70,329 results
Search Results
152. On the utmost importance of the geometry factor of accuracy in the quantum chemical calculations of 31P NMR chemical shifts: New efficient pecG-n (n = 1, 2) basis sets for the geometry optimization procedure.
- Author
-
Rusakov, Yu. Yu., Nikurashina, Yu. A., and Rusakova, I. L.
- Subjects
CHEMICAL shift (Nuclear magnetic resonance) ,NUCLEAR magnetic resonance ,ATOMIC clusters ,GEOMETRY ,CHEMICAL bond lengths - Abstract
31 P nuclear magnetic resonance (NMR) chemical shifts were shown to be very sensitive to the basis set used at the geometry optimization stage. Commonly used energy-optimized basis sets for a phosphorus atom containing only one polarization d-function were shown to be unable to provide correct equilibrium geometries for the calculations of phosphorus chemical shifts. The use of basis sets with at least two polarization d-functions on a phosphorus atom is strongly recommended. In this paper, an idea of creating the basis sets purposed for the geometry optimization that provide the least possible error coming from the geometry factor of accuracy in the resultant NMR shielding constants is proposed. The property-energy consisted algorithm with the target function in the form of the molecular energy gradient relative to P–P bond lengths was applied to create new geometry-oriented pecG-n (n = 1, 2) basis sets for a phosphorus atom. New basis sets have demonstrated by far superior performance as compared to the other commonly used energy-optimized basis sets in massive calculations of31 P NMR chemical shifts carried out at the gauge-including atomic orbital-coupled cluster singles and doubles/pecS-2 level of the theory by taking into account solvent, vibrational, and relativistic corrections. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
153. Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods.
- Author
-
Kalvoda, Tadeáš, Martinek, Tomas, Jungwirth, Pavel, and Rulíšek, Lubomír
- Subjects
SOLVATION ,MOLECULAR dynamics ,RADIAL distribution function ,HYDRATION ,GIBBS' free energy ,DENSITY functional theory - Abstract
Hydration and, in particular, the coordination number of a metal ion is of paramount importance as it defines many of its (bio)physicochemical properties. It is not only essential for understanding its behavior in aqueous solutions but also determines the metal ion reference state and its binding energy to (bio)molecules. In this paper, for divalent metal cations Ca 2 + , Cd 2 + , Cu 2 + , Fe 2 + , Hg 2 + , Mg 2 + , Ni 2 + , Pb 2 + , and Zn 2 + , we compare two approaches for predicting hydration numbers: (1) a mixed explicit/continuum DFT-D3//COSMO-RS solvation model and (2) density functional theory based ab initio molecular dynamics. The former approach is employed to calculate the Gibbs free energy change for the sequential hydration reactions, starting from [M( H 2 O)
2 ]2+ aqua complexes to [M( H 2 O)9 ]2+ , allowing explicit water molecules to bind in the first or second coordination sphere and determining the most stable [M( H 2 O)n ]2+ structure. In the latter approach, the hydration number is obtained by integrating the ion–water radial distribution function. With a couple of exceptions, the metal ion hydration numbers predicted by the two approaches are in mutual agreement, as well as in agreement with the experimental data. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
154. Diffusive dynamics of a model protein chain in solution.
- Author
-
Colberg, Margarita and Schofield, Jeremy
- Subjects
PROTEIN models ,MOLECULAR dynamics ,COLLISION broadening ,MARKOV processes - Abstract
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the transition rates among states that appear in the Markov model when the monomer dynamics is diffusive can be determined by computing the relative entropy of states and their mean first passage times, quantities that are unchanged by the specification of the energies of the relevant states. In this paper, we verify the folding dynamics described by a diffusive linear chain model of the crambin protein in three distinct solvent systems, each differing in complexity: a hard-sphere solvent, a solvent undergoing multi-particle collision dynamics, and an implicit solvent model. The predicted transition rates among configurations agree quantitatively with those observed in explicit molecular dynamics simulations for all three solvent models. These results suggest that the local monomer–monomer interactions provide sufficient friction for the monomer dynamics to be diffusive on timescales relevant to changes in conformation. Factors such as structural ordering and dynamic hydrodynamic effects appear to have minimal influence on transition rates within the studied solvent densities. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
155. Disentangling optical effects in 3D spiral-like, chiral plasmonic assemblies templated by a dark conglomerate liquid crystal.
- Author
-
Szepke, Dorota, Zarzeczny, Mateusz, Pawlak, Mateusz, Jarmuła, Paweł, Yoshizawa, Atsushi, Pociecha, Damian, and Lewandowski, Wiktor
- Subjects
LIQUID crystal films ,PLASMONICS ,CONGLOMERATE ,POLARIMETRY ,CIRCULAR dichroism ,MUELLER calculus - Abstract
Chiral thin films showing electronic and plasmonic circular dichroism (CD) are intensively explored for optoelectronic applications. The most studied chiral organic films are the composites exhibiting a helical geometry, which often causes entanglement of circular optical properties with unwanted linear optical effects (linearly polarized absorption or refraction). This entanglement limits tunability and often translates to a complex optical response. This paper describes chiral films based on dark conglomerate, sponge-like, liquid crystal films, which go beyond the usual helical type geometry, waiving the problem of linear contributions to chiroptical electronic and plasmonic properties. First, we show that purely organic films exhibit high electronic CD and circular birefringence, as studied in detail using Mueller matrix polarimetry. Analogous linear properties are two orders of magnitude lower, highlighting the benefits of using the bi-isotropic dark conglomerate liquid crystal for chiroptical purposes. Next, we show that the liquid crystal can act as a template to guide the assembly of chemically compatible gold nanoparticles into 3D spiral-like assemblies. The Mueller matrix polarimetry measurements confirm that these composites exhibit both electronic and plasmonic circular dichroisms, while nanoparticle presence is not compromising the beneficial optical properties of the matrix. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
156. Development of a dynamic gas lock inhibited model for EUV-induced carbon deposition.
- Author
-
Hao, Ming, Teng, Shuai, Liu, Jiaxing, Xie, Yuanhua, Ba, Dechun, Bian, Xin, Ba, Yaoshuai, Chen, Zhengwei, and Liu, Kun
- Abstract
The optical surface of extreme ultraviolet (EUV) lithography machines is highly vulnerable to contamination by hydrocarbons, resulting in the formation of carbon deposits that significantly degrade the quality and efficiency of lithography. The dynamic gas lock (DGL) has been proven as an effective approach to alleviate carbon deposition. However, the majority of existing studies on carbon deposition neglect the influence of the DGL. This paper is dedicated to investigating the phenomena of hydrocarbon adsorption, desorption, and cleavage with considering the effects of the DGL. A comprehensive mathematical model of the carbon deposition process is established, and the impact of radiation intensity, temperature, and hydrocarbon types on the depositing rate is considered. The results suggest that the primary cause of carbon deposition is the direct cracking of hydrocarbons induced by photons with a wavelength range between 12.5 and 14.5 nm. Additionally, it has been observed that the carbon deposition rate decreases exponentially as clean gas flow increases when EUV radiation intensity exceeds 50 mW/mm
2 . Conversely, at low EUV radiation intensity, clean gas flow has little effect on the carbon deposition rate. An effective approach to mitigate carbon deposition is to elevate the temperature of the optical surface and employ light hydrocarbon materials in the EUV process. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
