Enantiopure molecules form apparently racemic monolayers of chiral cyclic pentamers.

Ultra-high vacuum scanning tunneling microscopy (UHV-STM) was used to investigate two related molecules pulse-deposited onto Au(111) surfaces: indoline-2-carboxylic acid and proline (pyrrolidine-2-carboxylic acid). Indoline-2-carboxylic acid and proline form both dimers and -symmetric "pinwheel" pentamers. Enantiomerically pure -(-)-indoline-2-carboxylic acid and -proline were used, and the pentamer structures observed for both were chiral.

Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.

The inherent cross-reactivity of the T cell receptor (TCR) is balanced by high specificity, which often manifests in confounding ways not easily interpretable from static structures. We show here that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen derived from mutant and its wild-type (WT) counterpart emerges from motions within the HLA binding groove that vary with the identity of the peptide's first primary anchor. The motions form a dynamic gate that in the complex with the WT peptide impedes a large conformational change required for TCR binding.

Mechanism of Daunomycin Intercalation into DNA from Enhanced Sampling Simulations.

Daunomycin is a widely used anticancer drug, yet the mechanism underlying how it binds to DNA remains contested. 469 all-atom trajectories of daunomycin binding to the DNA oligonucleotide (GCG CAC GTG CGC) were collected using weighted ensemble (WE)-enhanced sampling. Mechanistic insights were revealed through analysis of the ensemble of trajectories.

The Energetic Landscape of Catch Bonds in TCR Interfaces.

Recognition of peptide/MHC complexes by αβ TCRs has traditionally been viewed through the lens of conventional receptor-ligand theory. Recent work, however, has shown that TCR recognition and T cell signaling can be profoundly influenced and tuned by mechanical forces. One outcome of applied force is the catch bond, where TCR dissociation rates decrease (half-lives increase) when limited force is applied.

Molecular Mechanism of Ligand Binding to the Minor Groove of DNA.

Although DNA-ligand binding is pervasive in biology, little is known about molecular-level binding mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling, an ensemble of 2562 binding trajectories of Hoechst 33258 (H33258) to d(CGC AAA TTT GCG) was generated from which the binding mechanism was extracted. In particular, the electrostatic interaction between the positively charged H33258 and the negatively charged DNA backbone drives the formation of initial H33258-DNA contacts.

Coupled local mode method for simulating vibrational spectroscopy.

Experimental and theoretical studies have highlighted protonated water clusters (PWCs) as important models of the excess proton in aqueous systems. A significant focus has been characterizing the spectral signatures associated with different excess proton solvation motifs. Accurate vibrational frequency calculations are crucial for connecting the measured spectra to the structure of PWCs.

Coupled Local-Mode Approach for the Calculation of Vibrational Spectra: Application to Protonated Water Clusters.

Spectroscopic studies of protonated water clusters (PWCs) have yielded enormous insights into the fundamental nature of the hydrated proton. Here, we introduce a new coupled local-mode (CLM) approach to calculate PWC OH stretch vibrational spectra. The CLM method combines a sampling of representative configurations from density functional theory (DFT)-based molecular dynamics (AIMD) simulations with DFT calculations of local-mode vibrational frequencies and couplings.

Local Electric Fields in Aqueous Electrolytes.

Vibrational Stark shifts were explored in aqueous solutions of organic molecules with carbonyl- and nitrile-containing constituents. In many cases, the vibrational resonances from these moieties shifted toward lower frequency as salt was introduced into solution. This is in contrast to the blue-shift that would be expected based upon Onsager's reaction field theory.

Nonlinear measurements of kinetics and generalized dynamical modes. II. Application to a simulation of solvation dynamics in an ionic liquid.

Solvation dynamics in ionic liquids show features that are often associated with supercooled liquids, including "stretched" nonexponential relaxation. To better understand the mechanism behind the stretching, the nonlinear mode-correlation methods proposed in Paper I [S. R.

