Zhaoru Sun

Ab initio molecular dynamics provides a first-principles framework for aqueous systems but is limited in accuracy by self-interaction error (SIE) in exchange-correlation functionals. While SIE corrections are known to reduce the over-structured hydrogen bonding in bulk water, their impact on ion hydration remains unclear. Here, we employ machine learning molecular dynamics to systematically compare the Perdew–Burke–Ernzerhof functional with Tkatchenko–Scheffler–van der Waals dispersion correction and the strongly constrained and appropriately normed (SCAN) functional, thereby investigating the effects of different treatments of exchange-correlation (including SIE) on the hydration structure and electronic properties of Na+ and Cl− in aqueous solutions. We find that the SCAN functional yields a more ordered and compact first hydration shell of Na+, while leaving the orientational distribution of water molecules largely unchanged. In contrast, for Cl−, the Cl–water correlation of the first hydration shell remains nearly unchanged, whereas the orientational distribution of surrounding water molecules is significantly modified. Charge density analysis reveals that these differences originate from ion-dependent electronic responses: the charge density is more localized around Na+ under the SCAN description, strengthening Na+–water interactions, whereas Cl− is comparatively less affected. These results reveal that ion-specific hydration responses are governed by electronic structure effects, particularly charge-density differences associated with reduced SIE, and highlight the importance of accurate treatment of electronic structure in aqueous simulations.

Antifreeze glycoproteins (AFGPs) are among the most potent ice recrystallization inhibition (IRI) agents, yet the molecular basis for their counterintuitive decline in activity with increasing glycosylated threonine (T*) content remains unresolved. Through molecular dynamics simulations of model glycoproteins with increasing T* content, we show that the potent IRI activity of AFGPs arises not only from the thermodynamic stability of strong ice-binding states but also from their kinetic accessibility. Specifically, the free energy barrier for forming strong ice-binding states from the unbound state constitutes a critical kinetic bottleneck. Increasing the T* content enhances the overall hydration capacity due to the additional glycan moieties, thereby imposing a greater desolvation penalty and elevating the adsorption barrier. This kinetic limitation, rather than the absence of strong ice-binding states, accounts for the observed decline in the IRI activity. To quantify the structural basis of this behavior, we introduce a facial amphiphilicity index that integrates both spatial segregation and compositional ratio of hydrophilic and hydrophobic residues and show that it correlates well with IRI activity. These findings highlight that facial amphiphilicity mediates a critical balance between binding stability and kinetic accessibility, providing a rational design principle for advanced IRI materials.

Oligoproline is a simple yet highly potent cryoprotectant, but the molecular basis underlying its nonmonotonic ice recrystallization inhibition (IRI) activity depending on the degree of polymerization (DP)─particularly the superior performance of DP = 8 (P8) over longer (e.g., P15) oligomers─remains elusive. Using molecular dynamics simulations, we show that the IRI activity originates from the combined effect of single-molecule conformation and multimolecule aggregation. P8 outperforms P15 primarily due to its higher proportion of the random coil (C) conformation, which effectively enhances ice-binding ability and resistance to ice engulfment than the linear (L) conformation with perfect PPII helix. Moreover, at high concentrations (>40 mg/mL), P15 tends to form soluble amorphous aggregates, reducing its effective coverage on the ice surface and thereby further diminishing its IRI efficiency. These findings provide atomistic insight into the structure-activity relationship of oligoprolines and offer a framework for understanding similar nonmonotonic effects in other antifreeze polymers.

