Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics

Ab initio molecular dynamics study of the keto-enol tautomerism of acetone in solution

We have studied the keto-enol interconversion of acetone to understand the mechanism of tautomerism relevant to numerous organic and biochemical processes. Applying the ab initio metadynamics method, we simulated the keto-enol isomerism both in the gas phase and in the presence of water. For the gas-phase intramolecular mechanism we show that no other hydrogen-transfer reactions can compete with the simple keto-enol tautomerism. We obtain an intermolecular mechanism and remarkable participation of water when acetone is solvated by neutral water. The simulations reveal that C deprotonation is the kinetic bottleneck of the keto-enol transformation, in agreement with experimental observations. The most interesting finding is the formation of short H-bonded chains of water molecules that provide the route for proton transfer from the carbon to the oxygen atom of acetone. The mechanistic picture that emerged from the present study involves proton migration and emphasizes the importance of active solvent participation in tautomeric interconversion.

Proton transfer 200 years after von Grotthuss: insights from ab initio simulations

In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.

Assessing the accuracy of metadynamics

Metadynamics is a powerful technique that has been successfully exploited to explore the multidimensional free energy surface of complex polyatomic systems and predict transition mechanisms in very different fields, ranging from chemistry and solid-state physics to biophysics. We here derive an explicit expression for the accuracy of the methodology and provide a way to choose the parameters of the method in order to optimize its performance.

Insight into the folding inhibition of the HIV-1 protease by a small peptide

It has recently been shown that the highly protected segments 24-34 (S2) and 83-93 (S8) of each of the two 99-mers of human immunodeficiency virus type 1 protease play an essential role in the folding of the monomers, giving rise to the so-called (postcritical) folding nucleus ((FN) minimum condensation unit ensuring folding) when they dock. This scenario received further support from model calculations that demonstrated that the peptide p-S8, displaying an amino acid sequence identical to the corresponding (83-93) segment of the monomer, can be used to interfere with the formation of the FN and eventually to inhibit folding by docking the fragment 24-34. Experiments in vitro and in cells infected with ex vivo wild-type and multiresistant HIV isolates confirm that the inhibition power of p-S8 is robust. On the other hand, there is no direct evidence demonstrating the validity of the proposed mechanism of inhibition associated with p-S8. To shed light on this question and to provide the basis for the design of a molecule mimetic to p-S8, to be used as lead of an eventual drug against AIDS, we study, in this paper, with the help of all-atom simulations in explicit solvent and the novel method of metadynamics combined with parallel tempering: a), the free energy and the equilibrium structure of each of the peptides p-S2 and p-S8; b), the details of the docking mechanism of the two peptides and the free energy associated with this process. Whereas p-S8 is found to be well structured, p-S2 is rather flexible, wrapping itself around p-S8 to give rise to the FN, which is stabilized by three particular hydrogen bonds.

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.

SASS: A symmetry adapted stochastic search algorithm exploiting site symmetry

A simple symmetry adapted search algorithm (SASS) exploiting point group symmetry increases the efficiency of systematic explorations of complex quantum mechanical potential energy surfaces. In contrast to previously described stochastic approaches, which do not employ symmetry, candidate structures are generated within simple point groups, such as C2, Cs, and C2v. This facilitates efficient sampling of the 3N-6 Pople's dimensional configuration space and increases the speed and effectiveness of quantum chemical geometry optimizations. Pople's concept of framework groups [J. Am. Chem. Soc. 102, 4615 (1980)] is used to partition the configuration space into structures spanning all possible distributions of sets of symmetry equivalent atoms. This provides an efficient means of computing all structures of a given symmetry with minimum redundancy. This approach also is advantageous for generating initial structures for global optimizations via genetic algorithm and other stochastic global search techniques. Application of the SASS method is illustrated by locating 14 low-lying stationary points on the cc-pwCVDZ ROCCSD(T) potential energy surface of Li5H2. The global minimum structure is identified, along with many unique, nonintuitive, energetically favorable isomers.

