5,429 results
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2. Limitations and generalizations of the first order kinetics reaction expression for modeling diffusion-driven exchange: Implications on NMR exchange measurements.
- Author
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Ordinola, Alfredo, Özarslan, Evren, Bai, Ruiliang, and Herberthson, Magnus
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CHEMICAL kinetics , *RATE coefficients (Chemistry) , *MAGNETIC relaxation , *MAGNETIC resonance , *GENERALIZATION - Abstract
The study and modeling of water exchange in complex media using different applications of diffusion and relaxation magnetic resonance (MR) have been of interest in recent years. Most models attempt to describe this process using a first order kinetics expression, which is appropriate to describe chemical exchange; however, it may not be suitable to describe diffusion-driven exchange since it has no direct relationship to diffusion dynamics of water molecules. In this paper, these limitations are addressed through a more general exchange expression that does consider such important properties. This exchange fraction expression features a multi-exponential recovery at short times and a mono-exponential decay at long times, both of which are not captured by the first order kinetics expression. Furthermore, simplified exchange expressions containing partial information of the analyzed system's diffusion and relaxation processes and geometry are proposed, which can potentially be employed in already established estimation protocols. Finally, exchange fractions estimated from simulated MR data and derived here were compared, showing qualitative similarities but quantitative differences, suggesting that the features of the derived exchange fraction in this paper can be partially recovered by employing an existing estimation framework. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Fractional Extended Diffusion Theory to capture anomalous relaxation from biased/accelerated molecular simulations.
- Author
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Rapallo, Arnaldo
- Subjects
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BROWNIAN motion , *MOLECULAR rotation , *ROTATIONAL motion , *STATISTICAL correlation , *PEPTIDES , *MOLECULAR dynamics , *GENERALIZATION - Abstract
Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586–599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head–tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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4. NMR spectroscopy of a 18O-labeled rhodium paddlewheel complex: Isotope shifts, 103Rh–103Rh spin–spin coupling, and 103Rh singlet NMR.
- Author
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Harbor-Collins, Harry, Sabba, Mohamed, Bengs, Christian, Moustafa, Gamal, Leutzsch, Markus, and Levitt, Malcolm H.
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ISOTOPE shift , *SPIN-spin coupling constants , *RHODIUM , *GYROMAGNETIC ratio , *NUCLEAR magnetic resonance , *CHEMICAL shift (Nuclear magnetic resonance) , *NUCLEAR magnetic resonance spectroscopy - Abstract
Despite the importance of rhodium complexes in catalysis, and the favorable 100% natural abundance of the spin-1/2 103Rh nucleus, there are few reports of 103Rh nuclear magnetic resonance (NMR) parameters in the literature. In part, this is the consequence of the very low gyromagnetic ratio of 103Rh and its dismal NMR sensitivity. In a previous paper [Harbor-Collins et al., J. Chem. Phys. 159, 104 307 (2023)], we demonstrated an NMR methodology for 1H-enhanced 103Rh NMR and demonstrated an application to the 103Rh NMR of the dirhodium formate paddlewheel complex. In this paper, we employ selective 18O labeling to break the magnetic equivalence of the 103Rh spin pair of dirhodium formate. This allows the estimation of the 103Rh–103Rh spin–spin coupling and provides access to the 103Rh singlet state. We present the first measurement of a 18O-induced 103Rh secondary isotope shift as well as the first instance of singlet order generated in a 103Rh spin pair. The field-dependence of 103Rh singlet relaxation is measured by field-cycling NMR experiments. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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5. Superadiabatic dynamical density functional theory for colloidal suspensions under homogeneous steady-shear.
- Author
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Tschopp, S. M. and Brader, J. M.
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COLLOIDAL suspensions , *DENSITY functional theory , *COLLOIDS , *DISTRIBUTION (Probability theory) , *VISCOSITY , *RHEOLOGY - Abstract
The superadiabatic dynamical density functional theory (superadiabatic-DDFT) is a promising new method for the study of colloidal systems out-of-equilibrium. Within this approach, the viscous forces arising from interparticle interactions are accounted for in a natural way by explicitly treating the dynamics of the two-body correlations. For bulk systems subject to spatially homogeneous shear, we use the superadiabatic-DDFT framework to calculate the steady-state pair distribution function and the corresponding viscosity for low values of the shear-rate. We then consider a variant of the central approximation underlying this superadiabatic theory and obtain an inhomogeneous generalization of a rheological bulk theory due to Russel and Gast. This paper thus establishes for the first time a connection between DDFT approaches, formulated to treat inhomogeneous systems, and existing work addressing nonequilibrium microstructure and rheology in bulk colloidal suspensions. [ABSTRACT FROM AUTHOR]
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- 2024
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6. Using a pruned basis and a sparse collocation grid with more points than basis functions to do efficient and accurate MCTDH calculations with general potential energy surfaces.
- Author
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Wodraszka, Robert and Carrington Jr., Tucker
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COLLOCATION methods , *POTENTIAL energy surfaces - Abstract
We propose a new collocation multi-configuration time-dependent Hartree (MCTDH) method. It reduces point-set error by using more points than basis functions. Collocation makes it possible to use MCTDH with a general potential energy surface without computing any integrals. The collocation points are associated with a basis larger than the basis used to represent wavefunctions. Both bases are obtained from a direct product basis built from single-particle functions by imposing a pruning condition. The collocation points are those on a sparse grid. Heretofore, collocation MCTDH calculations with more points than basis functions have only been possible if both the collocation grid and the basis set are direct products. In this paper, we exploit a new pseudo-inverse to use both more points than basis functions and a pruned basis and grid. We demonstrate that, for a calculation of the lowest 50 vibrational states (energy levels and wavefunctions) of CH2NH, errors can be reduced by two orders of magnitude by increasing the number of points, without increasing the basis size. This is true also when unrefined time-independent points are used. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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7. General framework for quantifying dissipation pathways in open quantum systems. II. Numerical validation and the role of non-Markovianity.
- Author
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Kim, Chang Woo and Franco, Ignacio
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QUANTUM theory , *EQUATIONS of motion , *SYSTEM dynamics , *ENERGY dissipation - Abstract
In the previous paper [C. W. Kim and I. Franco, J. Chem. Phys. 160, 214111-1–214111-13 (2024)], we developed a theory called MQME-D, which allows us to decompose the overall energy dissipation process in open quantum system dynamics into contributions by individual components of the bath when the subsystem dynamics is governed by a Markovian quantum master equation (MQME). Here, we contrast the predictions of MQME-D against the numerically exact results obtained by combining hierarchical equations of motion (HEOM) with a recently reported protocol for monitoring the statistics of the bath. Overall, MQME-D accurately captures the contributions of specific bath components to the overall dissipation while greatly reducing the computational cost compared to exact computations using HEOM. The computations show that MQME-D exhibits errors originating from its inherent Markov approximation. We demonstrate that its accuracy can be significantly increased by incorporating non-Markovianity by exploiting time scale separations (TSS) in different components of the bath. Our work demonstrates that MQME-D combined with TSS can be reliably used to understand how energy is dissipated in realistic open quantum system dynamics. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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8. Floquet nonadiabatic mixed quantum–classical dynamics in periodically driven solid systems.
- Author
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Chen, Jingqi, Wang, Yu, and Dou, Wenjie
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PHONONS , *SURFACE dynamics , *POPULATION dynamics , *FORWARD error correction - Abstract
In this paper, we introduce the Floquet mean-field dynamics and Floquet surface hopping approaches to study the nonadiabatic dynamics in periodically driven solid systems. We demonstrate that these two approaches can be formulated in both real and reciprocal spaces. Using the two approaches, we are able to simulate the interaction between electronic carriers and phonons under periodic drivings, such as strong light–matter interactions. Employing the Holstein and Peierls models, we show that strong light–matter interactions can effectively modulate the dynamics of electronic population and mobility. Notably, our study demonstrates the feasibility and effectiveness of modeling low-momentum carriers' interactions with phonons using a truncated reciprocal space basis, an approach impractical in real space frameworks. Moreover, we reveal that even with a significant truncation, carrier populations derived from surface hopping maintain greater accuracy compared to those obtained via mean-field dynamics. These results underscore the potential of our proposed methods in advancing the understanding of carrier–phonon interactions in various periodically driven materials. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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9. On-the-fly training of polynomial machine learning potentials in computing lattice thermal conductivity.
