Michael L Klein

Covalent and non-covalent molecular binding are two strategies to tailor surface properties and functions. However, the lack of responsiveness and requirement for specific binding groups makes spatiotemporal control challenging. Here, we report the adaptive insertion of a hydrophobic anchor into a poly(ethylene glycol) (PEG) host as a non-covalent binding strategy for surface functionalization. By using polycyclic aromatic hydrocarbons as the hydrophobic anchor, hydrophilic charged and non-charged functional modules were spontaneously loaded onto PEG corona in 2 min without the assistance of any catalysts and binding groups. The thermodynamically favourable insertion of the hydrophobic anchor can be reversed by pulling the functional module, enabling programmable surface functionalization. We anticipate that the adaptive molecular recognition between the hydrophobic anchor and the PEG host will …

Transition metal oxide materials are of great utility, with a diversity of topical applications ranging from catalysis to electronic devices. Because of their widespread importance in materials science, there is increasing interest in developing computational tools capable of reliable prediction of transition metal oxide phase behavior and properties. The workhorse of materials theory is density functional theory (DFT). Accordingly, we have investigated the impact of various correlation and exchange approximations on their ability to predict the properties of NiO using DFT. We have chosen NiO as a particularly challenging representative of transition metal oxides in general. In so doing, we have provided validation for the use of the r2SCAN density functional for predicting the materials properties of oxides. r2SCAN yields accurate structural properties of NiO and a local spin moment that notably persists under pressure …

The diffusivity of water in aqueous cesium iodide solutions is larger than that in neat liquid water and vice versa for sodium chloride solutions. Such peculiar ion-specific behavior, called anomalous diffusion, is not reproduced in typical force field based molecular dynamics (MD) simulations due to inadequate treatment of ion–water interactions. Herein, this hurdle is tackled by using machine learned atomic potentials (MLPs) trained on data from density functional theory calculations. MLP based atomistic MD simulations of aqueous salt solutions reproduce experimentally determined thermodynamic, structural, dynamical, and transport properties, including their varied trends in water diffusivities across salt concentration. This enables an examination of their intermolecular structure to unravel the microscopic underpinnings of the differences in their transport properties. While both ions in CsI solutions contribute to the …

Water is an integral component in electrochemistry, in the generation of the electric double layer, and in the propagation of the interfacial electric fields into the solution; however, probing the molecular-level structure of interfacial water near functioning electrode surfaces remains challenging. Due to the surface-specificity, sum-frequency-generation (SFG) spectroscopy offers an opportunity to investigate the structure of water near working electrochemical interfaces but probing the hydrogen-bonded structure of water at this buried electrode–electrolyte interface was thought to be impossible. Propagating the laser beams through the solvent leads to a large attenuation of the infrared light due to the absorption of water, and interrogating the interface by sending the laser beams through the electrode normally obscures the SFG spectra due to the large nonlinear response of conduction band electrons. Here, we show …

The dielectric permittivity of salt water decreases on dissolving more salt. For nearly a century, this phenomenon has been explained by invoking saturation in the dielectric response of the solvent water molecules. Herein, we employ an advanced deep neural network (DNN), built using data from density functional theory, to study the dielectric permittivity of sodium chloride solutions. Notably, the decrease in the dielectric permittivity as a function of concentration, computed using the DNN approach, agrees well with experiments. Detailed analysis of the computations reveals that the dominant effect, caused by the intrusion of ionic hydration shells into the solvent hydrogen-bond network, is the disruption of dipolar correlations among water molecules. Accordingly, the observed decrease in the dielectric permittivity is mostly due to increasing suppression of the collective response of solvent waters.

The dielectric constant is one of the most important properties of salt water, which determines the Coulomb interactions between the solution components and therefore regulates the microstructures and the physicochemical properties of the solution. Since the last century, it has been widely reported in experiments that the dielectric constant of salt solutions decreases nonlinearly with increasing solute concentration, a phenomenon called dielectric decrement. In this work, we study the dielectric decrement using the advanced deep potential long range (DPLR) method, which enables efficient ab initio-level simulations. Moreover, DPLR includes long-range electrostatic interactions explicitly, which is essential for the correct description of long-range dipole-dipole interactions. The computed dielectric constant agrees well with experimental data. The detailed analyses indicate that the dielectric decrement is mostly due …

The dielectric permittivity of salt water decreases on dissolving more salt. For nearly a century, this phenomenon has been explained by invoking saturation in the dielectric response of the solvent water molecules. Herein, we employ an advanced deep neural network (DNN), built using data from density functional theory, to study the dielectric permittivity of sodium chloride solutions. Notably, the decrease in the dielectric permittivity as a function of concentration, computed using the DNN approach, agrees well with experiments. Detailed analysis of the computations reveals that the dominant effect, caused by the intrusion of ionic hydration shells into the solvent hydrogen-bond network, is the disruption of dipolar correlations among water molecules. Accordingly, the observed decrease in the dielectric permittivity is mostly due to increasing suppression of the collective response of solvent waters.

