Tunneling and delocalization in hydrogen bonded systems: a study in position and momentum space

Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.Comment: 14 pages, 13 figure

A first principles simulation of rigid water

We present the results of Car-Parrinello (CP) simulations of water at ambient conditions and under pressure, using a rigid molecule approximation. Throughout our calculations, water molecules were maintained at a fixed intramolecular geometry corresponding to the average structure obtained in fully unconstrained simulations. This allows us to use larger time steps than those adopted in ordinary CP simulations of water, and thus to access longer time scales. In the absence of chemical reactions or dissociation effects, these calculations open the way to ab initio simulations of aqueous solutions that require timescales substantially longer than presently feasible (e.g. simulations of hydrophobic solvation). Our results show that structural properties and diffusion coefficients obtained with a rigid model are in better agreement with experiment than those determined with fully flexible simulations. Possible reasons responsible for this improved agreement are discussed

Elucidating the NuclearQuantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene

We address the double hydrogen transfer (DHT) dynamics of the porphycene molecule: A complex paradigmatic system where the making and breaking of H-bonds in a highly anharmonic potential energy surface requires a quantum mechanical treatment not only of the electrons, but also of the nuclei. We combine density-functional theory calculations, employing hybrid functionals and van der Waals corrections, with recently proposed and optimized path-integral ring-polymer methods for the approximation of quantum vibrational spectra and reaction rates. Our full-dimensional ring-polymer instanton simulations show that below 100 K the concerted DHT tunneling pathway dominates, but between 100 K and 300 K there is a competition between concerted and stepwise pathways when nuclear quantum effects are included. We obtain ground-state reaction rates of $2.19 \times 10^{11} \mathrm{s}^{-1}$ at 150 K and $0.63 \times 10^{11} \mathrm{s}^{-1}$ at 100 K, in good agreement with experiment. We also reproduce the puzzling N-H stretching band of porphycene with very good accuracy from thermostatted ring-polymer molecular dynamics simulations. The position and lineshape of this peak, centered at around 2600 cm$^{-1}$ and spanning 750 cm$^{-1}$, stems from a combination of very strong H-bonds, the coupling to low-frequency modes, and the access to $cis$-like isomeric conformations, which cannot be appropriately captured with classical-nuclei dynamics. These results verify the appropriateness of our general theoretical approach and provide a framework for a deeper physical understanding of hydrogen transfer dynamics in complex systems

Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges

Nuclear quantum effects influence the structure and dynamics of hydrogen-bonded systems, such as water, which impacts their observed properties with widely varying magnitudes. This review highlights the recent significant developments in the experiment, theory, and simulation of nuclear quantum effects in water. Novel experimental techniques, such as deep inelastic neutron scattering, now provide a detailed view of the role of nuclear quantum effects in water's properties. These have been combined with theoretical developments such as the introduction of the principle of competing quantum effects that allows the subtle interplay of water's quantum effects and their manifestation in experimental observables to be explained. We discuss how this principle has recently been used to explain the apparent dichotomy in water's isotope effects, which can range from very large to almost nonexistent depending on the property and conditions. We then review the latest major developments in simulation algorithms and theory that have enabled the efficient inclusion of nuclear quantum effects in molecular simulations, permitting their combination with on-the-fly evaluation of the potential energy surface using electronic structure theory. Finally, we identify current challenges and future opportunities in this area of research

Recent achievements in ab initio modelling of liquid water

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.Comment: 23 pages, 17 figure

