Mark E Tuckerman

Mark E Tuckerman
New York University | NYU · Department of Chemistry

Ph.D., Professor of Chemistry and Mathematics

About

249
Publications
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28,057
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Publications

Publications (249)
Article
Full-text available
Deep eutectic solvents (DESs) are an emerging class of non-aqueous solvents that are potentially scalable, easy to prepare and functionalize for many applications ranging from biomass processing to energy storage technologies. Predictive understanding of the fundamental correlations between local structure and macroscopic properties is needed to ex...
Article
Exposing anion exchange membrane (AEM) fuel cells to ambient air is known to decrease fuel cell efficiency significantly due to the presence of CO 2 .
Article
Reversible multiple timescale (MTS) integration algorithms have long been recognized as a straightforward way to increase efficiency and extend accessible timescales in molecular dynamics simulations without altering the ensemble distribution sampled. MTS methods are based on the idea that interatomic forces in a system drive motion on numerous tim...
Preprint
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Imidazole and 1,2,3-triazole are promising hydrogen-bonded heterocycles that conduct protons via a structural mechanism and whose derivatives are present in systems ranging from biological proton channels to proton exchange membrane fuel cells. Here, we leverage multiple time-stepping to perform ab initio molecular dynamics of imidazole and 1,2,3-t...
Preprint
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Imidazole is a promising anhydrous proton conductor with a high conductivity comparable to that of water at a similar temperature relative to its melting point. Previous theoretical studies of the mechanism of proton transport in imidazole have relied either on empirical models or on ab initio trajectories that have been too short to draw significa...
Article
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Fuel cell-based anion-exchange membranes (AEMs) and proton exchange membranes (PEMs) are considered to have great potential as cost-effective, clean energy conversion devices. However, a fundamental atomistic understanding of the hydroxide and hydronium diffusion mechanisms in the AEM and PEM environment is an ongoing challenge. In this work, we ai...
Article
Extended phase-space isokinetic methods in their deterministic [Minary et al., Phys. Rev. Lett. 93, 150201 (2004)] and stochastic forms [Leimkuhler et al., Mol. Phys. 111, 3579 (2013)] have proved tremendously successful in allowing multiple time-scale molecular dynamics simulations to be performed with very large time steps. These methods work by...
Article
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Reversible temperature-mediated solid phase changes, otherwise known as enantiotropic transformations, occur in many molecular crystals. These transformations take place as a result of the free-energy stabilization through entropic contributions at finite temperatures and can often have significant implications for the properties of crystalline sol...
Article
Fuel-cell deployable proton exchange membranes (PEMs) are considered to be a promising technology for clean and efficient power generation. However, a fundamental atomistic understanding of the hydronium diffusion process in the PEM environment is an ongoing challenge. In this work, we employ fully atomistic ab initio molecular dynamics to simulate...
Article
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The high cost of ab initio molecular dynamics (AIMD) simulations to model complex physical and chemical systems limits its ability to address many key questions. However, new machine learning‐based representations of complex potential energy surfaces have been introduced in recent years to circumvent computationally demanding AIMD simulations while...
Article
Deep eutectic solvents (DESs) are an emerging class of mixtures characterized by significant depressions in melting points compared to those of the neat constituent components. These materials are promising for applications as inexpensive "designer" solvents exhibiting a host of tunable physicochemical properties. A detailed review of the current l...
Article
Predicting structures of organic molecular cocrystals is a challenging task when considering the immense number of possible intermolecular orientations. Use of the Shannon information entropy, constructed from an intermolecular orientational spatial distribution function, to drive a search for crystal structures via enhanced molecular dynamics can...
Article
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Kohn-Sham density functional theory (DFT) is a standard tool in most branches of chemistry, but accuracies for many molecules are limited to 2-3 kcal ⋅ mol⁻¹ with presently-available functionals. Ab initio methods, such as coupled-cluster, routinely produce much higher accuracy, but computational costs limit their application to small molecules. In...
Article
The hydrated morphology of anion exchange membranes (used in alkaline membrane fuel cells) is a key aspect in determining their ion conductivity. Here we examine changes in the morphology of hydrated polystyrene-b-poly(ethylene-co-butylene)-b-polystyrene (SEBS) functionalized with quaternary ammonium groups in the polystyrene phase. The effects of...
Article
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In functionalized nanoconfined environments of the type employed in the study of anion exchange membranes (AEMs), a unique set of water layers forms as a result of the presence of cations and the proximity of the waters to the edges of the confining volume. In this work, we employ fully atomistic ab initio molecular dynamics in order provide a clea...
Article
Free energy surfaces of chemical and physical systems are often generated using a popular class of enhanced sampling methods that target a set of collective variables (CVs) chosen to distinguish the characteristic features of these surfaces. While some of these approaches are typically limited to low ($\sim$1-3)-dimensional CV subspaces, methods su...
Article
Benzamide, a simple derivative of benzoic acid and a common intermediate of pharmaceutical compounds, was reported to form two polymorphs in 1832, but the single crystal structure of the more stable form was not solved until 1959. Nearly 50 years later, the second form was characterized by powder diffraction, followed shortly thereafter by characte...