157. Superconductivity of cubic MB6 (M = Na, K, Rb, Cs).
- Author
-
Chen, Shi, Xie, Hui, Xu, Dan, Chen, Jiajin, Cao, Bohan, Liang, Min, Sun, Yibo, Gai, Xiaoqian, Wang, Xinwei, Yang, Mengxin, Zhang, Mengrui, Duan, Defang, Li, Da, and Tian, Fubo
- Abstract
Previous studies have shown that NaB
6 , KB6 , and RbB6 adopting Pm 3 ̄ m are superconductors with a relatively high Tc under ambient conditions. In this paper, we conducted systematic structural and related properties research on CsB6 through a genetic evolution algorithm and total energy calculations based on density functional theory between 0 and 20 GPa. Our results reveal a cubic Pm 3 ̄ m CsB6 , which is dynamically stable under the pressures we studied. We systematically calculated the formation enthalpies, electronic properties, and superconducting properties of Pm 3 ̄ m MB6 (M = Na, K, Rb, Cs). They all exhibit metallic features, and boron has high contributions to band structures, density of states, and electron–phonon coupling (EPC). The calculated results about the Helmholtz free energy difference of Pm 3 ̄ m CsB6 at 0, 10, and 20 GPa indicate that it is stable upon chemical decomposition (decomposition to simple substances Cs and B) from 0 to 400 K. The phonon density of states indicates that boron atoms occupy the high frequency area. The EPC results show that Pm 3 ̄ m CsB6 is a superconductor with Tc = 11.7 K at 0 GPa, close to NaB6 (13.1 K), KB6 (11.7 K), and RbB6 (11.3 K) at 0 GPa in our work, which indicates that boron atoms play an essential role in superconductivity: vibrations of B6 regular octagons lead to the high Tc of Pm 3 ̄ m MB6 . Our work about Pm 3 ̄ m hexaborides provides a supplementary study on the borides of the group IA elements (without Fr and Li) and has an important guiding significance for the experimental synthesis of CsB6 . [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
158. Second quantization-based symmetry-adapted perturbation theory: Generalizing exchange beyond single electron pair approximation.
- Author
-
Tyrcha, Bartosz, Brzęk, Filip, and Żuchowski, Piotr S.
- Abstract
This paper presents a general second-quantized form of a permutation operator interchanging n pairs of electrons between interacting subsystems in the framework of the symmetry-adapted perturbation theory (SAPT). We detail the procedure for constructing this operator through the consecutive multiplication of single-pair permutation operators. This generalized form of the permutation operator has enabled the derivation of universal formulas for S
2n approximations of the exchange energies in the first and second order of the interaction operator. We present expressions for corrections of S4 approximations and assess its efficacy on a selection of systems anticipated to exhibit a slowly converging overlap expansion. Additionally, we outline a method to sum the overlap expansion series to infinity in second-quantization, up to the second order in V. This new approach offers an alternative to the existing formalism based on density-matrix formulations. When combined with a symbolic algebra program for automated derivations, it paves the way for advancements in SAPT theory, particularly for intricate wavefunction theories. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
159. Efficient formulation of multitime generalized quantum master equations: Taming the cost of simulating 2D spectra.
- Author
-
Sayer, Thomas and Montoya-Castillo, Andrés
- Abstract
Modern 4-wave mixing spectroscopies are expensive to obtain experimentally and computationally. In certain cases, the unfavorable scaling of quantum dynamics problems can be improved using a generalized quantum master equation (GQME) approach. However, the inclusion of multiple (light–matter) interactions complicates the equation of motion and leads to seemingly unavoidable cubic scaling in time. In this paper, we present a formulation that greatly simplifies and reduces the computational cost of previous work that extended the GQME framework to treat arbitrary numbers of quantum measurements. Specifically, we remove the time derivatives of quantum correlation functions from the modified Mori–Nakajima–Zwanzig framework by switching to a discrete-convolution implementation inspired by the transfer tensor approach. We then demonstrate the method's capabilities by simulating 2D electronic spectra for the excitation-energy-transfer dimer model. In our method, the resolution of data can be arbitrarily coarsened, especially along the t
2 axis, which mirrors how the data are obtained experimentally. Even in a modest case, this demands O (1 0 3 ) fewer data points. We are further able to decompose the spectra into one-, two-, and three-time correlations, showing how and when the system enters a Markovian regime where further measurements are unnecessary to predict future spectra and the scaling becomes quadratic. This offers the ability to generate long-time spectra using only short-time data, enabling access to timescales previously beyond the reach of standard methodologies. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
160. The energies and charge and spin distributions in the low-lying levels of singlet and triplet N2V defects in diamond from direct variational calculations of the excited states.
- Author
-
Mackrodt, William C., Platonenko, Alexander, Pascale, Fabien, and Dovesi, Roberto
- Subjects
EXCITED states ,ELECTRONIC excitation ,DIAMONDS ,PLANE wavefronts ,ELECTRONS ,CHARGE transfer - Abstract
This paper reports the energies and charge and spin distributions of the low-lying excited states in singlet and triplet N
2 V defects in diamond from direct Δ-SCF calculations based on Gaussian orbitals within the B3LYP, PBE0, and HSE06 functionals. They assign the observed absorption at 2.463 eV, first reported by Davies et al. [Proc. R. Soc. London 351, 245 (1976)], to the excitation of a N(sp3 ) lone-pair electron in the singlet and triplet states, respectively, with estimates of ∼1.1 eV for that of the unpaired electrons, C(sp3 ). In both cases, the excited states are predicted to be highly local and strongly excitonic with 81% of the C(sp3 ) and 87% of the N(sp3 ) excited charges localized at the three C atoms nearest neighbor (nn) to the excitation sites. Also reported are the higher excited gap states of both the N lone pair and C unpaired electron. Calculated excitation energies of the bonding sp3 hybrids of the C atoms nn to the four inner atoms are close to that of the bulk, which indicates that the N2 V defect is largely a local defect. The present results are in broad agreement with those reported by Udvarhelyi et al. [Phys. Rev. B 96, 155211 (2017)] from plane wave HSE06 calculations, notably for the N lone pair excitation energy, for which both predict an energy of ∼2.7 eV but with a difference of ∼0.5 eV for the excitation of the unpaired electron. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
161. Computing equilibrium free energies through a nonequilibrium quench.
- Author
-
Liu, Kangxin, Rotskoff, Grant M., Vanden-Eijnden, Eric, and Hocky, Glen M.
- Subjects
MOLECULAR shapes ,PARTITION functions ,EQUILIBRIUM ,FREE surfaces ,HIGH temperatures - Abstract
Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using reweighting or through Monte Carlo exchanges between replicas at higher temperatures. A recent paper [G. M. Rotskoff and E. Vanden-Eijnden, Phys. Rev. Lett. 122, 150602 (2019)] demonstrated that accurate equilibrium densities of states can also be computed through a nonequilibrium "quench" process, where sampling is performed at a higher temperature to encourage rapid mixing and then quenched to lower energy states with dissipative dynamics. Here, we provide an implementation of the quench dynamics in LAMMPS and evaluate a new formulation of nonequilibrium estimators for the computation of partition functions or free energy surfaces (FESs) of molecular systems. We show that the method is exact for a minimal model of N-independent harmonic springs and use these analytical results to develop heuristics for the amount of quenching required to obtain accurate sampling. We then test the quench approach on alanine dipeptide, where we show that it gives an FES that is accurate near the most stable configurations using the quench approach but disagrees with a reference umbrella sampling calculation in high FE regions. We then show that combining quenching with umbrella sampling allows the efficient calculation of the free energy in all regions. Moreover, by using this combined scheme, we obtain the FES across a range of temperatures at no additional cost, making it much more efficient than standard umbrella sampling if this information is required. Finally, we discuss how this approach can be extended to solute tempering and demonstrate that it is highly accurate for the case of solvated alanine dipeptide without any additional modifications. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
162. Efficient characterization of double-cross-linked networks in hydrogels using data-inspired coarse-grained molecular dynamics model.
- Author
-
Zong, Ting, Liu, Xia, Zhang, Xingyu, and Yang, Qingsheng
- Subjects
POLYMER networks ,MOLECULAR dynamics ,CROSSLINKED polymers ,FATIGUE limit ,HYDROGELS ,DEGREES of freedom - Abstract
The network structure within polymers significantly influences their mechanical properties, including their strength, toughness, and fatigue resistance. All-atom molecular dynamics (AAMD) simulations offer a method to investigate the energy dissipation mechanism within polymers during deformation and fracture; Such an approach is, however, computationally inefficient when used to analyze polymers with complex network structures, such as the common chemically double-networked hydrogels. Alternatively, coarse-grained molecular dynamics (CGMD) models, which reduce the computational degrees of freedom by concentrating a set of adjacent atoms into a coarse-grained bead, can be employed. In CGMD simulations, a coarse-grained force field (CGFF) is a critical factor affecting the simulation accuracy. In this paper, we proposed a data-based method for predicting the CGFF parameters to improve the simulation efficiency of complex cross-linked network in polymers. Here, we utilized a typical chemically double-networked hydrogel as an example. An artificial neural network was selected, and it was trained with the tensile stress–strain data from the CGMD simulations using different CGFF parameters. The CGMD simulations using the predicted CGFF parameters show good agreement with the AAMD simulations and are almost fifty times faster. The data-inspired CGMD model presented here broadens the applicability of molecular dynamics simulations to cross-linked polymers and has the potential to provide insights that will aid the design of polymers with desirable mechanical properties. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
163. Highly efficient creation and detection of deeply bound molecules via invariant-based inverse engineering with feasible modified drivings.
