arXiv subjects

Thomas E. Markland

Publications and source records attributed to Thomas E. Markland.

At least 55 records · Page 3Linked to original sources

arXiv2017

Decoding the spectroscopic features and timescales of aqueous proton defects

Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton defects in the water hydrogen bond network and the mechanisms for their interconversion remains a formidable challenge. Here, we use simulations treating the quantum nature of both the electrons and nuclei to show how the experimentally observed spectroscopic features and relaxation timescales can be elucidated using a physically transparent coordinate that encodes the overall asymmetry of the solvation environment of the proton defect. We demonstrate that this coordinate can be used both to discriminate the extremities of the features observed in the linear vibrational spectrum and to explain the molecular motions that give rise to the interconversion timescales observed in recent nonlinear experiments. This analysis provides a unified condensed-phase picture of proton structure and dynamics that, at its extrema, encompasses proton sharing and spectroscopic features resembling the limiting Eigen [H$_{3}$O(H$_{2}$O)$_{3}$]$^{+}$ and Zundel [H(H$_{2}$O)$_{2}$]$^{+}$ gas-phase structures, while also describing the rich variety of interconverting environments in the liquid phase.

physics.chem-ph↗

arXiv2017

Proton network flexibility enables robustness and large electric fields in the ketosteroid isomerase active site

Hydrogen bond networks play vital roles in biological functions ranging from protein folding to enzyme catalysis. Here we combine electronic structure calculations and ab initio path integral molecular dynamics simulations, which incorporate both nuclear and electronic quantum effects, to show why the network of short hydrogen bonds in the active site of ketosteroid isomerase is remarkably robust to mutations along the network and how this gives rise to large local electric fields. We demonstrate that these properties arise from the network's ability to respond to a perturbation by shifting proton positions and redistributing electronic charge density. This flexibility leads to small changes in properties such as the partial ionization of residues and $pK_a$ isotope effects upon mutation of the residues, consistent with recent experiments. This proton flexibility is further enhanced when an extended hydrogen bond network forms in the presence of an intermediate analog, which allows us to explain the chemical origins of the large electric fields in the enzyme's active site observed in recent experiments.

physics.bio-ph↗

arXiv2017

Quantum dynamics and spectroscopy of ab initio liquid water: the interplay of nuclear and electronic quantum effects

Understanding the reactivity and spectroscopy of aqueous solutions at the atomistic level is crucial for the elucidation and design of chemical processes. However, the simulation of these systems requires addressing the formidable challenges of treating the quantum nature of both the electrons and nuclei. Exploiting our recently developed methods that provide acceleration by up to two orders of magnitude, we combine path integral simulations with on-the-fly evaluation of the electronic structure at the hybrid density functional theory level to capture the interplay between nuclear quantum effects and the electronic surface. Here we show that this combination provides accurate structure and dynamics, including the full infra-red and Raman spectra of liquid water. This allows us to demonstrate and explain the failings of lower-level density functionals for dynamics and vibrational spectroscopy when the nuclei are treated quantum mechanically. These insights thus provide a foundation for the reliable investigation of spectroscopy and reactivity in aqueous environments.

physics.chem-ph↗

arXiv2016

Generalized Quantum Master Equations In and Out of Equilibrium: When Can One Win?

Generalized quantum master equations (GQMEs) are an important tool in modeling chemical and physical processes. For a large number of problems it has been shown that exact and approximate quantum dynamics methods can be made dramatically more efficient, and in the latter case more accurate, by proceeding via the GQME formalism. However, there are many situations where utilizing the GQME approach seems to offer no advantage over a direct evaluation of the property of interest. Here we provide a more detailed understanding of the conditions under which these methods will offer benefits. In particular, we derive exact expressions for the memory kernel for systems both in and out of equilibrium, and show the conditions under which these expressions will be guaranteed to return a result identical to that obtained from direct simulation. We also show the conditions which approximate methods must satisfy if they are to offer different results when used in conjunction with the GQME formalism. These exact analytical results thus provide new insights as to when proceeding via the GQME approach can improve the accuracy or efficiency of simulations.

physics.chem-ph↗

arXiv2016

Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, our implementation is as fast as a typical classical ab initio molecular dynamics simulation and 35$\times$ faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

physics.chem-ph↗

arXiv2015

Accurate nonadiabatic quantum dynamics on the cheap: making the most of mean field theory with master equations

In this article we show how Ehrenfest mean field theory can be made both a more accurate and efficient method to treat nonadiabatic quantum dynamics by combining it with the generalized quantum master equation framework. The resulting mean field generalized quantum master equation (MF-GQME) approach is a non-perturbative and non-Markovian theory to treat open quantum systems without any restrictions on the form of the Hamiltonian that it can be applied to. By studying relaxation dynamics in a wide range of dynamical regimes, typical of charge and energy transfer, we show that MF-GQME provides a much higher accuracy than a direct application of mean field theory. In addition, these increases in accuracy are accompanied by computational speed-ups of between one and two orders of magnitude that become larger as the system becomes more nonadiabatic. This combination of quantum-classical theory and master equation techniques thus makes it possible to obtain the accuracy of much more computationally expensive approaches at a cost lower than even mean field dynamics, providing the ability to treat the quantum dynamics of atomistic condensed phase systems for long times.