- Author
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Togo, Atsushi and Seko, Atsuto
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MACHINE learning , *THERMAL conductivity , *BOLTZMANN'S equation , *MOLECULAR force constants , *SPHALERITE - Abstract
The application of first-principles calculations for predicting lattice thermal conductivity (LTC) in crystalline materials, in conjunction with the linearized phonon Boltzmann equation, has gained increasing popularity. In this calculation, the determination of force constants through first-principles calculations is critical for accurate LTC predictions. For material exploration, performing first-principles LTC calculations in a high-throughput manner is now expected, although it requires significant computational resources. To reduce computational demands, we integrated polynomial machine learning potentials on-the-fly during the first-principles LTC calculations. This paper presents a systematic approach to first-principles LTC calculations. We designed and optimized an efficient workflow that integrates multiple modular software packages. We applied this approach to calculate LTCs for 103 compounds of wurtzite, zinc blende, and rocksalt types to evaluate the performance of the polynomial machine learning potentials in LTC calculations. We demonstrate a significant reduction in the computational resources required for the LTC predictions. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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10. A remarkably simple dispersion damping scheme and the DH24 double hybrid density functional.
- Author
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Becke, Axel D.
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ATOMIC number , *DENSITY , *DISPERSION (Chemistry) , *DATABASES , *THERMOCHEMISTRY - Abstract
In recent papers, Becke et al. [J. Chem. Phys. 158, 151103 (2023)] and then Becke [J. Chem. Phys. 159, 241101 (2023)] have developed a novel double hybrid density functional, "DH23," whose terms are based on good local physics. Its 12 coefficients are 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 (1.73 kcal/mol for the revDH23 variant). Here, we simplify DH23 by introducing a dispersion damping scheme involving atomic numbers only and one global parameter. The resulting new functional, "DH24," performs as well as its predecessors. [ABSTRACT FROM AUTHOR]
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- 2024
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11. Performance of range-separated long-range SOPPA short-range density functional theory method for vertical excitation energies.
- Author
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Fuglsbjerg, Juliane H., Nagy, Dániel, Jensen, Hans Jørgen Aa., and Sauer, Stephan P. A.
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DENSITY functionals , *DENSITY functional theory , *ELECTRONIC excitation , *REFERENCE values - Abstract
In this paper, benchmark results are presented on the calculation of vertical electronic excitation energies using a long-range second-order polarization propagator approximation (SOPPA) description with a short-range density functional theory description based on the Perdew–Burke–Ernzerhof (PBE) functional. The excitation energies are investigated for 132 singlet states and 71 triplet states across 28 medium-sized organic molecules. The results show that overall SOPPA-srPBE always performs better than PBE and that SOPPA-srPBE performs better than SOPPA for singlet states, but slightly worse than SOPPA for triplet states when CC3 results are the reference values. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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12. The initial sticking of high velocity water onto graphite under non-equilibrium supersonic flow conditions.
- Author
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Gibson, Kevin D., Luo, Yuheng, Kang, Christopher, Sun, Rui, and Sibener, Steven J.
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PYROLYTIC graphite , *NONEQUILIBRIUM flow , *SUPERSONIC flow , *MOLECULAR dynamics , *GRAPHITE , *DEGREES of freedom - Abstract
In this paper, we present a combined experimental and theoretical study that explored the initial sticking of water on cooled surfaces. Specifically, these ultra-high vacuum gas–surface scattering experiments utilized supersonic molecular beam techniques in conjunction with a cryogenically cooled highly oriented pyrolytic graphite crystal, giving control over incident kinematic conditions. The D2O translational energy spanning 300–750 meV, the relative D2O flux, and the incident angle could all be varied independently. Three different experimental measurements were made. One involved measuring the total amount of D2O scattering as a function of surface temperature to determine the onset of sticking under non-equilibrium gas–surface collision conditions. Another measurement used He specular scattering to assess structural and coverage information for the interface during D2O adsorption. Finally, we used time-of-flight (TOF) measurements of the scattered D2O to determine how energy is exchanged with the graphite surface at surface temperatures above and near the conditions needed for gaseous condensation. For comparison and elaboration of the roles that internal degrees of freedom play in this process, we also did similar TOF measurements using another mass 20 incident particle, atomic neon. Enriching this study are precise molecular dynamics simulations that elaborate on gas–surface energy transfer and the roles of molecular degrees of freedom in gas–surface collisional energy exchange processes. This study furthers our fundamental understanding of energy exchange and the onset of sticking and ultimately gaseous condensation for gas–surface encounters occurring under high-velocity flows. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
13. Hydrodynamic slip characteristics of shear-driven water flow in nanoscale carbon slits.
- Author
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Shuvo, Abdul Aziz, Paniagua-Guerra, Luis E., Yang, Xiang, and Ramos-Alvarado, Bladimir
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RHEOLOGY , *MOLECULAR dynamics , *INTERFACIAL friction , *ELECTRONIC structure , *VISCOSITY , *FRICTION - Abstract
This paper reports on the effects of shear rate and interface modeling parameters on the hydrodynamic slip length (LS) for water–graphite interfaces calculated using non-equilibrium molecular dynamics. Five distinct non-bonded solid–liquid interaction parameters were considered to assess their impact on LS. The interfacial force field derivations included sophisticated electronic structure calculation-informed and empirically determined parameters. All interface models exhibited a similar and bimodal LS response when varying the applied shear rate. LS in the low shear rate regime (LSR) is in good agreement with previous calculations obtained through equilibrium molecular dynamics. As the shear rate increases, LS sharply increases and asymptotes to a constant value in the high shear regime (HSR). It is noteworthy that LS in both the LSR and HSR can be characterized by the density depletion length, whereas solid–liquid adhesion metrics failed to do so. For all interface models, LHSR calculations were, on average, ∼28% greater than LLSR, and this slip jump was confirmed using the SPC/E and TIP4P/2005 water models. To address the LS transition from the LSR to the HSR, the viscosity of water and the interfacial friction coefficient were investigated. It was observed that in the LSR, the viscosity and friction coefficient decreased at a similar rate, while in the LSR-to-HSR transition, the friction coefficient decreased at a faster rate than the shear viscosity until they reached a new equilibrium, hence explaining the LS-bimodal behavior. This study provides valuable insights into the interplay between interface modeling parameters, shear rate, and rheological properties in understanding hydrodynamic slip behavior. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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14. ℏ4 quantum corrections to semiclassical transmission probabilities.
- Author
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Pollak, Eli and Upadhyayula, Sameernandan
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QUANTUM perturbations , *PERTURBATION theory , *HARMONIC oscillators , *LOW temperatures - Abstract
The combination of vibrational perturbation theory with the replacement of the harmonic oscillator quantization condition along the reaction coordinate with an imaginary action to be used in the uniform semiclassical approximation for the transmission probability has been shown in recent years to be a practical method for obtaining thermal reaction rates. To date, this theory has been developed systematically only up to second order in perturbation theory. Although it gives the correct leading order term in an ℏ2 expansion, its accuracy at lower temperatures, where tunneling becomes important, is not clear. In this paper, we develop the theory to fourth order in the action. This demands developing the quantum perturbation theory up to sixth order. Remarkably, we find that the fourth order theory gives the correct ℏ4 term in the expansion of the exact thermal rate. The relative magnitude of the fourth order correction as compared to the second order term objectively indicates the accuracy of the second order theory. We also extend the previous modified second order theory to the fourth order case, creating an ℏ2 modified potential for this purpose. The resulting theory is tested on the standard examples—symmetric and asymmetric Eckart potentials and a Gaussian potential. The modified fourth order theory is remarkably accurate for the asymmetric Eckart potential. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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15. Predicting the artificial dynamical acceleration of binary hydrocarbon mixtures upon coarse-graining with roughness volumes and simple averaging rules.
