We present a heterogeneous central processing unit (CPU) + graphical processing unit (GPU) algorithm for the direct variational optimization of the two-electron reduced-density matrix (2RDM) under ...two-particle N-representability conditions. This variational 2RDM (v2RDM) approach is the driver for a polynomially scaling approximation to configuration-interaction-driven complete active-space self-consistent field (CASSCF) theory. For v2RDM-based CASSCF computations involving an active space consisting of 50 electrons in 50 orbitals, we observe a speedup of a factor of 3.7 when the code is executed on a combination of an NVIDIA TITAN V GPU and an Intel Core i7-6850k CPU, relative to the case when the code is executed on the CPU alone. We use this GPU-accelerated v2RDM-CASSCF algorithm to explore the electronic structure of the 3,k-circumacene and 3,k-periacene series (k = 2–7) and compare indicators of polyradical character in the lowest-energy singlet states to those observed for oligoacene molecules. The singlet states in larger circumacene and periacene molecules display the same polyradical characteristics observed in oligoacenes, with the onset of this behavior occurring at smallest k for periacenes, followed by the circumacenes and then the oligoacenes. However, the unpaired electron density that accumulates along the zigzag edge of the circumacenes is slightly less than that which accumulates in the oligoacenes, while periacenes clearly exhibit the greatest buildup of unpaired electron density in this region.
Recent experimental and computational evidence indicates that singlet oxygen (1O2) attacks the ethylene group (−CH2–CH2−) in ethylene carbonate (EC) leading to degradation in Li-ion batteries ...employing EC as the electrolyte solvent J. Phys. Chem. A 2018, 122, 8828-8839. Here, we employ computational quantum chemistry to explore this mechanism in detail for a large set of organic molecules. Benchmark calculations comparing density functional theory to the complete active space second-order perturbation theory and internally contracted multireference configuration interaction indicate that the M11 functional adequately captures trends in the transition-state energies for this mechanism. Based on our results, we recommend that solvents which include the ethylene group should be avoided in Li-ion and Li–O2 batteries where 1O2 is generated unless neighboring functional groups raise the reaction barrier to avoid this decomposition pathway.
We employ density functional theory (DFT) to examine reaction mechanisms involving singlet oxygen 1Δg (1O2) and 1,2-dimethoxyethane (DME) to probe potential parasitic reactions occurring in Li–O2 ...batteries. First, we investigate the attack of 1O2 on the ethylene group (−CH2–CH2−) to form H2O2 and a C–C double bond in a single step. Second, we look at hydroperoxide formation that occurs via a two-step mechanism. We employ an implicit solvent model, Li+ coordination, and external electric fields to model the complex electrolyte environment near the cathode of a Li–O2 battery. The initial barriers for these reactions are decreasing functions of the dielectric constant of the implicit solvent model as well as the strength of the electric field. These initial barriers range between 17 and 26 kcal mol–1 for large dielectric constants and in the presence of electric fields. We discuss the implications of these results on ether-based electrolytes for Li–O2 batteries.
The present work introduces a generalized-Yvon−Born−Green (YBG) theory for calculating coarse-grained (CG) force fields directly from structure ensembles. The method is noniterative and determines ...the CG potentials from a system of coupled linear integral equations that are expressed in terms of structural correlation functions for the CG sites. The force field obtained by solving these linear equations provides a variationally optimal approximation to the many-body potential of mean force determined by the atomistic model and the CG mapping. The generalized-YBG theory is equivalent to the conventional YBG equation when applied to monatomic liquids but also correctly treats the many-body structural correlations present in more complex molecular systems. Additionally, this work introduces an analogous version of the theory for determining discrete force field parameters. Numerical calculations for a CG model of a propane−propanol mixture illustrate the method.
Recent experimental and computational evidence indicates that singlet oxygen (
O
) attacks the ethylene group (-CH
-CH
-) in ethylene carbonate (EC) leading to degradation in Li-ion batteries ...employing EC as the electrolyte solvent
,
, 8828-8839. Here, we employ computational quantum chemistry to explore this mechanism in detail for a large set of organic molecules. Benchmark calculations comparing density functional theory to the complete active space second-order perturbation theory and internally contracted multireference configuration interaction indicate that the M11 functional adequately captures trends in the transition-state energies for this mechanism. Based on our results, we recommend that solvents which include the ethylene group should be avoided in Li-ion and Li-O
batteries where
O
is generated unless neighboring functional groups raise the reaction barrier to avoid this decomposition pathway.
We employ a basis set representation for classical force fields to derive an original system of exact integral equations relating each mode in the force field to an associated set of structural ...correlation functions. This generalized Yvon-Born-Green theory provides a framework for interpreting complex many-body correlations and also for variationally determining optimal interaction potentials for proteins and other complex molecules directly from structural correlation functions.