An adaptive surface that can sense and respond to environmental stimuli is integral to smart functional materials. Here, we report pH-responsive anchoring systems onto the poly(ethylene glycol) (PEG) corona of polymer vesicles. The hydrophobic anchor, pyrene, is reversibly inserted into the PEG corona through the reversible protonation of its covalently linked pH-sensing group. Depending on the pKa of the sensor, the pH-responsive region is engineered from acidic to neutral and basic conditions. The switchable electrostatic repulsion between the sensors contributes to the responsive anchoring behavior. Our findings provide a new responsive binding chemistry for the creation of smart nanomedicine and a nanoreactor.

The mission of the DOE Energy Frontier Research Centers CCDM (2014-2018) and CCM (2018-2021) was to theoretically develop, computationally apply, and experimentally validate electronic structure methods for all materials, with a focus on the complex materials, especially layered and two-dimensional materials, strongly-correlated materials, and liquid water. This was achieved by over 200 published journal articles authored by about 17 senior investigators from physics and chemistry and from theory, computation, and experiment, plus their collaborators. In particular, the Centers confirmed the predictive power of the SCAN (strongly constrained and appropriately normed) density functional, which was constructed to satisfy 17 known exact constraints and several appropriate norms. Without being fitted to real bonded systems, and at a modest computational cost, SCAN correctly predicted covalent, ionic, metallic, hydrogen, and van der Waals bonds in many challenging materials. SCAN gave an improved description of defects in semiconductors, surface properties of metals, seven phases of ice, liquid water, liquid and supercooled silicon, subtle structural distortions in ferroelectrics, formation energies and structural predictions for solids, and critical pressures for structural phase transitions. Perhaps most remarkably, SCAN correctly described some strongly-correlated materials that were previously believed to be beyond the reach of density-functional approximations. SCAN is the only density functional that correctly predicts the band gap closing under chemical doping of the cuprate high-temperature superconducting materials. SCAN also …

The accurate spatial segregation into distinct phases within cell membranes coordinates vital biochemical processes and functionalities in living organisms. One of nature’s strategies to localize reactivity is the formation of dynamic raft domains. Most raft models rely on liquid-ordered L0 phases in a liquid-disordered Ld phase lacking correlation and remaining static, often necessitating external agents for phase separation. Here, we introduce a synthetic system of bicomponent glycodendrimersomes coassembled from Janus dendrimers and Janus glycodendrimers (JGDs), where lactose–lactose interactions exclusively drive lateral organization. This mechanism results in modulated phases across two length scales, yielding raft-like microdomains featuring nanoarrays at the nanoscale. By varying the density of lactose and molecular architecture of JGDs, the nanoarray type and size, shape, and spacing of the …

Vitamin E acetate, which is used as a diluent of tetrahydrocannabinol (THC), has been reported as the primary causative agent of e-cigarette, or vaping, product use-associated lung injury (EVALI). Here, we employ in vitro assays, docking, and molecular dynamics (MD) computer simulations to investigate the interaction of vitamin E with the membrane-bound cannabinoid 2 receptor (CB2R), and its role in modulating the binding affinity of THC to CB2R. From the MD simulations, we determined that vitamin E interacts with both CB2R and membrane phospholipids. Notably, the synchronized effect of these interactions likely facilitates vitamin E acting as a lipid modulator for the cannabinoid system. Furthermore, MD simulation and trajectory analysis show that when THC binds to CB2R in the presence of vitamin E, the binding cavity widens, facilitating the entry of water molecules into it, leading to a reduced interaction of THC with CB2R. Additionally, the interaction between THC and vitamin E in solution is stabilized by several H bonds, which can directly limit the interaction of free THCs with CB2R. Overall, both the MD simulations and the in vitro dissociation assay results indicate that THC binding to CB2R is reduced in the presence of vitamin E. Our study discusses the role of vitamin E in limiting the effect of THCs and its implications on the reported pathology of EVALI.

Polyethylene is a material with a range of applications which depend less on its intrinsic chemistry and more upon its structure on the nano-to micro-meter scale. Low-density polyethylene, with its more open, disordered structure and yields softer, more ductile materials. High-density and ultra-high molecular weight polyethylene (UHMWPE) can be used to make materials strong enough to for body armor and soldier protection. It is therefore paramount to understand how the mechanical properties of UHMWPE depend on its microstructure and how defects can impair the strength and lead to material failure. This is a difficult task however, given that we require a potential which can model bond breaking while being efficient and accurate enough to simulate bulk PE over nanosecond timescales. We have thus trained a neural network potential (NNP) based on the SCAN density functional potential energy surface which …

SARS-CoV-2 has raised the alarm to search for effective therapy for this virus. To date several vaccines have been approved but few available drugs reported recently still need approval from FDA. Remdesivir was approved for emergency use only. In this report, the SARS-CoV-2 3CLpro was expressed and purified. By using a FRET-based enzymatic assay, we have screened a library consisting of more than 300 different niclosamide derivatives and identified three molecules JMX0286, JMX0301, and JMX0941 as potent allosteric inhibitors against SARS-CoV-2 3CLpro, with IC50 values similar to that of known covalent inhibitor boceprevir. In a cell-based antiviral assay, these inhibitors can inhibit the virus growth with EC50 in the range of 2–3 μM. The mechanism of action of JMX0286, JMX0301, and JMX0941 were characterized by enzyme kinetics, affinity binding and protein-based substrate digestion. Molecular …

Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. Contact angles at the alumina (0001) and (112‾0) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces. Translational and rotational dynamics of interfacial water molecules are slower than in bulk water. Hydrogen bonds between water and both surfaces are asymmetric, water-to-aluminol ones are stronger than aluminol-to-water ones. Molecular dynamics simulations eliminate the impacts of surface contamination when measuring contact angles and the results reveal the microscopic origin of the macroscopic superhydrophilicity of alumina surfaces: strong water-to-aluminol hydrogen bonds.