- Author
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Meinel, Melissa K. and Müller-Plathe, Florian
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DIFFUSION coefficients , *DEGREES of freedom , *SURFACE roughness , *BINARY mixtures , *MOLECULAR models , *LIQUID hydrocarbons , *MIXTURES - Abstract
Coarse-grained (CG) molecular models greatly reduce the computational cost of simulations allowing for longer and larger simulations, but come with an artificially increased acceleration of the dynamics when compared to the parent atomistic (AA) simulation. This impedes their use for the quantitative study of dynamical properties. During coarse-graining, grouping several atoms into one CG bead not only reduces the number of degrees of freedom but also reduces the roughness on the molecular surfaces, leading to the acceleration of dynamics. The RoughMob approach [M. K. Meinel and F. Müller-Plathe, J. Phys. Chem. B 126(20), 3737–3747 (2022)] quantifies this change in geometry and correlates it to the acceleration by making use of four so-called roughness volumes. This method was developed using simple one-bead CG models of a set of hydrocarbon liquids. Potentials for pure components are derived by the structure-based iterative Boltzmann inversion. In this paper, we find that, for binary mixtures of simple hydrocarbons, it is sufficient to use simple averaging rules to calculate the roughness volumes in mixtures from the roughness volumes of pure components and add a correction term quadratic in the concentration without the need to perform any calculation on AA or CG trajectories of the mixtures themselves. The acceleration factors of binary diffusion coefficients and both self-diffusion coefficients show a large dependence on the overall acceleration of the system and can be predicted a priori without the need for any AA simulations within a percentage error margin, which is comparable to routine measurement accuracies. Only if a qualitatively accurate description of the concentration dependence of the binary diffusion coefficient is desired, very few additional simulations of the pure components and the equimolar mixture are required. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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16. Deep learning path-like collective variable for enhanced sampling molecular dynamics.
- Author
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Fröhlking, Thorben, Bonati, Luigi, Rizzi, Valerio, and Gervasio, Francesco Luigi
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MOLECULAR dynamics , *SAMPLING (Process) , *DEEP learning , *ALANINE - Abstract
Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. The existing variables that describe the progression along a reactive pathway offer an elegant solution but face a number of limitations. In this paper, we address these challenges by introducing a new path-like collective variable called the "deep-locally non-linear-embedding," which is inspired by principles of the locally linear embedding technique and is trained on a reactive trajectory. The variable mimics the ideal reaction coordinate by automatically generating a non-linear combination of features through a differentiable generalized autoencoder that combines a neural network with a continuous k-nearest neighbor selection. Among the key advantages of this method is its capability to automatically choose the metric for searching neighbors and to learn the path from state A to state B without the need to handpick landmarks a priori. We demonstrate the effectiveness of DeepLNE by showing that the progression along the path variable closely approximates the ideal reaction coordinate in toy models, such as the Müller-Brown potential and alanine dipeptide. Then, we use it in the molecular dynamics simulations of an RNA tetraloop, where we highlight its capability to accelerate transitions and estimate the free energy of folding. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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17. Simple and efficient methods for local structural analysis in polydisperse hard disk systems.
- Author
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Mugita, Daigo, Souno, Kazuyoshi, Koyama, Hiroaki, Nakamura, Taisei, and Isobe, Masaharu
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STATISTICAL physics - Abstract
In nonequilibrium statistical physics, quantifying the nearest (and higher-order) neighbors and free volumes of particles in many-body systems is crucial to elucidating the origin of macroscopic collective phenomena, such as glass/granular jamming transitions and various aspects of the behavior of active matter. However, conventional techniques (based on a fixed-distance cutoff or the Voronoi construction) have mainly been applied to equilibrated, homogeneous, and monodisperse particle systems. In this paper, we implement simple and efficient methods for local structure analysis in nonequilibrium, inhomogeneous, and polydisperse hard disk systems. We show how these novel methods can overcome the difficulties encountered by conventional techniques as well as demonstrate some applications. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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18. Photodissociation dynamics of SO2 via the G̃1B1 state: The O(1D2) and O(1S0) product channels.
- Author
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Wu, Yucheng, Sun, Jitao, Li, Zhenxing, Zhang, Zhaoxue, Luo, Zijie, Chang, Yao, Wu, Guorong, Zhang, Weiqing, Yu, Shengrui, Yuan, Kaijun, and Yang, Xueming
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PHOTODISSOCIATION , *NATURAL satellites , *UPPER atmosphere , *ATMOSPHERE , *EXCITED states , *PLANETARY atmospheres - Abstract
Produced by both nature and human activities, sulfur dioxide (SO2) is an important species in the earth's atmosphere. SO2 has also been found in the atmospheres of other planets and satellites in the solar system. The photoabsorption cross sections and photodissociation of SO2 have been studied for several decades. In this paper, we reported the experimental results for photodissociation dynamics of SO2 via the G ̃ 1B1 state. By analyzing the images from the time-sliced velocity map ion imaging method, the vibrational state population distributions and anisotropy parameters were obtained for the O(1D2) + SO(X3Σ−, a1Δ, b1Σ+) and O(1S0) + SO(X3Σ−) channels, and the branching ratios for the channels O(1D2) + SO(X3Σ−), O(1D2) + SO(a1Δ), and O(1D2) + SO(b1Σ+) were determined to be ∼0.3, ∼0.6, and ∼0.1, respectively. The SO products were dominant in electronically and rovibrationally excited states, which may have yet unrecognized roles in the upper planetary atmosphere. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
19. Molecular chirality quantification: Tools and benchmarks.
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Abraham, Ethan and Nitzan, Abraham
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CHIRALITY , *POLYMERS , *MOLECULES - Abstract
Molecular chirality has traditionally been viewed as a binary property where a molecule is classified as either chiral or achiral, yet in recent decades, mathematical methods for quantifying chirality have been explored. Here, we use toy molecular systems to systematically compare the performance of two state-of-the-art chirality measures: (1) the Continuous Chirality Measure (CCM) and (2) the Chirality Characteristic (χ). We find that both methods exhibit qualitatively similar behavior when applied to simple molecular systems such as a four-site molecule or the polymer double-helix, but we show that the CCM may be more suitable for evaluating the chirality of arbitrary molecules or abstract structures such as normal vibrational modes. We discuss a range of considerations for applying these methods to molecular systems in general, and we provide links to user-friendly codes for both methods. We aim for this paper to serve as a concise resource for scientists attempting to familiarize themselves with these chirality measures or attempting to implement chirality measures in their own work. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
20. Self-assembly of chemical shakers.
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Qiao, Liyan and Kapral, Raymond
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CHEMICAL reactions , *NON-equilibrium reactions , *CHEMOSTAT , *SURFACE reactions , *VELOCITY - Abstract
Chemical shakers are active particles with zero propulsion velocity whose activity derives from chemical reactions on portions of their surfaces. Although they do not move, except through Brownian motion, the nonequilibrium concentration and velocity fields that they generate endow them with properties that differ from their equilibrium counterparts. In particular, collections of such shakers can actively move, reorient, and self-assemble into various cluster states, which are the subject of this paper. Elongated chemical shakers constructed from linked catalytic and noncatalytic spheres are considered, and it is shown how hydrodynamic, chemotactic, and shape-dependent interactions give rise to various self-assembled shaker structures. The chemical forces responsible for cluster formation are described in terms of a model based on pair-wise additive contributions. The forms of the self-assembled structures can be varied by changing the chemostat concentrations that control the nonequilibrium state. The resulting structures and their manipulation through chemical means suggest ways to construct a class of active materials for applications. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
21. Enhanced thermal conductivity of epoxy resin by incorporating three-dimensional boron nitride thermally conductive network.
