A Doubly Nudged Elastic Band Method for Finding Transition States

A modification of the nudged elastic band (NEB) method is presented that enables stable optimisations to be run using both the limited-memory quasi-Newton (L-BFGS) and slow-response quenched velocity Verlet (SQVV) minimisers. The performance of this new `doubly nudged' DNEB method is analysed in conjunction with both minimisers and compared with previous NEB formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be quicker by up to two orders of magnitude. Applications to permutational rearrangements of the seven-atom Lennard-Jones cluster (LJ7) and highly cooperative rearrangements of LJ38 and LJ75 are presented. We also outline an updated algorithm for constructing complicated multi-step pathways using successive DNEB runs.Comment: 13 pages, 8 figures, 2 table

Improving double-ended transition state searches for soft-matter systems.

Transitions between different stable configurations of biomolecules are important in understanding disease mechanisms, structure-function relations, and novel molecular-scale engineering. The corresponding pathways can be characterized efficiently using geometry optimization schemes based on double-ended transition state searches. An interpolation is first constructed between the known states and then refined, yielding a band that contains transition state candidates. Here, we analyze an example where various interpolation schemes lead to bands with a single step transition, but the correct pathway actually proceeds via an intervening, low-energy minimum. We compare a number of different interpolation schemes for this problem. We systematically alter the number of discrete images in the interpolations and the spring constants used in the optimization and test two schemes for adjusting the spring constants and image distribution, resulting in a total of 2760 different connection attempts. Our results confirm that optimized bands are not necessarily a good description of the transition pathways in themselves, and further refinement to actually converge transition states and establish their connectivity is required. We see an improvement in the optimized bands if we employ the adjustment of spring constants with doubly-nudged elastic band and a smaller improvement from the image redistribution. The example we consider is representative of numerous cases we have encountered in a wide variety of molecular and condensed matter systems

CHARMM: The biomolecular simulation program

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2009.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63074/1/21287_ftp.pd

QMCube (QM3): An all‐purpose suite for multiscale QM/MM calculations

QMCube (QM3) is a suite written in the Python programming language, initially focused on multiscale QM/MM simulations of biological systems, but open enough to address other kinds of problems. It allows the user to combine highly efficient QM and MM programs, providing unified access to a wide range of computational methods. The suite also supplies additional modules with extra functionalities. These modules facilitate common tasks such as performing the setup of the models or process the data generated during the simulations. The design of QM3 has been carried out considering the least number of external dependencies (only an algebra library, already included in the distribution), which makes it extremely portable. Also, the modular structure of the suite should help to expand and develop new computational methods

Analysis and optimisation of the basis set filtration algorithm

PhD ThesisThe ltration algorithm has recently been introduced as a way of increasing the speed of ab initio modelling calculations using Cartesian Gaussian basis functions. It works by developing a novel set of basis functions which are constructed specifically for the system being modelled. It has been implemented in the ab initio density functional theory based modelling package AIMPRO. The standard ltration process is found to be accurate when the ltration radius is increased to at least 10 Bohr radii in silicon. The standard ltration process uses all the basis functions centred on points inside a sphere centred on each atom in turn. By rejecting some of these functions (a trimming process), the ltration process can be speeded up, however there will be a resulting loss of accuracy. Three approaches to developing a ltered basis for an atom are considered, and compared. The most successful criterion for function trimming is found to be where functions are kept which exceed a threshold value on the surface of a sphere. Structural optimisation using ltration produce accurate nal structures, even when using parameters that give rise to poorly converged absolute energies. For the most time consuming elements of a calculation, a rapid ltration process is possible. However, very poor ltration thresholds introduce small inconsistencies between energies and forces, which can make optimisation difficult if algorithms are chosen that use both the energy and force. Algorithms that only use forces are implemented, and shown to be stable and produce accurate structures. This is further demonstrated using a new implementation of the Lanczos method for determining transition states. This is compared against the current AIMPRO method, the nudged elastic band. The new method is far superior in terms of speed, and offers greater stability towards the end of calculations

Direct conversion of methane-to-methanol: transition-metal dimer sites in small-pore zeolites: First-principles calculations and microkinetic modeling

