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Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD
An effective hybrid single-dual-topology protocol is designed for the calculation of relative binding affinities of small ligands to a receptor. The protocol was developed as an extension of the NAMD molecular dynamics program, which exclusively supports a dual-topology framework for relative alchemical free-energy perturbation (FEP) calculations. Here, the alchemical end states are represented as two separate molecules sharing a common substructure identified through maximum structural mapping. Within the substructure, an atom-to-atom correspondence is established, and each pair of corresponding atoms is holonomically constrained to share identical coordinates at all time throughout the simulation. The forces are projected and combined at each step for propagation. Following this formulation, a set of illustrative calculations of reliable experiment/simulation data, including relative solvation free energies of small molecules and relative binding affinities of drug compounds to proteins, are presented. To enhance sampling of the dual-topology region, the FEP calculations were carried out within a replica-exchange MD scheme supported by the multiple-copy algorithm module of NAMD, with periodically attempted swapping of the thermodynamic coupling parameter lambda between neighboring states. The findings are consistent with experiments and benchmarks reported in the literature, lending support to the validity of the current protocol. In summary, this hybrid single-dual-topology approach combines the conceptual simplicity of the dual-topology paradigm with the advantageous sampling efficiency of the single-topology method, making it an ideal strategy for high-throughput in silico drug design.
A Comparison of Electronic Structure Methods for Predicting the Hydrogenation Energies of Candidate Molecules for Hydrogen Storage
The development of novel energy materials and fuels is required to expand current available energy sources. Aiming to reach this goal, there is growing interest in using molecular hydrogen as an energy carrier due to its abundance and high energy density. Liquid organic hydrogen carriers (LOHCs) are a promising route to the large-scale storage and transport of hydrogen for use in the energy economy. The search for thermodynamically viable LOHC molecules for real world use has led to a set of constraints on the dehydrogenation enthalpy and the minimum gravimetric hydrogen capacity. These constraints allow one to formulate the search for an ideal LOHC candidate molecule as an optimization problem well suited to the strengths of machine learning and artificial intelligence computational approaches. A critical barrier to a large-scale, high-throughput screening of LOHC candidate molecules is the lack of reliable training data. Computational electronic structure methods including density functional theory, coupled cluster approximations, and diffusion Monte Carlo can be used to provide training data where experimental data are either unreliable or do not exist. In this work, we use these methods to calculate the dehydrogenation energies and enthalpies of candidate LOHC molecules.
Equipartition and the Temperature of Maximum Density of TIP4P/2005 Water
Here, we simulate TIP4P/2005 water in the temperature range of 257 to 318 K with time-steps δ = 0.25, 0.50, 1.00, 2.00, and 4.00 fs. The density–temperature behavior obtained using 0.25 or 0.50 fs is in excellent agreement with each other but differs from those obtained using time steps that have been shown earlier to lead to a breakdown of equipartition. For δt = 0.25 or 0.50 fs, the temperature of maximum density (TMD) is 277.15 K and the density value is in close agreement with experiments. For δt = 1.00 fs, the TMD is 277.15 K, but the density value is shifted higher. For the other time steps considered here, the TMD is shifted to progressively lower values for longer time steps, a trend that holds for different thermostat/barostat combinations. Enhancing the water–water dispersion interaction, as has been recommended for simulating disordered proteins in TIP4P/2005, degrades the description of the liquid–vapor phase envelope. We present a simple physically transparent explanation that highlights the separation of the time scales between translational and rotational motion. We also develop a metric, χ, that we term the equipartition anomaly, to detect equipartition violations in simulations that include molecules that are treated as rigid objects. Calculating χ is shown to be straightforward and sensitive to equipartition violations. A key takeaway from this study is that using sufficiently short time steps (≤0.5 fs) to preserve equipartition is essential for obtaining meaningful liquid water properties and for producing reliable simulation data, as correct ensemble sampling is fundamental to ensure reproducibility across codes and simulation algorithms.
Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis
We report that replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional (2D) replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559-2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional (1D) unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a pre-identified “solute”, and a second one via the introduction of flattening torsional free energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of pxylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. Lastly, the tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free energy computations.
In-depth investigation on quantitative characterization of pyrolysis oil by 31 P NMR
The characterization of different heteroatom functional groups by employing 31 P NMR has been developed for almost 30 years. In this study, an in-depth investigation of this commonly used method has been accomplished for the analysis of pyrolysis oil. Several commonly used internal standards for 31 P NMR have been examined by in situ monitoring. The results indicated that endo-N-hydroxy-5-norbornene-2,3-dicarboximide (NHND) is not stable after a long period of storage or experiment (>12 hours), but both cyclohexanol and triphenylphosphine oxide (TPPO) can be used as internal standards if a long experiment or storage is required. The pyrolysis oil has also been investigated by both short time (16 hours) in situ monitoring and long time (14 days) ex situ monitoring. The results showed that aliphatic OH, carboxylic acids and water contents are not very stable after 2 hours, and thus a short time of preparation, storage, and experiment need to be considered to ensure a precise quantitative measurement. The decomposition products are still unclear, but some preliminary investigations for different acids, (e.g. formic acid) have been accomplished. The results indicated that the aromatic carboxylic acids (benzoic acid and vanillic acid) are more stable than formic acid and acetic acid. Interestingly, the formic acid will even decompose to some other compounds at the very beginning of the in situ monitoring test. Further characterization found that water is one of the major products for the decomposition of formic acid in the 31 P NMR solution. Finally, as far as we know, this is the first report on such time-dependent changes when using 31 P NMR to analyze the pyrolysis oil, and these results show that proper application of this method is essential to achieve reliable quantitative data.
Damping of lower hybrid waves in large spectral gap configurations
Extensive experimental data support reliable power deposition and current drive by lower-hybrid (LH) waves in conditions where a large spectral gap exists between the nominal parallel index of refraction prescribed by the antenna characteristics and phasing, and that required for significant Landau damping to take place. We argue that only a significant modification of the initial spectrum at the plasma edge could explain experimental observations. Based on this assumption, a new prescription for reliable simulations of LH current drive using ray-tracing and Fokker-Planck modelling is proposed. A remarkable agreement between experimental observations in the Tore Supra tokamak and simulations is obtained for relevant parametric scans, including electron density and LH waveguide phasing. In an effort to investigate the possible role of fluctuations, it is shown that the spectral gap can be bridged dynamically in the presence of a fluctuating LH spectrum.
Assessing the density functional theory-based multireference configuration interaction (DFT/MRCI) method for transition metal complexes
We report an assessment of the performance of density functional theory-based multireference configuration interaction (DFT/MRCI) calculations for a set of 3d- and 4d-transition metal (TM) complexes. The DFT/MRCI results are compared to published reference data from reliable high-level multi-configurational ab initio studies. The assessment covers the relative energies of different ground-state minima of the highly correlated CrF{sub 6} complex, the singlet and triplet electronically excited states of seven typical TM complexes (MnO{sub 4}{sup −}, Cr(CO){sub 6}, [Fe(CN){sub 6}]{sup 4−}, four larger Fe and Ru complexes), and the corresponding electronic spectra (vertical excitation energies and oscillator strengths). It includes comparisons with results from different flavors of time-dependent DFT (TD-DFT) calculations using pure, hybrid, and long-range corrected functionals. The DFT/MRCI method is found to be superior to the tested TD-DFT approaches and is thus recommended for exploring the excited-state properties of TM complexes.