physics.chem-ph↗

arXiv2015

Efficient and accurate surface hopping for long time nonadiabatic quantum dynamics

The quantum-classical Liouville equation offers a rigorous approach to nonadiabatic quantum dynamics based on surface hopping type trajectories. However, in practice the applicability of this approach has been limited to short times owing to unfavorable numerical scaling. In this paper we show that this problem can be alleviated by combining it with a formally exact generalized quantum master equation treatment. This allows dramatic improvements in the efficiency of the approach in nonadiabatic regimes, making it computationally tractable to treat the quantum dynamics of complex systems for long times. We demonstrate our approach by applying it to a model of condensed phase charge transfer where our method is shown to be numerically exact in regimes where fewest-switches surface hopping and mean field approaches fail to obtain the either the correct rates or long-time populations.

physics.chem-ph↗

arXiv2015

Quantum delocalization of protons in the hydrogen bond network of an enzyme active site

Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

physics.chem-ph↗

arXiv2014

Quantum fluctuations and isotope effects in ab initio descriptions of water

Nuclear quantum effects, such as zero-point energy and tunneling, cause significant changes to the structure and dynamics of hydrogen bonded systems such as liquid water. However, due to the current inability to simulate liquid water using an exact description of its electronic structure, the interplay between nuclear and electronic quantum effects remains unclear. Here we use simulations that incorporate the quantum mechanical nature of both the nuclei and electrons to provide a fully ab initio determination of the particle quantum kinetic energies, free energy change upon exchanging hydrogen for deuterium and the isotope fractionation ratio in water. These properties, which selectively probe the quantum nature of the nuclear degrees of freedom, allow us to make direct comparison to recent experiments and elucidate how electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water.

physics.chem-ph↗

arXiv2013

Interface limited growth of heterogeneously nucleated ice in supercooled water

Heterogeneous ice growth exhibits a maximum in freezing rate arising from the competition between kinetics and the thermodynamic driving force between the solid and liquid states. Here, we use molecular dynamics simulations to elucidate the atomistic details of this competition, focusing on water properties in the interfacial region along the secondary prismatic direction. The crystal growth velocity is maximized when the efficiency of converting interfacial water molecules to ice, collectively known as the attachment kinetics, is greatest. We find water molecules that contact the intermediate ice layer in concave regions along the atomistically roughened surface are more likely to freeze directly. The increased roughening of the solid surface at large undercoolings consequently plays an important limiting role on the rate of ice growth, as water molecules are unable to integrate into increasingly deeper surface pockets. These results provide insights into the molecular mechanisms for self-assembly of solid phases that are important in many biological and atmospheric processes.

cond-mat.soft↗

arXiv2013

Multiple Time Step Integrators in Ab Initio Molecular Dynamics

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we show that such a timescale separation is possible using two different schemes: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

physics.comp-ph↗

arXiv2013

Unraveling quantum mechanical effects in water using isotopic fractionation

When two phases of water are at equilibrium, the ratio of hydrogen isotopes in each is slightly altered due to their different phase affinities. This isotopic fractionation process can be utilized to analyze water's movement in the world's climate. Here we show that equilibrium fractionation ratios, an entirely quantum mechanical property, also provide a sensitive probe to assess the magnitude of nuclear quantum fluctuations in water. By comparing the predictions of a series of water models, we show that those describing the OH chemical bond as rigid or harmonic greatly over-predict the magnitude of isotope fractionation. Models that account for anharmonicity in this coordinate are shown to provide much more accurate results due to their ability to give partial cancellation between inter and intra-molecular quantum effects. These results give evidence of the existence of competing quantum effects in water and allow us to identify how this cancellation varies across a wide range of temperatures. In addition, this work demonstrates that simulation can provide accurate predictions and insights into hydrogen fractionation.

physics.chem-ph↗

arXiv2012

Efficient methods and practical guidelines for simulating isotope effects

The shift in chemical equilibria due to isotope substitution is often exploited to gain insight into a wide variety of chemical and physical processes. It is a purely quantum mechanical effect, which can be computed exactly using simulations based on the path integral formalism. Here we discuss how these techniques can be made dramatically more efficient, and how they ultimately outperform quasi-harmonic approximations to treat quantum liquids not only in terms of accuracy, but also in terms of computational efficiency. To achieve this goal we introduce path integral quantum mechanics estimators based on free energy perturbation, which enable the evaluation of isotope effects using only a single path integral molecular dynamics trajectory of the naturally abundant isotope. We use as an example the calculation of the free energy change associated with H/D and 16O/18O substitutions in liquid water, and of the fractionation of those isotopes between the liquid and the vapor phase. In doing so, we demonstrate and discuss quantitatively the relative benefits of each approach, thereby providing a set of guidelines that should facilitate the choice of the most appropriate method in different, commonly encountered scenarios. The efficiency of the estimators we introduce and the analysis that we perform should in particular facilitate accurate ab initio calculation of isotope effects in condensed phase systems.