Article
The investigation of the microscopic processes underlying structural phase transformations in solids is extremely challenging for both simulation and experiment. Atomistic simulations of solid-solid phase transitions require extensive sampling of the corresponding high-dimensional and often rugged energy landscape. Here, we propose a rigorous const...
Article
Operation of anion exchange membrane (AEM) fuel cells results in gradients in the cell that can lead to low-hydration conditions within the cell. It is therefore important to investigate hydroxide ion diffusion in AEMs with low water-to-cation ratios (λ≤4, λ≡H2O/cation). In this work, ab initio molecular dynamics simulations are presented to explor...
Article
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We have recently proposed a new unified theoretical scheme (the "middle" scheme) for thermostat algorithms for efficient and accurate configurational sampling of the canonical ensemble. In this paper we extend the "middle" scheme to molecular dynamics algorithms for configurational sampling in systems subject to constraints. Holonomic constraints a...
Preprint
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div> Kohn-Sham density functional theory (DFT) is a standard tool in most branches of chemistry, but accuracies for many molecules are limited to 2-3 kcal/mol with presently-available functionals. Ab initio methods, such as coupled-cluster, routinely produce much higher accuracy, but computational costs limit their application to small molecules....
Preprint
We propose a rigorous construction of a 1D path collective variable to sample structural phase transformations in condensed matter. The path collective variable is defined in a space spanned by global collective variables that serve as classifiers derived from local structural units. A reliable identification of local structural environments is ach...
Article
In order to accelerate molecular dynamics simulations using polarizable force fields, we combine a new extended Lagrangian approach that eliminates the self-consistent field step (iEL/0-SCF) with a stochastic integration scheme that allows for a long time step using a multi-time stepping algorithm (SIN(R)). We consider different algorithms for the...
Preprint
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The Kohn-Sham scheme of density functional theory is one of the most widely used methods to solve electronic structure problems for a vast variety of atomistic systems across different scientific fields. While the method is fast relative to other first principles methods and widely successful, the computational time needed is still not negligible,...
Article
We propose a novel approach to search for free energy landmarks, i.e., minima and the saddle points, of chemical reactions in an automated manner, using a combination of steepest descent and gentlest ascent methods. A numerical approach is suggested to improve the sampling efficiency on the second derivatives of the free energy surface, which is re...
Article
A method for calculating the free energy difference between two structurally defined conformational states of a chemical system is developed. A path is defined using a previously reported collective variable that interpolates between two or more conformations, and a restraint is introduced in order to keep the system close to the path. The evolutio...
Article
Water exhibits numerous anomalous properties, many of which remain poorly understood. One of its intriguing behaviors is that it exhibits a temperature of maximum density (TMD) at 4 °C. We provide here new experimental evidence for hitherto unknown abrupt changes in proton transfer kinetics at the TMD. In particular, we show that the lifetime of OH...
Article
We introduce a scheme for approximating quantum time correlation functions numerically within the Feynman path integral formulation. Starting with the symmetrized version of the correlation function expressed as a discretized path integral, we introduce a change of integration variables often used in the derivation of trajectory-based semiclassical...
Article
Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires th...
Article
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The generation of free energy landscapes corresponding to conformational equilibria in complex molecular systems remains a significant computational challenge. Adding to this challenge is the need to represent, store, and manipulate the often high-dimensional surfaces that result from rare-event sampling approaches employed to compute them. In this...
Article
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Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formu...
Article
Equilibrium fractionation of stable isotopes is critically important in fields ranging from chemistry, including medicinal chemistry, electrochemistry, geochemistry, and nuclear chemistry, to environmental science. The dearth of reliable estimates of equilibrium fractionation factors, from experiment or from natural observations, has created a need...
Article
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Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms...
Article
Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H$_2$ and D$_2$ diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the f...
Article
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulati...
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The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range o...
Article
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Prediction and exploration of possible polymorphism in organic crystal compounds are of great importance for industries ranging from organic electronics to pharmaceuticals to high-energy materials. Here we apply our crystal structure prediction procedure and the enhanced molecular dynamics based sampling approach called the Crystal-Adiabatic Free E...
Article
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range o...
Article
Two isostructural energetic cocrystals containing 1,3,5-trinitrobenzene (TNB) were obtained with the energetic materials 1,3,5-triiodo-2,4,6-trinitrobenzene (TITNB) and 1,3,5-tribromo-2,4,6-trinitrobenzene (TBTNB) in ratios of 2:1 TNB/TITNB (1) and 2:1 TNB/TBTNB (2). These materials contain the shortest nitro-iodo and second shortest nitro-bromo in...