Fluorite oxides such as HfO$_2$ exhibit rich and tunable phase behavior, making them promising candidates for next generation electronic devices. A key challenge is to design amorphous HfO$_2$-based high-$k$ materials with both structural and performance stability. Here, using molecular dynamics simulations supported by experimental measurements, we reveal that Ba doping stimulates a polyamorphic transition in HfO$_2$, yielding a semi-ordered amorphous (SA) phase characterized by disordered oxygens embedded within an ordered metal sublattice. We find that this phase arises from degenerate short-range symmetry breaking modes, consistent with Pauling's parsimony rule. Notably, the SA structure is thermodynamically stable and displays a wider bandgap and higher dielectric constant than conventional random-packing amorphous structure, owing to suppressed subgap states and increased Born effective charges. We further demonstrate that this structural motif generalizes to Ba-, Sr-, and Ca-doped HfO$_2$ and ZrO$_2$, establishing a broadly applicable strategy for designing high-performance amorphous dielectrics.

Carbonic acid (H ₂ CO ₃ ), rather than water, serves as the primary protonating buffer regulating pH in biological systems and oceans. Its dissociation dynamics, driven by three conformers—cis-cis (CC), cis-trans (CT), and trans-trans (TT)—pose substantial experimental and theoretical challenges. Using deep potential molecular dynamics simulations with ab initio accuracy, we explored the dissociation dynamics of H ₂ CO ₃ in solution on the nanosecond timescale. While the CC conformer is the most abundant, the CT conformer is the dominant proton donor. This enhanced deprotonation ability arises from the CT conformer’s involvement in more hydrogen-bonding ring structures, enabling diverse proton transfer pathways, and its greater electronic asymmetry, which increases hydrophilicity and destabilizes the hydroxyl group. Furthermore, protons dissociated from the CT conformer demonstrate a stronger preference for the homing pathway. Our findings underscore the critical role of the topology and electronic properties of the CT conformer in aqueous H ₂ CO ₃ dissociation and proton transfer.

Nanofluidics exhibits ultrafast transport, highly sensitive to confinement size and surface interactions. This transport behavior is particularly prominent in graphene nanoslits, but its molecular origin remains elusive. Here, we utilize machine learning-based molecular dynamics simulations with ab initio accuracy to probe water transport between graphene sheets. We find that interlayer distance (H)-dependent transport variations result from the competition between parallel transport and fluctuations perpendicular to sheet, a universal mechanism across various graphene surfaces, regardless of strain. At H ≤ 12.5 Å, large variations are dominated by the parallel transport of the interfacial layer, stemming from the distribution of severely undercoordinated “fast water”. At H > 12.5 Å, variations become subtler as increased intermediate water leads to more perpendicular fluctuations. Moreover, we demonstrate that reducing interfacial friction at specific confinement sizes can further enhance nanofluidic transport several times over. Our findings suggest an effective strategy for regulating nanofluidic transport.

QAPPT shares a similar chemical structure with QAQPP but exhibits higher OH⁻ conductivity due to larger ion-conducting channels, resulting from greater fluctuations in water-sensitive phenyl rings.

The antifreeze mechanism of antifreeze glycoproteins (AFGPs) remains incompletely understood, which limits the design of new antifreeze molecules for practical applications. For instance, the ice growth inhibition of AFGP8 (the shortest AFGPs) is primarily driven by hydrophobic methyl and hydrogen-bonding hydroxyl groups. However, altering the C3-β linkage in the disaccharide moiety of AFGP8, denoted as variant GP8-LacNAc, significantly reduces its antifreeze activity. This challenges the conventional understanding of the antifreeze activity of AFGP8 because no group is removed. Here, we revisit the antifreeze mechanism using molecular dynamics simulations of two AFGPs as an example, revealing the relation between conformation, ice-binding group, and ice growth inhibition activity. The PPII helix is not the reason for the weak activity of GP8-LacNAc, while the cooperativity of the conformation and group matters. AFGP8 maintains a dominant conformation with all four disaccharides on the same side, which maximizes the binding with ice. While GP8-LacNAc undergoes frequent conformational transitions, leading to a methyl-hydroxyl distance mismatch with the ice surface. Our results reveal the cooperative role of conformation and ice-binding groups, providing new insights into the antifreeze mechanism of flexible proteins.