Performance and characteristics of a high pressure, high temperature capillary cell with facile construction for operando x-ray absorption spectroscopy
We demonstrate the use of commercially available fused silica capillary and fittings to construct a cell for operando X-ray absorption spectroscopy (XAS) for the study of heterogeneously catalyzed reactions under high pressure (up to 200 bars) and high temperature (up to 280 °C) conditions. As the first demonstration, the cell was used for CO{sub 2} hydrogenation reaction to examine the state of copper in a conventional Cu/ZnO/Al{sub 2}O{sub 3} methanol synthesis catalyst. The active copper component of the catalyst was shown to remain in the metallic state under supercritical reaction conditions, at 200 bars and up to 260 °C. With the coiled heating system around the capillary, one can easily change the length of the capillary and control the amount of catalyst under investigation. With precise control of reactant(s) flow, the cell can mimic and serve as a conventional fixed-bed micro-reactor system to obtain reliable catalytic data. This high comparability of the reaction performance of the cell and laboratory reactors is crucial to gain insights into the nature of actual active sites under technologically relevant reaction conditions. The large length of the capillary can cause its bending upon heating when it is only fixed at both ends because of the thermal expansion. The degree of the bending can vary depending on the heating mode, and solutions to this problem are also presented. Furthermore, the cell is suitable for Raman studies, nowadays available at several beamlines for combined measurements. A concise study of CO{sub 2} phase behavior by Raman spectroscopy is presented to demonstrate a potential of the cell for combined XAS-Raman studies.
Damping of lower hybrid waves in large spectral gap configurations
Extensive experimental data support reliable power deposition and current drive by lower-hybrid (LH) waves in conditions where a large spectral gap exists between the nominal parallel index of refraction prescribed by the antenna characteristics and phasing, and that required for significant Landau damping to take place. We argue that only a significant modification of the initial spectrum at the plasma edge could explain experimental observations. Based on this assumption, a new prescription for reliable simulations of LH current drive using ray-tracing and Fokker-Planck modelling is proposed. A remarkable agreement between experimental observations in the Tore Supra tokamak and simulations is obtained for relevant parametric scans, including electron density and LH waveguide phasing. In an effort to investigate the possible role of fluctuations, it is shown that the spectral gap can be bridged dynamically in the presence of a fluctuating LH spectrum.
A four-probe thermal transport measurement method for nanostructures
Several experimental techniques reported in recent years have enabled the measurement of thermal transport properties of nanostructures. However, eliminating the contact thermal resistance error from the measurement results has remained a critical challenge. Here, we report a different four-probe measurement method that can separately obtain both the intrinsic thermal conductance and the contact thermal resistance of individual nanostructures. The measurement device consists of four microfabricated, suspended metal lines that act as resistive heaters and thermometers, across which the nanostructure sample is assembled. The method takes advantage of the variation in the heat flow along the suspended nanostructure and across its contacts to the four suspended heater and thermometer lines, and uses sixteen sets of temperature and heat flow measurements to obtain nine of the thermal resistances in the measurement device and the nanostructure sample, including the intrinsic thermal resistance and the two contact thermal resistances to the middle suspended segment of the nanostructure. Two single crystalline Si nanowires with different cross sections are measured in this work to demonstrate the effectiveness of the method. This four-probe thermal transport measurement method can lead to future discoveries of unique size-dependent thermal transport phenomena in nanostructures and low-dimensional materials, in addition to providing reliable experimental data for calibrating theoretical models.
Two-temperature transport coefficients of SF{sub 6}–N{sub 2} plasma
Sulfur hexafluoride (SF{sub 6}) is widely adopted in electric power industry, especially in high-voltage circuit breakers and gas-insulated switchgear. However, the use of SF{sub 6} is limited by its high liquidation temperature and high global warming potential. Recently, research shows SF{sub 6}–N{sub 2} mixture, which shows environmental friendliness and good electrical properties, may be a feasible substitute for pure SF{sub 6}. This paper is devoted to the calculation of and transport coefficients of SF{sub 6}–N{sub 2} mixture under both LTE (local thermodynamic equilibrium) and non-LTE condition. The two–temperature mass action law was used to determine the composition. The transport coefficients were calculated by classical Chapman–Enskog method simplified by Devoto. The thermophysical properties are presented for electron temperatures of 300–40 000 K, ratios of electron to heavy species temperature of 1–10 and N{sub 2} mole fraction of 0%–100% at atmospheric pressure. The ionization processes under both LTE and non-LTE have been discussed. The results show that deviations from local thermodynamic equilibrium significantly affect the properties of SF{sub 6}–N{sub 2} plasma, especially before the plasma is fully ionized. The different influence of N{sub 2} on properties for SF{sub 6}–N{sub 2} plasma in and out of LTE has been found. The results will serve as reliable reference data for computational simulation of the behavior of SF{sub 6}–N{sub 2} plasmas.