Spectroscopic and Structural Characterization of Water-Shared Ion-Pairs in Aqueous Sodium and Lithium Hydroxide.

The structures of the ion-pairs formed in aqueous NaOH and LiOH solutions are elucidated by combining Raman multivariate curve resolution (Raman-MCR) experiments and molecular dynamics (AIMD) simulations. The results extend prior findings to reveal that the initially formed ion-pairs are predominantly water-shared, with the hydroxide ion retaining its full first hydration-shell, while direct contact ion-pairing only becomes significant at higher concentrations. Our results confirm previous experiments and simulations indicating greater ion-pairing in aqueous LiOH than NaOH as well as at high temperatures.

DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site.

Understanding the dynamic interactions of ligands to DNA is important in DNA-based nanotechnologies. By structurally tracking the dissociation of Hoechst 33258-bound DNA (d(CGCAAATTTGCG)) complex (H-DNA) with T-jump 2D-IR spectroscopy, the ligand is found to strongly disturb the stability of the three C:G base pairs adjacent to A:T the binding site, with the broken base pairs being more than triple at 100 ns. The strong stabilization effect of the ligand on DNA duplex makes this observation quite striking, which dramatically increases the melting temperature and dissociation time.

Hydrogen Bond Exchange and Ca Binding of Aqueous -Methylacetamide Revealed by 2DIR Spectroscopy.

Cation effects on proteins have been a challenge to understand. Herein, we present two-dimensional infrared (2DIR) spectroscopic measurements, coupled with molecular dynamics and spectroscopic calculations, of -methylacetamide (NMA), a common model of the peptide backbone, in aqueous CaCl. The 2DIR spectra reveal that the dynamics of the amide carbonyl of NMA is dominated by exchange between two states of varying hydration, one possessing a structure similar to aqueous NMA and one that is dehydrated by one hydrogen bond.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation.

Machine Learning for Vibrational Spectroscopic Maps.

Maps that relate spectroscopic properties of a vibrational mode and collective solvent coordinates have proven useful in theoretical vibrational spectroscopy of condensed-phase systems. It has been realized that the predictive power of such an approach is limited and there is no clear systematic way to improve its accuracy. Here, we propose an adaptation of Δ-machine-learning methodology that goes beyond the spectroscopic maps.

Dynamics and Vibrational Spectroscopy of Alcohols in Ionic Liquids: Methanol and Ethanol.

The structure, dynamics, and vibrational spectroscopy of dilute HOD, methanol, and ethanol in the 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [emim][NTf], ionic liquid (IL) are investigated with molecular dynamics (MD) simulations. The structure of the ILs around the solutes is qualitatively similar, where the OD bond of the deuterated alcohols donates an interaction to an [NTf] anion and the [emim] cations interact with the oxygen atom of the OD group. The slowest time scale for the reorientational dynamics of the OD bond varied considerably for HOD, methanol, and ethanol (27, 71, and 87 ps, respectively).

Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility.

T cell receptor (TCR) recognition of antigenic peptides bound and presented by class I major histocompatibility complex (MHC) proteins underlies the cytotoxic immune response to diseased cells. Crystallographic structures of TCR-peptide/MHC complexes have demonstrated how TCRs simultaneously interact with both the peptide and the MHC protein. However, it is increasingly recognized that, beyond serving as a static platform for peptide presentation, the physical properties of class I MHC proteins are tuned by different peptides in ways that are not always structurally visible.

Counter Cations Affect Transport in Aqueous Hydroxide Solutions with Ion Specificity.

The anomalously high mobility of hydroxide and hydronium ions in aqueous solutions is related to proton transfer and structural diffusion. The role of counterions in these solutions, however, is often considered to be negligible. Herein, we explore the impact of alkali metal counter cations on hydroxide solvation and mobility.

Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: IV. Temperature Dependence.