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Wang, Xubin, Zhang, Changhai, Zhang, Tiandong, Tang, Chao, and Chi, Qingguo
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THERMAL conductivity , *THERMAL insulation , *POWER semiconductors , *FOURIER transform spectrometers , *BORON nitride , *SCANNING electron microscopes , *PACKAGING materials , *EPOXY resins - Abstract
Packaging insulation materials with high thermal conductivity and excellent dielectric properties are favorable to meet the high demand and rapid development of third generation power semiconductors. In this study, we propose to improve the thermal conductivity of epoxy resin (EP) by incorporating a three-dimensional boron nitride thermally conductive network. Detailedly, polyurethane foam (PU) was used as a supporter, and boron nitride nanosheets (BNNSs) were loaded onto the PU supporter through chemical bonding (BNNS@PU). After immersing BNNS@PU into the EP resin, EP-based thermally conductive composites were prepared by vacuum-assisted impregnation. Fourier transform infrared spectrometer and scanning electron microscope were used to characterize the chemical bonding and morphological structure of BNNS@PU, respectively. The content of BNNS in BNNS@PU/EP composites was quantitatively analyzed by TGA. The results show that the thermal conductivity of the BNNS@PU/EP composites reaches 0.521 W/m K with an enhancement rate η of 30.89 at an ultra-low BNNS filler content (5.93 wt. %). Additionally, the BNNS@PU/EP composites have excellent dielectric properties with the frequency range from 101 to 106 Hz. This paper provides an interesting idea for developing high thermal conductivity insulating materials used for power semiconductor packaging. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
22. Characterization of environmental airborne hydrocarbon contaminants by surface-enhanced Raman scattering.
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Tolman, Nathan L., Li, Sunny, Zlotnikov, Samuel B., McQuain, Alex D., and Liu, Haitao
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RAMAN scattering , *SERS spectroscopy , *POLLUTANTS , *AMORPHOUS carbon , *HYDROCARBONS , *FACTOR analysis - Abstract
This paper explores the unintentional contamination of Surface-Enhanced Raman Scattering (SERS) substrates by ambient hydrocarbon contaminants and their contribution to SERS spectra. Previous studies have identified amorphous carbon as a potential complicating factor in data analysis in SERS experiments, although its origin has been elusive. Our work showed that ambient hydrocarbon contamination and its decomposition products can be detected by SERS on a gold substrate. We propose that ambient air itself is a source of amorphous carbon contamination on SERS substrates. This understanding is crucial for the correct interpretation of SERS data and highlights the need for careful consideration of potential environmental contaminants in SERS analysis. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
23. Liquid lasing from solutions of ligand-engineered semiconductor nanocrystals.
- Author
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Tan, Max J. H., Patel, Shreya K., Chiu, Jessica, Zheng, Zhaoyun Tiffany, and Odom, Teri W.
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SEMICONDUCTOR nanocrystals , *NANOCRYSTALS , *SIGNAL detection , *LIQUIDS , *CELLULAR signal transduction , *AQUEOUS solutions - Abstract
Semiconductor nanocrystals (NCs) can function as efficient gain materials with chemical versatility because of their surface ligands. Because the properties of NCs in solution are sensitive to ligand–environment interactions, local chemical changes can result in changes in the optical response. However, amplification of the optical response is technically challenging because of colloidal instability at NC concentrations needed for sufficient gain to overcome losses. This paper demonstrates liquid lasing from plasmonic lattice cavities integrated with ligand-engineered CdZnS/ZnS NCs dispersed in toluene and water. By taking advantage of calcium ion-induced aggregation of NCs in aqueous solutions, we show how lasing threshold can be used as a transduction signal for ion detection. Our work highlights how NC solutions and plasmonic lattices with open cavity architectures can serve as a biosensing platform for lab-on-chip devices. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
24. Responses of assembled structures of block polyelectrolytes to electrostatic interaction strength.
- Author
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Wang, Fujia, Liu, Xinyi, Yang, Wei, Chen, Yao, and Liu, Liyan
- Subjects
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ELECTROSTATIC interaction , *REVERSED micelles , *POLYELECTROLYTES , *HYDROPHOBIC interactions , *MICELLES - Abstract
In this paper, the responses of assembled behaviors of block polyelectrolytes (PEs) to the strength of electrostatic interactions are studied through molecular dynamic simulations. The results show that the assembled structures closely depend on the electrostatic strength. It should be noted that PE coacervation can outweigh the nucleation of hydrophobic blocks and invert the micelle structures at strong electrostatic strengths, leading to the formation of inverted micelles of PE cores and hydrophobic coronas. In the poor solvent condition for neutral block, diverse anisotropic micelles are presented; candy-like conventional micelles of hydrophobic cores and PE patches coexist with inverted candy-like micelles of PE cores and hydrophobic patches and with Janus micelles of semi-neutral aggregate and semi-PE cluster in the presence of divalent and trivalent counterions. The formation of conventional or inverted micelle is largely determined by the type of micellar fusion, which results from the nucleation competition between electrostatic correlation and hydrophobic interaction. The merge of micelles mediated by hydrophobic attraction leads to conventional hydrophobic cores, and the fusion induced by electrostatic correlations results in PE cores micelles. At strong electrostatic strengths, the PE chains exhibit rich conformations at trivalent counterions, ranging from a fully collapsed state to a rod-like state, and parallel alignment of PE chains is found. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
25. Dynamics accelerate the kinetics of ion diffusion through channels: Continuous-time random walk models beyond the mean field approximation.
- Author
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Mondal, Ronnie and Vaissier Welborn, Valerie
- Subjects
- *
RANDOM walks , *DIFFUSION kinetics , *ION channels , *PROTEIN conformation , *CELL membranes , *DIFFUSION coefficients - Abstract
Ion channels are proteins that play a significant role in physiological processes, including neuronal excitability and signal transduction. However, the precise mechanisms by which these proteins facilitate ion diffusion through cell membranes are not well understood. This is because experimental techniques to characterize ion channel activity operate on a time scale too large to understand the role of the various protein conformations on diffusion. Meanwhile, computational approaches operate on a time scale too short to rationalize the observed behavior at the microscopic scale. In this paper, we present a continuous-time random walk model that aims to bridge the scales between the atomistic models of ion channels and the experimental measurement of their conductance. We show how diffusion slows down in complex systems by using 3D lattices that map out the pore geometry of two channels: Nav1.7 and gramicidin. We also introduce spatial and dynamic site disorder to account for system heterogeneity beyond the mean field approximation. Computed diffusion coefficients show that an increase in spatial disorder slows down diffusion kinetics, while dynamic disorder has the opposite effect. Our results imply that microscopic or phenomenological models based on the potential of mean force data overlook the functional importance of protein dynamics on ion diffusion through channels. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
26. Electronic spectroscopy of gemcitabine and derivatives for possible dual-action photodynamic therapy applications.
- Author
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Abdelgawwad, Abdelazim M. A., Roca-Sanjuán, Daniel, and Francés-Monerris, Antonio
- Subjects
- *
PHOTODYNAMIC therapy , *GEMCITABINE , *SPIN-orbit interactions , *LIGHT absorption , *SPECTROMETRY , *REDSHIFT , *ATOMS - Abstract
In this paper, we explore the molecular basis of combining photodynamic therapy (PDT), a light-triggered targeted anticancer therapy, with the traditional chemotherapeutic properties of the well-known cytotoxic agent gemcitabine. A photosensitizer prerequisite is significant absorption of biocompatible light in the visible/near IR range, ideally between 600 and 1000 nm. We use highly accurate multiconfigurational CASSCF/MS-CASPT2/MM and TD-DFT methodologies to determine the absorption properties of a series of gemcitabine derivatives with the goal of red-shifting the UV absorption band toward the visible region and facilitating triplet state population. The choice of the substitutions and, thus, the rational design is based on important biochemical criteria and on derivatives whose synthesis is reported in the literature. The modifications tackled in this paper consist of: (i) substitution of the oxygen atom at O2 position with heavier atoms (O → S and O → Se) to red shift the absorption band and increase the spin–orbit coupling, (ii) addition of a lipophilic chain at the N7 position to enhance transport into cancer cells and slow down gemcitabine metabolism, and (iii) attachment of aromatic systems at C5 position to enhance red shift further. Results indicate that the combination of these three chemical modifications markedly shifts the absorption spectrum toward the 500 nm region and beyond and drastically increases spin–orbit coupling values, two key PDT requirements. The obtained theoretical predictions encourage biological studies to further develop this anticancer approach. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
27. Synergetic enhancement effect of two-dimensional MoS2 nanosheets and metal organic framework-derived porous ZnO nanorods for photodegradation performance.
