Chemical Physics
An embedding method with constant potential boundary conditions
Lisa Hetzel, Martin Head-Gordon and Christopher J. Stein
We present a self-consistent field framework for finite embedded
quantum-chemical clusters with constant potential boundary conditions. The coupling is realized through an energy-independent self-energy commonly employed in
quantum-transport calculations within the wide-band approximation. Starting from the corresponding non-
equilibrium Green's function formalism, we derive an analytic expression for the one-particle density
matrix update that can be incorporated into conventional Hartree–Fock and density functional theory. The resulting non-Hermitian self-consistent field equations are solved using adapted Pulay-type mixing schemes. Applications to a quasi-periodic hydrogen ring demonstrate that a finite fragment coupled through an optimized self-energy accurately reproduces the polarization response of the extended system, while calculations on a lithium cluster capture metallic charge transfer and fractional occupations under open-boundary conditions. The proposed framework establishes practical grand-canonical boundary conditions for finite
quantum-chemical clusters and lays the methodological foundation for
quantum embedding methods for electrochemical systems.
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Chemical Physics
Exploring electron transport in carbon wire systems using a wave function-based multiconfigurational non-equilibrium Green's function approach
Pranesh Raghavendran, Gabriela E. Campbell, Erik P. Hoy et al. (+1 more)
One-dimensional carbon wire materials are an interesting class of materials which have potentially useful applications in sub-nanoscale junction technology due to their unique
quantum transport properties. In this work, we apply a non-
equilibrium Green's function approach based on multiconfiguration pair-density functional theory (NEGF-MCPDFT). NEGF-MCPDFT is a wave-function-based non-periodic framework to study electron transport in systems exhibiting strong correlation. The advantage of this approach is multiconfigurational wave functions are used which offer enhanced abilities to describe strong electron correlation beyond single-determinant approaches. MC-PDFT necessitates the use of an active space, and a key step in such calculations is the determination of which orbitals to include. In application of this theory to carbon wire junctions of various lengths, we find that NEGF-MCPDFT is capable of reproducing trends from recent experimental results, and we use our findings to further the development of best practices in active space design for transport calculations of this type.
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All authors Pranesh Raghavendran, Gabriela E. Campbell, Erik P. Hoy, Andrew M. Sand
Chemical Physics
Visualizing and Quantifying Atomic Contributions to Raman Intensities governed by Spatially-Resolved Atomic Interferences
Marc Bröckel, Johannes Gierschner, Alfred J Meixner et al. (+1 more)
Raman spectroscopy is commonly reduced to molecular fingerprint sensing, neglecting Raman intensities. Atomic Raman intensity contributions trace Raman intensities back to their microscopic origin and act as local electronic structure descriptors; however, a both physical but intuitive framework is missing by now. Therefore, in this work, we combine the two main lines of decomposing Raman intensities: atomic Raman tensors and atomic Raman Intensity Densities (RIDs). The former are used to define atomic Raman intensities which quantify both the magnitude and the phase of each atom's contribution to the global Raman signal, demonstrating that weak Raman bands may arise from destructive interference of individually strong atomic contributions. The latter build on redefined atomic Raman Polarizability Densities, RPDs, and are defined in analogy to our atomic Raman intensities. They show how the motion of an individual atom modulates the polarizability of the entire molecule. Atomic RIDs thus show local interferences of different atomic contributions. They integrate to the atomic Raman intensities bridging the two main lines. Additional (atomic) Charge Density Differences (CDDs) extend the RIDs to electronic structure effects. Finally, we apply the methodology to experimental surface-enhanced Raman spectra of substituted 2-mercaptobenzothiazole derivatives and discuss substituent-induced Raman intensity changes. We show that such changes do not necessarily stem from globally altered polarizabilities but from changes in the relative phase of atomic contributions. However, this method is not limited to SERS but widely applicable to all kinds of Raman, SERS or picocavity TERS experiments offering a basis for atomically resolved investigations of molecular processes such as adsorption, catalysis, and chemical reactions
