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Size-dependent wettability of carboxyl alkyl chain-modified gold nanoparticles
The wettability of organic ligand-capped metal nanoparticles plays a crucial role in determining their behavior in diverse applications, including protein adsorption, protein corona formation, cellular uptake, toxicity, immune system recognition, drug release kinetics, and bioavailability. However, a comprehensive understanding of the size-dependent effects in metal nanoparticles with specific ligand modifications remains elusive. Here, we leverage molecular dynamics simulations to delineate the size-dependent wettability of Au nanocrystals modified with carboxyl-terminated alkyl chains at the same grafting density. Our results reveal a negative correlation between the water contact angle of gold nanoparticles and the radius of the Au-core for a given ligand length. This trend is determined by the spatial arrangement of carboxyl groups, where an increase in the size of Au-core leads to a reduction in the intermolecular spacing between carboxyl groups, promoting the formation of hydrogen bonds between the carboxyl groups and water molecules, thereby conferring a more hydrophilic character to the nanoparticles. Conversely, for a fixed Au-core radius, the water contact angle of nanoparticles increases as the length of alkyl chains increases. This distinct relationship arises from the extended separation between carboxyl groups in longer alkyl ligands, which reduces the hydrogen bond formation with water molecules and renders the nanoparticle more hydrophobic. These findings lay the groundwork for how nanoparticle wettability can be precisely modulated, a critical factor for optimizing their performance in various biomedical and industrial applications.
Minimal pole representation for spectral functions
Representing spectral densities, real-frequency, and real-time Green’s functions of continuous systems by a small discrete set of complex poles is a ubiquitous problem in condensed matter physics, with applications ranging from quantum transport simulations to the simulation of strongly correlated electron systems. This paper introduces a method for obtaining a compact, approximate representation of these functions, based on their parameterization on the real axis and a given approximate precision. We show applications to typical spectral functions and results for structured and unstructured correlation functions of model systems.
Structural comparison of homomolecular systems on surfaces using a fingerprint-based method
This work presents an adaptation of the Smooth Overlap of Atomic Positions (SOAP) method to improve the efficiency of (dis)similarity quantification in homogeneous molecular (homomolecular) systems. SOAP, a fingerprint-based approach, is widely used to measure molecular similarity. We propose variants of SOAP kernels that leverage the structural architecture of homomolecular systems to minimize irrelevant comparisons of atomic environments. To evaluate its performance, we apply this adapted SOAP-based method to a synthetic dataset consisting of two identical tripeptides deposited on a copper surface, simulating different molecular states. The results demonstrate that the adapted method not only improves computational efficiency but also yields more meaningful clustering outcomes by better capturing the key structural differences between states. These findings suggest that the proposed method is well-suited for the study of homomolecular systems, particularly those involving surface interactions, and has the potential to enhance the use of diverse types of molecular modeling and analysis methods that rely on (dis)similarity measures.
Modeling the impact of drug-nanocarriers in lipid membranes
A coarse-grained framework for molecular dynamics (CG-MD) simulations based on the MARTINI force field was developed to tackle interactions between ionic G5 dendrimers and nonionic Pluronic micelles with diverse amphiphilic characters as drug-loaded nanocarriers in contact with two biological membranes, the anionic 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) + 1-palmitoyl-2-oleoyl-glycero-3-phosphatidylglycerol (POPG) and the neutral dipalmitoyl phosphatidylcholine. Simulations showed that drug-nanocarrier stability relies on a delicate balance of their amphiphilic character and Coulombic interactions. Pluronic micelles yielded lower undesired drug leaks into the water phase compared with the cationic G5 dendrimers, which either remained attached to Pluronic moieties or remained between them and the membrane surface. An interesting feature of Pluronic micelles was their tendency to be disrupted and absorbed into the membranes. Hydrophilic micelles showed improved drug stability, avoiding early release of doxorubicin and gemcitabine drugs. When the Pluronic micelles are disrupted and absorbed into the charged membrane, the hydrophilic pluronic segments were depleted toward the membrane surface, retaining the drugs within. Overall, the CG-MD framework yields a detailed molecule-scale picture of the cooperative Coulombic and amphiphilic effects between charged moieties in contact with membrane surfaces.