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulations with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. An elastic network model was adopted to maintain the secondary structure within a single chain. The side-chain analogues reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable association free energy (potential of mean force) in …

Metal-chelating ligands such as nitrilotriacetic acid (NTA) bind to polyhistidine-tagged (His-tagged) proteins. Lipids conjugated to NTA are widely used to decorate the surface of liposomes with proteins in cell biology applications. Multivalent NTA ligands such as tris-nitrilotriacetic acid (TrisNTA) display higher affinities than the monovalent NTA when co-assembled with phospholipids and cholesterol in liposomes. However, there is a limited number of available lipids conjugated to NTA and only few are commercially available. Additionally, their activity diminishes during storage or upon exposure to air. Here we report a library of five amphiphilic Janus dendrimers conjugated to NTA (JD-NTA) and three to TrisNTA (JD-TrisNTA). Both JD-NTA and JD-TrisNTA are indefinitely stable at room temperature in air and preliminary results demonstrate that they co-assemble with phospholipids and cholesterol into liposomes …

The cannabinoid receptors CB1R and CB2R are members of the G protein-coupled receptor (GPCR) family. These receptors have recently come to light as possible therapeutic targets for conditions affecting the central nervous system. However, because CB1R is known to have psychoactive side effects, its potential as a drug target is constrained. Therefore, targeting CB2R has become the primary focus of recent research. Using various molecular modeling studies, we analyzed the active, inactive, and intermediate states of both CBRs in this study. We conducted in-depth research on the binding properties of various groups of cannabinoid modulators, including agonists, antagonists, and inverse agonists, with all of the different conformational states of the CBRs. The binding effects of these modulators were studied on various CB structural features, including the movement of the transmembrane helices, the volume of the binding cavity, the internal fluids, and the important GPCR properties. Then, using in vitro experiments and computational modeling, we investigated how vitamin E functions as a lipid modulator to influence THC binding. This comparative examination of modulator binding to CBRs provides significant insight into the mechanisms of structural alterations and ligand affinity, which can directly help in the rational design of selective modulators that target either CB1R or CB2R.

Traditional farming lifestyle has been shown to be protective against asthma and allergic diseases. The individual factors that appear to be associated with this “farm-life effect” include consumption of unpasteurized farm milk and exposure to farm animals and stables. However, the biomarkers of the protective immunity and those associated with early development of allergic diseases in infancy remain unclear. The “Zooming in to Old Order Mennonites (ZOOM)” study was designed to assess the differences in the lifestyle and the development of the microbiome, systemic and mucosal immunity between infants born to traditional farming lifestyle at low risk for allergic diseases and those born to urban/suburban atopic families with a high risk for allergic diseases in order to identify biomarkers of development of allergic diseases in infancy. 190 mothers and their infants born to Old Order Mennonite population protected from or in Rochester families at high risk for allergic diseases were recruited before birth from the Finger Lakes Region of New York State. Questionnaires and samples are collected from mothers during pregnancy and after delivery and from infants at birth and at 1-2 weeks, 6 weeks, 6, 12, 18 and 24 months, with 3-, 4- and 5-year follow-up ongoing. Samples collected include maternal blood, stool, saliva, nasal and skin swabs and urine during pregnancy; breast milk postnatally; infant blood, stool, saliva, nasal and skin swabs. Signs and symptoms of allergic diseases are assessed at every visit and serum specific IgE is measured at 1 and 2 years of age. Allergic diseases are diagnosed by clinical history, exam, and sensitization by skin …

Sodium chloride (NaCl) solutions, also known as saltwater, are ubiquitous in nature. Understanding the effect of the dissolved Na+ and Cl-ions on the tetrahedral hydrogen-bond network of water is essential to uncover the mechanisms underlying various physical, chemical, biological, and geological processes. Although the effect of ions on water has long been the focus of scientific interest during the past century, the way and the extent of ionic effects on the H-bond network of water is still an unsolved problem. In this work, we study the effect of increasing NaCl solute concentration on the structure of solvent water and compare it with the effect of increasing pressure on pure water using deep potential molecular dynamics (DPMD). In particular, the deep neural network potential is trained with the density functional theory data based on the strongly constrained and appropriately normed functional. Therefore, our …

Hypothesis Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. Experiments and simulations Contact angles at the alumina (0001) and (11 2‾ 0) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. Findings Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces …