Chemical Physics
- [1] arXiv:2405.09681 [pdf, ps, other]
-
Title: Inactive Overhang in Silicon AnodesAidin I. OBrien, Stephen E. Trask, Devashish Salpekar, Seoung-Bum Son, Alison R. Dunlop, Gabriel M. Veith, Wenquan Lu, Brian J. Ingram, Daniel P. Abraham, Andrew N. Jansen, Marco-Tulio F. RodriguesSubjects: Chemical Physics (physics.chem-ph)
Li-ion batteries contain excess anode area to improve manufacturability and prevent Li plating. These overhang areas in graphite electrodes are active but experience decreased Li+ flux during cycling. Over time, the overhang and the anode portions directly opposite to the cathode can exchange Li+, driven by differences in local electrical potential across the electrode, which artificially inflates or decreases the measured cell capacity. Here, we show that lithiation of the overhang is less likely to happen in silicon anodes paired with layered oxide cathodes. The large voltage hysteresis of silicon creates a lower driving force for Li+ exchange as lithium ions transit into the overhang, rendering this exchange highly inefficient. For crystalline Si particles, Li+ storage at the overhang is prohibitive, because the low potential required for the initial lithiation can act as thermodynamic barrier for this exchange. We use micro-Raman spectroscopy to demonstrate that crystalline Si particles at the overhang are never lithiated even after cell storage at 45 oC for four months. Since the anode overhang can affect the forecasting of cell life, cells using silicon anodes may require different methodologies for life estimation compared to those used for traditional graphite-based Li-ion batteries.
- [2] arXiv:2405.09692 [pdf, ps, html, other]
-
Title: Graph automorphism group of the dissociation microequilibrium of polyprotic acidsComments: 27 pages, 5 figuresSubjects: Chemical Physics (physics.chem-ph)
The dissociation micro-states (DMS) of an $N$-protic acid are described using set theory notation. This facilitates the mathematical description of the dissociation micro-equilibrium (DME). In particular, the DME constants are easily obtained in terms of the dissociation equilibrium constants and the molar fractions of the DMSs. Representing of the DMEs in terms of graph theory allows to identify permutations between DMSs that preserve the vertex-edge connectivity of the graph. These permutations, along with their composition, allow us to identify the direct product of the cyclic group $C_2$, and the symmetric group $S_N$, $C_2\times S_N$, as the graph automorphism group of the micro-dissociation of $N$-protic acids.
- [3] arXiv:2405.09731 [pdf, ps, other]
-
Title: Impacts of Hot Electron Diffusion, Electron-Phonon Coupling, and Surface Atoms on Metal Surface Dynamics Revealed by Reflection Ultrafast Electron DiffractionComments: 25 pages, 5 figuresSubjects: Chemical Physics (physics.chem-ph); Materials Science (cond-mat.mtrl-sci)
Metals exhibit nonequilibrium electron and lattice subsystems at transient times following femtosecond laser excitation. In the past four decades, various optical spectroscopy and time-resolved diffraction methods have been used to study electron-phonon coupling and the effects of underlying dynamical processes. Here, we take advantage of the surface specificity of reflection ultrafast electron diffraction (UED) to examine the structural dynamics of photoexcited metal surfaces, which are apparently slower in recovery than predicted by thermal diffusion from the profile of absorbed energy. Fast diffusion of hot electrons is found to critically reduce surface excitation and affect the temporal dependence of the increased atomic motions on not only the ultrashort but sub-nanosecond times. Whereas the two-temperature model with the accepted physical constants of platinum can reproduce the observed surface lattice dynamics, gold is found to exhibit appreciably larger-than-expected dynamic vibrational amplitudes of surface atoms while keeping the commonly used electron-phonon coupling constant. Such surface behavioral difference at transient times can be understood in the context of the different strengths of binding to surface atoms for the two metals. In addition, with the quantitative agreements between diffraction and theoretical results, we provide convincing evidence that surface structural dynamics can be reliably obtained by reflection UED even in the presence of laser-induced transient electric fields.