Additive strategy for nucleation pathway control based on the understanding of molecular size effect on crystallization
Understanding mechanisms involved in particle formation processes is crucial to effectively control crystalline particle characteristics. This study highlights the significant effect of slight changes in molecular size on the crystallization pathway. Molecular dynamics simulations are performed in a binary Lennard-Jones system as a model for systems that undergo two-step nucleation via an intermediate droplet structure. This study analyzed two cases with different solute–solute interaction strengths and found that a larger solute-to-solvent size ratio delayed droplet crystallization in both cases. In systems with strong solute–solute interactions, this delay shifted the pathway from one-step-like to two-step-like nucleation, as droplets with larger solute molecules incorporated more solvent, thereby hindering crystallization. We explained this change in droplet composition by considering the mixing free energy between the solute and solvent. Larger solute molecules form entropically and enthalpically favorable structures by accommodating solvent molecules, which increase the solvent fraction of the droplet. We used a thermodynamic model based on the classical nucleation theory with a core–shell nucleus and revealed that this increased solvent fraction in the droplet lowered the freezing point of the droplet and raised the solid–liquid interfacial tension, ultimately delaying and suppressing crystallization. Based on these findings, we proposed a strategy to control the nucleation pathway using additives. Introducing appropriate additives to modify the stability of intermediates is a promising strategy to control nucleation pathways in various systems.
Noncollinear generalization of nonlocal pure exchange–correlation functionals
We have recently proposed a method for extending collinear functionals to noncollinear functionals, referred to as the multicollinear approach. While previous studies have applied this method to local and semilocal functionals, demonstrating its effectiveness, the present work extends the approach to nonlocal pure functionals via a novel implementation scheme. As an example, we generalize the weighted spin density approximation functional from its original collinear form to a noncollinear one, introducing the first pure functional that is both nonlocal and noncollinear. Our numerical tests demonstrate that the generalized noncollinear functional satisfies the correct collinear limit, preserves spin rotational invariance, provides nonzero local torque, and maintains numerical stability. This work highlights the broad applicability of the multicollinear approach and provides a reference for developing more sophisticated noncollinear functionals beyond local and semilocal forms.
Theoretical investigation into the interaction mechanism of hexavalent americium with covalent organic framework (PyN-DAB)
The separation of radionuclide americium (Am) is a crucial challenge in the reprocessing of spent nuclear fuel, due to the complex speciation. Selective coordination of hexavalent americium [Am (VI)] with covalent organic frameworks (COFs) has emerged as a promising strategy to address this issue. In this work, we employed first-principles simulations combined with density functional theory (DFT) to investigate the adsorption stability of COF (PyN-DAB) for the linear americyl ion AmO22+. Our results demonstrate that COFs can effectively and stably coordinate with Am (VI), highlighting their potential for Am separation. Furthermore, we explored the high-oxidation-state model of AmO22+ complexes with the PyN-DAB ligand to elucidate the underlying microscopic interaction mechanisms between AmO22+ and the PyN-DAB monomer. Comprehensive analyses revealed a strong attraction between the PyN-DAB and AmO22+, which is attributed to the synergistic effects of electrostatic interactions, orbital interactions, and π-electron-rich aromatic rings within the PyN-DAB framework. These findings not only provide fundamental insights into the Am separation process but also offer a novel perspective on the potential applications of COFs in the efficient extraction of actinides. Thus, this study contributes to the ongoing efforts to develop advanced materials for nuclear fuel reprocessing and waste management.
Fast calculation of the permittivities of gold thin films in the frequency range of 0–6 eV
The permittivity tensor of gold nanofilms of different orientations and thicknesses in the frequency range of 0–6 eV is theoretically studied, revealing significant differences from the bulk gold permittivity. Two models are proposed to calculate the longitudinal ɛ‖(h, ω) and transverse ɛ⊥(h, ω) parts of the permittivity tensor in the specified frequency range for gold nanofilms of different thicknesses and surface orientations (001), (110), and (111). These models explain intense peaks in the real and imaginary parts of permittivity at 0–2 eV. The model for calculating the transverse permittivity does not use the Drude model but uses the interband contribution of the bulk material determined through DFT calculations and the contribution of electron motion perpendicular to the nanoslab surface. This contribution takes into account the electron motion inside an infinitely deep one-dimensional potential well with a set of discrete electron levels and makes it possible to calculate the imaginary part of the permittivity using Fermi’s golden rule. The model for calculating the longitudinal permittivity employs an interpolation scheme using the tabulated permittivity of bulk gold and that of several plates with different thicknesses. The difference between experimental permittivity values and those calculated using DFT and the proposed models is discussed. The proposed algorithms enabled a Python program for fast calculation of ɛ⊥(h, ω) and ɛ‖(h, ω) of gold nanofilms of any thickness and above-mentioned orientations in the 0–6 eV range without computationally expensive DFT calculations. This program is included in the supplementary material. The proposed approaches can be easily applied to nanofilms made of other metals.
