Cu-Catalyzed Three-Component Alkene Carboamination: Mechanistic Insights and Rational Design to Overcome Limitations.

Herein, we report mechanistic investigations into the Cu-catalyzed three-component carboamination of alkenes with α-halo carbonyls and aryl amines via an oxocarbenium intermediate. Monitoring the reaction reveals the formation of transient atom transfer radical addition (ATRA) intermediates with both electron-neutral and deficient vinyl arenes as well as unactivated alkenes. Based on our experimental studies and density functional theory calculations, the oxocarbenium is generated through atom transfer and subsequent intramolecular substitution.

Structural Insight on Supramolecular Polyion Salts: Inositol Hexaphosphate Enclosed in Cationic Macrocyclic Clusters.

Supramolecular macrocyclic forces have been used to trap phytate, myo-inositol-1,2,3,4,5,6-hexakisphosphate, a key bioanion with multiple roles in metabolic processes. Due to the complex chemistry of six multivalent phosphates surrounding the small, cyclic inositol framework, crystallographic information of simple phytate salts has been elusive. This report represents a combined crystallographic, theoretical, and solution binding investigation of a supramolecular macrocyclic complex of phytate.

Self-Assembly and Micellar Transition in CTAB Solutions Triggered by 1-Octanol.

This study exploits higher-order micellar transition ranging from ellipsoidal to rodlike to wormlike induced by 1-octanol (COH) in an aqueous solution of cetyltrimethylammonium bromide (CTAB), characterizing phase behavior, rheology, and small-angle neutron scattering (SANS). The phase diagram for the ternary system CTAB-COH-water was constructed, which depicted the varied solution behavior. Such performance was further inferred from the rheology study (oscillatory-shear frequency sweep (ω) and viscosity (η)) that displayed an interesting solution behavior of CTAB solutions as a function of COH.

Newly identified C-H⋯O hydrogen bond in histidine.

New Cδ-H⋯O histidine hydrogen bonding interactions in various proteins are identified by neutron diffraction and computationally characterized. Neutron diffraction data shows several H-bond motifs with the Cδ-H moiety in histidine side chains, including interactions in β-sheets and with coordinated waters, mostly with histidinium and τ-tautomers. In yellow protein, an active site histidine H-bonds Cδ-H to a main chain carbonyl while the Cε-H bond coordinates a water molecule.

Probing Adaptation of Hydration and Protein Dynamics to Temperature.

Protein dynamics is strongly influenced by the surrounding environment and physiological conditions. Here we employ broadband megahertz-to-terahertz spectroscopy to explore the dynamics of water and myoglobin protein on an extended time scale from femto- to nanosecond. The dielectric spectra reveal several relaxations corresponding to the orientational polarization mechanism, including the dynamics of loosely bound, tightly bound, and bulk water, as well as collective vibrational modes of protein in an aqueous environment.

Contrasting effect of 1-butanol and 1,4-butanediol on the triggered micellar self-assemblies of C-type cationic surfactants.

The self-assembly in aqueous solutions of three quaternary salt-based C-type cationic surfactants with different polar head groups and identical carbon alkyl chain , cetylpyridinium bromide (CPB), cetyltrimethylammonium tosylate (CTAT), and cetyltriphenylphosphonium bromide (CTPPB) in the presence of 1-butanol (BuOH) and 1,4-butanediol (BTD) was investigated using tensiometry, 2D-nuclear Overhauser enhancement spectroscopy (2D-NOESY) and small angle neutron scattering (SANS) techniques. The adsorption parameters and micellar characteristics evaluated at 303.15 K distinctly showed that BuOH promotes the mixed micelle formation while BTD interfered with the micellization phenomenon.

Tuning Cationic Micelle Properties with an Antioxidant Additive: A Molecular Perspective.

In this work, we characterize the micellization and morphology transition induced in aqueous cetyltrimethylammonium bromide (CTAB) solution by the addition of the antioxidant propyl gallate (PG) using tensiometry, rheology, and small-angle neutron scattering (SANS) techniques combined with the molecular dynamics (MD) simulation approach. The adsorption of CTAB at the air-water interface in the presence of varying [PG] revealed a progressive decrease in the critical micelle concentration (CMC), while the changes in different interfacial parameters indicated enhancement of the hydrophobicity induced by PG in the CTAB micellar system. The dynamic rheology behavior indicated an increase in the flow viscosity (η) as a function of [PG].

Dynamic Preference for NADP/H Cofactor Binding/Release in YqhD Oxidoreductase.

YqhD, an alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release.

The study and application of biomolecules in deep eutectic solvents.

Biomolecules have been thoroughly investigated in a multitude of solvents historically in order to accentuate or modulate their superlative properties in an array of applications. Ionic liquids have been extensively explored over the last two decades as potential replacements for traditional organic solvents, however, they are sometimes associated with a number of limitations primarily related to cost, convenience, accessibility, and/or sustainability. One potential solvent which is gaining considerable traction in recent years is the so-called deep eutectic solvent which holds a number of striking advantages, including biodegradability, inherently low toxicity, and a facile, low-cost, and solventless preparation from widely available natural feedstocks.

Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics.

The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer.

How Does Solvation Layer Mobility Affect Protein Structural Dynamics?

Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations.

