acylation is largely determined by the ß-lactam reactivity with one exception, as the enzyme catalytic pocket fully compensated for the detrimental effect of carbapenem methylation.

Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences.

Norovirus (NV) RNA-dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer-template duplex was investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the post-incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435-1445. © 2017 Wiley Periodicals, Inc.

Experimental and Theoretical Insight into Electrocatalytic Hydrogen Evolution with Nickel Bis(aryldithiolene) Complexes as Catalysts.

A series of neutral and monoanionic nickel dithiolene complexes with p-methoxyphenyl-substituted 1,2-dithiolene ligands have been prepared and characterized with physicochemical methods. Two of the complexes, the monoanion of the symmetric [Ni{S2C2(Ph-p-OCH3)2}2] (3(-)) with NBu4(+) as a counterion and the neutral asymmetric [Ni{S2C2(Ph)(Ph-p-OCH3)}2] (2), have been structurally characterized by single-crystal X-ray crystallography. All complexes have been employed as proton-reducing catalysts in N,N-dimethylformamide with trifluoroacetic acid as the proton source. The complexes are active catalysts with good faradaic yields, reaching 83% for 2 but relatively high overpotential requirements (0.91 and 1.55 V measured at the middle of the catalytic wave for two processes observed depending on the different routes of the mechanism). The similarity of the experimental data regardless of whether the neutral or anionic form of the complexes is used indicates that the neutral form acts as a precatalyst. On the basis of detailed density functional theory calculations, the proposed mechanism reveals two different main routes after protonation of the dianion of the catalyst in accordance with the experimental data, indicating the role of the concentration of the acid and the influence of the methoxy groups. Protonation at sulfur seems be more favorable than that at the metal, which is in marked contrast with the catalytic mechanism proposed for analogous cobalt dithiolene complexes.

Multiple proton relay routes in the reaction mechanism of RNAP II: assessing the effect of structural model.

RNA polymerase II catalyzes the nucleotidyl transfer reaction for messenger RNA synthesis in eukaryotes. Two crystal structures of this system have been resolved, each with its own defects in the coordination sphere of Mg(2+) (A) resulting from chemical modifications. We have used both structures and also a novel hybrid of the two that allows a better exploration of the parts of configuration space that reflect substrate-enzyme interactions. MD and QM/MM calculations have been performed, the latter with the semiempirical AM1/d-PhoT method, calibrated against density functional theory. Reaction path scans in 1-D provided insights about the role of Mg(2+) (A) which turns out to be more structural than catalytic. In contrast, 1-D scans of the incorporation of the nucleotidyl group yielded barriers that were much too high, necessitating the use of 2-D reaction coordinates. Three different proton acceptors for the initial reaction step were examined. For those models based on the two PDB structures the 2-D scans continued to yield very high barriers, indicating that the reaction is unlikely to proceed from these configurations. On the other hand, two hybrid models, chosen from the early and late parts of a 12 ns molecular dynamics simulation yielded greatly reduced barriers in the range of ∼ 17 to ∼ 27 kcal/mol for the three proton acceptors, as compared to the experimental estimate of 18 kcal/mol. The final step, release of pyrophosphate, was found to be facile. Our overall mechanism involves only active site residues or water without the need for external reactive agents such as the hydroxide ion previously proposed.

Technical advances in molecular simulation since the 1980s.

This review describes how the theory and practice of molecular simulation have evolved since the beginning of the 1980s when the author started his career in this field. The account is of necessity brief and subjective and highlights the changes that the author considers have had significant impact on his research and mode of working.

Pcetk: A pDynamo-based Toolkit for Protonation State Calculations in Proteins.

Pcetk (a pDynamo-based continuum electrostatic toolkit) is an open-source, object-oriented toolkit for the calculation of proton binding energetics in proteins. The toolkit is a module of the pDynamo software library, combining the versatility of the Python scripting language and the efficiency of the compiled languages, C and Cython. In the toolkit, we have connected pDynamo to the external Poisson-Boltzmann solver, extended-MEAD. Our goal was to provide a modern and extensible environment for the calculation of protonation states, electrostatic energies, titration curves, and other electrostatic-dependent properties of proteins. Pcetk is freely available under the CeCILL license, which is compatible with the GNU General Public License. The toolkit can be found on the Web at the address http://github.com/mfx9/pcetk. The calculation of protonation states in proteins requires a knowledge of pKa values of protonatable groups in aqueous solution. However, for some groups, such as protonatable ligands bound to protein, the pKa aq values are often difficult to obtain from experiment. As a complement to Pcetk, we revisit an earlier computational method for the estimation of pKa aq values that has an accuracy of ± 0.5 pKa-units or better. Finally, we verify the Pcetk module and the method for estimating pKa aq values with different model cases.