- Author
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Yin, Huimin, Zhou, Suyu, Liu, Junhui, and Huang, Mingju
- Subjects
- *
MOLYBDENUM sulfides , *NANORODS , *METAL oxide semiconductors , *NANOSTRUCTURED materials , *ORGANOMETALLIC compounds , *ZINC oxide - Abstract
Two-dimensional transition metal dichalcogenides and semiconductor metal oxides have shown great potential in photocatalysis. However, their stability and efficiency need to be further improved. In this paper, porous ZnO nanorods with high specific surface area were prepared from metal-organic framework ZIF-8 by a simple hydrothermal method. A MoS2/ZnO composite was constructed by loading MoS2 onto the surface of porous ZnO nanorods. Compared with ZnO materials prepared by other methods, MoS2/ZnO prepared in this paper exhibits superior photocatalytic performance. The enhanced photocatalytic activity of the MoS2/ZnO composite can be attributed to the formation of heterojunctions and strong interaction between them, which greatly facilitate the separation of electrons and holes at the contact interface. In addition, due to the wide absorption region of the visible spectrum, MoS2 can greatly broaden the light absorption range of the material after the formation of the composite material, increase the utilization rate of visible light, and reduce the combination of electrons and holes. This study provides a new way to prepare cheap and efficient photocatalysts. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
28. Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. I. Response function theory.
- Author
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Whaley-Mayda, Lukas, Guha, Abhirup, and Tokmakoff, Andrei
- Subjects
- *
INFRARED spectroscopy , *OPTIMAL designs (Statistics) , *VIBRONIC coupling , *DIPOLE moments , *SINGLE molecules , *ULTRA-short pulsed lasers - Abstract
Fluorescence-encoded infrared (FEIR) spectroscopy is an emerging technique for performing vibrational spectroscopy in solution with detection sensitivity down to single molecules. FEIR experiments use ultrashort pulses to excite a fluorescent molecule's vibrational and electronic transitions in a sequential, time-resolved manner, and are therefore sensitive to intervening vibrational dynamics on the ground state, vibronic coupling, and the relative orientation of vibrational and electronic transition dipole moments. This series of papers presents a theoretical treatment of FEIR spectroscopy that describes these phenomena and examines their manifestation in experimental data. This first paper develops a nonlinear response function description of Fourier-transform FEIR experiments for a two-level electronic system coupled to multiple vibrations, which is then applied to interpret experimental measurements in the second paper [L. Whaley-Mayda et al., J. Chem. Phys. 159, 194202 (2023)]. Vibrational coherence between pairs of modes produce oscillatory features that interfere with the vibrations' population response in a manner dependent on the relative signs of their respective Franck–Condon wavefunction overlaps, leading to time-dependent distortions in FEIR spectra. The orientational response of population and coherence contributions are analyzed and the ability of polarization-dependent experiments to extract relative transition dipole angles is discussed. Overall, this work presents a framework for understanding the full spectroscopic information content of FEIR measurements to aid data interpretation and inform optimal experimental design. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
29. Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. II. Analysis of early-time signals.
- Author
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Whaley-Mayda, Lukas, Guha, Abhirup, and Tokmakoff, Andrei
- Subjects
- *
INFRARED spectroscopy , *VIBRONIC coupling , *SIGNALS & signaling , *NONLINEAR functions , *SPECTROMETRY - Abstract
Developing fluorescence-encoded infrared (FEIR) vibrational spectroscopy for single-molecule applications requires a detailed understanding of how the molecular response and external experimental parameters manifest in the detected signals. In Paper I [L. Whaley-Mayda, A. Guha, and A. Tokmakoff, J. Chem. Phys. 159, 194201 (2023)] we introduced a nonlinear response function theory to describe vibrational dynamics, vibronic coupling, and transition dipole orientation in FEIR experiments with ultrashort pulses. In this second paper, we apply the theory to investigate the role of intermode vibrational coherence, the orientation of vibrational and electronic transition dipoles, and the effects of finite pulse durations in experimental measurements. We focus on measurements at early encoding delays—where signal sizes are largest and therefore of most value for single-molecule experiments, but where many of these phenomena are most pronounced and can complicate the appearance of data. We compare experiments on coumarin dyes with finite-pulse response function simulations to explain the time-dependent behavior of FEIR spectra. The role of the orientational response is explored by analyzing polarization-dependent experiments and their ability to resolve relative dipole angles in the molecular frame. This work serves to demonstrate the molecular information content of FEIR experiments, and develop insight and guidelines for their interpretation. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
30. Polarization-dependent intensity ratios in double resonance spectroscopy.
- Author
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Lehmann, Kevin K.
- Subjects
- *
RESONANCE , *QUANTUM numbers , *DOPPLER broadening , *SPECTROMETRY - Abstract
Double Resonance is a powerful spectroscopic method that unambiguously assigns the rigorous quantum numbers of one state of a transition. However, there is often ambiguity as to the branch (ΔJ) of that transition. Spectroscopists have resolved this ambiguity by using the dependence of the double resonance intensity on the relative polarization directions of pump and probe radiation. However, published theoretical predictions for this ratio are based upon a weak (i.e., non-saturating) field approximation. This paper presents theoretical predictions for these intensity ratios for cases where the pump field is strongly saturating in the two limits of transitions dominated by homogeneous or of inhomogeneous broadening. Saturation reduces but does not eliminate the magnitude of the polarization effect (driving the intensity ratio closer to unity) even with strong pump saturation. For the case of an inhomogeneously broadened line, such as when Doppler broadened linewidth dominates over the power-broadened homogeneous line width, a large fraction of the low pump power polarization anisotropy remains. This paper reports predicted polarization ratios for both linear and circular pump and probe field polarizations. The present predictions are compared with experimental measurements on CH4 ground state → ν3 → 3ν3 transitions recently reported by de Oliveira et al.63 and these are in better agreement than with the weak field predictions. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
31. Multicomponent solutions: Combining rules for multisolute osmotic virial coefficients.
- Author
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Binyaminov, Hikmat and Elliott, Janet A. W.
- Subjects
- *
OSMOTIC coefficients , *VIRIAL coefficients , *THERMODYNAMICS , *GIBBS' free energy , *SOLUTION (Chemistry) , *BINARY mixtures , *CAHN-Hilliard-Cook equation - Abstract
This paper presents an exploration of a specific type of a generalized multicomponent solution model, which appears to be first given by Saulov in the current explicit form. The assumptions of the underlying theory and a brief derivation of the main equation have been provided preliminarily for completeness and notational consistency. The resulting formulae for the Gibbs free energy of mixing and the chemical potentials are multivariate polynomials with physically meaningful coefficients and the mole fractions of the components as variables. With one additional assumption about the relative magnitudes of the solvent–solute and solute–solute interaction exchange energies, combining rules were obtained that express the mixed coefficients of the polynomial in terms of its pure coefficients. This was done by exploiting the mathematical structure of the asymmetric form of the solvent chemical potential equation. The combining rules allow one to calculate the thermodynamic properties of the solvent with multiple solutes from binary mixture data only (i.e., each solute with the solvent), and hence, are of practical importance. Furthermore, a connection was established between the osmotic virial coefficients derived in this work and the original osmotic virial coefficients of Hill found by employing a different procedure, illustrating the equivalency of what appears to be two different theories. A validation of the combining rules derived here has been provided in a separate paper where they were successfully used to predict the freezing points of ternary salt solutions of water. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
32. Understanding dynamics in coarse-grained models. III. Roles of rotational motion and translation-rotation coupling in coarse-grained dynamics.