In previous papers in the series, the vibrational spectroscopy of CO in ionic liquids (ILs) was investigated at ambient conditions. Here, we extend these studies to understand the temperature dependence of the structure, dynamics, and thermodynamics of CO in the 1-butyl-3-methylimidazolium hexafluorophosphate, [bmim][PF], IL. Using spectroscopic mapping techniques, the infrared absorption spectrum of the CO asymmetric stretch mode is simulated at a number of temperatures, and the results are found to be consistent with similar experimental studies.

Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: III. Dynamics and Spectroscopy.

In recent years, interest in carbon capture and sequestration has led to numerous investigations of the ability of ionic liquids to act as recyclable CO-sorbent materials. Herein, we investigate the structure and dynamics of a model physisorbing ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([CCIm][PF]), from the perspective of CO using two-dimensional (2D) IR spectroscopy and molecular dynamics simulations. A direct comparison of experimentally measured and calculated 2D IR line shapes confirms the validity of the simulations and spectroscopic calculations.

Reaction Ensemble Monte Carlo Simulations of CO Absorption in the Reactive Ionic Liquid Triethyl(octyl)phosphonium 2-Cyanopyrrolide.

The absorption of CO into an aprotic heterocyclic anion ionic liquid (IL) is modeled using reaction ensemble Monte Carlo (RxMC) with the semigrand reaction move. RxMC has previously been unable to sample chemical equilibrium involving molecular ions in nanostructured liquids due to the high free-energy requirements to open and close cavities and restructure the surrounding environment. Our results are validated by experiments in the modeled IL, triethyl(octyl)phosphonium 2-cyanopyrrolide ([P][cnp]), and in a close analog with longer alkyl chains on the cation.

Decompositions of Solvent Response Functions in Ionic Liquids: A Direct Comparison of Equilibrium and Nonequilibrium Methodologies.

Time-dependent Stokes shift (TDSS) measurements provide crucial insights into the dynamics of liquids. The interpretation of TDSS measurements is often aided by molecular dynamics simulations, where solvent response functions are computed either with an equilibrium or nonequilibrium approach. In the nonequilibrium approach, the solvent is at equilibrium with the ground electronic state of the solute and its charge distribution is instantaneously changed to that of the first excited state.

Enthalpic Driving Force for the Selective Absorption of CO by an Ionic Liquid.

Molecular dynamics (MD) simulations validated against two-dimensional infrared (2D-IR) measurements of CO in an imidazolium-based ionic liquid have revealed new insights into the mechanism of CO solvation. The first solvation shell around CO has a distinctly quadrupolar structure, with strong negative charge density around the CO carbon atom and positive charge density near the CO oxygen atoms. When CO is modeled without atomic charges (thus removing its strong quadrupole moment), its solvation shell weakens and changes significantly into a structure that is similar to that of N in the same liquid.

Structural Polymorphism as the Result of Kinetically Controlled Self-Assembly.

Traditionally, the goal of self-assembly and supramolecular chemistry is to engineer an equilibrium structure with a desired geometry and functionality; this is achieved through careful choice of molecular monomers, growth conditions, and substrate. Supramolecular assemblies produced under nonequilibrium conditions, in contrast, can form metastable structures with conformations quite different from those accessible in equilibrium self-assembly. The study of nonequilibrium growth of clusters potentially impacts the study of nucleation in atmospheric aerosols, nucleation in organic crystallization, and mesoscale organization for systems ranging from biological molecules to molecular electronics.

Effect of pH and Salt on Surface pK of Phosphatidic Acid Monolayers.

The pH-induced surface speciation of organic surfactants such as fatty acids and phospholipids in monolayers and coatings is considered to be an important factor controlling their interfacial organization and properties. Yet, correctly predicting the surface speciation requires the determination of the surface dissociation constants (surface pK) of the protic functional group(s) present. Here, we use three independent methods-compression isotherms, surface tension pH titration, and infrared reflection-absorption spectroscopy (IRRAS)-to study the protonation state of dipalmitoylphosphatidic acid (DPPA) monolayers on water and NaCl solutions.