Hsc70 ATPase: an insight into water dissociation and joint catalytic role of K+ and Mg2+ metal cations in the hydrolysis reaction

Hybrid quantum mechanics/molecular mechanics simulations, coupled to the recently introduced metadynamics method, performed on the adenosine triphosphate (ATP) of the bovine Hsc70 ATPase protein, show which specific water molecule of the solvation shell of the Mg2+ metal cation acts as a trigger in the initial phase of the ATP hydrolysis reaction in ATP synthase. Furthermore, we provide a detailed picture of the reaction mechanism, not accessible to experimental probes, that allows us to address two important issues not yet unraveled: (i) the pathway followed by a proton and a hydroxyl anion, produced upon dissociation of a putative catalytic H2O molecule, that is crucial in the selection of the reaction channel leading to the hydrolysis; (ii) the unique and cooperative role of K+ and Mg2+ metal ions in the reaction, acting as co-catalysts and promoting the release of the inorganic phosphate via an exchange of the OH- hydroxyl anion between their respective solvation shells. This is deeply different from the proton wire mechanism evidenced, for instance, in actin and lowers significantly the free energy barrier of the reaction.

Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases

Metallo beta-lactamases (MbetaL) are enzymes naturally evolved by bacterial strains under the evolutionary pressure of beta-lactam antibiotic clinical use. They have a broad substrate spectrum and are resistant to all the clinically useful inhibitors, representing a potential risk of infection if massively disseminated. The MbetaL scaffold is designed to accommodate one or two zinc ions able to activate a nucleophilic hydroxide for the hydrolysis of the beta-lactam ring. The role of zinc content on the binding and reactive mechanism of action has been the subject of debate and still remains an open issue despite the large amount of data acquired. We report herein a study of the reaction pathway for binuclear CcrA from Bacteroides fragilis using density functional theory based quantum mechanics-molecular mechanics dynamical modeling. CcrA is the prototypical binuclear enzyme belonging to the B1 MbetaL family, which includes several harmful chromosomally encoded and transferable enzymes. The involvement of a second zinc ion in the catalytic mechanism lowers the energetic barrier for beta-lactam hydrolysis, preserving the essential binding features found in mononuclear B1 enzymes (BcII from Bacillus cereus) while providing a more efficient single-step mechanism. Overall, this study suggests that uptake of a second equivalent zinc ion is evolutionary favored.

From A to B in free energy space

The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

There is considerable interest in developing methodologies for the accurate evaluation of free energies, especially in the context of biomolecular simulations. Here, we report on a reexamination of the recently developed metadynamics method, which is explicitly designed to probe "rare events" and areas of phase space that are typically difficult to access with a molecular dynamics simulation. Specifically, we show that the accuracy of the free energy landscape calculated with the metadynamics method may be considerably improved when combined with umbrella sampling techniques. As test cases, we have studied the folding free energy landscape of two prototypical peptides: Ace-(Gly)(2)-Pro-(Gly)(3)-Nme in vacuo and trialanine solvated by both implicit and explicit water. The method has been implemented in the classical biomolecular code AMBER and is to be distributed in the next scheduled release of the code.

Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics

Photoinduced proton transfer in the Watson-Crick guanine (G)-cytosine (C) base pair has been studied using Car-Parrinello molecular dynamics (CP-MD). A flexible mechanical constraint acting on all three hydrogen bonds in an unbiased fashion has been devised to explore the free energy profile along the proton transfer coordinate. The lowest barrier has been found for proton transfer from G to C along the central hydrogen bond. The resulting charge transfer excited state lies energetically close to the electronic ground state suggesting the possibility of efficient radiationless decay. It is found that dynamic, finite temperature fluctuations significantly reduce the energy gap between the ground and excited states for this charge transfer product, promoting the internal conversion process. A detailed analysis of the internal degrees of freedom reveals that the energy gap is considerably reduced by out-of-plane molecular vibrations, in particular. Consequently, it appears that considering only the minimum energy path provides an upper-bound estimate of the associated energy gap compared to the full-dimension dynamical reaction coordinate. Furthermore, the first CP-MD simulations of the G-C base pair in liquid water are presented, and the effects of solvation on its electronic structure are analyzed.