- Author
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Jin, Jaehyeok, Lee, Eok Kyun, and Voth, Gregory A.
- Subjects
- *
ROTATIONAL diffusion , *TRANSLATIONAL motion , *DIFFUSION coefficients , *MOLECULAR dynamics , *MOTION capture (Human mechanics) , *ROTATIONAL motion - Abstract
This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in CG systems using a hard sphere mapping, the absence of rotational motions in single-site CG models introduces differences between FG and CG dynamics. In this third paper, our objective is to faithfully recover atomistic diffusion coefficients from CG dynamics by incorporating rotational dynamics. By extracting FG rotational diffusion, we unravel, for the first time reported to our knowledge, a universality in excess entropy scaling between the rotational and translational diffusion. Once the missing rotational dynamics are integrated into the CG translational dynamics, an effective translation-rotation coupling becomes essential. We propose two different approaches for estimating this coupling parameter: the rough hard sphere theory with acentric factor (temperature-independent) or the rough Lennard-Jones model with CG attractions (temperature-dependent). Altogether, we demonstrate that FG diffusion coefficients can be recovered from CG diffusion coefficients by (1) incorporating "entropy-free" rotational diffusion with translation-rotation coupling and (2) recapturing the missing entropy. Our findings shed light on the fundamental relationship between FG and CG dynamics in molecular fluids. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
33. Can classical mechanics sense conical intersection?
- Author
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Karmakar, Sourav, Thakur, Saumya, and Jain, Amber
- Subjects
- *
FLUORESCENCE resonance energy transfer , *HAMILTONIAN systems , *CLASSICAL mechanics - Abstract
Conical intersection (CI) leads to fast electronic energy transfer. However, Hamm and Stock [Phys. Rev. Lett. 109, 173201 (2012)] showed the existence of a vibrational CI and its role in vibrational energy relaxation. In this paper, we further investigate the vibrational energy relaxation using an isolated model Hamiltonian system of four vibrational modes with two distinctively different timescales (two fast modes and two slow modes). We show that the excitation of the slow modes plays a crucial role in the energy relaxation mechanism. We also analyze the system from a mixed quantum-classical (surface hopping method) and a completely classical point of view. Notably, surface hopping and even classical simulations also capture fast energy relaxation, which is a signature of CI's existence. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
34. Extending the definition of atomic basis sets to atoms with fractional nuclear charge.
- Author
-
Domenichini, Giorgio
- Subjects
- *
NUCLEAR charge , *ATOMS , *ATOMIC orbitals , *PERTURBATION theory , *ATOMIC charges - Abstract
Alchemical transformations showed that perturbation theory can be applied also to changes in the atomic nuclear charges of a molecule. The alchemical path that connects two different chemical species involves the conceptualization of a non-physical system in which an atom possess a non-integer nuclear charge. A correct quantum mechanical treatment of these systems is limited by the fact that finite size atomic basis sets do not define exponents and contraction coefficients for fractional charge atoms. This paper proposes a solution to this problem and shows that a smooth interpolation of the atomic orbital coefficients and exponents across the periodic table is a convenient way to produce accurate alchemical predictions, even using small size basis sets. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
35. New physical insights into the supporting subspace factorization of XMS-CASPT2 and generalization to multiple spin states via spin-free formulation.
- Author
-
Song, Chenchen
- Subjects
- *
MAGNETIC field effects , *GENERALIZATION , *FACTORIZATION - Abstract
This paper introduces a spin-free formulation of the supporting subspace factorization [C. Song and T. J. Martínez, J. Chem. Phys. 149, 044108 (2018)], enabling a reduction in the computational scaling of the extended multi-state complete active space second-order perturbation (XMS-CASPT2) method for arbitrary spins. Compared to the original formulation that is defined in the spin orbitals and is limited to singlet states, the spin-free formulation in this work treats different spin states equivalently, thus naturally generalizing the idea beyond singlet states. In addition, we will present a new way of deriving the supporting subspace factorization with the purpose of understanding its physical interpretation. In this new derivation, we separate the sources that make CASPT2 difficult into the "same-site interactions" and "inter-site interactions." We will first show how the Kronecker sum can be used to remove the same-site interactions in the absence of inter-site interactions, leading to MP2 energy in dressed orbitals. We will then show how the inter-site interactions can be exactly recovered using Löwdin partition, where the supporting subspace concept will naturally arise. The new spin-free formulation maintains the main advantage of the supporting subspace factorization, i.e., allowing XMS-CASPT2 energies to be computed using highly optimized MP2 energy codes and Fock build codes, thus reducing the scaling of XMS-CASPT2 to the same scaling as MP2. We will present and discuss results that benchmark the accuracy and performance of the new method. To demonstrate how the new method can be useful in studying real photochemical systems, the supporting subspace XMS-CASPT2 is applied to a photoreaction sensitive to magnetic field effects. The new spin-free formulation makes it possible to calculate the doublet and quartet states required in this particular photoreaction mechanism. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
36. A simple one-electron expression for electron rotational factors.
- Author
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Qiu, Tian, Bhati, Mansi, Tao, Zhen, Bian, Xuezhi, Rawlinson, Jonathan, Littlejohn, Robert G., and Subotnik, Joseph E.
- Subjects
- *
ELECTRONS , *ALGORITHMS , *WISHES , *MATRICES (Mathematics) - Abstract
Within the context of fewest-switch surface hopping (FSSH) dynamics, one often wishes to remove the angular component of the derivative coupling between states J and K . In a previous set of papers, Shu et al. [J. Phys. Chem. Lett. 11, 1135–1140 (2020)] posited one approach for such a removal based on direct projection, while we isolated a second approach by constructing and differentiating a rotationally invariant basis. Unfortunately, neither approach was able to demonstrate a one-electron operator O ̂ whose matrix element J O ̂ K was the angular component of the derivative coupling. Here, we show that a one-electron operator can, in fact, be constructed efficiently in a semi-local fashion. The present results yield physical insight into designing new surface hopping algorithms and are of immediate use for FSSH calculations. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
37. Hybrid programming-model strategies for GPU offloading of electronic structure calculation kernels.
- Author
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Fattebert, Jean-Luc, Negre, Christian F. A., Finkelstein, Joshua, Mohd-Yusof, Jamaludin, Osei-Kuffuor, Daniel, Wall, Michael E., Zhang, Yu, Bock, Nicolas, and Mniszewski, Susan M.
- Subjects
- *
ELECTRONIC structure , *DENSITY matrices , *LINEAR algebra , *DENSITY functional theory , *BENCHMARK problems (Computer science) , *GRAPH algorithms , *SATISFIABILITY (Computer science) - Abstract
To address the challenge of performance portability and facilitate the implementation of electronic structure solvers, we developed the basic matrix library (BML) and Parallel, Rapid O(N), and Graph-based Recursive Electronic Structure Solver (PROGRESS) library. The BML implements linear algebra operations necessary for electronic structure kernels using a unified user interface for various matrix formats (dense and sparse) and architectures (CPUs and GPUs). Focusing on density functional theory and tight-binding models, PROGRESS implements several solvers for computing the single-particle density matrix and relies on BML. In this paper, we describe the general strategies used for these implementations on various computer architectures, using OpenMP target functionalities on GPUs, in conjunction with third-party libraries to handle performance critical numerical kernels. We demonstrate the portability of this approach and its performance in benchmark problems. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
38. Effect of penetrant–polymer interactions and shape on the motion of molecular penetrants in dense polymer networks.
- Author
-
Lin, Tsai-Wei and Sing, Charles E.