Ferric-Thiolate Bond Dissociation Studied with Electronic Structure Calculations.

The stability and reactivity of iron-sulfur clusters are fundamental properties for the biological function of these prosthetic groups. Here, we investigate the ferric-thiolate bond dissociation of model iron-sulfur tetrahedral complexes with high-level ab initio multiconfigurational electronic structure calculations. We find that the reaction mechanism is homolytic with a spin-crossing from the sextet state in the reactant to quartet state in the product. We also compare several density functionals and semiempirical configuration interaction with the high-level ab initio results to find an accurate but computationally more efficient method to describe the reaction. The functionals M06 and those based on the OPTX exchange functional show the best performance and may reasonably describe the various electron correlation effects involved in ferric-thiolate bond dissociation.

Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations.

Peptidoglycan deacetlyase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori, is the enzyme responsible for a peptidoglycan modification that counteracts the host immune response. In a recent study, we determined the crystallographic structure of the enzyme, which is a homo-tetramer (Shaik et al., PloS One 2011;6:e19207). The metal-binding site, which is essential for the enzyme's catalytic activity, is visible within the structure, but we were unable to identify the nature of the metal itself. In this study, we have obtained a higher-resolution crystal structure of the enzyme, which shows that the ion bound is, in fact, zinc. Analysis of the structure of the four sites, one per monomer, and quantum chemical calculations of models of the site in the presence of different divalent metal ions show an intrinsic preference for zinc, but also significant flexibility of the site so that binding of other ions can eventually occur.

Theoretical modeling of low-energy electronic absorption bands in reduced cobaloximes.

The reduced Co(I) states of cobaloximes are powerful nucleophiles that play an important role in the hydrogen-evolving catalytic activity of these species. In this work we analyze the low-energy electronic absorption bands of two cobaloxime systems experimentally and use a variety of density functional theory and molecular orbital ab initio quantum chemical approaches. Overall we find a reasonable qualitative understanding of the electronic excitation spectra of these compounds but show that obtaining quantitative results remains a challenging task.

Cobaloxime-based artificial hydrogenases.

Cobaloximes are popular H2 evolution molecular catalysts but have so far mainly been studied in nonaqueous conditions. We show here that they are also valuable for the design of artificial hydrogenases for application in neutral aqueous solutions and report on the preparation of two well-defined biohybrid species via the binding of two cobaloxime moieties, {Co(dmgH)2} and {Co(dmgBF2)2} (dmgH2 = dimethylglyoxime), to apo Sperm-whale myoglobin (SwMb). All spectroscopic data confirm that the cobaloxime moieties are inserted within the binding pocket of the SwMb protein and are coordinated to a histidine residue in the axial position of the cobalt complex, resulting in thermodynamically stable complexes. Quantum chemical/molecular mechanical docking calculations indicated a coordination preference for His93 over the other histidine residue (His64) present in the vicinity. Interestingly, the redox activity of the cobalt centers is retained in both biohybrids, which provides them with the catalytic activity for H2 evolution in near-neutral aqueous conditions.

QM/MM through the 1990s: The First Twenty Years of Method Development and Applications.

The 2013 Nobel Prize in Chemistry was awarded to the authors of the first two publications utilizing the concept of combined quantum mechanical and molecular mechanical (QM/MM) methods. In celebrating this great event in computational chemistry, we review the early development of combined QM/MM techniques and the associated events that took place through the mid-1990s. We also offer some prospects for the future development of quantum mechanical techniques for macromolecular systems.

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open-source graphical plug-in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations.

A computational study of the mechanism of hydrogen evolution by cobalt(diimine-dioxime) catalysts.

Cobalt(diimine-dioxime) complexes catalyze hydrogen evolution with low overpotentials and remarkable stability. In this study, DFT calculations were used to investigate their catalytic mechanism, to demonstrate that the initial active state was a Co(I) complex and that H2 was evolved in a heterolytic manner through the protonation of a Co(II)-hydride intermediate. In addition, these catalysts were shown to adjust their electrocatalytic potential for hydrogen evolution to the pH value of the solution and such a property was assigned to the presence of a H(+)-exchange site on the oxime bridge. It was possible to establish that protonation of the bridge was directly involved in the H2-evolution mechanism through proton-coupled electron-transfer steps. A consistent mechanistic scheme is proposed that fits the experimentally determined electrocatalytic and electrochemical potentials of cobalt(diimine-dioxime) complexes and reproduces the observed positive shift of the electrocatalytic potential with increasing acidity of the proton source.