Gold(I)–N–heterocyclic carbene hydration process; <i>ab initio</i>, DFT, and QM/MM molecular dynamics study
This study investigates the hydration reaction of a gold(I)–N-heterocyclic carbene [Au(I)–NHC] complex at both the quantum mechanical (QM) level and combined Quantum Mechanics/Molecular Mechanics (QM/MM) MD simulations. The main goals are to analyze the differences between implicit (PCM) and explicit solvation models and to compare the advantages and disadvantages of both approaches. Regarding the QM part, the B97D3 and B3PW91 functionals are combined with double-zeta basis sets and the C-PCM/UFF implicit solvation model and compared with the CCSD(T)/TZP computational level supplemented with the C-PCM (COSMO/Klamt radii) or D-PCM/scaled-UAKS solvation model. In addition, reaction force and reaction electronic flux (REF) analyses are performed along the intrinsic reaction coordinate (IRC) determined at the B3PW91/6-31+G(d)/SDD/C-PCM/UFF computational model for deeper insights into the reaction mechanism. Despite relatively high endergonicity, the TS structure is quite close to the center of the reaction coordinate, contrary to the Hammond principle. In the QM/MM MD part of the study, the B97D3 computational setting from the previous part is used as a QM core, and several different explicit water solvation models are explored in the MM environment. The TIP3P water model is compared with the OPC, POL3, TIP4P, and SPCE ones. Nevertheless, they all lead to very low activation barriers and mild endergonicity. Both ΔGr and ΔGa energies are visibly reduced compared to QM values when PCM models are applied. Since partial charges of water atoms within the QM calculations are visibly smaller than point charges in all the explored force-field water models, a modified TIP3P (with partial charges close to DFT RESP values and a LJ parameter conserving the correct water density) is used. In this manner, the energy profile is closer to QM results (with ΔGa = 8.2 and ΔGr = 6.4 kcal mol−1)—especially to the CCSD(T)/TZP/D-PCM/scaled-UAKS model (ΔGa = 14.6 and ΔGr = 9.1). Nevertheless, the hydration process is predicted to be endoergic in all explored models.
Investigating ferromagnetic response in monolayer CVD grown MoS2 flakes using quantum weak measurement
We synthesize MoS2 atomic layer flakes at different growth conditions to tailor S-terminated and Mo-terminated edge defect states that are investigated for their ferromagnetic response. We leverage quantum weak measurement principles to construct a spin Hall effect of light-based magneto-optic Kerr effect (SHEL-MOKE) setup to sense the ultra-small magnetic response from the synthesized atomic layers. We establish that Mo-terminated edge states are the primary source of ferromagnetic response from MoS2 flakes, which is consistent with x-ray photoelectron, Raman, and photoluminescence spectroscopic results. In the process, we demonstrate SHEL-MOKE to be a robust technique to investigate ultra-weak magnetic properties in novel atomic-scale materials. Our findings highlight the importance of controlling edge terminations in engineering magnetism at the nanoscale and underscore the potential of weak value amplification based optical measurements.
Uniaxial ordering by self-assembly of isotropic octahedral junctions
We demonstrate that isotropic octahedral (sixfold branched) junctions with three diagonal end point pairs of different colors almost inevitably form a macroscopic assembly of uniaxial order, exhibiting the perfect order of a single color. Monte Carlo simulations of the antiferromagnetic three-state Potts model on the tripartite reo net, consisting of corner-sharing regular octahedrons, confirm this counterintuitive prediction while showcasing switching self-assembly upon an ordering phase transition. The possible inequivalence of three directions, i.e., more symmetry breaking than uniaxiality, is found and discussed for the ordered phase of this model at finite temperatures. Some additional analyses of the model are provided, including the possibility of a metastable isotropic order, which aligns better with intuition.
Experimental evidences for the correlation between chair-to-chair conversion and dynamic fragility in poly(cyclohexyl methacrylate)/hindered phenol blends
Polymers with cyclic or ring topologies are typically endowed with unusual molecular dynamics considerably different from their linear or branched counterparts. Here, the primary and secondary dynamics of neat poly(cyclohexyl methacrylate) (PCHMA) and its blends with hindered phenols were systematically investigated by a combination of dielectric and enthalpy relaxation. Notably, neat PCHMA owns a glass transition temperature Tg ∼ 299 K, while the segmental fragility m can be as low as about 42. After introducing hindered phenols capable of forming intermolecular hydrogen bonds, m increases in the same direction as Tg. Surprisingly, the observed increase in segmental fragility exhibits a strong correlation with the suppression of the dielectric γ-relaxation process, which has been previously attributed to chair-to-chair transitions of the cyclohexyl side groups. The concomitant decrease in accessible configurational states is further evidenced by enthalpy relaxation. We suppose that the γ-relaxation may involve less degree of intermolecular freedom, which can be speculated from its increased activation energy that is comparable to that of the Johari–Goldstein secondary process, as well as the broadened γ-peak breadth. These results provide solid experimental evidence that a correlation does exist between the conformational change and fragility and therefore pave a new routine to fabricate strong polymeric glass formers by introducing the ring-containing topology structures.