- Author
-
Zhang, Jiahui
- Subjects
LASER pulses ,EXCITED states ,MOLECULES ,ENGINEERING - Abstract
Stimulated Raman Adiabatic Passage (STIRAP) and its variants, such as M-type chainwise-STIRAP, allow for efficiently transferring the populations in a multilevel system and have widely been used to prepare molecules in their rovibrational ground state. However, their transfer efficiencies are generally imperfect. The main obstacle is the presence of losses and the requirement to make the dynamics adiabatic. To this end, in the present paper, a new theoretical method is proposed for the efficient and robust creation and detection of deeply bound molecules in three-level Λ-type and five-level M-type systems via "Invariant-based shortcut-to-adiabaticity." In the regime of large detunings, we first reduce the dynamics of three- and five-level molecular systems to those of effective two- and three-level counterparts. By doing so, the major molecular losses from the excited states can be well suppressed. Consequently, the effective two-level counterpart can be directly compatible with two different "Invariant-based Inverse Engineering" protocols; the results show that both protocols give a comparable performance and have a good experimental feasibility. For the effective three-level counterpart, by considering a relation among the four incident pulses, we show that this model can be further generalized to an effective Λ-type one with the simplest resonant coupling. This generalized model permits us to borrow the "Invariant-based Inverse Engineering" protocol from a standard three-level Λ-type system to a five-level M-type system. Numerical calculations show that the weakly bound molecules can be efficiently transferred to their deeply bound states without strong laser pulses, and the stability against parameter variations is well preserved. Finally, the detection of ultracold deeply bound molecules is discussed. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
164. Internal friction as a factor in the anomalous chain length dependence of DNA transcriptional dynamics.
- Author
-
Cherayil, Binny J.
- Subjects
INTERNAL friction ,DNA ,PATH integrals ,POLYMERS ,MONOMERS - Abstract
Recent experiments by Brückner et al. [Science 380, 1357 (2023)] have observed an anomalous chain length dependence of the time of near approach of widely separated pairs of genomic elements on transcriptionally active chromosomal DNA. In this paper, I suggest that the anomaly may have its roots in internal friction between neighboring segments on the DNA backbone. The basis for this proposal is a model of chain dynamics formulated in terms of a continuum scaled Brownian walk (sBw) of polymerization index N. The sBw is an extension of the simple Brownian walk model widely used in path integral calculations of polymer properties, differing from it in containing an additional parameter H (the Hurst index) that can be tuned to produce varying degrees of correlation between adjacent monomers. A calculation using the sBw of the mean time τ
c for chain closure predicts—under the Wilemski–Fixman approximation for diffusion-controlled reactions—that at early times, τc varies as the 2/3 power of N, in close agreement with the findings of the Brückner et al. study. Other scaling relations of that study, including those related to the probability of loop formation and the mean square displacements of terminal monomers, are also satisfactorily accounted for by the model. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
165. Solvent-mediated modification of thermodynamics and kinetics of monoethanolamine regeneration reaction in amine-stripping carbon capture: Computational chemistry study.
- Author
-
Afify, N. D. and Sweatman, M. B.
- Subjects
COMPUTATIONAL chemistry ,THERMODYNAMICS ,NONAQUEOUS solvents ,PERMITTIVITY ,ROUTE choice ,ZWITTERIONS - Abstract
A major limitation of amine-based post-combustion carbon capture technology is the necessity to regenerate amines at high temperatures, which dramatically increases operating costs. This paper concludes the effect of solvent choice as a possible route to modify the thermodynamics and kinetics characterizing the involved amine regeneration reactions and discusses whether these modifications can be economically beneficial. We report experimentally benchmarked computational chemistry calculations of monoethanolamine regeneration reactions employing aqueous and non-aqueous solvents with a wide range of dielectric constants. Unlike previous studies, our improved computational chemistry framework could accurately reproduce the right experimental activation energy of zwitterion formation. From the thermodynamics and kinetics of the predicted reactions, the use of non-aqueous solvents with small dielectric constants led to reductions in regeneration Gibbs free energies, activation barriers, and enthalpy changes. This can reduce energy consumption and give an opportunity to run desorption columns at relatively lower temperatures, thus offering the possibility of relying on low-grade waste heat as an energy input. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
166. On committor functions in milestoning.
- Author
-
Ji, Xiaojun, Wang, Ru, Wang, Hao, and Liu, Wenjian
- Subjects
PHASE space ,FUNCTION spaces ,BIOCHEMICAL substrates - Abstract
As an optimal one-dimensional reaction coordinate, the committor function not only describes the probability of a trajectory initiated at a phase space point first reaching the product state before reaching the reactant state but also preserves the kinetics when utilized to run a reduced dynamics model. However, calculating the committor function in high-dimensional systems poses significant challenges. In this paper, within the framework of milestoning, exact expressions for committor functions at two levels of coarse graining are given, including committor functions of phase space point to point (CFPP) and milestone to milestone (CFMM). When combined with transition kernels obtained from trajectory analysis, these expressions can be utilized to accurately and efficiently compute the committor functions. Furthermore, based on the calculated committor functions, an adaptive algorithm is developed to gradually refine the transition state region. Finally, two model examples are employed to assess the accuracy of these different formulations of committor functions. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
167. Direct measurement of the structural change associated with amorphous solidification using static scattering of coherent radiation.
- Author
-
Petersen, Charlotte F. and Harrowell, Peter
- Subjects
COHERENT radiation ,COHERENT scattering ,SUPERCOOLED liquids ,SOLIDIFICATION ,FACTOR structure ,SPECKLE interference ,GLASS transitions - Abstract
In this paper, we demonstrate that the weak temperature dependence of the structure factor of supercooled liquids, a defining feature of the glass transition, is a consequence of the averaging of the scattering intensity due to angular averaging. We show that the speckle at individual wavevectors, calculated from a simulated glass former, exhibits a Debye–Waller factor with a sufficiently large temperature dependence to represent a structural order parameter capable of distinguishing liquid from glass. We also extract from the speckle intensities a quantity proportional to the variance of the local restraint, i.e., a direct experimental measure of the amplitude of structural heterogeneity. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
168. Performance of point charge embedding schemes for excited states in molecular organic crystals.
- Author
-
Sidat, Amir, Ingham, Michael, Rivera, Miguel, Misquitta, Alston J., and Crespo-Otero, Rachel
- Subjects
MOLECULAR crystals ,EXCITED states ,TIME-dependent density functional theory ,APPROXIMATION theory ,ATOMIC charges - Abstract
Modeling excited state processes in molecular crystals is relevant for several applications. A popular approach for studying excited state molecular crystals is to use cluster models embedded in point charges. In this paper, we compare the performance of several embedding models in predicting excited states and S
1 –S0 optical gaps for a set of crystals from the X23 molecular crystal database. The performance of atomic charges based on ground or excited states was examined for cluster models, Ewald embedding, and self-consistent approaches. We investigated the impact of various factors, such as the level of theory, basis sets, embedding models, and the level of localization of the excitation. We consider different levels of theory, including time-dependent density functional theory and Tamm–Dancoff approximation (TDA) (DFT functionals: ωB97X-D and PBE0), CC2, complete active space self-consistent field, and CASPT2. We also explore the impact of selection of the QM region, charge leakage, and level of theory for the description of different kinds of excited states. We implemented three schemes based on distance thresholds to overcome overpolarization and charge leakage in molecular crystals. Our findings are compared against experimental data, G0 W0 -BSE, periodic TDA, and optimally tuned screened range-separated functionals. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
169. Doubling down on density-functional theory.
- Author
-
Becke, Axel D.