- [4] arXiv:2405.10012 [pdf, ps, other]
-
Title: Electron Spin Dynamics of the Intersystem Crossing in Aminoanthraquinone Derivatives: The Spectral Telltale of Short Triplet Excited StatesRuilei Wang, Andrey A. Sukhanov, Yue He, Aidar Mambetov, Jianzhang Zhao, Daniel Escudero, Violeta K. Voronkova, Mariangela Di DonatodSubjects: Chemical Physics (physics.chem-ph)
Herein we studied the excited state dynamics of two bis-amino substituted anthraquinone (AQ) derivatives. Femtosecond transient absorption spectra show that intersystem crossing (ISC) takes place in 190-320 ps, and nanosecond transient absorption spectra demonstrated unusually short triplet state lifetime (2.1-5.4 us) for the two AQ derivatives at room temperature. Pulsed laser excited time-resolved electron paramagnetic resonance (TREPR) spectra shows an inversion of the electron spin polarization (ESP) phase pattern of the triplet state at longer delay time. Spectral simulations show that the faster decay of the Ty sublevel (x = 15.0 us, y = 1.50 us, z = 15.0 us) rationalizes the short T1 state lifetime and the ESP inversion. Computations taking into account the electron-vibrational coupling, i.e., the Herzberg-Teller effect, successfully rationalize the TREPR experimental observations.
- [5] arXiv:2405.10032 [pdf, ps, html, other]
-
Title: On the use of complex GTOs for the evaluation of radial integrals involving oscillating functionsComments: 19 pages, 4 figuresJournal-ref: Advances in Quantum Chemistry 88, 133-149 (2023)Subjects: Chemical Physics (physics.chem-ph); Quantum Physics (quant-ph)
We study two classes of radial integrals involving a product of bound and continuum one-electron states. Using a representation of the continuum part with an expansion on complex Gaussian Type Orbitals, such integrals can be performed analytically. We investigate the reliability of this scheme for low-energy physical parameters. This study serves as a premise in view of potential applications in molecular scattering processes.
- [6] arXiv:2405.10197 [pdf, ps, html, other]
-
Title: Forte: A Suite of Advanced Multireference Quantum Chemistry MethodsFrancesco A. Evangelista, Chenyang Li, Prakash Verma, Kevin P. Hannon, Jeffrey B. Schriber, Tianyuan Zhang, Chenxi Cai, Shuhe Wang, Nan He, Nicholas H. Stair, Meng Huang, Renke Huang, Jonathon P. Misiewicz, Shuhang Li, Kevin Marin, Zijun Zhao, Lori A. BurnsSubjects: Chemical Physics (physics.chem-ph)
Forte is an open-source library specialized in multireference electronic structure theories for molecular systems and the rapid prototyping of new methods. This paper gives an overview of the capabilities of Forte, its software architecture, and examples of applications enabled by the methods it implements.
New submissions for Friday, 17 May 2024 (showing 6 of 6 entries )
- [7] arXiv:2405.09759 (cross-list from cond-mat.mtrl-sci) [pdf, ps, other]
-
Title: Ferroelectricity Driven by Orbital Resonance of Protons in CH$_3$NH$_3$Cl and CH$_3$NH$_3$BrComments: 5 pages, 5 figuresJournal-ref: J. Mater. Chem. C, 10, 1334-1338 (2022)Subjects: Materials Science (cond-mat.mtrl-sci); Chemical Physics (physics.chem-ph)
The $\beta$ and $\gamma$ phases of methylammonium chloride CH$_3$NH$_3$Cl and methylammonium bromide CH$_3$NH$_3$Br are identified to be ferroelectric $via$ pyroelectric current and dielectric constant measurements. The magnetic susceptibility also exhibits pronounced discontinuities at the Curie temperatures. We attribute the origin of spontaneous polarization to the emergence of two groups of proton orbital magnetic moments from the uncorrelated motion of the CH$_3$ and NH$_3$ groups in the $\beta$ and $\gamma$ phases. The two inequivalent frameworks of intermolecular orbital resonances interact with each other to distort the lattice in a non-centrosymmetric fashion. Our findings indicate that the structural instabilities in molecular frameworks are magnetic in origin as well as provide a new pathway toward uncovering new organic ferroelectrics.
- [8] arXiv:2405.10023 (cross-list from cond-mat.soft) [pdf, ps, html, other]
-
Title: On the selective formation of cubic tetrastack crystals from tetravalent patchy particlesJournal-ref: The Journal of Chemical Physics 160, 194707 (2024)Subjects: Soft Condensed Matter (cond-mat.soft); Chemical Physics (physics.chem-ph)
Achieving the formation of target open crystalline lattices from colloidal particles is of paramount importance for their potential application in photonics. Examples of such desired structures are the diamond, tetrastack, and pyrochlore lattices. Here, we demonstrate that the self-assembly of tetravalent patchy particles results in the selective formation of cubic tetrastack crystals, both in the bulk and in the systems subjected to external fields exerted by the solid substrate. It is demonstrated that the presence of an external field allows for the formation of well-defined single crystals with a low density of defects. Moreover, depending on the strength of the applied external field, the mechanism of epitaxial growth changes. For weakly attractive external fields, the crystallization occurs in a similar manner as in the bulk, since the fluid does not wet the substrate. Nonetheless, the formed crystal is considerably better ordered than the crystals formed in bulk, since the surface induces the ordering in the first layer. On the other hand, it is demonstrated that the formation of well-ordered cubic tetrastack crystals is considerably enhanced by the increase in external field strength, and the formation of the thick crystalline film occurs via a series of layering transitions.