Ab Initio Exploration of Rearrangement Reactions: Intramolecular Hydrogen Scrambling Processes in Acetone

The recently developed metadynamics method is applied to the intramolecular hydrogen migration reactions of acetone in the gas phase. Comparison of different sets of collective coordinates allows efficient description of the underlying free energy surface. The simulations yielded numerous reactions: the enol-oxo tautomerism, the decomposition of acetone to various products, and rearrangement reactions. On the basis of the calculated activation barriers it is concluded that the enol-oxo tautomerism is the most frequent intramolecular proton-exchange process the acetone undergoes in the gas phase.

Ab initio Simulation of the Grafting of Phenylacetylene on Hydrogenated Surfaces of Crystalline Silicon Catalyzed by a Lewis Acid

Car-Parrinello simulations have been carried out to identify the grafting mechanism of phenylacetylene, a prototypical alkyne, on the hydrogenated surfaces of crystalline silicon, catalyzed by a Lewis acid (AlCl3). To this purpose, we have made use of a new technique, metadynamics, devised recently to deal with complex chemical reactions in first principles simulations. The reaction mechanism, leading to a styrenyl-terminated surface, turns out to be equivalent to the corresponding gas-phase hydrosilylation reaction by silanes that we have identified in a previous work. The activation energies for the surface reactions (0.43, 0.42, 0.35 eV, for H-Si(111), H-Si(100)2 x 1, and H-Si(100)1 x 1, respectively) are very close to that of the corresponding gas-phase reaction (0.37 eV). The estimated activation free energy at room temperature is sufficiently low for the grafting reaction to be viable at normal conditions and at low coverage on the crystalline silicon surfaces, as already well documented to occur on the surface of porous silicon. However, the conformation of the transition state shadows a large area of the surface, which might contribute to making the grafting process self-limiting.

Glycine at the Pyrite−Water Interface: The Role of Surface Defects

Ab initio molecular dynamics simulations were performed in order to study chemisorption, electronic properties, and desorption of glycine at wet pyrite surfaces focusing on the role of surface point defects. The change in the electronic structure and its influence on the chemical reactivity of the free FeS(2)(100) surface due to sulfur vacancies was studied in detail yielding several adsorption modes of glycine and water molecules. Energetically preferred adsorption modes were furthermore investigated in the presence of hot pressurized water mimicking "Iron Sulfur World" prebiotic conditions. The metadynamics Car-Parrinello technique was employed to map the free energy landscape including paths and barriers for desorption of glycine from such wet defective surfaces. The ubiquitous sulfur vacancies are found to increase the retention time of the adsorbed amino acid by many orders of magnitudes in comparison to the ideal pyrite-water interface. The importance of these findings in terms of a possible two-dimensional primordial chemistry on mineral surfaces is discussed.

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations

The deprotonation of solvated formic acid was investigated theoretically with ab initio simulations. With the Car-Parrinello method, deprotonation and reprotonation by means of a proton wire were observed. The microscopics of these reactions were analyzed, and reveal the key role played by nearby water molecules in catalyzing the reactions. A constrained molecular dynamics calculation was carried out to estimate the dissociation free energy. Deprotonation of formic acid was further investigated with the recently developed metadynamics method using the formic acid oxygen coordination numbers as the collective variables. The determined free-energy landscape gives barriers similar to that obtained with the constrained free-energy calculation.

Dissociation Mechanism of Acetic Acid in Water

The reaction mechanism for acetic acid dissociation in aqueous solution has been investigated by combining the metadynamics method with transition path sampling (TPS). By using collective variables that describe not only the deprotonation of the acid but also the solvation state of the hydronium ion and its distance from the acetate, a reactive trajectory in which stable separated ions were produced was obtained. More transition trajectories were sampled by using the TPS technique, taking the metadynamics trajectory as the initial trajectory. Two different dissociation reaction pathways were determined, one driven by the breaking of an H-bond formed by the water molecule in contact with the hydroxyl and involving the formation of a metastable contact ion pair and the other characterized by a direct transfer of the proton to the solution through an unstable Zundel-ion-like intermediate.

Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail

The ability of calcium-bound calmodulin (CaM) to recognize most of its target peptides is caused by its binding to two hydrophobic residues ('anchors'). In most of the CaM complexes, the anchors pack against the hydrophobic pockets of the CaM domains and are surrounded by fully conserved Met side chains. Here, by using metadynamics simulations, we investigate quantitatively the energetics of the final step of this process using the M13 peptide, which has a high affinity and spans the sequence of the skeletal myosin light chain kinase, an important natural CaM target. We established the accuracy of our calculations by a comparison between calculated and NMR-derived structural and dynamical properties. Our calculations provide novel insights into the mechanism of protein/peptide recognition: we show that the process is associated with a free energy gain similar to that experimentally measured for the CaM complex with the homologous smooth muscle MLCK peptide (Ehrhardt et al., 1995, Biochemistry 34, 2731). We suggest that binding is dominated by the entropic effect, in agreement with previous proposals. Furthermore, we explain the role of conserved methionines by showing that the large flexibility of these side chains is a key feature of the binding mechanism. Finally, we provide a rationale for the experimental observation that in all CaM complexes the C-terminal domain seems to be hierarchically more important in establishing the interaction.

Solid-State Phase Transition Induced by Pressure in LiOH·H2O

When the free energy surface of the lithium hydroxide monohydrate crystal was explored, the high-pressure solid-state phase transition was determined. The high-pressure phase has been obtained through ab initio Car-Parrinello molecular dynamics simulation in the isothermic-isobaric ensemble. The recent metadynamics method has been applied to overcome the high activation energy barriers typical of rare events, like solid-state phase transition at high pressures. In the LiOH x H2O system, there are two kinds of H bonds: water-water and hydroxyl-water. The effect of the pressure has been investigated, to give further insight into the high-pressure phase. The strengthening of the H bonds of the system produces modifications in the water and the hydroxyl ion dipole electronic environment. The infrared spectra of both phases have been calculated and compared with experiments, and the assignment of the external modes has been discussed.

Proton transfer in imidazole-based molecular crystals

Heterocycles' aggregates show rather good proton conductivity. In particular, condensed structures formed by imidazole rings that are held together by polymeric chains have attracted some interest as possible candidate materials for fuel cell membranes. However, the details of the proton diffusion process could not be resolved by means of experimental measurements because of the fast rearrangement of the structure after each proton exchange. In this work, we report in detail the results of ab initio molecular dynamics calculations, which were briefly presented in a previous Letter [M. Iannuzzi and M. Parrinello, Phys. Rev. Lett. 93, 025901 (2004)]. The conformational changes associated with the diffusion of protons in model crystalline structures containing chains of imidazole rings are described in the framework of an atomistic approach. In particular, the bonding pattern characterizing the structure of imidazole-2-ethylene-oxide doped by an excess proton is also studied through the calculation of the 1H NMR chemical shifts. The unresolved resonances appearing in the experimental spectra could be associated with specific structural features, in connection with the fluctuating hydrogen bonding. The analysis of the distortions that induce or are induced by the mobility of the protons offers some new hints for the engineering of new proton conducting materials.

Ab Initio Molecular Dynamics Simulation of NO Reactivity on the CaO(001) Surface

Ab initio molecular dynamics (MD) is used to investigate NO reaction processes on the (001) surface of CaO. A novel path is proposed for the first steps of nitrogen oxides reactivity catalyzed by the CaO surface. The mechanism consists of the formation of anionic dimers, adsorbing on the surface cations, at the expense of oxidized NO species adsorbed on surface anions. The complete charge-transfer process takes place in two steps, producing first monovalent anionic dimers (NO)2- and, later on, divalent anionic dimers (NO)2(2-). These redox processes cause spin quenching and are observed in the short time scale of the ab initio MD simulation at 300 K. The results presented provide a rationalization of a recent electron spin resonance (ESR) investigation indicating that the spectroscopy is silent to most of the nitrogen oxide species adsorbed on CaO powders, despite deposition of paramagnetic NO molecules at room temperature.