Isomers and band assignments in the cryogenic vibrational spectrum of the binary complex between water and protonated formic acid using two color, IR–IR photobleaching and H/D isotopic substitution
Protonated formic acid (PFA) is purported to be the active species in the catalytic activation of condensation reactions at the acidic interface of microdroplets. Here, we investigate the fundamental interaction between PFA and water with cryogenic ion vibrational spectroscopy of the binary PFA–H2O complexes generated via electrospray ionization followed by buffer gas cooling to about 20 K. The patterns displayed by the isomer-specific IR spectra of D2-tagged PFA–H2O indicate that two distinct, non-interconverting rotamers are present at low temperatures based on the cis and trans structures of the HCO2H2+ core ion. Both of these occur with the water molecule attached to the OH that is in a cis-configuration relative to the CH group (denoted E), but differ in the E vs Z (cis vs trans relative to the CH group) orientation of the spectator OH. This assignment scheme corrects a previous theoretical analysis that invoked a scenario in which structures with E- and Z-bound water molecules interconvert at low (20 K) temperatures. Isomer-specific bands arising from the OH stretches and water bending modes are deconvoluted using isotopomer-specific spectroscopy of the complexes with partial H/D exchange. The dependence of the nominal shared proton OH stretch frequency on the deuteration of the tethered water confirms strong coupling between this mode and the water bending fundamental.
Dynamic fluctuations in a highly cross-linked polybutadiene rubber
Using a combined approach of different neutron scattering techniques that allows experimental separation of the self and collective dynamics, we investigated the various types of motion in a highly cross-linked 1,2-polybutadiene rubber. As a reference, the neat, fully deuterated melt was also studied. In the latter, the collective segmental relaxation around the structure factor peak S(Qmax) exhibits pronounced de Gennes narrowing, with a collective relaxation time τc(Q) that increases without plateauing toward lower momentum transfers Q. Apparently, due to the very bulky monomer structure, the correlation length ξc for the crossover to viscoelastic homogeneity is unusually large. In the highly cross-linked d1,2-PB rubber, the original structure factor peak of the pure d1,2-PB is significantly reduced. Instead, a strong low-Q peak emerges, which we attribute to correlations between the hydrogen-containing cross-linkers. Both the collective d1,2-PB relaxation rates around the former S(Qmax) and the relaxation around the new crosslink correlation peak are significantly slowed down compared to the neat melt. Finally, the cross-linking strands exhibit their own fast dynamics, which is well described by diffusion within a spherical Gaussian well, with a corresponding radius R ≅ 4 Å.
Static and dynamic theory of polarization under internal and directing electric fields: Fixed-charge and fixed-potential conditions
We present a continuum theory on statics and dynamics of polar fluids, where the orientational polarization p1 and the induced polarization p2 are governed by the Onsager directing field Ed and the Lorentz internal field F, respectively. We start with a dielectric free energy functional F with a cross term ∝∫drp1 · p2, which was proposed by Felderhof [J. Phys. C: Solid State Phys. 12, 2423 (1979)]. With this cross-coupling, our theory can yield the theoretical results by Onsager and Kirkwood. We also present dynamic equations using the functional derivatives δF/δpi to calculate the space-time correlations of pi. We then obtain analytic expressions for various frequency-dependent quantities, including the Debye formula. We find that the fluctuations of the total polarization drastically depend on whether we fix the electrode charge or the applied potential difference between parallel metal electrodes. In the latter fixed-potential condition, we obtain a nonlocal (long-range) polarization correlation inversely proportional to the cell volume V, which is crucial to understanding the dielectric response. It is produced by nonlocal charge fluctuations on the electrode surfaces and is sensitive to the potential drops in the Stern layers in small systems. These nonlocal correlations in the bulk and on the surfaces are closely related due to the global constraint of fixed potential difference. We also add some results in other boundary conditions, including the periodic one, where nonlocal correlations also appear.
