skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


This content will become publicly available on May 26, 2026

Title: Synergistic Density Functional Theory and Molecular Dynamics Approach to Elucidate PNIPAM–Water Interaction Mechanisms
This study employs Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations to investigate interactions between water molecules and Poly(Nisopropylacrylamide) (PNIPAM). DFT reveals preferential water binding sites, with enhanced binding energy observed in the linker zone. Quantum Theory of Atoms in Molecules (QTAIM) and electron localization function (ELF) analyses highlight the roles of hydrogen bonding and steric hindrance. MD simulations unveil temperature-dependent hydration dynamics, with structural transitions marked by changes in the radius of gyration (Rg) and the radial distribution function (RDF), aligning with DFT findings. Our work goes beyond prior studies by combining a DFT, QTAIM and MD simulations approach across different PNIPAM monomer-to-30mer structures. It introduces a systematic quantification of pseudo-saturation thresholds and explores water clustering dynamics with structural specificity, which have not been previously reported in the literature. These novel insights establish a more complete molecular-level picture of PNIPAM hydration behavior and temperature responsiveness, emphasizing the importance of amide hydrogen and carbonyl oxygen sites in hydrogen bonding, which weakens above the lower critical solution temperature (LCST), resulting in increased hydrophobicity and paving the way for understanding water sorption mechanisms, offering guidance for future applications such as dehumidification and atmospheric water harvesting.  more » « less
Award ID(s):
2318720
PAR ID:
10639225
Author(s) / Creator(s):
; ; ; ; ; ;
Publisher / Repository:
MDPI
Date Published:
Journal Name:
Materials
ISSN:
1996-1944
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. A classical model in the framework of the INTERFACE force field has been developed for treating the LiCoO$$_2$$ (LCO) (001)/water interface. In comparison to {\em ab initio} molecular dynamics (MD) simulations based on density functional theory, MD simulations using the classical model lead to generally reliable descriptions of interfacial properties, such as the density distribution of water molecules. Water molecules in close contact with the LCO surface form a strongly adsorbed layer, which leads to a free energy barrier for the absorption of polar or charged molecules to the LCO surface. Moreover, due to the strong hydrogen bonding interactions with the LCO surface, the first water layer forms an interface that exhibits hydrophobic characters, leading to favorable adsorption of non-polar molecules to the interface. Therefore, despite its highly polar nature, the LCO (001) surface binds not only polar/charged but also non-polar solutes. As an application, the model is used to analyze the adsorption of reduced nicotinamide adenine dinucleotide (NADH) and its molecular components to the LCO (001) surface in water. The results suggests that recently observed redox activity of NADH at the LCO/water interface was due to the co-operativity between the ribose component, which drives binding to the LCO surface, and the nicotinamide moiety, which undergoes oxidation. 
    more » « less
  2. A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a −1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2. 
    more » « less
  3. Abstract Achieving selective molecular recognition of hydrophilic anions in water remains a formidable challenge due to the competitive nature of water and the high hydration energies of target anions such as sulfate. Here, we report the design, synthesis, and characterization of a simple dicationic tetralactam macrocycle (BPTL2⁺·2Cl⁻) capable of binding highly hydrated anions in water via charge‐assisted hydrogen bonding. Structural, spectroscopic, thermodynamic, and computational studies reveal that BPTL2⁺ exhibits a strong binding affinity for sulfate (Ka = 2892 M⁻¹), driven primarily by entropic gain from water release and reinforced by electrostatic and hydrogen bonding interactions. Single‐crystal X‐ray diffraction and DFT‐optimized structures confirm the formation of directional [N─H•••O] and [C─H•••O] hydrogen bonds. Comparative studies with a control macrocycle (6Na+•HCTL6−) that has a charge‐neutral binding cavity underscore the essential role of cationic charge in overcoming desolvation enthalpic penalties. The receptor displays anti‐Hofmeister selectivity, preferentially binding more hydrophilic anions. This work provides fundamental insights into the mechanisms of anion recognition in water. It establishes charge‐assisted hydrogen bonding as a powerful strategy for developing next‐generation receptors for sensing, separation, sequestration, transport, and catalysis in aqueous environments. 
    more » « less
  4. The hydration shells of proteins mediate interactions, such as small molecule binding, that are vital to their biological function or in some cases their dysfunction. However, even when the structure of a protein is known, the properties of its hydration environment cannot be easily predicted due to the complex interplay between protein surface heterogeneity and the collective structure of water’s hydrogen bonding network. This manuscript presents a theoretical study of the influence of surface charge heterogeneity on the polarization response of the liquid water interface. We focus our attention on classical point charge models of water, where the polarization response is limited to molecular reorientation. We introduce a new computational method for analyzing simulation data that is capable of quantifying water’s collective polarization response and determining the effective surface charge distribution of hydrated surfaces over atomistic length scales. To illustrate the utility of this method, we present the results of molecular dynamics simulations of liquid water in contact with a heterogeneous model surface and the CheY protein. 
    more » « less
  5. Zwitterionic materials are an important class of antifouling biomaterials for various applications. Despite such desirable antifouling properties, molecular-level understanding of the structure–property relationship associated with surface chemistry/topology/hydration and antifouling performance still remains to be elucidated. In this work, we computationally studied the packing structure, surface hydration, and antifouling property of three zwitterionic polymer brushes of poly(carboxybetaine methacrylate) (pCBMA), poly(sulfobetaine methacrylate) (pSBMA), and poly((2-(methacryloyloxy)ethyl)phosporylcoline) (pMPC) brushes and a hydrophilic PEG brush using a combination of molecular mechanics (MM), Monte Carlo (MC), molecular dynamics (MD), and steered MD (SMD) simulations. We for the first time determined the optimal packing structures of all polymer brushes from a wide variety of unit cells and chain orientations in a complex energy landscape. Under the optimal packing structures, MD simulations were further conducted to study the structure, dynamics, and orientation of water molecules and protein adsorption on the four polymer brushes, while SMD simulations to study the surface resistance of the polymer brushes to a protein. The collective results consistently revealed that the three zwitterionic brushes exhibited stronger interactions with water molecules and higher surface resistance to a protein than the PEG brush. It was concluded that both the carbon space length between zwitterionic groups and the nature of the anionic groups have a distinct effect on the antifouling performance, leading to the following antifouling ranking of pCBMA > pMPC > pSBMA. This work hopefully provides some structural insights into the design of new antifouling materials beyond traditional PEG-based antifouling materials. 
    more » « less