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All authors Marc Bröckel, Johannes Gierschner, Alfred J Meixner, Kai Braun
Chemical Physics · Cross-listed from cond-mat.soft
Persistence length of short homopolymeric single-stranded DNA sequences in polyvalent cations
Balaka Mondal and D. Thirumalai
We used simulations of short single stranded DNA (ssDNA) homopolymers, based on the sequence dependent Three Interaction Site (TIS) model, to calculate the persistence length ($l_p$) in polyvalent cations. The TIS model accounts for stacking interactions and electrostatic interactions are treated using the Coulomb potential. We find that $l_p$ for $\mathrm{dT_{30}}$ (T is thymine) and $\mathrm{dA_{30}}$ (A is adenine) is quantitatively fit using $l_p = l_p^0 + \lambda \kappa^{-1}$ ($l_p^0$ is the bare persistence length, $\lambda$ is a dimensionless constant, and $\kappa$ is the inverse Debye length) in the divalent cations $\mathrm{Mg^{2+}}$ and $\mathrm{Ca^{2+}}$. The dependence of $l_p$ on $\kappa$ is surprising because it was derived for long flexible polyelectrolytes in which the charges interact via the Debye-Hückel potential. The $l_p^0$ values are 0.4 nm and 1.1 nm for polyT and polyA, respectively. Strikingly, $l_p$ is almost independent of the tetravalent spermine concentration. There is no clear theoretical explanation although simulations suggest that the number of spermine molecules that bind to the ssDNA saturates at a small value. A qualitative picture, based on the restrictions of access to the phosphate groups due to volume exclusion of the anisotropic structure of $\mathrm{Spm^{4+}}$, rationalizes the simulation results. The predicted dependence of $l_p$ in spermine awaits experimental test.
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Chemical Physics
Dynamical Consequences of Nontrivial Topology of Molecular Conical Intersections
Indranil Ghosh, Kush Banker and Gregory S. Engel
The
topology of the electronic structure for an avoided crossing and a conical intersection (CI) is different and is characterized by the presence of the
geometric phase in the electronic wavefunction in the latter. Using the linear Jahn-Teller model, we show that an avoided crossing can be created from the conical intersection while preserving the nontrivial
topology of the latter by adding a Pauli $\sigma_y$ term to the
Hamiltonian. Analogously to solid state systems, we derive a half-integer topological invariant as the integral of the Berry
curvature over the CI nuclear branching space. We investigate the influence of electronic
topology on chemical dynamics by conducting fewest-switches surface hopping simulations and find distinct hopping rates on identical eigensurfaces but with different
topologies. Our work extends the influence of
topology on molecular excited state dynamics beyond the Berry phase that can be practically realized through electron-nuclear and
spin-orbit coupling.
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Chemical Physics · Cross-listed from physics.flu-dyn
Effects of pressure on the chemical sooting structure of equi-diffusive counterflow diffusion flames
Rajat Sawanni and Ömer L. Gülder
The effects of pressure on the chemical sooting structure of equi-diffusive soot formation (SF) in a counterflow
diffusion flame (CDF) are explored in a combined experimental and numerical study over pressures ranging from 1 bar to 6 bar. Experiments preserve the diffusive flame structure and carbon flux at increasing pressures and utilize measurements of soot concentrations, dispersion exponents and soot production rates. Numerical simulations are completed in OpenSMOKE++ with detailed \ce{C1}-\ce{C16} chemistry, lumped PAH consideration up to \ce{C160}, sectional soot model and tracking of the C/H ratio in particulates. Network-based tools are utilized to study the organization and
evolution of carbon routing pathways. Results show that for equi-diffusive flames, soot concentration increases with residence time and pressure, whereas soot production rates are influenced only by pressure. Soot C/H ratio is observed to increase with pressure using numerical and experimental methods, but numerical solutions underestimate the increase in hydrogen abstraction reactions. The soot-forming network undergoes a percolation-like organization of its pathways before soot inception. The network then continues to grow by adding connections through its influential nodes. Acetylene is identified as a highly influential node in the carbon transfer graph, with its influence increasing with pressure.
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Chemical Physics · Cross-listed from cond-mat.stat-mech
Kinetic Turnover in the Early-Stage Nucleation of Multi-Shell Condensed Clusters
Kaicheng Zhu and Haibin Su
Nucleation is a key rate-limiting process in phase transition and phase separation. Recent studies highlight a significant discrepancy between experimentally measured nucleation rates and theoretical predictions, particularly when dynamic structural reordering occurs along multi-step pathways. To bridge this gap, we develop a multi-shell model with a space-time-dependent order-parameter field to describe the reordering-nucleation process, where structural reorganization couples with the early growth of condensed clusters. Through
stochastic simulations, we track the time-resolved
evolution of heterogeneous structural order inside growing clusters. Path analysis of the first-passage problem in early-stage nucleation demonstrates that shifting the reordering rate alters the nucleation rate by several orders of magnitude. Furthermore, as the coupling strength increases, the relationship between the mean first-passage time and reordering susceptibility shifts from monotonic to non-monotonic, exhibiting a turnover effect. We quantitatively rationalize these behaviors with an effective nucleation barrier that accounts for non-
equilibrium properties. Our findings elucidate the mechanisms behind multi-step nucleation and offer a predictive framework for future studies.
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Chemical Physics
Collective intermolecular Coulombic decay beyond Coulomb
Alan G. Falkowski and Lorenz S. Cederbaum
Intermolecular Coulombic decay (ICD) is a widely spread phenomenon in nature and laboratory in which the excess energy of a donor is utilized to ionize a nearby acceptor. If the excess energy is insufficiently large to enable ICD, two (or more) donors can collectively transfer their combined excess energy to ionize the acceptor. Experiments show that this collective ICD is, surprisingly, operative in gases. Recently, it has been demonstrated that standard ICD can efficiently take place at large distances between the donors and acceptors due to retardation. Here, we derive the theory of collective ICD including retardation.
Quantum electrodynamics (QED) perturbation theory is used and it is shown that the theory can be substantially simplified and the process also made more amenable to interpretation by introducing two-body interaction potentials which include retardation. Explicit formulas for the rate of collective ICD are derived and interpreted by expressing the rate in terms of measurable quantities and
geometric factors. It is demonstrated that the change of the permanent dipole moments of the species upon excitation is a relevant ingredient in collective ICD.
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Chemical Physics
Efficient, precise DFT calculations of NMR shieldings: Revisiting the finite field approach
Xiao Liu, Kaushik D. Nanda, Jiashu Liang et al. (+1 more)
Absolute nuclear
magnetic shielding constants and relative chemical shifts are second-derivative response properties that underpin the interpretation of Nuclear
Magnetic Resonance (NMR) spectra and provide critical insights into the structural and electronic environments of diverse chemical systems. However, their accurate computation is often constrained by the need for method-specific, analytical response implementation, and therefore is particularly challenging for non-variational, correlated wavefunction methods where analytical second derivatives are frequently unavailable. Here we present a scalable framework that computes NMR shielding tensors through finite
magnetic field differentiation of complex-valued, gauge-including atomic-orbital (GIAO) based self-consistent field (SCF) calculations. By combining hybrid MPI and OpenMP parallelization and resolution-of-identity (RI) approximation-based Coulomb (J) and Exchange (K) implementation and mixed numerical/analytical derivatives computational scheme, we achieve very good efficiency for hybrid density functional theory (DFT) NMR shielding, relative to existing state-of-the-art analytic implementations across realistic chemical systems of various sizes. Forward differentiation with optimal step sizes derived from rigorous error analysis retains favorable numerical errors much smaller than experimental uncertainty or intrinsic DFT errors. The results demonstrate that RI-accelerated finite
magnetic field calculations can obtain DFT-level NMR shielding constants very precisely, providing a scalable foundation for extensions to more advanced
quantum chemistry methods in future work.