High-Precision Megahertz-to-Terahertz Dielectric Spectroscopy of Protein Collective Motions and Hydration Dynamics.

The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of the hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here, we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz.

Entropy connects water structure and dynamics in protein hydration layer.

The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, and loop structure. Heterogeneous hydration dynamics were observed around the surface of the enzyme, in line with spectroscopic observations of other proteins.

Evaluating electronic structure methods for accurate calculation of F chemical shifts in fluorinated amino acids.

The ability of electronic structure methods (11 density functionals, HF, and MP2 calculations; two basis sets and two solvation models) to accurately calculate the F chemical shifts of 31 structures of fluorinated amino acids and analogues with known experimental F NMR spectra has been evaluated. For this task, BHandHLYP, ωB97X, and Hartree-Fock with scaling factors (provided within) are most accurate. Additionally, the accuracy of methods to calculate relative changes in fluorine shielding across 23 sets of structural variants, such as zwitterionic amino acids versus side chains only, was also determined.

Tautomeric stabilities of 4-fluorohistidine shed new light on mechanistic experiments with labeled ribonuclease A.

Ribonuclease A is the oldest model for studying enzymatic mechanisms, yet questions remain about proton transfer within the active site. Seminal work by Jackson (Science, 1994) labeled Ribonuclease A with 4-fluorohistidine, concluding that active-site histidines act as general acids and bases. Calculations of 4-fluorohistidine indicate that the π-tautomer is predominant in all simulated environments (by ~17 kJ/mol), strongly suggesting that fluoro-labeled ribonuclease A functions with His119 in π-tautomer.

The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties.

Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pK values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer.

New Insights into the Dynamics of Zwitterionic Micelles and Their Hydration Waters by Gigahertz-to-Terahertz Dielectric Spectroscopy.

Gigahertz-to-terahertz spectroscopy of macromolecules in aqueous environments provides an important approach for identifying their global and transient molecular structures, as well as directly assessing hydrogen-bonding. We report dielectric properties of zwitterionic dodecylphosphocholine (DPC) micelles in aqueous solutions over a wide frequency range, from 50 MHz to 1.12 THz.

To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent.

The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties.

Molecular Modeling of Cetylpyridinium Bromide, a Cationic Surfactant, in Solutions and Micelle.

Cationic surfactants are widely used in biological and industrial processes. Notably, surfactants with pyridinium salts, such as cetylpyridinium bromide (CPB), have diverse applications. The cetylpyridium cation has a quaternary nitrogen in the aromatic heterocyclic ring of the headgroup and 16 carbons in the hydrocarbon tail.

Demystifying fluorine chemical shifts: electronic structure calculations address origins of seemingly anomalous (19)F-NMR spectra of fluorohistidine isomers and analogues.

Fluorine NMR spectroscopy is a powerful tool for studying biomolecular structure, dynamics, and ligand binding, yet the origins of (19)F chemical shifts are not well understood. Herein, we use electronic structure calculations to describe the changes in (19)F chemical shifts of 2F- and 4F-histidine/(5-methyl)-imidazole upon acid titration. While the protonation of the 2F species results in a deshielded chemical shift, protonation of the 4F isomer results in an opposite, shielded chemical shift.

On the reorientation and hydrogen-bond dynamics of alcohols.

The mechanism of the OH bond reorientation in liquid methanol and ethanol is examined. It is found that the extended jump model, recently developed for water, describes the OH reorientation in these liquids. The slower reorientational dynamics in these alcohols compared to water can be explained by two key factors.

Infrared spectra of a model phenol-amine proton transfer complex in nanoconfined CH3Cl.

The vibrational spectra of a model phenol-amine proton transfer complex dissolved in CH3Cl solvent confined in a 12 A radius spherical hydrophobic cavity were calculated using mixed quantum-classical molecular dynamics simulations. The reaction free energy of the proton transfer complex was varied in order to explore the contributions to the vibrational absorption band from product and reactant species. The vibrational spectra of the model proton transfer complex resulted in motionally narrowed spectral linewidths with two distinct peaks for products and reactants in cases where the system undergoes chemical exchange.

Evaluating computational predictions of the relative stabilities of polymorphic pharmaceuticals.

The ability of computational methods to describe the relative energies of polymorphic pharmaceuticals is investigated for a diverse array of compounds. The initial molecular geometries were taken from crystal structures, and energy differences between polymorphic pairs were calculated with various geometry optimization methods. Results using molecular mechanics were compared to experimental calorimetric data and periodic density functional theory (DFT) calculations.

Utilization of hydrogen bonds to stabilize M-O(H) units: synthesis and properties of monomeric iron and manganese complexes with terminal oxo and hydroxo ligands.

Non-heme iron and manganese species with terminal oxo ligands are proposed to be key intermediates in a variety of biological and synthetic systems; however, the stabilization of these types of complexes has proven difficult because of the tendency to form oxo-bridged complexes. Described herein are the design, isolation, and properties for a series of mononuclear Fe(III) and Mn(III) complexes with terminal oxo or hydroxo ligands. Isolation of the complexes was facilitated by the tripodal ligand tris[(N'-tert-butylureaylato)-N-ethyl]aminato ([H(3)1](3-)), which creates a protective hydrogen bond cavity around the M(III)-O(H) units (M(III) = Fe and Mn).