Brownian motion of snowman-shaped colloidal particles
We investigate the Brownian motion of isolated snowman-shaped particles consisting of pairs of large and small spheres by video microscopy. Our observations reveal that the particle exhibits varying degrees of anisotropic translational diffusion depending on the reference point used for tracking. In particular, when tracking the snowman’s geometrical center, the diffusion coefficient along the particle’s long axis (Da) is greater than that along the short axis (Db). When tracking the large sphere’s center, Da and Db are identical, while tracking the small sphere’s center results in Da being smaller than Db. Since Da remains constant across these geometrical centers, the higher Db thus leads to the fastest diffusion for the small sphere’s center. These differences in diffusion arise from the varying coupling between translational and rotational motions, determined by the tracking points relative to the center of hydrodynamic stress (CoH). The CoH has been experimentally confirmed to be the geometrical center of the snowman-shaped particle. Our findings are consistent with the Langevin theory for the Brownian motion of anisotropic particles.
Higher order relationships in the canonical ensemble for local reactivity indices
In this paper, higher order relations derived from the canonical ensemble N,νr⃗ are presented in the framework of Density Functional Theory (DFT), with a focus on the Fukui function [f(r⃗)], dual descriptor [f2(r⃗)], and the function t(r⃗) introduced by Fuentealba and Parr. These relationships extend existing theoretical models, providing a more detailed understanding of local and non-local chemical reactivity. The equations developed establish direct connections between higher order reactivity indices, such as hyperhardness (γ), the fourth order energy function f3r⃗, and non-local response functions, offering new insights into the activation and deactivation of molecular systems under external perturbations. These findings are particularly relevant in the study of activation processes by the presence of n bodies generating external perturbations. The results highlight the fundamental role of higher-order kernels in describing changes in reactivity, contributing to the development of a more refined theoretical framework in conceptual DFT.
Depicting a neoteric family of biocompatible ionic liquids: A look through a molecular dynamics prism
The organization of Ionic Liquids (ILs) at the nanoscale has been demonstrated to be invaluable knowledge to understand and even rationally develop novel applications. In this line, this work aims at the deeper structural comprehension of five model ionic solvents from the recently presented family of biocompatible ILs based on cholinium cation ([Ch]+) and peptide anions ([Pep]−). To do this, a molecular dynamics approach was employed. The use of different [Pep]− allowed us to evaluate the influence of (i) incrementing an oligopeptide chain through the glycyl (Gly) unit and (ii) employing a more complex functionalization based on the phenylalanyl (Phe) group. The simulations show that the additional peptide group from [Ch][Pep] adds a new anchoring point for inter-anionic association through H-bonding, and while the peptide hydrogen is interacting with other anions, the peptide oxygen seems to approach cation charged centers. This stronger H-bonding grid may explain the boost in viscosity observed when transitioning from [Ch][AA] to [Ch][Pep]. On the other hand, the nano-segregation of ILs built with Phe is distinguished by two continuous mesophases, polar and apolar. Both these networks have their impact on each other since, when the peptide chain is incremented from 1 to 2 Phe residues, (i) the polar domain is slightly less continuous and (ii) the apolar one presents different phenyl ring (Pher) solvation profiles depending on their position in the peptide chain. In addition, the edge-to-face configurations dominate the Pher–Pher aggregation, suggesting an electrostatic influence in the internal organization of this domain, and π–cation complexes appear to disturb apolar accumulation.
Spin-polarized alkali-metal trimers revisited
Homonuclear spin-polarized alkali-metal trimers in their lowest-lying electronic state are investigated theoretically. Their equilibrium geometries and binding energies are determined with the state-of-the-art quantum chemical methods at three levels of approximation. The equilibrium geometries obtained Req(Li3) = 3.100 Å, Req(Na3) = 4.353 Å, Req(K3) = 4.996 Å, Req(Rb3) = 5.391 Å, and Req(Cs3) = 5.730 Å are compared to the other theoretical results and also to the very recent experimental results obtained through the laser-induced Coulomb explosion. Further theoretical studies are proposed, which could help with better interpretation of the experimental results for the sodium and cesium trimers.
From all-atom to rigid monomer treatment of molecular clusters
Given a system of M molecular monomers, represented with a presumably accurate all-atom potential energy surface (PES), V(r), we partition the configuration space by setting a one-to-one correspondence r ↔ (R, q), where R describes the centers and orientations of all the M monomers and q describes all the vibrational intra-molecular degrees of freedom. We then define a temperature-dependent free-energy surface of the corresponding rigid monomer system, F(R;T), by averaging over the intra-molecular degrees of freedom. F(R;T) is here estimated directly using the local harmonic approximation. While conceptually simple and numerically inexpensive, the coarse-grained PES defined in this manner turns out to be surprisingly accurate for the model systems considered, namely water and ammonia clusters. The proposed framework can be used in a more general context for local rigidification of other molecular systems in non-uniform environments.