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1. Implementing Reactivity in Molecular Dynamics Simulations with the Interface Force Field (IFF-R) and Other Harmonic Force Fields

   Jordan J. Winetrout, Krishan Kanhaiya ( July 2021 , ArXivorg)

   The Interface force field (IFF) enables accurate simulations of bulk and interfacial properties of compounds and multiphase materials. However, the simulation of reactions and mechanical properties up to failure remains challenging and expensive. Here we introduce the Reactive Interface Force Field (IFF-R) to analyze bond breaking and failure of complex materials using molecular dynamics simulations. IFF-R uses a Morse potential instead of a harmonic potential as typically employed in molecular dynamics force fields to describe the bond energy, which can render any desired bond reactive by specification of the curve shape of the potential energy and the bond dissociation energy. This facile extension of IFF and other force fields that utilize a harmonic bond energy term allows the description of bond breaking without loss in functionality, accuracy, and speed. The method enables quantitative, on-the-fly computations of bond breaking and stress-strain curves up to failure in any material. We illustrate accurate predictions of mechanical behavior for a variety of material systems, including metals (iron), ceramics (carbon nanotubes), polymers (polyacrylonitrile and cellulose I\b{eta}), and include sample parameters for common bonds based on using experimental and high-level (MP2) quantum mechanical reference data. Computed structures, surface energies, elastic moduli, and tensile strengths are inmore »excellent agreement with available experimental data. Non-reactive properties are shown to be essentially identical to IFF values. Computations are approximately 50 times faster than using ReaxFF and require only a single set of parameters. Compatibility of IFF and IFF-R with biomolecular force fields allows the quantitative analysis of the mechanics of proteins, DNA, and other biological molecules.« less
2. Lithium niobate photonics: Unlocking the electromagnetic spectrum

   https://doi.org/10.1126/science.abj4396  

   Boes, Andreas ; Chang, Lin ; Langrock, Carsten ; Yu, Mengjie ; Zhang, Mian ; Lin, Qiang ; Lončar, Marko ; Fejer, Martin ; Bowers, John ; Mitchell, Arnan ( January 2023 , Science)

   BACKGROUND Electromagnetic (EM) waves underpin modern society in profound ways. They are used to carry information, enabling broadcast radio and television, mobile telecommunications, and ubiquitous access to data networks through Wi-Fi and form the backbone of our modern broadband internet through optical fibers. In fundamental physics, EM waves serve as an invaluable tool to probe objects from cosmic to atomic scales. For example, the Laser Interferometer Gravitational-Wave Observatory and atomic clocks, which are some of the most precise human-made instruments in the world, rely on EM waves to reach unprecedented accuracies. This has motivated decades of research to develop coherent EM sources over broad spectral ranges with impressive results: Frequencies in the range of tens of gigahertz (radio and microwave regimes) can readily be generated by electronic oscillators. Resonant tunneling diodes enable the generation of millimeter (mm) and terahertz (THz) waves, which span from tens of gigahertz to a few terahertz. At even higher frequencies, up to the petahertz level, which are usually defined as optical frequencies, coherent waves can be generated by solid-state and gas lasers. However, these approaches often suffer from narrow spectral bandwidths, because they usually rely on well-defined energy states of specific materials, which results inmore »a rather limited spectral coverage. To overcome this limitation, nonlinear frequency-mixing strategies have been developed. These approaches shift the complexity from the EM source to nonresonant-based material effects. Particularly in the optical regime, a wealth of materials exist that support effects that are suitable for frequency mixing. Over the past two decades, the idea of manipulating these materials to form guiding structures (waveguides) has provided improvements in efficiency, miniaturization, and production scale and cost and has been widely implemented for diverse applications. ADVANCES Lithium niobate, a crystal that was first grown in 1949, is a particularly attractive photonic material for frequency mixing because of its favorable material properties. Bulk lithium niobate crystals and weakly confining waveguides have been used for decades for accessing different parts of the EM spectrum, from gigahertz to petahertz frequencies. Now, this material is experiencing renewed interest owing to the commercial availability of thin-film lithium niobate (TFLN). This integrated photonic material platform enables tight mode confinement, which results in frequency-mixing efficiency improvements by orders of magnitude while at the same time offering additional degrees of freedom for engineering the optical properties by using approaches such as dispersion engineering. Importantly, the large refractive index contrast of TFLN enables, for the first time, the realization of lithium niobate–based photonic integrated circuits on a wafer scale. OUTLOOK The broad spectral coverage, ultralow power requirements, and flexibilities of lithium niobate photonics in EM wave generation provides a large toolset to explore new device functionalities. Furthermore, the adoption of lithium niobate–integrated photonics in foundries is a promising approach to miniaturize essential bench-top optical systems using wafer scale production. Heterogeneous integration of active materials with lithium niobate has the potential to create integrated photonic circuits with rich functionalities. Applications such as high-speed communications, scalable quantum computing, artificial intelligence and neuromorphic computing, and compact optical clocks for satellites and precision sensing are expected to particularly benefit from these advances and provide a wealth of opportunities for commercial exploration. Also, bulk crystals and weakly confining waveguides in lithium niobate are expected to keep playing a crucial role in the near future because of their advantages in high-power and loss-sensitive quantum optics applications. As such, lithium niobate photonics holds great promise for unlocking the EM spectrum and reshaping information technologies for our society in the future. Lithium niobate spectral coverage. The EM spectral range and processes for generating EM frequencies when using lithium niobate (LN) for frequency mixing. AO, acousto-optic; AOM, acousto-optic modulation; χ (2) , second-order nonlinearity; χ (3) , third-order nonlinearity; EO, electro-optic; EOM, electro-optic modulation; HHG, high-harmonic generation; IR, infrared; OFC, optical frequency comb; OPO, optical paramedic oscillator; OR, optical rectification; SCG, supercontinuum generation; SHG, second-harmonic generation; UV, ultraviolet.« less
3. Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations

   https://doi.org/10.1039/C7CP06709G  

   Liang, Dongyue ; Hong, Jiewei ; Fang, Dong ; Bennett, Joseph W. ; Mason, Sara E. ; Hamers, Robert J. ; Cui, Qiang ( January 2018 , Physical Chemistry Chemical Physics)

   We describe a strategy of integrating quantum mechanical (QM), hybrid quantum mechanical/molecular mechanical (QM/MM) and MM simulations to analyze the physical properties of a solid/water interface. This protocol involves using a correlated ab initio (CCSD(T)) method to first calibrate Density Functional Theory (DFT) as the QM approach, which is then used in QM/MM simulations to compute relevant free energy quantities at the solid/water interface using a mean-field approximation of Yang et al. that decouples QM and MM thermal fluctuations; gas-phase QM/MM and periodic DFT calculations are used to determine the proper QM size in the QM/MM simulations. Finally, the QM/MM free energy results are compared with those obtained from MM simulations to directly calibrate the force field model for the solid/water interface. This protocol is illustrated by examining the orientations of an alkyl amine ligand at the gold/water interface, since the ligand conformation is expected to impact the chemical properties ( e.g. , charge) of the solid surface. DFT/MM and MM simulations using the INTERFACE force field lead to consistent results, suggesting that the effective gold/ligand interactions can be adequately described by a van der Waals model, while electrostatic and induction effects are largely quenched by solvation. The observed differencesmore »among periodic DFT, QM/MM and MM simulations, nevertheless, suggest that explicitly including electronic polarization and potentially charge transfer in the MM model can be important to the quantitative accuracy. The strategy of integrating multiple computational methods to cross-validate each other for complex interfaces is applicable to many problems that involve both inorganic/metallic and organic/biomolecular components, such as functionalized nanoparticles.« less
4. Multifactor theoretical modeling of solar thermal fuels built on azobenzene and norbornadiene scaffolds

   https://doi.org/10.1039/d1se00041a  

   Szabo, Reuben ; Le, Khoa N. ; Kowalczyk, Tim ( April 2021 , Sustainable Energy & Fuels)

   Solar thermal fuels (STFs) offer a unique way of harnessing energy from the sun by absorbing photons and storing the energy in a metastable photoisomerized state. The reverse isomerization process can then be catalytically or thermally triggered to release the stored energy and return the fuel to its stable configuration. Functionalization of these compounds is necessary to reach practical energy storage densities, but substitutions that increase the energy storage density may adversely impact performance at other steps along the fuel cycle. Recent computational screening efforts to identify high-performance STF candidates have focused on properties that can be estimated from ground-state electronic structure methods. Here we argue that computational screening of STF candidates across the full fuel cycle benefits from a multifactor approach with excited-state properties like excitation energies and photoisomerization quantum yields addressed alongside key ground-state properties like energy storage densities and reverse isomerization barriers. As a critical step toward multifactor high-throughput screening and optimization of STFs, in this work we first systematically simulate the specific storage energy and excitation energy of substituted azobenzene- and norbornadiene-based STFs through electronic structure calculations. Density-functional tight-binding (DFTB) predictions are benchmarked against density functional theory (DFT) and experimental measurements where available. To encompass themore »complete solar thermal fuel cycle in these compounds, we then apply DFT methods to analyze the reverse isomerization process and its relationship to the photoisomerization quantum yield. We find that DFTB provides a useful balance between accuracy and computational efficiency for virtual screening of STF photoabsorption and energy storage, while isomerization barrier and quantum yield predictions require more sophisticated approaches.« less
5. Comparative assessment of QM-based and MM-based models for prediction of protein–ligand binding affinity trends

   https://doi.org/10.1039/d2cp00464j  

   Maier, Sarah ; Thapa, Bishnu ; Erickson, Jon ; Raghavachari, Krishnan ( June 2022 , Physical Chemistry Chemical Physics)

   Methods which accurately predict protein – ligand binding strengths are critical for drug discovery. In the last two decades, advances in chemical modelling have enabled steadily accelerating progress in the discovery and optimization of structure-based drug design. Most computational methods currently used in this context are based on molecular mechanics force fields that often have deficiencies in describing the quantum mechanical (QM) aspects of molecular binding. In this study, we show the competitiveness of our QM-based Molecules-in-Molecules (MIM) fragmentation method for characterizing binding energy trends for seven different datasets of protein – ligand complexes. By using molecular fragmentation, the MIM method allows for accelerated QM calculations. We demonstrate that for classes of structurally similar ligands bound to a common receptor, MIM provides excellent correlation to experiment, surpassing the more popular Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) methods. The MIM method offers a relatively simple, well-defined protocol by which binding trends can be ascertained at the QM level and is suggested as a promising option for lead optimization in structure-based drug design.