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What is Dispersity (Ð), and how does it differ between traditional and sequence-defined polymers?

Dispersity (Ð) is a quantitative measure that describes the spread or distribution of molecular weights within a polymer sample. Traditional polymers typically exhibit dispersity due to variations in chain lengths, while sequence-defined polymers are synthesized with precise control over chain length, resulting in a uniform molecular weight and thus no dispersity.

What defines a sequence-defined polymer, and what unique characteristic does it possess regarding molecular weight?

A sequence-defined polymer is a synthetic polymer where the exact order of its monomer units and its precise molecular weight are deterministically controlled during synthesis, thereby eliminating the characteristic of dispersity entirely.

How is the stiffness of a polymer chain quantitatively described, and what determines it?

Persistence length is a quantitative Metric that describes the inherent stiffness or rigidity of a polymer chain, which is significantly influenced by the chemical identity and structural characteristics of its repeating monomer units.

What is the radius of gyration in the context of polymers, and what does it indicate?

The radius of gyration is a physical parameter that represents the average spatial distribution of all monomer units around a polymer’s center of mass, providing a measure of the overall size or compactness of a polymer chain in solution.

What is static light scattering used for, and what properties of polymers can it determine?

Static light scattering is an optical technique utilized to determine the absolute molecular weight and overall size (e.g., radius of gyration) of polymers dissolved in solution by measuring the intensity of light scattered by the macromolecules.

What is SAXS (Small-Angle X-ray Scattering), and what structural information does it provide for macromolecules?

SAXS (Small-Angle X-ray Scattering) is an X-ray scattering method employed to probe and analyze the nanometer-scale structure, overall shape, and conformational dynamics of macromolecules, including polymers, in solution.

What is SANS (Small-Angle Neutron Scattering), and how is it similar to and different from SAXS?

SANS (Small-Angle Neutron Scattering) is a neutron-based analogue to SAXS that uses neutrons instead of X-rays to study the structure, conformation, and dynamics of polymers and biomolecules in solution, often providing complementary information that can be enhanced through deuteration.

What type of detailed structural information can be obtained using NMR spectroscopy?

NMR spectroscopy (Nuclear Magnetic Resonance) is a powerful analytical method that provides highly detailed information about the atomic environment, interatomic distances, and dihedral angles within a molecule, making it invaluable for elucidating the precise three-dimensional structure of polymers and biomolecules.

How does smFRET (single-molecule FRET) function, and what unique insights does it offer at the molecular level?

smFRET (single-molecule FRET) is an advanced technique that measures distances and monitors conformational changes in individual molecules by observing the energy transfer efficiency between two fluorescent labels (fluorophores) attached to specific sites on the molecule.

What is EPR (Electron Paramagnetic Resonance) spectroscopy, and what can it reveal about labeled polymers?

EPR (Electron Paramagnetic Resonance) spectroscopy is a spectroscopic technique exquisitely sensitive to the presence of unpaired electrons, which is used to investigate the dynamics, conformations, and interactions within labeled polymers or biomolecules by attaching spin labels.

How does IMS-MS (Ion Mobility Spectrometry–Mass Spectrometry) work, and what unique information does it provide about polymer chain architecture?

IMS-MS (Ion Mobility Spectrometry–Mass Spectrometry) is a coupled analytical technique that first separates ions based on their shape-to-charge ratio in the gas phase using ion mobility spectrometry, followed by mass analysis, which provides insights into the intricate chain architecture and conformation of polymers without the need for extrinsic probes.

What is Edman degradation primarily used for in protein analysis?

Edman degradation is a sequential chemical method used to determine the amino acid sequence of a peptide or protein. It involves cleaving and identifying the N-terminal amino acid one at a time from the polypeptide chain.

What is Circular Dichroism (CD) spectroscopy, and what kind of structural information does it typically provide?

Circular Dichroism (CD) spectroscopy is a method that measures the differential absorption of left and right circularly polarized light by a molecule, primarily used to assess the secondary structure (e.g., alpha-helices, beta-sheets) of proteins and other chiral molecules, though it lacks site-specific structural details.

What is a Protein-Protein Interaction (PPI), and why are they often difficult to inhibit with small molecules?

A Protein-Protein Interaction (PPI) refers to the specific physical association between two or more proteins, which is often challenging to inhibit effectively with small molecules due to their typically broad and flat interfacial surfaces.

What defines an obligate PPI (Protein-Protein Interaction)?

An obligate PPI describes a protein complex whose individual constituent subunits are inherently unstable, misfolded, or non-functional unless they are bound together as part of the larger complex.

What characterizes a non-obligate PPI (Protein-Protein Interaction)?

A non-obligate PPI describes protein partners that are capable of existing stably and maintaining their biological function even when not bound together within their complex.

What is SPR (Surface Plasmon Resonance), and how does it monitor biomolecular binding kinetics?

SPR (Surface Plasmon Resonance) is a label-free, real-time biosensing technique that monitors biomolecular binding events, such as protein-ligand interactions, by detecting changes in the refractive index near a sensor surface, which alters the surface plasmon resonance signal.

How does BLI (Biolayer Interferometry) work to track binding events?

BLI (Biolayer Interferometry) is an optical interference method that directly tracks biomolecular binding and dissociation events in real-time on the tip of a fiber optic biosensor, by measuring changes in the white light interference pattern reflected from the sensor surface.