Thermodynamic properties and transport coefficients of air thermal plasmas mixed with ablated vapors of Cu and polytetrafluoroethylene
Because the fault arc in aircraft electrical system often causes a fire, it is particularly important to analyze its energy and transfer for aircraft safety. The calculation of arc energy requires the basic parameters of the arc. This paper is mainly devoted to the calculations of equilibrium composition, thermodynamic properties (density, molar weight, enthalpy, and specific heat at constant pressure) and transport coefficients (thermal conductivity, electrical conductivity, and viscosity) of plasmas produced by a mixture of air, Cu, and polytetrafluoroethylene under the condition of local thermodynamic equilibrium. The equilibrium composition is determined by solving a system of equations around the number densities of each species. The thermodynamic properties are obtained according to the standard thermodynamic relationships. The transport coefficients are calculated using the Chapman-Enskog approximations. Results are presented in the temperature range from 3000 to 30 000 K for pressures of 0.08 and 0.1 MPa, respectively. The results are more accurate and are reliable reference data for theoretical analysis and computational simulation of the behavior of fault arc.
Equation of state and transport properties of warm dense helium via quantum molecular dynamics simulations
The equation of state, self-diffusion, and viscosity coefficients of helium have been investigated by quantum molecular dynamics (QMD) simulations in the warm dense matter regime. Our simulations are validated through the comparison with the reliable experimental data. The calculated principal and reshock Hugoniots of liquid helium are in good agreement with the gas-gun data. On this basis, we revisit the issue for helium, i.e., the possibility of the instabilities predicted by chemical models at around 2000 GPa and 10 g/cm{sup 3} along the pressure isotherms of 6309, 15 849, and 31 623 K. Our calculations show no indications of instability in this pressure-temperature region, which reconfirm the predictions of previous QMD simulations. The self-diffusion and viscosity coefficients of warm dense helium have been systematically investigated by the QMD simulations. We carefully test the finite-size effects and convergences of statistics, and obtain numerically converged self-diffusion and viscosity coefficients by using the Kubo-Green formulas. The present results have been used to evaluate the existing one component plasma models. Finally, the validation of the Stokes-Einstein relationship for helium in the warm dense regime is discussed.
How strongly do hydrogen and water molecules stick to carbon nanomaterials?
The interaction strength of molecular hydrogen and water to carbon nanomaterials is relevant to, among many applications, hydrogen storage, water treatment, and water flow. Yet, accurate interaction energies for hydrogen and water with carbon nanotubes (CNTs) remain scarce despite the importance of having reliable benchmark data to inform experiments and to validate computational models. Here, benchmark fixed-node diffusion Monte Carlo (DMC) interaction energies are provided for hydrogen and water monomers inside and outside a typical zigzag CNT. The DMC interaction energies provide valuable insight into molecular interactions with CNTs in general and are also expected to be particularly relevant to gas uptake studies on CNTs. In addition, a selection of density functional theory (DFT) exchange-correlation (xc) functionals and force field potentials that ought to be suitable for these systems is compared. An unexpected variation is found in the performance of DFT van der Waals (vdW) models in particular. An analysis of the peculiar discrepancy between different vdW models indicates that medium-range correlation (at circa 3 to 5 Å) plays a key role inside CNTs and is poorly predicted by some vdW models. Using accurate reference information, this work reveals which xc functionals and force fields perform well for molecules interacting with CNTs. The results will be valuable to future work on these and related systems that involve molecules interacting with low-dimensional systems.
