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Yang, Sheng‐Chun; Li, Bin; Zhu, You‐Liang; Laaksonen, Aatto; Wang, Yong‐Lei
doi: 10.1002/jcc.26395pmid: 32808686
Computer simulations of model systems are widely used to explore striking phenomena in promising applications spanning from physics, chemistry, biology, to materials science and engineering. The long range electrostatic interactions between charged particles constitute a prominent factor in determining structures and states of model systems. How to efficiently calculate electrostatic interactions in simulation systems subjected to partial or full periodic boundary conditions has been a grand challenging task. In the past decades, a large variety of computational schemes has been proposed, among which the Ewald summation method is the most reliable route to accurately deal with electrostatic interactions between charged particles in simulation systems. In addition, extensive efforts have been done to improve computational efficiencies of the Ewald summation based methods. Representative examples are approaches based on cutoffs, reaction fields, multi‐poles, multi‐grids, and particle‐mesh schemes. We sketched an ENUF method, an abbreviation for the Ewald summation method based on the nonuniform fast Fourier transform technique, and have implemented this method in particle‐based simulation packages to calculate electrostatic energies and forces at micro‐ and mesoscopic levels. Extensive computational studies of conformational properties of polyelectrolytes, dendrimer‐membrane complexes, and ionic fluids demonstrated that the ENUF method and its derivatives conserve both energy and momentum to floating point accuracy, and exhibit a computational complexity of ONlogN with optimal physical parameters. These ENUF based methods are attractive alternatives in molecular simulations where high accuracy and efficiency of simulation methods are needed to accelerate calculations of electrostatic interactions at extended spatiotemporal scales.
Klaja, Oskar; Frank, James A.; Trauner, Dirk; Bondar, Ana‐Nicoleta
doi: 10.1002/jcc.26387pmid: 32749723
Photo‐switchable lipids are synthetic lipid molecules used in photo‐pharmacology to alter membrane lateral pressure and thus control opening and closing of mechanosensitive ion channels. The molecular picture of how photo‐switchable lipids interact with membranes or ion channels is poorly understood. To facilitate all‐atom simulations that could provide a molecular picture of membranes with photo‐switchable lipids, we derived force field parameters for atomistic computations of the azobenzene‐based fatty acid FAAzo‐4. We implemented a Phyton‐based algorithm to make the optimization of atomic partial charges more efficient. Overall, the parameters we derived give good description of the equilibrium structure, torsional properties, and non‐bonded interactions for the photo‐switchable lipid in its trans and cis intermediate states, and crystal lattice parameters for trans‐FAAzo‐4. These parameters can be extended to all‐atom descriptions of various photo‐switchable lipids that have an azobenzene moiety.
doi: 10.1002/jcc.26394pmid: 32798279
The DLPNO‐CCSD(T1)/CBS method combined with simple reactions containing small reference species leads to an improvement in the accuracy of theoretically evaluated enthalpies of formation of medium‐sized polyalicyclic hydrocarbons when compared with the widely used composite approach. The efficiency of the DLPNO‐CCSD(T1)/CBS method is most vividly demonstrated by comparing with the results of G4 calculations for adamantane. The most important factor in choosing appropriate working reaction is the same number of species on both sides of the equation. Among these reactions, the reactions with small enthalpy change usually provide a better cancellation of errors. The DLPNO‐CCSD(T1)/CBS method was used to calculate the enthalpies of formation of compounds belonging to the norbornadiene cycle (norbornadiene, quadricyclane, norbornene, nortricyclane, and norbornane). The most reliable experimental enthalpies of formation are recommended for these compounds by comparing calculated values with conflicting experimental data.
Ammar, Abdallah; Leclerc, Arnaud; Ancarani, Lorenzo Ugo
doi: 10.1002/jcc.26396pmid: 32822517
We implement a full nonlinear optimization method to fit continuum states with complex Gaussians. The application to a set of regular scattering Coulomb functions allows us to validate the numerical feasibility, to explore the range of convergence of the approach, and to demonstrate the relative superiority of complex over real Gaussian expansions. We then consider the photoionization of atomic hydrogen, and ionization by electron impact in the first Born approximation, for which the closed form cross sections serve as a solid benchmark. Using the proposed complex Gaussian representation of the continuum combined with a real Gaussian expansion for the initial bound state, all necessary matrix elements within a partial wave approach become analytical. The successful numerical comparison illustrates that the proposed all‐Gaussian approach works efficiently for ionization processes of one‐center targets.
Per, Manolo C.; Fletcher, Emily K.; Swann, Ellen T.; Cleland, Deidre M.
doi: 10.1002/jcc.26397pmid: 32780429
We assess the performance of variational (VMC) and diffusion (DMC) quantum Monte Carlo methods for calculating the radical stabilization energies of a set of 43 carbon‐centered radical species. Even using simple single‐determinant trial wavefunctions, both methods perform exceptionally well, with mean absolute deviations from reference values well under the chemical accuracy standard of 1 kcal/mol. In addition, the use of DMC results in a highly concentrated spread of errors, with all 43 results within chemical accuracy at the 95% confidence level. These results indicate that DMC is an extremely reliable method for calculating radical stabilization energies and could be used as a benchmark method for larger systems in future.
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