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All authors Xiao Liu, Kaushik D. Nanda, Jiashu Liang, Martin Head-Gordon
Chemical Physics
Quantum Vibronic Dynamics Shape Catalytically Relevant Au-Ligand Interfaces in Atomically Precise Gold Nanoclusters
Mengyuan Cui, Tianrui Chen, Junhua Zhou et al. (+6 more)
Atomically precise gold nanoclusters are versatile for photocatalysis and energy conversion because their electronic structure stems from strong metal-ligand interactions. However, these interactions are mostly discussed statically, leaving dynamic reorganization of Au-ligand interfaces under photoexcitation unclear. We investigate rod-shaped [Au25(PPh3)10(SC2H5)5Cl2]2+ using ultrafast transient-grating spectroscopy, two-dimensional electronic spectroscopy, ab initio calculations, and hierarchical equations-of-motion simulations. The multidimensional spectra resolve multiple electronic relaxation pathways and a hierarchy of coherent structural motions, from localized Au-ligand distortions to collective framework vibrations. Wavelet analysis reveals that high-frequency Au-ligand vibrations emerge immediately after excitation, whereas low-frequency collective modes appear later through interstate vibronic coupling, indicating sequential redistribution of structural coherence. Simulations reproduce the nonlinear response and identify the microscopic vibronic couplings responsible. The results show that photoexcitation drives continuous ultrafast reorganization of the Au-ligand bonding network, transiently reshaping interfacial electronic structure before thermalization. This work establishes dynamic Au-ligand interfaces as the microscopic link between excited-state energy flow and photochemical function in atomically precise nanoclusters.
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All authors Mengyuan Cui, Tianrui Chen, Junhua Zhou, Xiangmei Duan, Vandana Tiwari, Chao Mei, Ajay Jha, Fulu Zheng, Hong-Guang Duan
Chemical Physics · Cross-listed from cond-mat.soft
Conformation-Mediated Kinetics of Polymer Chain Scission under Tension
Jie Zhu and Laurence Brassart
Chain scission is a key molecular process underlying damage and fracture in
polymer networks. In this Letter, we develop a statistical-mechanical framework for predicting chain-scission kinetics while accounting for three-dimensional (3D) conformational fluctuations. Within transition-state theory, scission is formulated as a multichannel first-rupture problem, with bond-specific rates governed primarily by self-consistent potentials of mean force. In the freely jointed limit, the additional 3D configurational freedom enhances rupture relative to the collinear 1D reference. Finite bending stiffness introduces orientational correlations that can reverse this enhancement and, at high stiffness, reduce rupture rates by orders of magnitude. These correlations also make rupture bond-position dependent, with higher rates near the chain ends and a common interior rate. For sufficiently long chains, the interior contribution dominates, yielding linear scaling of the chain-scission rate with chain length. These molecularly resolved rates provide physically grounded inputs for future network-scale models of
polymer damage and fracture.
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Chemical Physics · Cross-listed from cond-mat.stat-mech
A Minimal Thermodynamically Consistent Chemical Oscillator
Benedikt Remlein, Luca Monari, Beatrice Bartolomei et al. (+3 more)
Inspired by the chemical reaction network considered as the smallest system featuring a Hopf bifurcation and its reversible extension, we introduce an even more minimal reaction network that is thermodynamically consistent and exhibits autonomous oscillations under nonequilibrium driving. The model combines three features that are rarely realized simultaneously in compact oscillator networks: a chemically plausible structure restricted to uni- and bimolecular reactions, reversibility of such reactions, and analytical tractability. The system consists of three internal species coupled to two chemostatted species and still undergoes a supercritical Hopf bifurcation when a chemostat concentration is varied. To analyze the dynamics and thermodynamics near the onset of oscillations, we employ the mathematical technique of normal-form reduction, which allows obtaining a controlled irreversible approximation that preserves the leading phase-space structure of the full reversible network while enabling explicit calculations. This framework provides analytical access to the bifurcation structure and the leading contributions governing thermodynamic observables. Within this setting, we use the onset of oscillations to characterize the thermodynamic response of the system. In particular, we offer an analytical description of key thermodynamic quantities such as the semi-grand Gibbs free energy and the non-conservative work rate, which exhibit a kink-like discontinuity at the Hopf bifurcation. We thus provide an analytical description of a phenomenon previously characterized only through numerical simulations of more complex networks.
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All authors Benedikt Remlein, Luca Monari, Beatrice Bartolomei, Giulio Ragazzon, Massimiliano Esposito, Emanuele Penocchio