Computational 17O-NMR spectroscopy of organic acids and peracids: comparison of solvation models.

We examine several computational strategies for the prediction of the (17)O-NMR shielding constants for a selection of organic acids and peracids in aqueous solution. In particular, we consider water (the solvent and reference for the chemical shifts), hydrogen peroxide, acetic acid, lactic acid and peracetic acid. First of all, we demonstrate that the PBE0 density functional in combination with the 6-311+G(d,p) basis set provides an excellent compromise between computational cost and accuracy in the calculation of the shielding constants. Next, we move on to the problem of the solvent representation. Our results confirm the shortcomings of the Polarizable Continuum Model (PCM) in the description of systems susceptible to strong hydrogen bonding interactions, while at the same time they demonstrate its usefulness within a molecular-continuum approach, whereby PCM is applied to describe the solvation of the solute surrounded by some explicit solvent molecules. We examine different models of the solvation shells, sampling their configurations using both energy minimizations of finite clusters and molecular dynamics simulations of bulk systems. Hybrid molecular dynamics simulations, in which the solute is described at the PM6 semiempirical level and the solvent by the TIP3P model, prove to be a promising sampling method for medium-to-large sized systems. The roles of solvent shell size and structure are also briefly discussed.

Combined experimental-theoretical characterization of the hydrido-cobaloxime [HCo(dmgH)2(PnBu3)].

A combined theoretical and experimental approach has been employed to characterize the hydrido-cobaloxime [HCo(dmgH)(2)(PnBu(3))] compound. This complex was originally investigated by Schrauzer et al. [Schrauzer et al., J. Am. Chem. Soc. 1971, 93,1505] and has since been referred to as a key, stable analogue of the hydride intermediate involved in hydrogen evolution catalyzed by cobaloxime compounds [Artero, V. et al. Angew. Chem., Int. Ed. 2011, 50, 7238-7266]. We employed quantum chemical calculations, using density functional theory and correlated RI-SCS-MP2 methods, to characterize the structural and electronic properties of the compound and observed important differences between the calculated (1)H NMR spectrum and that reported in the original study by Schrauzer and Holland. To calibrate the theoretical model, the stable hydrido tetraamine cobalt(III) complex [HCo(tmen)(2)(OH(2))](2+) (tmen = 2,3-dimethyl-butane-2,3-diamine) [Rahman, A. F. M. M. et al. Chem. Commun. 2003, 2748-2749] was subjected to a similar analysis, and, in this case, the calculated results agreed well with those obtained experimentally. As a follow-up to the computational work, the title hydrido-cobaloxime compound was synthesized and recharacterized experimentally, together with the Co(I) derivative, giving results that were in agreement with the theoretical predictions.

Comparative DFT study to determine if α-oxoaldehydes are precursors for pentosidine formation.

We report a comprehensive density functional theory (DFT) study of the mechanism of pentosidine formation. This work is a continuation of our earlier studies in which we proposed pathways for formation of glucosepane (J. Mol. Model. 2011, pp 1-15, DOI 10.1007/s00894-011-1161-x), GODIC (glyoxal-derived imidazolium cross-link), and MODIC (methyl glyoxal-derived imidazolium cross-link; J. Phys. Chem. 2011, 115, pp 13542-13555). Here we show that formation of pentosidine via reaction of α-oxoaldehydes with lysine and arginine in aqueous solution is possible thermodynamically and kinetically, in good agreement with the available experimental evidence. Five pathways, A-E, were characterized, as in our previous GODIC and MODIC work. In pathways A and B, a Schiff base is first formed from lysine and methyl glyoxal (MGO), and this is followed by addition of arginine and glyoxal (GO). By contrast, in pathways C, D, and E, addition of arginine to MGO occurs first, resulting in the formation of imidazolone, which then reacts with lysine and GO to give pentosidine. Our calculations show that the reaction process is highly exergonic and that the three pathways A, C, and E are competitive. These results serve to underline the potentially important role that α-oxoaldehydes play as precursors in pentosidine formation in the complex field of glycation.