Computational studies on fatty acid synthesis: from mechanisms to drug design

The first committed steps of the Fatty Acid synthesis pathway involves the de/carboxylation reactions of biotin. By understanding this step, potential novel antimicrobial agents could be discovered. The current tools of drug discovery can only help the research in finding and modifying potential hits. Finding a lead candidate from these programs are often equated to finding a needle in a haystack, which is due to the many assumptions used in molecular docking. The fundamental reaction kinetics can not be described by these techniques and a detailed study of the decarboxylation reaction is investigated using ab initio molecular dynamics. In this particular study, Car-Parrinello molecular dynamics is used and how the biotin model is protonated was found to play an important role in its reaction barrier. Although stable in low acidic solutions, a crucial nitrogen protonation is shown to have the lowest free energy barrier which could play a pivotal role in the enzymatic mechanism. The molecular docking knowledge of potential ligand inhibitors via a low level modeling technique connected to high level quantum mechanical reaction modeling provides a synergistic route in the search for inhibitors

The Coupled Electron-Ion Monte Carlo Method

In these Lecture Notes we review the principles of the Coupled Electron-Ion Monte Carlo methods and discuss some recent results on metallic hydrogen.Comment: 38 pages, 6 figures, Lecture notes for the International School of Solid State Physics, 34th course: "Computer Simulation in Condensed Matter: from Materials to Chemical Biology", 20 July-1 August 2005 Erice (Italy). To appear in Lecture Notes in Physics (2006

Elementary steps in aqueous proton transfer reactions : a first principles molecular dynamics study

La nature des acides dans un environnement aqueux est primordiale dans de nombreux aspects de la chimie et de la biologie. La caractéristique principale d'un acide est sa capacité à transférer un proton vers une molécule d'eau ou vers n'importe quelle base, mais ce procédé n'est pas aussi simple qu'il y paraît. Il peut au contraire être extrêmement complexe et dépendre de manière cruciale de la solvatation des différents intermédiaires de réaction impliqués. Cette thèse décrit les études computationnelles basées sur des simulations de dynamique moléculaire ab initio qui ont pour but d'obtenir une description à l'échelle moléculaire des divers procédés de transferts de proton entre acide et bases dans un milieu aqueux. Pour cela, nous avons étudié une serie de système, dont l'acide hydrofluorique aqueux, l'acide trifluoroacétique aqueux, et un système modèle constitué d'un phénol et d'une entité carboxylate reliés entre eux par une molécule d'eau en solution aqueuse. Deux états intermédiaires ont été identifiés pour le transfert d'un proton depuis un acide. Ces intermédiaires apparaissent stabilisés par un motif local de solvatation via des ponts H. Leurs signatures spectroscopiques ont été caractérisées au moyen de la spectroscopie infrarouge, en utilisant le formalisme de la dynamique moléculaire ab initio, qui inclut l'effet quantique nucléaire de manière explicite. Cette étude a aussi identifié trois chemins de réaction élémentaire, qui sont responsable pour le transfert d'un proton d'un acide à une base, ainsi que leurs échelles de temps caractéristiques. Les conclusions tirées de ces études sont discutées dans les détails, au niveau moléculaire, avec une emphase sur les comparaisons entre les résultats théoriques et les mesures expérimentales obtenues dans a littérature ou via des collaborateurs.The nature of acids in an aqueous environment is fundamental to many aspects of chemistry and biology. The defining feature of an acid is its ability to transfer a proton to water or to any accepting base, but this seemingly simple process can be complex and highly dependent on the solvation involving different reaction intermediate species. This thesis describes computational studies based on first principles molecular dynamics simulations aimed at obtaining molecular-level descriptions of diverse proton transfer process involving acids and bases in liquid water. For that, we have investigated a variety of systems including aqueous hydrofluoric acid, aqueous trifluoroacetic acid and a model system comprising of a phenol and a carboxyate molecule bridged by a water molecule in aqueous solution. Two different intermediate stages of proton transfer from an acid were identified which are found to be stabilized by distinct local H-bond solvation pattern. Their spectroscopic signatures were characterized using infrared spectroscopy computed from first principles molecular dynamics simulations which incorporate nuclear quantum effects explicitly. This study also identified three elementary reaction pathways that are responsible for proton translocation from acid to the base and their characteristic time scales. Conclusions drawn from this study are discussed in molecular detail, highlighting experimental comparisons