- Subjects
ACTIVATION energy ,DATABASES ,THERMOCHEMISTRY - Abstract
In a recent paper, Becke et al. [J. Chem. Phys. 158, 151103 (2023)] presented a novel double hybrid density functional, "DH23," whose terms are based on good physics. Its 12 coefficients were trained on the GMTKN55 (general main-group thermochemistry, kinetics, and noncovalent interactions) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)]. The lowest GMTKN55 "WTMAD2" error to date for any hybrid or double hybrid density functional was obtained (1.76 kcal/mol). Here, we make some revisions to DH23 and test its efficacy on reference data beyond GMTKN55, namely, organometallic reaction energies and barrier heights. The results confirm that DH23 is robust outside its training set. In the process, a slightly smaller GMTKN55 WTMAD2 of 1.73 kcal/mol is achieved. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
170. TurboGenius: Python suite for high-throughput calculations of ab initio quantum Monte Carlo methods.
- Author
-
Nakano, Kousuke, Kohulák, Oto, Raghav, Abhishek, Casula, Michele, and Sorella, Sandro
- Subjects
QUANTUM Monte Carlo method ,AB-initio calculations ,PYTHON programming language ,DENSITY functional theory ,PYTHONS ,QUANTUM chemistry - Abstract
TurboGenius is an open-source Python package designed to fully control ab initio quantum Monte Carlo (QMC) jobs using a Python script, which allows one to perform high-throughput calculations combined with TurboRVB [Nakano et al. J. Phys. Chem. 152, 204121 (2020)]. This paper provides an overview of the TurboGenius package and showcases several results obtained in a high-throughput mode. For the purpose of performing high-throughput calculations with TurboGenius, we implemented another open-source Python package, TurboWorkflows, that enables one to construct simple workflows using TurboGenius. We demonstrate its effectiveness by performing (1) validations of density functional theory (DFT) and QMC drivers as implemented in the TurboRVB package and (2) benchmarks of Diffusion Monte Carlo (DMC) calculations for several datasets. For (1), we checked inter-package consistencies between TurboRVB and other established quantum chemistry packages. By doing so, we confirmed that DFT energies obtained by PySCF are consistent with those obtained by TurboRVB within the local density approximation (LDA) and that Hartree–Fock (HF) energies obtained by PySCF and Quantum Package are consistent with variational Monte Carlo energies obtained by TurboRVB with the HF wavefunctions. These validation tests constitute a further reliability check of the TurboRVB package. For (2), we benchmarked the atomization energies of the Gaussian-2 set, the binding energies of the S22, A24, and SCAI sets, and the equilibrium lattice parameters of 12 cubic crystals using DMC calculations. We found that, for all compounds analyzed here, the DMC calculations with the LDA nodal surface give satisfactory results, i.e., consistent either with high-level computational or with experimental reference values. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
171. Correlation functions for confined wormlike chains.
- Author
-
Gard, Joel and Morrison, Greg
- Subjects
STATISTICAL correlation ,MONTE Carlo method ,POLYMERS ,BENT functions ,BIOMOLECULES - Abstract
Polymer models describing the statistics of biomolecules under confinement have applications to a wide range of single-molecule experimental techniques and give insight into biologically relevant processes in vivo. In this paper, we determine the transverse position and bending correlation functions for a wormlike chain confined within slits and cylinders (with one and two confined dimensions, respectively) using a mean-field approach that enforces rigid constraints on average. We show the theoretical predictions accurately capture the statistics of a wormlike chain from Monte Carlo simulations in both confining geometries for both weak and strong confinement. We also show that the longitudinal correlation function is accurately computed for a chain confined to a slit and leverages the accuracy of the model to suggest an experimental technique to infer the (often unobservable) transverse statistics from the (directly observable) longitudinal end-to-end distance. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
172. A global 2A″ state potential energy surface for the Al (2P) + O2 (Σg−3) → AlO (2Σ+) + O (3P) reaction based on the doubly hybrid functional XYG3.
- Author
-
Chen, Jun, Wang, Fengyan, and Xu, Xin
- Subjects
POTENTIAL energy surfaces ,ENERGY policy ,ELECTRONIC structure - Abstract
In this paper, a global and full-dimensional potential energy surface at the
2 A″ ground state for the Al + O2 → AlO + O reaction was constructed, for the first time, based on extensive electronic structure calculations using the doubly hybrid functional XYG3 and potential energy surface fittings by neural networks. Details of the reaction paths have been analyzed. It was found that both two intermediates, the cyclic-AlO2 and the linear-OAlO, were able to dissociate to the AlO + O products, and the isomerization process between these two intermediates was controlled by conical intersections between two2 A″ states. Ro-vibrational state resolved integral cross sections have also been calculated at collision energies from 1.0 to 10.0 kcal/mol. The results support the harpooning mechanism in this metal-oxidant-involved reaction. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
173. Multidimensional uniform semiclassical instanton thermal rate theory.
- Author
-
Pollak, Eli
- Subjects
INSTANTONS ,SEMICLASSICAL limits ,SYSTEMS theory ,TUNNEL design & construction - Abstract
Instanton-based rate theory is a powerful tool that is used to explore tunneling in many-dimensional systems. Yet, it diverges at the so-called "crossover temperature." Using the uniform semiclassical transmission probability of Kemble [Phys. Rev. 48, 549 (1935)], we showed recently that in one dimension, one might derive a uniform semiclassical instanton rate theory, which has no divergence. In this paper, we generalize this uniform theory to many-dimensional systems. The resulting theory uses the same input as in the previous instanton theory, yet does not suffer from the divergence. The application of the uniform theory to dissipative systems is considered and used to revise Wolynes' well-known analytical expression for the rate [P. G. Wolynes, Phys. Rev. Lett. 47, 968 (1981)] so that it does not diverge at the "crossover temperature." [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
174. Coupled cluster cavity Born–Oppenheimer approximation for electronic strong coupling.
- Author
-
Angelico, Sara, Haugland, Tor S., Ronca, Enrico, and Koch, Henrik
- Subjects
BORN-Oppenheimer approximation ,POTENTIAL energy surfaces ,SCHRODINGER equation ,DEGREES of freedom ,INTERMOLECULAR interactions - Abstract
Chemical and photochemical reactivity, as well as supramolecular organization and several other molecular properties, can be modified by strong interactions between light and matter. Theoretical studies of these phenomena require the separation of the Schrödinger equation into different degrees of freedom as in the Born–Oppenheimer approximation. In this paper, we analyze the electron–photon Hamiltonian within the cavity Born–Oppenheimer approximation (CBOA), where the electronic problem is solved for fixed nuclear positions and photonic parameters. In particular, we focus on intermolecular interactions in representative dimer complexes. The CBOA potential energy surfaces are compared with those obtained using a polaritonic approach, where the photonic and electronic degrees of freedom are treated at the same level. This allows us to assess the role of electron–photon correlation and the accuracy of CBOA. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
175. A first principles derivation of energy-conserving momentum jumps in surface hopping simulations.
- Author
-
Huang, Dorothy Miaoyu, Green, Austin T., and Martens, Craig C.
- Subjects
QUANTUM trajectories ,MOLECULAR dynamics ,ENERGY conservation - Abstract
The fewest switches surface hopping (FSSH) method proposed by Tully in 1990 [Tully, J. Chem. Phys. 93, 1061 (1990)]—along with its many later variations—forms the basis for most practical simulations of molecular dynamics with electronic transitions in realistic systems. Despite its popularity, a rigorous formal derivation of the algorithm has yet to be achieved. In this paper, we derive the energy-conserving momentum jumps employed by FSSH from the perspective of quantum trajectory surface hopping (QTSH) [Martens, J. Phys. Chem. A 123, 1110 (2019)]. In the limit of localized nonadiabatic transitions, simple mathematical and physical arguments allow the FSSH algorithm to be derived from first principles. For general processes, the quantum forces characterizing the QTSH method provide accurate results for nonadiabatic dynamics with rigorous energy conservation, at the ensemble level, within the consistency of the underlying stochastic surface hopping without resorting to the artificial momentum rescaling of FSSH. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
176. Reworking the Tao–Mo exchange–correlation functional. II. De-orbitalization.
- Author
-
Francisco, H., Cancio, A. C., and Trickey, S. B.