- Abstract
The diffusion of dilute molecular penetrants within polymers plays a crucial role in the advancement of material engineering for applications such as coatings and membrane separations. The potential of highly cross-linked polymer networks in these applications stems from their capacity to adjust the size and shape selectivity through subtle changes in network structures. In this paper, we use molecular dynamics simulation to understand the role of penetrant shape (aspect ratios) and its interaction with polymer networks on its diffusivity. We characterize both local penetrant hopping and the long-time diffusive motion for penetrants and consider different aspect ratios and penetrant–network interaction strengths at a variety of cross-link densities and temperatures. The shape affects the coupling of penetrant motion to the cross-link density- and temperature-dependent structural relaxation of networks and also affects the way a penetrant experiences the confinement from the network meshes. The attractive interaction between the penetrant and network primarily affects the former since only the system of dilute limit is of present interest. These results offer fundamental insights into the intricate interplay between penetrant characteristics and polymer network properties and also suggest future directions for manipulating polymer design to enhance the separation efficiency. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
39. Comparing machine learning potentials for water: Kernel-based regression and Behler–Parrinello neural networks.
- Author
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Montero de Hijes, Pablo, Dellago, Christoph, Jinnouchi, Ryosuke, Schmiedmayer, Bernhard, and Kresse, Georg
- Abstract
In this paper, we investigate the performance of different machine learning potentials (MLPs) in predicting key thermodynamic properties of water using RPBE + D3. Specifically, we scrutinize kernel-based regression and high-dimensional neural networks trained on a highly accurate dataset consisting of about 1500 structures, as well as a smaller dataset, about half the size, obtained using only on-the-fly learning. This study reveals that despite minor differences between the MLPs, their agreement on observables such as the diffusion constant and pair-correlation functions is excellent, especially for the large training dataset. Variations in the predicted density isobars, albeit somewhat larger, are also acceptable, particularly given the errors inherent to approximate density functional theory. Overall, this study emphasizes the relevance of the database over the fitting method. Finally, this study underscores the limitations of root mean square errors and the need for comprehensive testing, advocating the use of multiple MLPs for enhanced certainty, particularly when simulating complex thermodynamic properties that may not be fully captured by simpler tests. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
40. Diagonalizing the Born–Oppenheimer Hamiltonian via Moyal perturbation theory, nonadiabatic corrections, and translational degrees of freedom.
- Author
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Littlejohn, Robert, Rawlinson, Jonathan, and Subotnik, Joseph
- Abstract
This article describes a method for calculating higher order or nonadiabatic corrections in Born–Oppenheimer theory and its interaction with the translational degrees of freedom. The method uses the Wigner–Weyl correspondence to map nuclear operators into functions on the classical phase space and the Moyal star product to represent operator multiplication on those functions. These are explained in the body of the paper. The result is a power series in κ2, where κ = (m/M)1/4 is the usual Born–Oppenheimer parameter. The lowest order term is the usual Born–Oppenheimer approximation, while higher order terms are nonadiabatic corrections. These are needed in calculations of electronic currents, momenta, and densities. The separation of nuclear and electronic degrees of freedom takes place in the context of the exact symmetries (for an isolated molecule) of translations and rotations, and these, especially translations, are explicitly incorporated into our discussion. This article presents an independent derivation of the Moyal expansion in molecular Born–Oppenheimer theory. We show how electronic currents and momenta can be calculated within the framework of Moyal perturbation theory; we derive the transformation laws of the electronic Hamiltonian, the electronic eigenstates, and the derivative couplings under translations; we discuss in detail the rectilinear motion of the molecular center of mass in the Born–Oppenheimer representation; and we show how the elimination of the translational components of the derivative couplings leads to a unitary transformation that has the effect of exactly separating the translational degrees of freedom. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
41. Situating the phosphonated calixarene–cytochrome C association by molecular dynamics simulations.
- Author
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Bartocci, Alessio and Dumont, Elise
- Subjects
- *
MOLECULAR dynamics , *CYTOCHROME c , *MOLECULAR association , *BINDING sites , *CYTOSKELETAL proteins , *CALIXARENES - Abstract
Protein–calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
42. Pseudo-marginal approximation to the free energy in a micro–macro Markov chain Monte Carlo method.
- Author
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Vandecasteele, Hannes and Samaey, Giovanni
- Subjects
- *
MARKOV processes , *GIBBS sampling , *BOLTZMANN factor , *MARKOV chain Monte Carlo , *DEGREES of freedom - Abstract
We introduce a generalized micro–macro Markov chain Monte Carlo (mM-MCMC) method with pseudo-marginal approximation to the free energy that is able to accelerate sampling of the microscopic Gibbs distributions when there is a time-scale separation between the macroscopic dynamics of a reaction coordinate and the remaining microscopic degrees of freedom. The mM-MCMC method attains this efficiency by iterating four steps: (i) propose a new value of the reaction coordinate, (ii) accept or reject the macroscopic sample, (iii) run a biased simulation that creates a microscopic molecular instance that lies close to the newly sampled macroscopic reaction coordinate value, and (iv) microscopic accept/reject step for the new microscopic sample. In the present paper, we eliminate the main computational bottleneck of earlier versions of this method: the necessity to have an accurate approximation of free energy. We show that the introduction of a pseudo-marginal approximation significantly reduces the computational cost of the microscopic accept/reject step while still providing unbiased samples. We illustrate the method's behavior on several molecular systems with low-dimensional reaction coordinates. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
43. Cluster perturbation theory IX: Perturbation series for the coupled cluster singles and doubles ground state energy.
- Author
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Hillers-Bendtsen, Andreas Erbs, Jensen, Frank, Mikkelsen, Kurt V., Olsen, Jeppe, and Jørgensen, Poul
- Subjects
- *
GROUND state energy , *PERTURBATION theory , *NATURAL orbitals , *RATE coefficients (Chemistry) , *BASE pairs - Abstract
In this paper, we develop and analyze a number of perturbation series that target the coupled cluster singles and doubles (CCSD) ground state energy. We show how classical Møller–Plesset perturbation theory series can be restructured to target the CCSD energy based on a reference CCS calculation and how the corresponding cluster perturbation series differs from the classical Møller–Plesset perturbation series. Subsequently, we reformulate these series using the coupled cluster Lagrangian framework to obtain series, where fourth and fifth order energies are determined only using parameters through second order. To test the methods, we perform a series of test calculations on molecular photoswitches of both total energies and reaction energies. We find that the fifth order reaction energies are of CCSD quality and that they are of comparable accuracy to state-of-the-art approximations to the CCSD energy based on local pair natural orbitals. The advantage of the present approach over local correlation methods is the absence of user defined threshold parameters for neglecting or approximating contributions to the correlation energy. Fixed threshold parameters lead to discontinuous energy surfaces, although this effect is often small enough to be ignored, but the present approach has a differentiable energy that will facilitate derivation and implementation of gradients and higher derivatives. A further advantage is that the calculation of the perturbation correction is non-iterative and can, therefore, be calculated in parallel, leading to a short time-to-solution. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
44. Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography.
- Author
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Perrett, Samuel, Chatrchyan, Viktoria, Buckup, Tiago, and van Thor, Jasper J.