Direct conversion of methane to methanol is a highly desired reaction. Partially oxidizing methane into a liquid fuel at ambient temperature and pressure would enable utilization of natural gas and biogas to a much larger extent than what is possible today. This is desirable since natural gas is the cleanest fossil energy source, and when in the form of biogas (or biomethane) has a net-zero carbon emission. The direct conversion of methane requires a catalyst; however, no material with high enough activity and selectivity towards methanol has been identified. Mimicking the enzyme methane monooxygenase (MMO), copper-exchanged zeolites are considered promising candidates. A plethora of different active sites have been suggested, but neither the detailed structure and composition of the active site, nor the mechanism for the reaction, are known.In this thesis, the catalytic properties of transition metal dimers in small-pore zeolites are studied using first-principles calculations, ab initio thermodynamics, and microkinetic modeling. As a first step, the stability of the Cu dimer structure in SSZ-13 is investigated under direct conversion conditions. The zeolite is found to be very humid, and the structure of the proposed active site is highly dependent on the temperature and partial pressure of relevant gases. The Cu2O and Cu2OH structures are found to be the energetically most preferred. The reaction over the sites is limited by a high free energy barrier of the C-H bond in methane and a slow methanol desorption rate. Adding water to the reaction facilitates desorption of the products, increasing the activity of the Cu2O site. The reaction mechanism for an entire reaction cycle over the Cu-dimer, including the formation of the active site, is investigated in dry and wet conditions. The oxidation of the Cu monomers, using molecular oxygen, is limited by the diffusion of the Cu species along the zeolite framework and the activity is increased when water is added to the reaction. To further investigate the composition of the active dimer site, transition-metal and transition-metal alloy configurations are investigated. The adsorption energy of atomic oxygen is identified as a descriptor for the activity of the dimer systems. Identified motifs showing activity towards direct methane to methanol conversion are the 2Cu, along with the AuPd and PdCu alloy dimer systems. The activity of these systems is comparable and, when excluding competing reactions, meets the high turn-over needed for a commercially viable catalyst

Modeling and Design of All-Solid-State Batteries: From Materials to Interfaces

All-solid-state batteries show its great potential for being the next-generation source of clean energy barely with safety issues. While current research progress suggests the bottleneck of commercialization of all-solid-state batteries is the high resistivity at the electrode/SE interfaces. The aim of this thesis is to demonstrate how computational efforts can help understand and tackle the interface issues. The content comprises the following three projects: the methodology development (Chapter 2), the optimization of bulk materials (Chapter 3), and combined experimental and theoretical investigation into reactive interfaces (Chapter 4 & 5).In the first project, we aimed to develop and improve the computational workflow in material science research, especially those related to the interfaces. In the first part of this project, the Nudged Elastic Band (NEB) workflow has been developed with high automation and flexibility; and in the second part, an extension to a traditional molecular dynamics workflow specifically for tracking interface reactions has been implemented.The intrinsic properties of bulk materials are important to the interfacial properties and, thus, the performance of the full-cell battery. In the second project, we illustrated a computational aided design of bulk material, the Mg-doped Na3V2(PO4)3 cathode Na3+xV2-xMgx(PO4)3/C.The third project includes chapters 4 & 5, which are interfacial investigations on Na-ion and Li-ion, respectively. In chapter 4, we have demonstrated how thermodynamic approximations based on assumptions of fast alkali diffusion and multi-species equilibrium can be used to effectively screen combinations of Na-ion electrodes, solid electrolytes and buffer oxides for electrochemical and chemical compatibility. In addition to the thermodynamic approximation, ab initio molecular dynamics simulations of the NaCoO 2 /Na 3 PS 4 interface model predict that the formation of [SO4]2- -containing compounds and Na3P are kinetically favored over the formation of [PO4]3- -containing compounds, which has been validated through XPS recently. Chapter 5 investigate the source of reactivity between the sulfide solid electrolyte Li6PS5Cl (LPSCl) and the high-voltage cathode LiNi0.85Co0.1Al0.05O2 (NCA). And both experimental and computational results demonstrated improved stability between NCA and LPSCl after incorporation of the LiNbO 3 coating