- Subjects
PERFORMANCE standards ,FUNCTIONALS - Abstract
In Paper I [H. Francisco, A. C. Cancio, and S. B. Trickey, J. Chem. Phys. 159, 214102 (2023)], we gave a regularization of the Tao–Mo exchange functional that removes the order-of-limits problem in the original Tao–Mo form and also eliminates the unphysical behavior introduced by an earlier regularization while essentially preserving compliance with the second-order gradient expansion. The resulting simplified, regularized (sregTM) functional delivers performance on standard molecular and solid state test sets equal to that of the earlier revised, regularized Tao–Mo functional. Here, we address de-orbitalization of that new sregTM into a pure density functional. We summarize the failures of the Mejía-Rodríguez and Trickey de-orbitalization strategy [Phys. Rev. A 96, 052512 (2017)] when used with both versions. We discuss how those failures apparently arise in the so-called z′ indicator function and in substitutes for the reduced density Laplacian in the parent functionals. Then, we show that the sregTM functional can be de-orbitalized somewhat well with a rather peculiarly parameterized version of the previously used deorbitalizer. We discuss, briefly, a de-orbitalization that works in the sense of reproducing error patterns but that apparently succeeds by cancelation of major qualitative errors associated with the de-orbitalized indicator functions α and z, hence, is not recommended. We suggest that the same issue underlies the earlier finding of comparatively mediocre performance of the de-orbitalized Tao–Perdew–Staroverov–Scuseri functional. Our work demonstrates that the intricacy of such two-indicator functionals magnifies the errors introduced by the Mejía-Rodríguez and Trickey de-orbitalization approach in ways that are extremely difficult to analyze and correct. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
177. Reworking the Tao–Mo exchange-correlation functional. I. Reconsideration and simplification.
- Author
-
Francisco, H., Cancio, A. C., and Trickey, S. B.
- Subjects
THERMOCHEMISTRY ,KINETIC energy ,PERFORMANCE standards ,INVESTIGATION reports ,ENERGY density - Abstract
The revised, regularized Tao–Mo (rregTM) exchange-correlation density functional approximation (DFA) [A. Patra, S. Jana, and P. Samal, J. Chem. Phys. 153, 184112 (2020) and Jana et al., J. Chem. Phys. 155, 024103 (2021)] resolves the order-of-limits problem in the original TM formulation while preserving its valuable essential behaviors. Those include performance on standard thermochemistry and solid data sets that is competitive with that of the most widely explored meta-generalized-gradient-approximation DFAs (SCAN and r
2 SCAN) while also providing superior performance on elemental solid magnetization. Puzzlingly however, rregTM proved to be intractable for de-orbitalization via the approach of Mejía-Rodríguez and Trickey [Phys. Rev. A 96, 052512 (2017)]. We report investigation that leads to diagnosis of how the regularization in rregTM of the z indicator functions (z = the ratio of the von-Weizsäcker and Kohn–Sham kinetic energy densities) leads to non-physical behavior. We propose a simpler regularization that eliminates those oddities and that can be calibrated to reproduce the good error patterns of rregTM. We denote this version as simplified, regularized Tao–Mo, sregTM. We also show that it is unnecessary to use rregTM correlation with sregTM exchange: Perdew–Burke–Ernzerhof correlation is sufficient. The subsequent paper shows how sregTM enables some progress on de-orbitalization. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
178. Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures.
- Author
-
Angelié, C. and Soudan, J.-M.
- Subjects
THERMODYNAMICS ,IRON clusters ,MONTE Carlo method ,CRYSTAL structure ,DENSITY functional theory - Abstract
The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, g
p (Ep ), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat 1/3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve. [ABSTRACT FROM AUTHOR]- Published
- 2017
- Full Text
- View/download PDF
179. Isothermal dehydration of thin films of water and sugar solutions.
- Author
-
Heyd, R., Rampino, A., Bellich, B., Elisei, E., Cesàro, A., and Saboungi, M.-L.
- Subjects
THIN films ,DEHYDRATION reactions ,GLUCOSE ,THERMODYNAMICS ,DIFFUSION ,COMPUTER simulation - Abstract
The process of quasi-isothermal dehydration of thin films of pure water and aqueous sugar solutions is investigated with a dual experimental and theoretical approach. A nanoporous paper disk with a homogeneous internal structure was used as a substrate. This experimental set-up makes it possible to gather thermodynamic data under well-defined conditions, develop a numerical model, and extract needed information about the dehydration process, in particular the water activity. It is found that the temperature evolution of the pure water film is not strictly isothermal during the drying process, possibly due to the influence of water diffusion through the cellulose web of the substrate. The role of sugar is clearly detectable and its influence on the dehydration process can be identified. At the end of the drying process, trehalose molecules slow down the diffusion of water molecules through the substrate in a more pronounced way than do the glucose molecules. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
180. Simulating energy transfer dynamics in the Fenna–Matthews–Olson complex via the modified generalized quantum master equation.
- Author
-
Mulvihill, Ellen, Lenn, Kristina M., Gao, Xing, Schubert, Alexander, Dunietz, Barry D., and Geva, Eitan
- Subjects
ENERGY transfer ,HAMILTONIAN systems ,ELECTRON donor-acceptor complexes ,DENSITY matrices ,DEGREES of freedom ,QUANTUM theory ,CHARGE transfer - Abstract
The generalized quantum master equation (GQME) provides a general and formally exact framework for simulating the reduced dynamics of open quantum systems. The recently introduced modified approach to the GQME (M-GQME) corresponds to a specific implementation of the GQME that is geared toward simulating the dynamics of the electronic reduced density matrix in systems governed by an excitonic Hamiltonian. Such a Hamiltonian, which is often used for describing energy and charge transfer dynamics in complex molecular systems, is given in terms of diabatic electronic states that are coupled to each other and correspond to different nuclear Hamiltonians. Within the M-GQME approach, the effect of the nuclear degrees of freedom on the time evolution of the electronic density matrix is fully captured by a memory kernel superoperator, which can be obtained from short-lived (compared to the time scale of energy/charge transfer) projection-free inputs. In this paper, we test the ability of the M-GQME to predict the energy transfer dynamics within a seven-state benchmark model of the Fenna–Matthews–Olson (FMO) complex, with the short-lived projection-free inputs obtained via the Ehrenfest method. The M-GQME with Ehrenfest-based inputs is shown to yield accurate results across a wide parameter range. It is also found to dramatically outperform the direct application of the Ehrenfest method and to provide better-behaved convergence with respect to memory time in comparison to an alternative implementation of the GQME approach previously applied to the same FMO model. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
181. Oxygen and vacancy defects in silicon. A quantum mechanical characterization through the IR and Raman spectra.
- Author
-
Platonenko, Alexander, Colasuonno, Fabio, Gentile, Francesco Silvio, Pascale, Fabien, and Dovesi, Roberto
- Subjects
RAMAN spectroscopy ,QUANTUM computing ,OXYGEN ,SILICON ,ELECTRONS - Abstract
The Infrared (IR) and Raman spectra of various defects in silicon, containing both oxygen atoms (in the interstitial position, O
i ) and a vacancy, are computed at the quantum mechanical level by using a periodic supercell approach based on a hybrid functional (B3LYP), an all-electron Gaussian-type basis set, and the Crystal code. The first of these defects is VO: the oxygen atom, twofold coordinated, saturates the unpaired electrons of two of the four carbon atoms on first neighbors of the vacancy. The two remaining unpaired electrons on the first neighbors of the vacancy can combine to give a triplet (Sz = 1) or a singlet (Sz = 0) state; both states are investigated for the neutral form of the defect, together with the doublet solution, the ground state of the negatively charged defect. Defects containing two, three, and four oxygen atoms, in conjunction with the vacancy V, are also investigated as reported in many experimental papers: VO2 and VOOi (two oxygen atoms inside the vacancy, or one in the vacancy and one in interstitial position between two Si atoms) and VO2 Oi and VO2 2Oi (containing three and four oxygen atoms). This study integrates and complements a recent investigation referring to Oi defects [Gentile et al., J. Chem. Phys. 152, 054502 (2020)]. A general good agreement is observed between the simulated IR spectra and experimental observations referring to VOx (x = 1–4) defects. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