- [9] arXiv:2405.10227 (cross-list from physics.plasm-ph) [pdf, ps, html, other]
-
Title: Experimental Validation of Collision-Radiation Dataset for Molecular Hydrogen in PlasmasKeisuke Fujii, Keiji Sawada, Kuzmin Arseniy, Motoshi Goto, Masahiro Kobayashi, Liam H. Scarlett, Dmitry V. Fursa, Igor Bray, Mark C. Zammit, Theodore M. BiewerSubjects: Plasma Physics (physics.plasm-ph); Chemical Physics (physics.chem-ph)
Quantitative spectroscopy of molecular hydrogen has generated substantial demand, leading to the accumulation of diverse elementary-process data encompassing radiative transitions, electron-impact transitions, predissociations, and quenching. However, their rates currently available are still sparse and there are inconsistencies among those proposed by different authors. In this study, we demonstrate an experimental validation of such molecular dataset by composing a collisional-radiative model (CRM) for molecular hydrogen and comparing experimentally-obtained vibronic populations across multiple levels. From the population kinetics of molecular hydrogen, the importance of each elementary process in various parameter space is studied. In low-density plasmas (electron density $n_\mathrm{e} \lesssim 10^{17}\;\mathrm{m^{-3}}$) the excitation rates from the ground states and radiative decay rates, both of which have been reported previously, determines the excited state population. The inconsistency in the excitation rates affects the population distribution the most significantly in this parameter space. On the other hand, in higher density plasmas ($n_\mathrm{e} \gtrsim 10^{18}\;\mathrm{m^{-3}}$), the excitation rates \textit{from} excited states become important, which have never been reported in the literature, and may need to be approximated in some way. In order to validate these molecular datasets and approximated rates, we carried out experimental observations for two different hydrogen plasmas; a low-density radio-frequency (RF) heated plasma ($n_\mathrm{e}\approx 10^{16}\;\mathrm{m^{-3}}$) and the Large Helical Device (LHD) divertor plasma ($n_\mathrm{e}\gtrsim 10^{18}\;\mathrm{m^{-3}}$)... [continued]
Cross submissions for Friday, 17 May 2024 (showing 3 of 3 entries )
- [10] arXiv:2312.09013 (replaced) [pdf, ps, html, other]
-
Title: ExROPPP: Fast, Accurate and Spin-Pure Calculation of the Electronically Excited States of Organic Hydrocarbon RadicalsComments: 39 pagesJournal-ref: J. Chem. Phys. 160, 164110 (2024)Subjects: Chemical Physics (physics.chem-ph)
Recent years have seen an explosion of interest in organic radicals due to their promise for highly efficient organic light-emitting diodes (OLEDs) and molecular qubits. However, accurately and inexpensively computing their electronic structure has been challenging, especially for excited states, due to the spin-contamination problem. Furthermore, while alternacy or `pseudoparity' rules have guided the interpretation and prediction of the excited states of closed-shell hydrocarbons since the 1950s, similarly general rules for hydrocarbon radicals have not to our knowledge yet been found. In this article we present solutions to both of these challenges. We firstly combine the extended configuration interaction singles (XCIS) method with Pariser-Parr-Pople (PPP) theory to obtain a method which we call ExROPPP (Extended Restricted Open-shell PPP theory). We find that ExROPPP computes spin-pure excited states of hydrocarbon radicals with comparable accuracy to experiment as high-level GMC-QDPT calculations but at a computational cost that is at least two orders of magnitude lower. We then use ExROPPP to derive widely-applicable rules for the spectra of alternant hydrocarbon radicals which are completely consistent with our computed results. These findings pave the way for the highly accurate and efficient computation and prediction of the excited states of organic radicals.
- [11] arXiv:2402.16621 (replaced) [pdf, ps, html, other]
-
Title: Uncertainty quantification by direct propagation of shallow ensemblesSubjects: Chemical Physics (physics.chem-ph)
Statistical learning algorithms provide a generally-applicable framework to sidestep time-consuming experiments, or accurate physics-based modeling, but they introduce a further source of error on top of the intrinsic limitations of the experimental or theoretical setup. Uncertainty estimation is essential to quantify this error, and make application of data-centric approaches more trustworthy. To ensure that uncertainty quantification is used widely, one should aim for algorithms that are reasonably accurate, but also easy to implement and apply. In particular, including uncertainty quantification on top of an existing architecture should be straightforward, and add minimal computational overhead. Furthermore, it should be easy to manipulate or combine multiple machine-learning predictions, propagating uncertainty over further modeling steps. We compare several well-established uncertainty quantification frameworks against these requirements, and propose a practical approach, which we dub direct propagation of shallow ensembles, that provides a good compromise between ease of use and accuracy. We present benchmarks for generic datasets, and an in-depth study of applications to the field of atomistic machine learning for chemistry and materials. These examples underscore the importance of using a formulation that allows propagating errors without making strong assumptions on the correlations between different predictions of the model.
- [12] arXiv:2403.19597 (replaced) [pdf, ps, html, other]
-
Title: Reference Energies for Double Excitations: Improvement and ExtensionComments: 25 pages, 3 figures (Supporting Information available)Subjects: Chemical Physics (physics.chem-ph); Materials Science (cond-mat.mtrl-sci); Strongly Correlated Electrons (cond-mat.str-el); Nuclear Theory (nucl-th)
In the realm of photochemistry, the significance of double excitations (also known as doubly-excited states), where two electrons are concurrently elevated to higher energy levels, lies in their involvement in key electronic transitions essential in light-induced chemical reactions as well as their challenging nature from the computational theoretical chemistry point of view. Based on state-of-the-art electronic structure methods (such as high-order coupled-cluster, selected configuration interaction, and multiconfigurational methods), we improve and expand our prior set of accurate reference excitation energies for electronic states exhibiting a substantial amount of double excitations [this http URL Loos et al. J. Chem. Theory Comput. 2019, 15, 1939]. This extended collection encompasses 47 electronic transitions across 26 molecular systems that we separate into two distinct subsets: (i) 28 "genuine" doubly-excited states where the transitions almost exclusively involve doubly-excited configurations and (ii) 19 "partial" doubly-excited states which exhibit a more balanced character between singly- and doubly-excited configurations. For each subset, we assess the performance of high-order coupled-cluster (CC3, CCSDT, CC4, and CCSDTQ) and multiconfigurational methods (CASPT2, CASPT3, PC-NEVPT2, and SC-NEVPT2). Using as a probe the percentage of single excitations involved in a given transition ($\%T_1$) computed at the CC3 level, we also propose a simple correction that reduces the errors of CC3 by a factor of 3, for both sets of excitations. We hope that this more complete and diverse compilation of double excitations will help future developments of electronic excited-state methodologies.
- [13] arXiv:2308.04098 (replaced) [pdf, ps, html, other]
-
Title: Molecular docking via quantum approximate optimization algorithmComments: 23 pages, 17 figures, All comments are welcomeJournal-ref: Phys. Rev. Applied 21, 034036 (2024)Subjects: Quantum Physics (quant-ph); Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)
Molecular docking plays a pivotal role in drug discovery and precision medicine, enabling us to understand protein functions and advance novel therapeutics. Here, we introduce a potential alternative solution to this problem, the digitized-counterdiabatic quantum approximate optimization algorithm (DC-QAOA), which utilizes counterdiabatic driving and QAOA on a quantum computer. Our method was applied to analyze diverse biological systems, including the SARS-CoV-2 Mpro complex with PM-2-020B, the DPP-4 complex with piperidine fused imidazopyridine 34, and the HIV-1 gp120 complex with JP-III-048. The DC-QAOA exhibits superior performance, providing more accurate and biologically relevant docking results, especially for larger molecular docking problems. Moreover, QAOA-based algorithms demonstrate enhanced hardware compatibility in the noisy intermediate-scale quantum era, indicating their potential for efficient implementation under practical docking scenarios. Our findings underscore quantum computing's potential in drug discovery and offer valuable insights for optimizing protein-ligand docking processes.