cond-mat.stat-mech↗

arXiv2012

Growing point-to-set length scale correlates with growing relaxation times in model supercooled liquids

It has been demonstrated recently that supercooled liquids sharing simple structural features (e.g. pair distribution functions) may exhibit strikingly distinct dynamical behavior. Here we show that a more subtle structural feature correlates with relaxation times in three simulated systems that have nearly identical radial distribution functions but starkly different dynamical behavior. In particular, for the first time we determine the thermodynamic "point-to-set" length scale in several canonical model systems and demonstrate the quantitative connection between this length scale and the growth of relaxation times. Our results provide clues necessary for distinguishing competing theories of the glass transition.

cond-mat.stat-mech↗

arXiv2011

Reduced density matrix hybrid approach: Application to electronic energy transfer

Electronic energy transfer in the condensed phase, such as that occurring in photosynthetic complexes, frequently occurs in regimes where the energy scales of the system and environment are similar. This situation provides a challenge to theoretical investigation since most approaches are accurate only when a certain energetic parameter is small compared to others in the problem. Here we show that in these difficult regimes, the Ehrenfest approach provides a good starting point for a dynamical description of the energy transfer process due to its ability to accurately treat coupling to slow environmental modes. To further improve on the accuracy of the Ehrenfest approach, we use our reduced density matrix hybrid framework to treat the faster environmental modes quantum mechanically, at the level of a perturbative master equation. This combined approach is shown to provide an efficient and quantitative description of electronic energy transfer in a model dimer and the Fenna-Matthews-Olson complex and is used to investigate the effect of environmental preparation on the resulting dynamics.

cond-mat.stat-mech↗

arXiv2011

Theory and simulations of quantum glass forming liquids

A comprehensive microscopic dynamical theory is presented for the description of quantum fluids as they transform into glasses. The theory is based on a quantum extension of mode-coupling theory. Novel effects are predicted, such as reentrant behavior of dynamical relaxation times. These predictions are supported by path integral ring polymer molecular dynamics simulations. The simulations provide detailed insight into the factors that govern slow dynamics in glassy quantum fluids. Connection to other recent work on both quantum glasses as well as quantum optimization problems is presented.

cond-mat.stat-mech↗

arXiv2011

Reduced density matrix hybrid approach: An efficient and accurate method for adiabatic and non-adiabatic quantum dynamics

We present a new approach to calculate real-time quantum dynamics in complex systems. The formalism is based on the partitioning of a system's environment into "core" and "reservoir" modes, with the former to be treated quantum mechanically and the latter classically. The presented method only requires the calculation of the system's reduced density matrix averaged over the quantum core degrees of freedom which is then coupled to a classically evolved reservoir to treat the remaining modes. We demonstrate our approach by applying it to the spin-boson problem using the noninteracting blip approximation to treat the system and core, and Ehrenfest dynamics to treat the reservoir. The resulting hybrid methodology is accurate for both fast and slow baths, since it naturally reduces to its composite methods in their respective regimes of validity. In addition, our combined method is shown to yield good results in intermediate regimes where neither approximation alone is accurate and to perform equally well for both strong and weak system-bath coupling. Our approach therefore provides an accurate and efficient methodology for calculating quantum dynamics in complex systems.

cond-mat.stat-mech↗

arXiv2010

Competing quantum effects in the dynamics of a flexible water model

Numerous studies have identified large quantum mechanical effects in the dynamics of liquid water. In this paper, we suggest that these effects may have been overestimated due to the use of rigid water models and flexible models in which the intramolecular interactions were described using simple harmonic functions. To demonstrate this, we introduce a new simple point charge model for liquid water, q-TIP4P/F, in which the O--H stretches are described by Morse-type functions. We have parameterized this model to give the correct liquid structure, diffusion coefficient, and infra-red absorption frequencies in quantum (path integral-based) simulations. By comparing classical and quantum simulations of the liquid, we find that quantum mechanical fluctuations increase the rates of translational diffusion and orientational relaxation in our model by a factor of around 1.15. This effect is much smaller than that observed in all previous simulations of simple empirical water models, which have found a quantum effect of at least 1.4 regardless of the quantum simulation method or the water model employed. The small quantum effect in our model is a result of two competing phenomena. Intermolecular zero point energy and tunneling effects destabilize the hydrogen bonding network, leading to a less viscous liquid with a larger diffusion coefficient. However this is offset by intramolecular zero point motion, which changes the average water monomer geometry resulting in a larger dipole moment, stronger intermolecular interactions, and slower diffusion. We end by suggesting, on the basis of simulations of other potential energy models, that the small quantum effect we find in the diffusion coefficient is associated with the ability of our model to produce a single broad O-H stretching band in the infra-red absorption spectrum.

cond-mat.soft↗