182. Efficient geometric integrators for nonadiabatic quantum dynamics. II. The diabatic representation.
- Author
-
Roulet, Julien, Choi, Seonghoon, and Vaníček, Jiří
- Subjects
INTEGRATORS ,QUANTUM theory ,HILBERT space ,HAMILTONIAN graph theory ,THREE-dimensional modeling ,PYRAZINES - Abstract
Exact nonadiabatic quantum evolution preserves many geometric properties of the molecular Hilbert space. In the first paper of this series ["Paper I," S. Choi and J. Vaníček, J. Chem. Phys. 150, 204112 (2019)], we presented numerical integrators of arbitrary-order of accuracy that preserve these geometric properties exactly even in the adiabatic representation, in which the molecular Hamiltonian is not separable into kinetic and potential terms. Here, we focus on the separable Hamiltonian in diabatic representation, where the split-operator algorithm provides a popular alternative because it is explicit and easy to implement, while preserving most geometric invariants. Whereas the standard version has only second-order accuracy, we implemented, in an automated fashion, its recursive symmetric compositions, using the same schemes as in Paper I, and obtained integrators of arbitrary even order that still preserve the geometric properties exactly. Because the automatically generated splitting coefficients are redundant, we reduce the computational cost by pruning these coefficients and lower memory requirements by identifying unique coefficients. The order of convergence and preservation of geometric properties are justified analytically and confirmed numerically on a one-dimensional two-surface model of NaI and a three-dimensional three-surface model of pyrazine. As for efficiency, we find that to reach a convergence error of 10
−10 , a 600-fold speedup in the case of NaI and a 900-fold speedup in the case of pyrazine are obtained with the higher-order compositions instead of the second-order split-operator algorithm. The pyrazine results suggest that the efficiency gain survives in higher dimensions. [ABSTRACT FROM AUTHOR]- Published
- 2019
- Full Text
- View/download PDF
183. The EXP pair-potential system. II. Fluid phase isomorphs.
- Author
-
Bacher, Andreas Kvist, Schrøder, Thomas B., and Dyre, Jeppe C.
- Subjects
POTENTIAL energy surfaces ,LIQUIDS ,ISOMORPHOUS structures ,THERMODYNAMIC potentials ,BORN approximation ,COULOMB potential ,MATHEMATICAL models - Abstract
This paper continues the investigation of the exponentially repulsive EXP pair-potential system of Paper I [A. K. Bacher et al., J. Chem. Phys. 149, 114501 (2018)] with a focus on isomorphs in the low- temperature gas and liquid phases. As expected from the EXP system's strong virial potential-energy correlations, the reduced-unit structure and dynamics are isomorph invariant to a good approximation. Three methods for generating isomorphs are compared: the small-step method that is exact in the limit of small density changes and two versions of the direct-isomorph-check method that allows for much larger density changes. Results from the latter two approximate methods are compared to those of the small-step method for each of the three isomorphs generated by 230 one percent density changes, covering one decade of density variation. Both approximate methods work well [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
184. Dynamic bounds on stochastic chemical kinetic systems using semidefinite programming.
- Author
-
Dowdy, Garrett R. and Barton, Paul I.
- Subjects
CHEMICAL kinetics ,SEMIDEFINITE programming ,CHEMICAL equations ,STOCHASTIC processes ,PROBLEM solving - Abstract
Applying the method of moments to the chemical master equation appearing in stochastic chemical kinetics often leads to the so-called closure problem. Recently, several authors showed that this problem can be partially overcome using moment-based semidefinite programs (SDPs). In particular, they showed that moment-based SDPs can be used to calculate rigorous bounds on various descriptions of the stochastic chemical kinetic system’s stationary distribution(s)—for example, mean molecular counts, variances in these counts, and so on. In this paper, we show that these ideas can be extended to the corresponding dynamic problem, calculating time-varying bounds on the same descriptions. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
185. CH4 dissociation on Ni(100): Comparison of a direct dynamical model to molecular beam experiments.
- Author
-
Luntz, A. C.
- Subjects
MOLECULAR beams ,DISSOCIATION (Chemistry) ,NUCLEAR chemistry - Abstract
This paper makes an extensive comparison of a dynamical model for a mechanism of direct dissociation to the detailed molecular beam experiments of CH4 dissociation on a Ni(100) surface reported in the previous paper. When a PES incorporating an ‘‘exit channel’’ barrier is used in the model and steric (multidimensional) aspects are included approximately via a ‘‘hole’’ approximation, excellent agreement is achieved between the model and experiments. This strengthens the qualitative mechanistic conclusions of Holmblad, Wambach, and Chorkendorff [J. Chem. Phys. 102, 8255 (1995)]. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]
- Published
- 1995
- Full Text
- View/download PDF
186. Comment on the paper ''The role of shallow traps on the mobility of electrons in liquid Ar, Kr, and Xe,'' by G. Ascarelli, J. Chem. Phys. 71, 5030 (1979).
- Author
-
Schmidt, W. F., Sowada, U., and Yoshino, K.
- Published
- 1981
- Full Text
- View/download PDF
187. Absolute coverage determination of CO on nickel crystal faces: Papers by Erley, Besocke, and Wagner [J. Chem. Phys. 66, 5269 (1977)] and by Klier, Zettlemoyer, and Leidheiser [J. Chem. Phys. 52, 589 (1970)].
- Author
-
Klier, K., Zettlemoyer, A. C., and Leidheiser, H.
- Published
- 1977
- Full Text
- View/download PDF
188. Comments on the paper ''Contraction effects in ideal networks of flexible chains'' by G. Ronca and G. Allegra.
- Author
-
Eichinger, B. E.
- Published
- 1976
- Full Text
- View/download PDF
189. Impact of the electric field on isotropic and anisotropic spin Hamiltonian parameters.
- Author
-
Pradines, Barthélémy, Cahier, Benjamin, Suaud, Nicolas, and Guihéry, Nathalie
- Subjects
ELECTRIC fields ,POLARIZATION (Electricity) ,MAGNETIC fields ,TRANSITION metal complexes ,ELECTRIC properties ,HYPERFINE structure ,SPIN-orbit interactions - Abstract
One may obviously think that the best way to control magnetic properties relies on using a magnetic field. However, it is not convenient to focus a magnetic field on a small object, whereas it is much easier to do so with an electric field. Magnetoelectric coupling allows one to control the magnetization with the electric field and the polarization with the magnetic field and could therefore provide a solution to this problem. This paper aims at quantifying the impact of the electric field on both the isotropic magnetic exchange and the Dzyaloshinskii–Moriya interaction in the case of a binuclear system of S = 1/2 spins. This study follows previous studies that showed that very high Dzyaloshinskii–Moriya interaction, i.e., the antisymmetric exchange, can be generated when close to first order spin orbit coupling. We will, therefore, explore this regime in a model Cu(II) complex that exhibits a quasi-degeneracy of the d x 2 − y 2 and d
xy orbitals. This situation is indeed the one that allows us to obtain the largest spin orbit couplings in transition metal complexes. We will show that both the magnetic exchange and the Dzyaloshinskii–Moriya interaction are very sensitive to the electric field and that it would therefore be possible to modulate and control magnetic properties by the electric field. Finally, rationalizations of the obtained results will be proposed. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
190. On the photorelease of nitric oxide by nitrobenzene derivatives: A CASPT2//CASSCF model.
- Author
-
Giussani, Angelo and Worth, Graham A.