What information can ITC (Isothermal Titration Calorimetry) provide about molecular binding interactions?

ITC (Isothermal Titration Calorimetry) is a highly sensitive thermodynamic technique used to directly quantify the binding affinity, enthalpy (heat), stoichiometry, and entropy of molecular interactions by precisely measuring the heat absorbed or released during a binding event.

What is a peptoid, and what are its key advantages over traditional peptides?

A peptoid is a synthetic oligomer structurally similar to a peptide, but composed of N-substituted glycine residues. This unique N-substitution eliminates backbone NH groups, which confers high cell permeability and remarkable resistance to proteolysis (enzymatic degradation).

What is proteolysis, and why are peptoids resistant to it?

Proteolysis is the enzymatic cleavage of peptide bonds within proteins or peptides, a process that peptoids are notably resistant to due to their unique N-substituted backbone, which prevents recognition by proteases.

What is FRET (Fluorescence Resonance Energy Transfer), and what is its primary application as a 'spectroscopic ruler'?

FRET (Fluorescence Resonance Energy Transfer) is a distance-dependent non-radiative energy transfer process between a donor fluorophore and an acceptor fluorophore when they are within close proximity (typically $1-10 \, nm$), functioning as a spectroscopic ruler to measure molecular distances and conformational changes.

What is Hydrogen Exchange (HX), and what structural and dynamic information does it provide about proteins?

Hydrogen Exchange (HX) is a biophysical technique where backbone amide protons (NH) exchange with solvent deuterons (deuterium oxide, D2O). The rate and extent of this exchange report on hydrogen bonding networks, solvent accessibility, and the burial of protein regions, thereby providing insights into protein dynamics and structure.

What information do NOESY and ROESY 2D NMR experiments provide for structural analysis?

NOESY (Nuclear Overhauser Effect Spectroscopy) and ROESY (Rotating-frame Overhauser Effect Spectroscopy) are 2D NMR experiments that provide crucial information on interproton distances ($<5 \, Å$) through the Nuclear Overhauser Effect, and, combined with scalar couplings, also reveal dihedral angle constraints, which are essential for determining the three-dimensional structure of molecules like peptides and proteins.

What is GPC (Gel Permeation Chromatography), and how does it separate polymers?

GPC (Gel Permeation Chromatography), also known as size-exclusion chromatography, is a chromatographic method that separates polymers in solution based on their hydrodynamic radius. Larger polymers with a larger hydrodynamic radius elute earlier, allowing for the estimation of their molecular weight distribution.

What is the hydrodynamic radius, and how does it relate to GPC elution volume?

The hydrodynamic radius is the effective radius a molecule or particle exhibits while diffusing in a solution, representing its apparent size in a solvated state. It directly correlates with the elution volume in GPC, where larger hydrodynamic radii correspond to earlier elution.

What is TEM (Transmission Electron Microscopy), and what kind of sample information does it provide?

TEM (Transmission Electron Microscopy) is a high-resolution imaging technique that transmits a beam of electrons through extremely thin samples, allowing for the visualization of internal morphology, ultrastructure, and crystalline arrangement at nanoscale resolution.

What is SEM (Scanning Electron Microscopy), and what visual information does it typically reveal?

SEM (Scanning Electron Microscopy) is an imaging method that scans a focused electron beam across the surface of a sample. It detects secondary electrons emitted from the sample to generate highly detailed, three-dimensional images of the surface topography and composition.

How does AFM (Atomic Force Microscopy) generate images, and what properties can it map?

AFM (Atomic Force Microscopy) is a high-resolution surface imaging technique that uses a sharp nanoscale probe attached to a cantilever to scan a sample's surface, mapping its topography, roughness, and various mechanical properties (e.g., stiffness, adhesion) at the atomic or molecular level.

What is MALDI-TOF, and what are its key advantages in mass spectrometry?

MALDI-TOF (Matrix-Assisted Laser Desorption Ionization Time-of-Flight) mass spectrometry is a soft ionization mass spectrometry technique that uses a laser to desorb and ionize molecules embedded in a solid matrix, followed by high-resolution mass analysis, enabling rapid and accurate determination of molecular weights, particularly for large biomolecules and polymers.

What is a reflectron in a TOF mass spectrometer, and what is its primary function?

A Reflectron is an electrostatic mirror component within time-of-flight (TOF) mass spectrometers that directs ions back towards the detector, simultaneously lengthening their flight path and correcting for initial kinetic energy spread, thereby significantly enhancing mass resolution and accuracy.

What is the purpose of a peptoid linker in MALDI, especially for small peptoids?

A peptoid linker in MALDI refers to a specifically designed mass-adding chemical moiety that is covalently attached to small peptoids (typically $<500 \, Da$). Its purpose is to increase their molecular weight sufficiently to move their mass signals above the low-mass region, which is often cluttered by signals from the MALDI matrix and solvent clusters, thus enabling accurate MS sequencing.

What is unique about Reichardt's dye, particularly concerning its fluorescence?

Reichardt's dye is a highly solvatochromic probe, meaning its light absorption properties are extremely sensitive to the polarity of the solvent it is in. Uniquely, it dissipates nearly all absorbed excitation energy as heat through internal conversion, rendering it essentially non-fluorescent.