Article
Quantum delocalization of atomic nuclei affects the physical properties of many hydrogen-rich liquids and biological systems even at room temperature. In computer simulations, quantum nuclei can be modeled via the path integral formulation of quantum statistical mechanics, which implies a substantial increase in computational overhead. By restricti...
Article
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The organisers and participants are very grateful to the crystallographers who supplied the candidate structures: Dr. Peter Horton (XXII), Dr. Brian Samas (XXIII), Prof. Bruce Foxman (XXIV), and Prof. Kraig Wheeler (XXV and XXVI). We are also grateful to Dr. Emma Sharp and colleagues at Johnson Matthey (Pharmorphix) for the polymorph screening of X...
Article
Full-text available
The sixth blind test of organic crystal-structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal, and a bulky flexible molecule. This blind test has seen substantial growth in the number of submissions, with the broad range o...
Article
Molecular dynamics remains one of the most widely used computational tools in the theoretical molecular sciences to sample an equilibrium ensemble distribution and/or to study the dynamical properties of a system. The efficiency of a molecular dynamics calculation is limited by the size of the time step that can be employed, which is dictated by th...
Article
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Structures of the α and β phases of resorcinol, a major commodity chemical in the pharmaceutical, agrichemical, and polymer industries, were the first polymorphic pair of molecular crystals solved by X-ray analysis. It was recently stated that "no additional phases can be found under atmospheric conditions" (Druzbicki, K. et al. J. Phys. Chem. B 20...
Article
We investigate systematically the manifestations of the condensed-phase environment of the structure II clathrate hydrate in the translation-rotation (TR) dynamics and the inelastic neutron scattering (INS) spectra of an H2 molecule confined in the small dodecahedral cage of the hydrate. The aim is to elucidate the extent to which these properties...
Article
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In computer simulations, quantum delocalization of atomic nuclei can be modeled making use of the Path Integral (PI) formulation of quantum statistical mechanics. This approach, however, comes with a large computational cost. By restricting the PI modeling to a small region of space, this cost can be significantly reduced. In the present work we de...
Article
Coarse graining of complex systems possessing many degrees of freedom can often be a useful approach for analyzing and understanding key features of these systems in terms of just a few variables. The relevant energy landscape in a coarse-grained description is the free energy surface as a function of the coarse-grained variables, which, despite th...
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The melting of a solid, like other first-order phase transitions, exhibits an intrinsic time-scale disparity: The time spent by the system in metastable states is orders of magnitude longer than the transition times between the states. Using rare-event sampling techniques, we find that melting of representative solids—here, copper and aluminum—occu...
Article
In molecular dynamics simulations, most enhanced sampling methods are traditionally associated with one particular estimator to calculate the free energy surface (FES), such as the histogram, the mean force, or the bias potential. Here, we start from the realization that four enhanced sampling methods, metadynamics and well-tempered metadynamics (i...
Chapter
Modern theoretical methods, aided by the emergence of increasingly powerful high-speed computing architectures, have advanced to a level such that the microscopic details of chemical processes in condensed phases can now be treated on a relatively routine basis.
Article
Full-text available
The problem of predicting polymorphism in atomic and molecular crystals constitutes a significant challenge both experimentally and theoretically. From the theoretical viewpoint, polymorphism prediction falls into the general class of problems characterized by an underlying rough energy landscape, and consequently, free energy based enhanced sampli...
Article
Many problems in biology, chemistry, and materials science require knowledge of saddle points on free energy surfaces. These saddle points act as transition states and are the bottlenecks for transitions of the system between different metastable states. For simple systems in which the free energy depends on a few variables, the free energy surface...
Article
The properties of the hydroperoxide anion, HOO-, in water play a key role in many biological systems and industrial processes. However the dynamics of HOO$^-$ and its solvation shell are largely unknown. We have undertaken an ab initio molecular dynamics study of aqueous HOO- at ambient temperature in liquid water. Two solvation structures for the...
Article
The quality of classical biomolecular simulations is inevitably limited by two problems: the cccuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converged free energy surfaces of dipeptides in the gas p...
Article
The problem of computing free energy differences due to isotopic substitution in chemical systems is discussed. The shift in the equilibrium properties of a system upon isotopic substitution is a purely quantum mechanical effect that can be quantified using the Feynman path integral approach. In this paper, we explore two developments that lead to...
Article
Abstract Phosphoric acid based polymer electrolyte membranes (e.g. poly(benzimidazole)/phosphoric acid) are the only quasi-anhydrous separator electrolytes for medium temperature fuel cells currently in use. Pure phosphoric acid has the highest known intrinsic proton conductivity of any substance, which is very sensitive towards doping with Brønste...
Article
We correct an error in our original paper. Calculations originally reported for the alanine tripeptide were performed using the earlier driven adiabatic free energy dynamics (d-AFED) approach rather than the new unified free energy dynamics (UFED) scheme. When UFED is applied to this system, the rate of convergence of the free energy surface improv...