- Subjects
NITROBENZENE ,NITROAROMATIC compounds ,MOLECULAR structure ,METHYL groups ,ACTIVATION energy ,NITRIC oxide - Abstract
Nitroaromatic compounds can photorelease nitric oxide after UV absorption. The efficiency of the photoreaction depends on the molecular structure, and two features have been pointed out as particularly important for the yield of the process: the presence of methyl groups at the ortho position with respect to the nitro group and the degree of conjugation of the molecule. In this paper, we provide a theoretical characterization at the CASPT2//CASSCF (complete active space second-order perturbation theory//complete active space self-consistent field) level of theory of the photorelease of NO for four molecules derived from nitrobenzene through the addition of ortho methyl groups and/or the elongation of the conjugation. Our previously described mechanism obtained for the photorelease of NO in nitrobenzene has been adopted as a model for the process. According to this model, the process proceeds through a reactive singlet–triplet crossing (STC) region that the system can reach from the triplet
3 (πO π*) minimum. The energy barrier that must be surmounted in order to populate the reactive STC can be associated with the efficiency of the photoreaction. Here, the obtained results display clear differences in the efficiency of the photoreaction in the studied systems and can be correlated with experimental results. Thus, the model proves its ability to highlight the differences in the photoreaction efficiency for the nitroaromatic compounds studied here. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
191. Persistence of an active asymmetric rigid Brownian particle in two dimensions.
- Author
-
Ghosh, Anirban, Mandal, Sudipta, and Chakraborty, Dipanjan
- Subjects
RANDOM variables ,ROTATIONAL motion ,ROTATIONAL diffusion ,PARTICLE motion - Abstract
We have studied the persistence probability p(t) of an active Brownian particle with shape asymmetry in two dimensions. The persistence probability is defined as the probability of a stochastic variable that has not changed its sign in a given fixed time interval. We have investigated two cases: (1) diffusion of a free active particle and (2) that of a harmonically trapped particle. In our earlier work, by Ghosh et al. [J. Chem. Phys. 152, 174901 (2020)], we had shown that p(t) can be used to determine the translational and rotational diffusion constant of an asymmetrically shaped particle. The method has the advantage that the measurement of the rotational motion of the anisotropic particle is not required. In this paper, we extend the study to an active anisotropic particle and show how the persistence probability of an anisotropic particle is modified in the presence of a propulsion velocity. Furthermore, we validate our analytical expression against the measured persistence probability from the numerical simulations of single particle Langevin dynamics and test whether the method proposed in our earlier work can help distinguish between active and passive anisotropic particles. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
192. Stable α‐FAPbI3 via porous PbI2 for efficient perovskite solar cells.
- Author
-
Xu, Tie, Cai, Hongkun, Ye, Xiaofang, Zhu, Yinbin, Ni, Jian, Li, Juan, and Zhang, Jianjun
- Subjects
SOLAR cells ,SPIN coating ,LEWIS bases ,LEAD iodide ,ARYL iodides ,PEROVSKITE ,MICROENCAPSULATION - Abstract
Black-phase formamidinium lead iodide (FAPbI
3 ), with a narrow bandgap and high thermal stability, has emerged as an in-demand material for highly efficient perovskite solar cells (PSCs). In a two-step sequential deposition, the PbI2 film plays an important role in the formation of a perovskite film with desirable qualities. This paper explores using N-methyl-2-pyrrolidone (NMP), a strong Lewis base, and N,N-dimethylformamide (DMF) as a mixed precursor solvent (DMF/NMP) of PbI2 and reports on preparing PbI2 films with a porous morphology by thermal treatment. Porous PbI2 films ensure the diffusion and sufficient reaction of the formamidinium iodide solution to form a smooth perovskite film. In addition, a dynamic spin coating method is also introduced to improve the uniformity of the perovskite film. Both methods yield a pure α-phase FAPbI3 film immediately in the unannealed state, which is necessary for the perovskite film to maintain phase stability. Finally, PSCs with a power conversion efficiency of 21.20% (0.13 cm2 ) are fabricated and optimized. The unencapsulated PSCs retain 90% of the initial efficiency for 1000 hours in dry air and exhibit a good thermal stability when heated to 85 °C. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
193. Impact of conjugated polymer addition on the properties of paraffin–asphaltene blends for heat storage applications: Insight from computer modeling and experiment.
- Author
-
Larin, S. V., Makarova, V. V., Gorbacheva, S. N., Yakubov, M. R., Antonov, S. V., Borzdun, N. I., Glova, A. D., Nazarychev, V. M., Gurtovenko, A. A., and Lyulin, S. V.
- Subjects
POLYMER blends ,CONJUGATED polymers ,HEAT storage ,HEAT storage devices ,PHASE change materials ,COMPUTER simulation ,THERMOPHYSICAL properties - Abstract
Adding carbon nanoparticles into organic phase change materials (PCMs) such as paraffin is a common way to enhance their thermal conductivity and to improve the efficiency of heat storage devices. However, the sedimentation stability of such blends can be low due to aggregation of aromatic carbon nanoparticles in the aliphatic paraffin environment. In this paper, we explore whether this important issue can be resolved by the introduction of a polymer agent such as poly(3-hexylthiophene) (P3HT) into the paraffin–nanoparticle blends: P3HT could ensure the compatibility of aromatic carbon nanoparticles with aliphatic paraffin chains. We employed a combination of experimental and computational approaches to determine the impact of P3HT addition on the properties of organic PCMs composed of paraffin and carbon nanoparticles (asphaltenes). Our findings clearly show an increase in the sedimentation stability of paraffin–asphaltene blends, when P3HT is added, through a decrease in average size of asphaltene aggregates as well as in an increase of the blends' viscosity. We also witness the appearance of the yield strength and gel-like behavior of the mixtures. At the same time, the presence of P3HT in the blends has almost no effect on their thermophysical properties. This implies that all properties of the blends, which are critical for heat storage applications, are well preserved. Thus, we demonstrated that adding polyalkylthiophenes to paraffin–asphaltene mixtures led to significant improvement in the performance characteristics of these systems. Therefore, the polymer additives can serve as promising compatibilizers for organic PCMs composed of paraffins and asphaltenes and other types of carbon nanoparticles. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
194. Advances in modeling plasmonic systems.
- Author
-
Della Sala, Fabio, Pachter, Ruth, and Sukharev, Maxim
- Subjects
RAMAN scattering ,POLARITONS ,SEMICONDUCTOR quantum dots ,PLASMONICS ,SURFACE plasmon resonance ,NONRELATIVISTIC quantum mechanics ,MATERIALS science - Abstract
More efficient excitation energy transfer is simulated for distances smaller than 5 nm, while at distances less than 1.5 nm, the opposite occurs, indicating an interplay between the excitation of the first nanoparticle and the back transfer from the second nanoparticle. In another article in this Special Issue, Herrera and Litinskaya[119] develop a macroscopic model of exciton-plasmon metamaterials composed of nanoparticle dimers with organic molecules (chromophores are considered in the paper) situated inside the gap. 155, 134117 (2021).10.1063/5.0060171 97 S. Wang, G. D. Scholes, and L.-Y. Hsu, "Quantum dynamics of a molecular emitter strongly coupled with surface plasmon polaritons: A macroscopic quantum electrodynamics approach", J. Chem. Phys. The field of plasmonics has been in the spotlight in physics,[1] materials science,[2] chemistry,[3] and biology[4] for more than a decade, with relevant applications in photovoltaics,[5] biosensing,[6] and nanoimaging.[7] Thanks to fascinating progress in nanofabrication, we now have tools to create artificial metal/dielectric interfaces with 1 nm precision,[[8]] while ultrafast optical detection techniques are now offering riveting time resolution as short as 2 fs.[10] Combined together, these tools are used to further advance our understanding of light-matter interaction at the nanoscale when the classical view collides and merges with quantum properties of matter and light.[11] The ability of plasmonic materials to sustain surface plasmon-polariton (SPP)[12] resonances results in a very small SPP mode volume. [Extracted from the article]
- Published
- 2022
- Full Text
- View/download PDF
195. Response to "Comment on 'Manifolds of quasi-constant SOAP and ACSF fingerprints and the resulting failure to machine learn four-body interactions'" [J. Chem. Phys. 156, 034302 (2022)].
- Author
-
Parsaeifard, Behnam, Krummenacher, Marco, and Goedecker, Stefan
- Subjects
MACHINE learning ,SOAP ,POTENTIAL energy surfaces - Abstract
It is uncontested that a machine learning scheme cannot correctly reproduce physical properties that vary on a manifold in configuration space if the fingerprint, used as an input for the machine learning scheme, is constant on this manifold. In our original paper, we found several manifolds whose fingerprint variation is sufficiently small to prevent machine learning based on a standard training scheme even if some 40 configurations on the manifold are included in the training set. Response to "Comment on 'Manifolds of quasi-constant SOAP and ACSF fingerprints and the resulting failure to machine learn four-body interactions'" [J. Chem. Phys. [Extracted from the article]
- Published
- 2022
- Full Text
- View/download PDF
196. Dual exponential coupled cluster theory: Unitary adaptation, implementation in the variational quantum eigensolver framework and pilot applications.