- Subjects
- *
DENSITY matrices , *X-ray crystallography , *FREE electron lasers , *COHERENCE (Optics) , *PHASE space , *LIGHT sources - Abstract
Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities of XFELs advance, we anticipate that a new range of coherent control and structural Raman measurements will become achievable. Shorter optical and x-ray pulse durations and increasingly more exotic pulse regimes are becoming available at free electron lasers. Moreover, with high repetition enabled by the superconducting technology of European XFEL (EuXFEL) and Linac Coherent Light Source (LCLS-II) , it will be possible to improve the signal-to-noise ratio of the light-induced differences, allowing for the observation of vibronic motion on the sub-Angstrom level. To predict and assign this coherent motion, which is measurable with a structural technique, new theoretical approaches must be developed. In this paper, we present a theoretical density matrix approach to model the various population and coherent dynamics of a system, which considers molecular system parameters and excitation conditions. We emphasize the use of the Wigner transform of the time-dependent density matrix, which provides a phase space representation that can be directly compared to the experimental positional displacements measured in a TR-SFX experiment. Here, we extend the results from simple models to include more realistic schemes that include large relaxation terms. We explore a variety of pulse schemes using multiple model systems using realistic parameters. An open-source software package is provided to perform the density matrix simulation and Wigner transformations. The open-source software allows us to define any arbitrary level schemes as well as any arbitrary electric field in the interaction Hamiltonian. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
45. Research on molecular dynamics and electrical properties of high heat-resistant epoxy resins.
- Author
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Zhang, Changhai, Liu, Zeyang, Wang, Xubin, Zhang, Qiyue, Xing, Wenjie, Zhang, Tiandong, and Chi, Qingguo
- Subjects
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EPOXY resins , *MOLECULAR dynamics , *PACKAGING materials , *GLASS transition temperature , *MOLECULAR orbitals , *CARBONYL group , *PHENOLIC resins - Abstract
In order to prepare highly heat-resistant packaging insulation materials, in this paper, bismaleimide/epoxy resin (BMI/EP55) composites with different contents of BMI were prepared by melt blending BMI into amino tetrafunctional and phenolic epoxy resin (at a ratio of 5:5). The microstructures and thermal and electrical properties of the composites were tested. The electrostatic potential distribution, energy level distribution, and molecular orbitals of BMI were calculated using Gaussian. The results showed that the carbonyl group in BMI is highly electronegative, implying that the carbonyl group has a strong electron trapping ability. The thermal decomposition temperature of the composites gradually increased with the increase of BMI content, and the 20% BMI/EP55 composites had the highest heat-resistance index, along with a glass transition temperature (Tg) of >250 °C. At different test temperatures, with increase in the BMI content, the conductivity of epoxy resin composites showed a tendency to first decrease and then increase, the breakdown field strength showed a tendency to first increase and then decrease, and the dielectric constant was gradually decreased. Two trap centers were present simultaneously in the composites, where the shallow trap energy level is the deepest in 20% BMI/EP composites and the deep trap energy level is the deepest in 10% BMI/EP55 composites. Correspondingly, the 10% BMI/EP55 composite had a slower charge decay rate, while the 20% BMI/EP55 had a faster charge decay rate. In summary, the BMI/EP55 composites with high heat resistance and insulating properties were prepared in this study, which provided ideas for preparing high-temperature packaging insulating materials. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
46. A molecular dynamics study on the boundary between homogeneous and heterogeneous nucleation.
- Author
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Men, Hua
- Subjects
- *
HOMOGENEOUS nucleation , *HETEROGENOUS nucleation , *MOLECULAR dynamics , *LIQUID metals , *ROUGH surfaces , *NUCLEATION , *GALLIUM alloys - Abstract
The large discrepancy among the nucleation kinetics extracted from experimental measurements and computer simulations and the prediction of the classical nucleation theory (CNT) has stimulated intense arguments about its origin in the past decades, which is crucially relevant to the validity of the CNT. In this paper, we investigate the atomistic mechanism of the nucleation in liquid Al in contact with amorphous substrates with atomic-level smooth/rough surfaces, using molecular dynamics (MD) simulations. This study reveals that the slightly distorted local fcc/hcp structures in amorphous substrates with smooth surfaces can promote heterogeneous nucleation through a structural templating mechanism, and on the other hand, homogeneous nucleation will occur at a larger undercooling through a fluctuation mechanism if the surface is rough. Thus, some impurities, previously thought to be impotent, could be activated in the homogeneous nucleation experiments. We further find that the initial growth of the nucleus on smooth surfaces of amorphous substrates is one order of magnitude faster than that in homogeneous nucleation. Both these factors could significantly contribute to the discrepancy in the nucleation kinetics. This study is also supported by a recent study of the synthesis of high-entropy alloy nanoparticles assisted with the liquid metal Ga [Cao et al., Nature 619, 73 (2023)]. In this study, we established that the boundary existed between homogeneous and heterogeneous nucleation, i.e., the structural templating is a general mechanism for heterogeneous nucleation, and in its absence, homogeneous nucleation will occur through the fluctuation mechanism. This study provides an in-depth understanding of the nucleation theory and experiments. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
47. Matrix-formation dynamics dictate methyl nitrite conformer abundance.
- Author
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Hockey, Emily K., McLane, Nathan, Vlahos, Korina, McCaslin, Laura M., and Dodson, Leah G.
- Subjects
- *
CONFORMATIONAL isomers , *DIHEDRAL angles , *QUANTUM chemistry , *CONFORMERS (Chemistry) , *SURFACE dynamics , *SURFACE properties - Abstract
Methyl nitrite has two stable conformational isomers resulting from rotation about the primary C–O–N–O dihedral angle: cis-CH3ONO and trans-CH3ONO, with cis being more stable by ∼5 kJ/mol. The barrier to rotational interconversion (∼45 kJ/mol) is too large for isomerization to occur under ambient conditions. This paper presents evidence of a change in conformer abundance when dilute CH3ONO is deposited onto a cold substrate; the relative population of the freshly deposited cis conformer is seen to increase compared to its gas-phase abundance, measured by in situ infrared spectroscopy. We observe abundance changes depending on the identity of the bath gas (N2, Ar, and Xe) and deposition angle. The observations indicate that the surface properties of the growing matrix influence conformer abundance—contrary to the widely held assumption that conformer abundance in matrices reflects gas-phase abundance. We posit that differences in the angle-dependent host-gas deposition dynamics affect the growing surfaces, causing changes in conformer abundances. Quantum chemistry calculations of the binding energies between CH3ONO and a single bath-gas component reveal that significant energetic stabilization is not observed in 1:1 complexes of N2:CH3ONO, Ar:CH3ONO, or Xe:CH3ONO. From our results, we conclude that the growing surface plays a significant role in trapping cis-CH3ONO more effectively than trans-CH3ONO, likely because cis-CH3ONO is more compact. Taken together, the observations highlight the necessity for careful characterization of conformers in matrix-isolated systems, emphasizing a need for further study into the deposition dynamics and surface structure of chemically inert matrices. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
48. The approximate coupled-cluster methods CC2 and CC3 in a finite magnetic field.
- Author
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Kitsaras, Marios-Petros, Grazioli, Laura, and Stopkowicz, Stella
- Subjects
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FINITE fields , *MAGNETIC fields , *WHITE dwarf stars , *EXCITED states , *SINGLE molecule magnets , *STELLAR magnetic fields - Abstract
In this paper, we report on the implementation of CC2 and CC3 in the context of molecules in finite magnetic fields. The methods are applied to the investigation of atoms and molecules through spectroscopic predictions and geometry optimizations for the study of the atmosphere of highly magnetized White Dwarf stars. We show that ground-state finite-field (ff) CC2 is a reasonable alternative to CCSD for energies and, in particular, for geometrical properties. For excited states, ff-CC2 is shown to perform well for states with predominant single-excitation character. Yet, for cases in which the excited state wavefunction has double-excitation character with respect to the reference, ff-CC2 can easily lead to completely unphysical results. Ff-CC3, however, is shown to reproduce the CCSDT behavior very well and enables the treatment of larger systems at a high accuracy. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
49. Coherent x-ray spontaneous emission spectroscopy of conical intersections.
- Author
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Jadoun, Deependra and Kowalewski, Markus
- Subjects
- *
X-ray emission spectroscopy , *BORN-Oppenheimer approximation , *EXCITED states - Abstract
Conical intersections are known to play a vital role in many photochemical processes. The breakdown of the Born–Oppenheimer approximation in the vicinity of a conical intersection causes exciting phenomena, such as the ultrafast radiationless decay of excited states. The passage of a molecule through a conical intersection creates a coherent superposition of electronic states via nonadiabatic couplings. Detecting this coherent superposition may serve as a direct probe of the conical intersection. In this paper, we theoretically demonstrate the use of coherent spontaneous emission in samples with long-range order for probing the occurrence of a conical intersection in a molecule. Our simulations show that the spectrum contains clear signatures of the created coherent superposition of electronic states. We investigate the bandwidth requirements for the x-ray probes, which influence the observation of coherent superposition generated by the conical intersection. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
50. Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods.
- Author
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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
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