- [14] arXiv:2403.09386 (replaced) [pdf, ps, html, other]
-
Title: Exploring the Interplay of Intrinsic Fluctuation and Complexity in Intracellular Calcium DynamicsSubjects: Adaptation and Self-Organizing Systems (nlin.AO); Chaotic Dynamics (nlin.CD); Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph)
The concentration of intracellular calcium ion (Ca$^{2+}$) exhibits complex oscillations, including bursting and chaos, as observed experimentally. These dynamics are influenced by inherent fluctuations within cells, which serve as crucial determinants in cellular decision-making processes and fate determination. In this study, we systematically explore the interplay between intrinsic fluctuation and the complexity of intracellular cytosolic Ca$^{2+}$ dynamics using complexity measures such as permutation entropy (PE) and statistical complexity (SC). Using the chemical Langevin equation, we simulate the stochastic dynamics of cytosolic Ca$^{2+}$. Our findings reveal that PE and SC effectively characterize the diverse, dynamic states of cytosolic Ca$^{2+}$ and illustrate their interactions with intrinsic fluctuation. PE analysis elucidates that the chaotic state is more sensitive to intrinsic fluctuation than the other periodic states. Furthermore, we identify distinct states of cytosolic Ca$^{2+}$ occupying specific locations within the theoretical bounds of the complexity-entropy causality plane. These locations indicate varying complexity and information content as intrinsic fluctuation varies. When adjusting the permutation order, the SC for the different states exhibits peaks in an intermediate range of intrinsic fluctuation values. Additionally, we identify scale-free or self-similar patterns in this intermediate range, which are further corroborated by multifractal detrended fluctuation analysis. These high-complexity states likely correspond to optimal Ca$^{2+}$ dynamics with biological significance, revealing rich and complex dynamics shaped by the interplay of intrinsic fluctuation and complexity. Our investigation enhances our understanding of how intrinsic fluctuation modulates the complexity of intracellular Ca$^{2+}$ dynamics that play crucial roles in biological cells.
- [15] arXiv:2404.16245 (replaced) [pdf, ps, other]
-
Title: Computationally Efficient Molecular Integrals of Solid Harmonic Gaussian Orbitals Using Quantum Entanglement of Angular MomentumSubjects: Quantum Physics (quant-ph); Chemical Physics (physics.chem-ph)
Evaluating multi-center molecular integrals with Cartesian Gaussian-type basis sets has been a long-standing bottleneck in electronic structure theory calculation for solids and molecules. We have developed a vector-coupling and vector-uncoupling scheme to solve molecular Coulomb integrals with solid harmonics basis functions(SHGO). Solid harmonics are eigenstates of angular momentum, making it possible to factorize molecular integrals. By combining solid harmonic addition, differential and product rules, the computationally costly multi-center four-center integrals can be factored into an angular part and a radial component dependent on the atomic positions. The potential speed-up ratio in evaluating molecular nuclear Coulomb integrals in our method can reach up to four orders of magnitude for atomic orbitals with high angular momentum quantum numbers. The foundation underpinning the mathematical efficiency is the quantum angular momentum theory, where both vector-coupling and vector-uncoupling schemes correspond to unitary Clebsch-Gordan transformations that act on quantum angular momentum states, influencing their degree of entanglement. By incorporating quantum angular momentum through these transformations, the entanglement of the states can be reduced, and the less entanglement there is for a quantum system, the easier it is to simulate. The highly efficient method unveiled here opens new avenues for accelerated material and molecule design and discovery.
- [16] arXiv:2405.07880 (replaced) [pdf, ps, html, other]
-
Title: On Hagedorn wavepackets associated with different GaussiansComments: 26 pages, 2 figuresSubjects: Quantum Physics (quant-ph); Mathematical Physics (math-ph); Chemical Physics (physics.chem-ph)
Hagedorn functions are carefully constructed generalizations of Hermite functions to the setting of many-dimensional squeezed and coupled harmonic systems. Wavepackets formed by superpositions of Hagedorn functions have been successfully used to solve the time-dependent Schrödinger equation exactly in harmonic systems and variationally in anharmonic systems. For evaluating typical observables, such as position or kinetic energy, it is sufficient to consider orthonormal Hagedorn functions with a single Gaussian center. Here, we instead derive various relations between Hagedorn bases associated with different Gaussians, including their overlaps, which are necessary for evaluating quantities nonlocal in time, such as time correlation functions needed for computing spectra. First, we use the Bogoliubov transformation to obtain commutation relations between the ladder operators associated with different Gaussians. Then, instead of using numerical quadrature, we employ these commutation relations to derive exact recurrence relations for the overlap integrals between Hagedorn functions with different Gaussian centers. Finally, we present numerical experiments that demonstrate the accuracy and efficiency of our algebraic method as well as its suitability to treat problems in spectroscopy and chemical dynamics.