Prediction of stability constants of metal–ligand complexes by machine learning for the design of ligands with optimal metal ion selectivity
The new LOGKPREDICT program integrates HostDesigner molecular design software with the machine learning (ML) program Chemprop. By supplying HostDesigner with predicted log K values, LOGKPREDICT enhances the computer-aided molecular design process by ranking ligands directly by metal–ligand binding strength. Harnessing reliable experimental data from a historic National Institute of Standards and Technology (NIST) database and data from the International Union of Pure and Applied Chemistry (IUPAC), we train message passing neural net algorithms. The multi-metal NIST-based ML model has a root mean square error (RMSE) of 0.629 ± 0.044 (R 2 of 0.960 ± 0.006), while two versions of lanthanide-only IUPAC-based ML models have, respectively, RMSE of 0.764 ± 0.073 (R 2 of 0.976 ± 0.005) and 0.757 ± 0.071 (R 2 of 0.959 ± 0.007). For relative log K predictions on an out-of-sample set of six ligands, demonstrating metal ion selectivity, the RMSE value reaches a commendably low 0.25. Here we showcase the use of LOGKPREDICT in identifying ligands with high selectivity for lanthanides in aqueous solutions, a finding supported by recent experimental evidence. We also predict new ligands yet to be verified experimentally. Therefore, our ML models implemented through LOGKPREDICT and interfaced with the ligand design software HostDesigner pave the way for designing new ligands with predetermined selectivity for competing metal ions in an aqueous solution.
Finite-temperature vibrational full configuration interaction
Thermodynamic functions of an ideal molecular gas due to its anharmonic vibrations are evaluated in a wide range of temperature (T) by the vibrational full-configuration-interaction (FCI) method using a quartic force field and a finite number (N) of harmonic-oscillator basis functions along each normal mode. The thermodynamic functions considered are the grand potential (Ω), internal energy (U), and entropy (S). They are compared with those obtained from the Bose–Einstein theory with or without truncation of the harmonic-oscillator basis functions after quantum number N–1. The comparison reveals that the finite-basis-set errors in Ω and U are, respectively, k B Tln(k B T/Nℏω) and k B T per mode in the high-T limit, obscuring anharmonic effects when k B T > ℏω, where ω is the lowest mode frequency. Here, the benchmark data for several low-order perturbation corrections to Ω, U, and S are also obtained as the numerical derivatives of their FCI values with respect to dimensionless perturbation strength, and the domain of T and N in which these data are reliable (for the N → ∞ limits) is discussed.
ENERGY RELAXATION OF HELIUM ATOMS IN ASTROPHYSICAL GASES
We report accurate parameters describing energy relaxation of He atoms in atomic gases, important for astrophysics and atmospheric science. Collisional energy exchange between helium atoms and atomic constituents of the interstellar gas, heliosphere, and upper planetary atmosphere has been investigated. Energy transfer rates, number of collisions required for thermalization, energy distributions of recoil atoms, and other major parameters of energy relaxation for fast He atoms in thermal H, He, and O gases have been computed in a broad interval of energies from 10 meV to 10 keV. This energy interval is important for astrophysical applications involving the energy deposition of energetic atoms and ions into atmospheres of planets and exoplanets, atmospheric evolution, and analysis of non-equilibrium processes in the interstellar gas and heliosphere. Angular- and energy-dependent cross sections, required for an accurate description of the momentum-energy transfer, are obtained using ab initio interaction potentials and quantum mechanical calculations for scattering processes. Calculation methods used include partial wave analysis for collisional energies below 2 keV and the eikonal approximation at energies higher than 100 eV, keeping a significant energy region of overlap, 0.1-2 keV, between these two methods for their mutual verification. The partial wave method and the eikonal approximation excellently match results obtained with each other as well as experimental data, providing reliable cross sections in the astrophysically important interval of energies from 10 meV to 10 keV. Analytical formulae, interpolating obtained energy- and angular-dependent cross sections, are presented to simplify potential applications of the reported database. Thermalization of fast He atoms in the interstellar gas and energy relaxation of hot He and O atoms in the upper atmosphere of Mars are considered as illustrative examples of potential applications of the new database.