The material behavior of the API‐60 epoxy resin was investigated using atomistic molecular dynamics simulations. In this study, a hybrid, reactive force field (M‐GAFF2), which combined Morse and ...harmonic bond potentials from GAFF2, was developed to understand the elastic/plastic response of the cured epoxy polymer. We found that elastic deformation was caused by epoxy network rearrangement at low strain while plastic deformation was observed by stretching and breaking covalent bonds after the yield point. Ab initio calculations at the CASPT2(2,2)/6‐311+G** level of theory were performed to compute parameters for M‐GAFF2. These are necessary for breaking covalent bonds in the epoxy network backbone when they are deformed. The M‐GAFF2 was effective in revealing the ductile‐like deformation behavior of the crosslinked epoxy polymer at the microscopic level, including elastic/plastic deformations and progressive failure. The effect of testing temperature at 300 and 400 K and degree of cure (DoC) on tensile properties such as Young's modulus, ultimate strength, and failure strain was evaluated to verify the feasibility of the M‐GAFF2 in different thermodynamic constraints. This new approach is easy to use for nonequilibrium MD simulations and computationally efficient for studying the microscopic deformation and failure behavior of thermosetting polymers at the atomistic scale.
Analytic energy gradients are presented for a variational two-electron reduced-density-matrix-driven complete active space self-consistent field (v2RDM-CASSCF) procedure that employs the density ...fitting (DF) approximation to the two-electron repulsion integrals. The DF approximation significantly reduces the computational cost of v2RDM-CASSCF gradient evaluation, in terms of both the number of floating-point operations and memory requirements, enabling geometry optimizations on much larger chemical systems than could previously be considered at this level of theory Maradzike et al., J. Chem. Theory Comput., 2017, 13, 4113−4122 . The efficacy of v2RDM-CASSCF for computing equilibrium geometries and harmonic vibrational frequencies is assessed using a set of 25 small closed- and open-shell molecules. Equilibrium bond lengths from v2RDM-CASSCF differ from those obtained from configuration-interaction-driven CASSCF (CI-CASSCF) by 0.62 and 0.05 pm, depending on whether the optimal reduced-density matrices from v2RDM-CASSCF satisfy two-particle N-representability conditions (PQG) or PQG plus partial three-particle conditions (PQG+T2), respectively. Harmonic vibrational frequencies, which are obtained by finite differences of v2RDM-CASSCF analytic energy gradients, similarly demonstrate that quantitative agreement between v2RDM- and CI-CASSCF requires the consideration of partial three-particle N-representability conditions. Lastly, optimized geometries are obtained for the lowest-energy singlet and triplet states of the linear polyacene series up to dodecacene (C50H28), in which case the active space is comprised of 50 electrons in 50 orbitals. The v2RDM-CASSCF singlet–triplet energy gap extrapolated to an infinitely long linear acene molecule is found to be 7.8 kcal mol–1.
Understanding the ecology of the often dense white-tailed deer populations in urban and suburban landscapes is important for mitigating a variety of conflicts that arise with dense human populations, ...such as issues surrounding zoonotic disease mitigation. We collared white-tailed deer in highly suburban areas of Howard County, Maryland with high-resolution GPS collars. Then, we created autocorrelated kernel density home ranges for broader land use analyses and concurrently used general additive models to characterize fine-scale hourly measures of speed, activity, and proximity to residential buildings. Suburban deer home ranges encompassed approximately 35% direct residential land, and an average of 71 and 129 residential properties were found within female and male core ranges, respectively. Sex, time of day, and day of year all influenced fine-scale speeds, activity levels, and proximity to residential property buildings. Deer moved into residential areas nightly, especially in winter, and exhibited bouts of increased speed and activity shortly after sunrise and sunset, with distinctive seasonal changes. We discuss how variation in home ranges and movements may influence population management success and explore year-round periods of increased risk of deer transporting ticks to residential areas. These findings focus our broad understanding of deer movements in suburban and urban landscapes to improve deer population management and to mitigate the spread of ticks into residential areas.
Knowledge-based approaches frequently employ empirical relations to determine effective potentials for coarse-grained protein models directly from protein databank structures. Although these ...approaches have enjoyed considerable success and widespread popularity in computational protein science, their fundamental basis has been widely questioned. It is well established that conventional knowledge-based approaches do not correctly treat many-body correlations between amino acids. Moreover, the physical significance of potentials determined by using structural statistics from different proteins has remained obscure. In the present work, we address both of these concerns by introducing and demonstrating a theory for calculating transferable potentials directly from a databank of protein structures. This approach assumes that the databank structures correspond to representative configurations sampled from equilibrium solution ensembles for different proteins. Given this assumption, this physics-based theory exactly treats many-body structural correlations and directly determines the transferable potentials that provide a variationally optimized approximation to the free energy landscape for each protein. We illustrate this approach by first constructing a databank of protein structures using a model potential and then quantitatively recovering this potential from the structure databank. The proposed framework will clarify the assumptions and physical significance of knowledge-based potentials, allow for their systematic improvement, and provide new insight into many-body correlations and cooperativity in folded proteins.
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