Equilibrium free energies from nonequilibrium metadynamics

In this Letter we propose a new formalism to map history-dependent metadynamics in a Markovian process. We apply this formalism to model Langevin dynamics and determine the equilibrium distribution of a collection of simulations. We demonstrate that the reconstructed free energy is an unbiased estimate of the underlying free energy and analytically derive an expression for the error. The present results can be applied to other history-dependent stochastic processes, such as Wang-Landau sampling.

Enol-to-keto Tautomerism of Peptide Groups

Density functional based simulations, performed on polyglycine containing an enol peptide group [-C(OH)N-] which is a structural isomer of a keto form [-CONH-], show that in the enol-to-keto tautomeric reaction, the enol peptide group is less stable than the keto form, and that the enol-to-keto tautomerism is characterized by a cis/trans isomerization of the C-N peptide bond. The rate-limiting step in the cis/trans isomerization is a hydrogen migration from O to N atoms in the peptide group with a transition state consisting of a four-membered ring in the cis configuration. An analysis of the cis/trans isomerization pathway shows that the mechanisms for the cis/trans isomerization are essentially different between the enol and keto forms.

Lithium Hydroxide Phase Transition under High Pressure: An Ab Initio Molecular Dynamics Study

The high-pressure phase transition in the deuterated lithium hydroxide crystalline state has been studied by Car-Parrinello molecular dynamics simulations, in the constant-pressure, constant-temperature ensemble. The recently developed metadynamics approach has been applied to encourage the system to transform into different phases in an affordable simulation time. A previously not completely characterized high-pressure phase has been obtained. The structural and spectroscopic properties have been studied and compared with the neutron scattering, infrared and Raman measurements. It has been found that the calculated structure differs slightly from the experimental hypothesis, and that the presence of strong hydrogen bonds is the source of the red shift and of the characteristic features of the OD-stretching bands in both IR and Raman spectra.

Toward a DFT-based molecular dynamics description of Co(ii) binding in sulfur-rich peptides

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.

Modeling anticancer drug–DNA interactions via mixed QM/MM molecular dynamics simulations

The development of anticancer drugs started over four decades ago, with the serendipitous discovery of the antitumor activity of cisplatin and its successful use in the treatment of various cancer types. Despite the efforts made in unraveling the mechanism of the action of cisplatin, as well as in the rational design of new anticancer compounds, in many cases detailed structural and mechanistic information is still lacking. Many of these drugs exert their anticancer activity by covalently binding to DNA inducing a distortion or simply impeding replication, thus triggering a cellular response, which eventually leads to cell death. A detailed understanding of the structural and electronic properties of drug-DNA complexes and their mechanism of binding is the key step in elucidating the principles of their anticancer activity. At the theoretical level, the description of covalent drug-DNA complexes requires the use of state-of-the-art computer simulation techniques such as hybrid quantum/classical molecular dynamics simulations. In this review we provide a general overview on: drugs which covalently bind to DNA duplexes, the basic concepts of quantum mechanics/molecular mechanics (QM/MM), molecular dynamics methods and a list of selected applications of these simulations to the study of drug-DNA adducts. Finally, the potential and the limitations of this approach to the study of such systems are critically evaluated.

Structure and Function of Vanadium Haloperoxidases

A quantum mechanics/molecular mechanics study of the resting state of the vanadium dependent chloroperoxidase from fungi Curvularia inaequalis and of the early intermediates of the halide oxidation is reported. The investigation of different protonation states indicates that the enzyme likely consists of an anionic H2VO4- vanadate moiety where one hydroxo group is in axial position. The calculations suggest that the hydrogen peroxide binding may not involve an initial protonation of the vanadate cofactor. A low free energy reactive path is found where the hydrogen peroxide directly attacks the axial hydroxo group, resulting in the formation of an hydrogen peroxide intermediate. This intermediate is promptly protonated to yield a peroxo species. The free energy barrier for the formation of the peroxo species does not depend significantly upon the protonation state of the cofactor. The most likely protonation states of the peroxo cofactor are neutral forms HVO2(O2) with a hydroxo group either H-bonded to Ser402 or coordinated to Arg360. The peroxo cofactor is also coordinated to an axial water molecule, which could be important for the stability of the peroxovanadate/His496 adduct. Our calculations strongly suggest that the halide oxidation may take place with the preliminary formation of a peroxovanadate/halogen adduct. Subsequently, the halogen reacts with the peroxo moiety yielding a hypohalogen vanadate. The most reactive protonation state of peroxovanadate is the neutral HVO2(O2) with the hydroxo group H-bonded to Ser402. The important role of Lys353 in determining the catalytic activity is also confirmed.

Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics

Recently, we have introduced a new method, metadynamics, which is able to sample rarely occurring transitions and to reconstruct the free energy as a function of several variables with a controlled accuracy. This method has been successfully applied in many different fields, ranging from chemistry to biophysics and ligand docking and from material science to crystal structure prediction. We present an important development that speeds up metadynamics calculations by orders of magnitude and renders the algorithm much more robust. We use multiple interacting simulations, walkers, for exploring and reconstructing the same free energy surface. Each walker contributes to the history-dependent potential that, in metadynamics, is an estimate of the free energy. We show that the error on the reconstructed free energy does not depend on the number of walkers, leading to a fully linear scaling algorithm even on inexpensive loosely coupled clusters of PCs. In addition, we show that the accuracy and stability of the method are much improved by combining it with a weighted histogram analysis. We check the validity of our new method on a realistic application.

The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge

We study the ligand (tetramethylammonium) recognition by the peripheral anionic site and its penetration of the human AChE gorge by using atomistic molecular dynamics simulations and our recently developed metadynamics method. The role of both the peripheral anionic site and the formation of cation-pi interactions in the ligand entrance are clearly shown. In particular, a simulation with the W286A mutant shows the fundamental role of this residue in anchoring the ligand at the peripheral anionic site of the enzyme and in positioning it prior to the gorge entrance. Once the ligand is properly oriented, the formation of specific and synchronized cation-pi interactions with W86, F295, and Y341 enables the gorge penetration. Eventually, the ligand is stabilized in a free energy basin by means of cation-pi interactions with W86.

Direct determination of reaction paths and stationary points on potential of mean force surfaces

A simulation approach is introduced for directly determining reaction paths and stationary points on potential of mean force (PMF) surfaces associated with molecular events that occur in complex environments. The nudged elastic band approach was employed to search for steepest descent paths on the PMF surface using the relevant PMF derivatives from a series of local simulations. The steepest descent path on the PMF surface corresponds to the minimum PMF path (i.e. the path with the lowest local PMF barrier), which contains important information about stationary points (e.g. saddle points) on the PMF surface, which in turn can provide useful insights into the thermodynamics and kinetics for the process of interest. By working with the PMF defined in a low-dimensional sub-space rather than a potential energy function of full molecular dimensionality, the main features of the process under study are concisely represented and the orthogonal degrees of freedom are adequately sampled with the appropriate canonical distribution at the desired temperature (e.g. 300 K). Therefore, minimum PMF paths carry statistically meaningful mechanistic information and are complementary to reaction paths of full molecular dimensionality proposed in previous studies. The NEB based path optimization method is direct in the sense that no information regarding the global PMF surface is necessary for the determination of the local reaction path and stationary points along this path. Since only low-dimensional quantities (paths) are searched for, the PMF-path method is expected to scale better in terms of dimension of the PMF sub-space than those aims to fully explore multi-dimensional PMF surfaces. Test applications on simple molecular systems, the alanine di-peptide in vacuum and in solution and a micro-solvated proton-wire, indicate that reliable PMF paths can be determined for both conformational isomerization and chemical reaction processes. However, highly accurate PMF derivatives are required for determining more quantitative observables, such as the free energy profile along the minimum PMF path. Therefore, effective numerical algorithms for calculating local PMF derivatives and systematic protocols for defining the relevant sub-space are the main focus in the near future. Finally, we emphasize that the minimum PMF path defined here includes thermal (e.g. entropic) effects associated with the orthogonal degrees of freedom, but finite kinetic energies associated with the PMF degrees of freedom are not included; this can be improved by adopting a different definition of the reaction path, such as the maximum flux path, on the PMF surface, or thermally sampling all degrees of freedom orthogonal to the one-dimensional path.