- Author
-
Halder, Dipanjali, Prasannaa, V. S., and Maitra, Rahul
- Subjects
POTENTIAL energy surfaces ,QUANTUM computers ,WATER clusters - Abstract
In this paper, we have developed a unitary variant of a double exponential coupled cluster theory, which is capable of handling molecular strong correlation with arbitrary electronic complexity. With the Hartree–Fock determinant taken as the reference, we introduce a sequential product of parameterized unitary Ansätze. While the first unitary, containing the excitation operators, acts directly on the reference determinant, the second unitary, containing a set of rank-two, vacuum-annihilating scattering operators, has nontrivial action only on certain entangled states. We demonstrate the theoretical bottleneck of such an implementation in a classical computer, whereas the same is implemented in the hybrid quantum–classical variational quantum eigensolver framework with a reasonably shallow quantum circuit without any additional approximation. We have further introduced a number of variants of the proposed Ansatz with different degrees of sophistication by judiciously approximating the scattering operators. With a number of applications on strongly correlated molecules, we have shown that all our schemes can perform uniformly well throughout the molecular potential energy surface without significant additional implementation cost over the conventional unitary coupled cluster approach with single and double excitations. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
197. Distinct impacts of polar and nematic self-propulsion on active unjamming.
- Author
-
Venkatesh, Varun, Mondal, Chandana, and Doostmohammadi, Amin
- Subjects
CONDENSED matter physics ,DYNAMIC simulation ,NEMATIC liquid crystals - Abstract
Though jamming transitions are long studied in condensed matter physics and granular systems, much less is known about active jamming (or unjamming), which commonly takes place in living materials. In this paper, we explore, by molecular dynamic simulations, the jamming–unjamming transition in a dense system of active semiflexible filaments. In particular, we characterize the distinct impact of polar vs nematic driving for different filament rigidities and at varying densities. Our results show that high densities of dynamic active filaments can be achieved by only changing the nature of the active force, nematic or polar. Interestingly, while polar driving is more effective at unjamming the system at high densities below confluency, we find that at even higher densities, nematic driving enhances unjamming compared to its polar counterpart. The effect of varying the rigidity of filaments is also significantly different in the two cases: While for nematic driving, lowering the bending rigidity unjams the system, we find an intriguing reentrant jamming–unjamming–jamming transition for polar driving as the filament rigidity is lowered. While the first transition (unjamming) is driven by softening due to reduced rigidity, the second transition (jamming) is a cooperative effect of ordering and coincides with the emergence of nematic order in the system. Together, through a generic model of self-propelled flexible filaments, our results demonstrate how tuning the nature of self-propulsion and flexibility can be employed by active materials to achieve high densities without getting jammed. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
198. Experimental and theoretical investigation of the ArICl van der Waals complexes in the valence and ion-pair states.
- Author
-
Lukashov, Sergei S., Martynov, Ivan I., Poretsky, Sergey A., Pravilov, Anatoly M., and Sivokhina, Mariia M.
- Subjects
VAN der Waals clusters ,LUMINESCENCE spectroscopy ,POTENTIAL energy surfaces ,PERTURBATION theory ,BINDING energy - Abstract
This paper presents the experimental and theoretical analyses of ArICl(IP,v
IP ,nIP ) states' population and decay at energies lower than the ArICl(E,vE = 0,nE ) dissociation limit (IP = E0+ , D′2, β1), vIP = 0, 1, and nIP are the quantum numbers of the van der Waals (vdW) modes. We have measured the excitation spectra of the ArICl(E,vE = 0,1,nE → X,vX ,nX ) and ArICl(β,0,nβ → A and/or D ′ , v D ′ , n D ′ → A ′ luminescence as well as luminescence spectra themselves. To construct potential energy surfaces (PESs) for valence (A1, A′2) and ion-pair (E, β, and D′) electronic states of the complex, we utilized the intermolecular diatomic-in-molecule perturbation theory first order method. The experimental and calculated spectroscopic characteristics of the T-shaped ArICl valence and E, β states agree well. The ArICl(D′) state PES has no vdW levels in the T-shaped configuration, and collinear ArICl(D′) binding energy is larger than that of the T-shaped ArICl(β) state. We calculated vibrational state energies and the ArICl(IP → valence states) luminescence excitation spectra, as well as luminescence spectra themselves, by using the Heidelberg MCTDH code. The comparison of the experimental and calculated excitation spectra shows that the latter describe their principal features. The bound–bound ArICl(E,0,nE → X and β,0,nβ → A) parts of experimental luminescence spectra are described adequately by the calculated spectra, whereas bound-free ArICl(E,0,nE → X, D′, 0, nD′ → A′) parts are not described since the bound-free transitions occur in repulsive parts of the ArICl(X, A ′ PESs, which we cannot describe accurately. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
199. Multiconfigurational short-range density functional theory for nuclear magnetic resonance shielding constants with gauge-including atomic orbitals.
- Author
-
Jørgensen, Frederik Kamper, Kjellgren, Erik Rosendahl, Jensen, Hans Jørgen Aagaard, and Hedegård, Erik Donovan
- Subjects
NUCLEAR magnetic resonance ,ATOMIC orbitals ,DENSITY functional theory ,MAGNETIC shielding ,RADIATION shielding - Abstract
In this paper, we present the theory and implementation of nuclear magnetic resonance shielding constants with gauge-including atomic orbitals for the hybrid multiconfigurational short-range density functional theory model. As a special case, this implementation also includes Hartree–Fock srDFT (HF-srDFT). Choosing a complete-active space (CAS) wave function as the multiconfigurational parameterization of the wave function, we investigate how well CAS-srDFT reproduces experimental trends of nuclear shielding constants compared to DFT and complete active space self-consistent field (CASSCF). Calculations on the nucleobases adenine and thymine show that CAS-srDFT performs on average the best of the tested methods, much better than CASSCF but only marginally better than HF-srDFT. The performance, compared to regular DFT, is similar when functionals containing exact exchange are used. We generally find that the inclusion of exact exchange is important for an accurate description of the shielding constants. In cases where no exact exchange is included, we observe that the HF- and CAS-srDFT often outperform regular DFT. For calculations on transition metal nuclei in organometallic compounds with significant static correlation, the CAS-srDFT method again outperforms CASSCF compared to experimental shielding constants, and the change from HF-srDFT is substantial. In conclusion, the static correlation posed by the metal complexes seems to be captured by CAS-srDFT, which is promising since this type of correlation is not well described by regular DFT. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
200. Nucleation and growth of crystals inside polyethylene nano-droplets.
- Author
-
Zerze, Hasan
- Subjects
DISCONTINUOUS precipitation ,CRYSTAL growth ,MOLECULAR dynamics ,PLASTICS ,RATE of nucleation ,POLYETHYLENE - Abstract
Polymer crystallization is a long-standing interesting problem both in fundamental polymer physics and in polymer manufacturing. Fundamentally, the connectivity of the macromolecules provides a unique feature for the study of nucleation and growth of crystals in contrast to the crystallization of smaller molecules. In addition, understanding the crystallization in polymers is industrially important due to the necessity of its control to achieve mechanically durable plastic materials. Molecular dynamics simulations offer a suitable way of studying this phenomenon due to their capability to probe the small time and length scales that are characteristic of nucleation. In this paper, we use a long alkane chain model to study nucleation and the growth of polyethylene crystals both within bulk and nano-droplets whose diameters range from about 6 to 11 nm. It is found that the droplets approach being more spherical during the nucleation whereas they deviate from this shape during the growth regime. Strikingly, a mean first passage time analysis indicates that the nucleation rate per unit volume decreases as the droplet size is increased. Finally, visual inspection of the simulation snapshots suggests that nuclei majorly emerged from the surface of the droplets. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.