Dissociation of water on defective carbon substrates

Using calculations from first principles, we found that water can dissociate over defective sites in graphene or nanotubes following many possible reaction pathways, some of which have activation barriers lower than half the value for the dissociation of bulk water. This reduction is caused by spin selection rules that allow the system to remain on the same spin surface throughout the reaction.

Blue Moon Sampling, Vectorial Reaction Coordinates, and Unbiased Constrained Dynamics

We give a new formula expressing the components of the mean force in terms of a conditional expectation which can be computed by Blue Moon sampling. This generalizes to the vectorial case a formula first derived by Ruiz-Montero et al. for a scalar reaction coordinate. We also discuss how to compute this conditional average by means of constrained stochastic dynamics which, unlike the usual constrained molecular dynamics, introduces no bias. Finally, we give a new perspective on bias removal by using constrained molecular dynamics.

Ab Initio Molecular Dynamics Study of Heterogeneous Oxidation of Graphite by Means of Gas-Phase Nitric Acid

The interaction between gas-phase nitric acid and the graphite surface is taken as a simple model of interactions occurring at the surface of atmospheric soot particles. In particular, we study the heterogeneous processes that lead to the dissociation of the nitric acid and the production of nitrous acid. The atomistic details of the reaction mechanisms are reproduced by use of the new metadynamics method. The binding interactions of the HNO3 molecule and its fragments with the graphite surface are calculated, and the role of the surface in catalyzing the reaction is taken into account. From the reactive trajectory generated by the metadynamics, it is seen that the path goes through several different intermediate states. We analyze in detail the electronic structures and spin density distributions of the relevant products and report on the mechanisms and the main features of the transition regions relative to all the activated processes observed.

Exploring Intramolecular Reactions in Complex Systems with Metadynamics: The Case of the Malonate Anions

We have determined the optimized structures, relative energies and intramolecular reactions for two anionic forms of malonic acid, anion malonate(-1) (HO(2)CCH(2)CO(2)(-)) and malonate(-2) ((-)O(2)CCH(2)CO(2)(-)). For this purpose we employed accurate quantum chemistry calculations using second-order Möller-Plesset perturbation theory and Density Functional Theory with an aug'-cc-p-VTZ basis set to determine the structures and energies, and a novel metadynamics method based on Car-Parrinello molecular dynamics for the thermal reactions. For both malonates, we found new isomers (keto and enol structures) characterized by CO(2) rotations and intramolecular proton transfers. These proton transfers characterize the keto-enol tautomerism that takes place both in the monoanion and dianion. In all cases, the keto tautomer is the more stable configuration. The metadynamics method allows the system to explore the potential energy surface in a few picoseconds, crossing activation barriers of 20-50 kcal/mol.

Nonperiodic boundary conditions for solvated systems

The simulation of charged and/or strongly polar solutes represents a challenge for standard molecular-dynamics techniques. The use of periodic boundary conditions (PBCs) leads to artifacts due to the interaction between two replicas in the presence of the long-range Coulomb forces. A way to avoid these problems is the use of nonperiodic boundary conditions. A possible realization is to consider a finite system, a sphere, embedded in a reaction field described by the method of the images. In the present work the modified image approximation has been implemented in a molecular-dynamics code and optimized for the use of two standard solvents, water and acetonitrile. The methodology has then been applied to investigate the conformational changes in water-solvated alanine dipeptide. The free-energy surface calculated with this method is comparable to that obtained with PBC.

Hydration structure of Y3+ and La3+ compared: An application of metadynamics

We studied the hydration structures of Y(3+) and La(3+) in aqueous solutions by applying the metadynamics method recently introduced as a tool to explore reaction pathways based on the Car-Parrinello molecular dynamics. By employing the metal-water oxygen coordination number as a collective variable of the metadynamics a couple of aqua and chloroaqua complexes are successfully generated within the time scale of 10 ps. The reconstructed free-energy surface captures the characteristics of the hydration of the light and heavy trivalent rare-earth ions. The present study demonstrates that the metadynamics based on the Car-Parrinello molecular dynamics is a promising tool for exploring the free-energy surface of complicated systems such as solutions.