Molecule

About: Molecule is a research topic. Over the lifetime, 52462 publications have been published within this topic receiving 1234914 citations.

Energy landscapes of receptor–ligand bonds explored with dynamic force spectroscopy

Abstract: Atomic force microscopy (AFM) has been used to measure the strength of bonds between biological receptor molecules and their ligands. But for weak noncovalent bonds, a dynamic spectrum of bond strengths is predicted as the loading rate is altered, with the measured strength being governed by the prominent barriers traversed in the energy landscape along the force-driven bond-dissociation pathway. In other words, the pioneering early AFM measurements represent only a single point in a continuous spectrum of bond strengths, because theory predicts that these will depend on the rate at which the load is applied. Here we report the strength spectra for the bonds between streptavidin (or avidin) and biotins-the prototype of receptor-ligand interactions used in earlier AFM studies, and which have been modelled by molecular dynamics. We have probed bond formation over six orders of magnitude in loading rate, and find that the bond survival time diminished from about 1 min to 0.001 s with increasing loading rate over this range. The bond strength, meanwhile, increased from about 5 pN to 170 pN. Thus, although they are among the strongest noncovalent linkages in biology (affinity of 10(13) to 10(15) M(-1)), these bonds in fact appear strong or weak depending on how fast they are loaded. We are also able to relate the activation barriers derived from our strength spectra to the shape of the energy landscape derived from simulations of the biotin-avidin complex.

Reference Data on Atoms, Molecules, and Ions

Abstract: 1. Introduction.- 2. Units of Physical Quantities.- 2.1 Systems of Units in Physics.- 2.2 Fundamental Physical Constants.- 2.3 Systems of Units Based on "Natural Standards".- 2.4 Tables of Conversion Factors.- I Atoms and Atomic Ions.- 3. Isotopic Composition, Atomic Mass Table and Atomic Weights of the Elements.- 3.1 Parameters of Stable and Long-Lived Isotopes.- 3.2 Atomic Weights of the Elements and Atomic Mass Table.- 4. Structure of Atomic Electron Shells.- 4.1 Electron Configurations and Ground-State Terms.- 4.2 The Periodic Table.- 4.3 Parameters of Wavefunctions for Valence Electrons in Atoms, Positive and Negative Ions.- 5. Energetics of Neutral Atoms.- 5.1 Ionization Potentials of Atoms.- 5.2 Quantum Defects of Atomic Rydberg States.- 5.3 Fine-Structure Splitting of Atomic Energy Levels.- 5.4 Hyperfine Structure of Atomic Energy Levels.- 5.5 Isotope Shifts of Low-Lying Atomic Levels.- 5.6 Atoms in Static Electric and Magnetic Fields. Atomic Polarizabilities and Magnetic Susceptibilities.- 6. Energetics of Atomic Ions.- 6.1 Ionization Potentials of Atomic Ions.- 6.2 Electron Affinities of Atoms.- 6.3 Energy Levels of Multiply Charged Atomic Ions.- 7. Spectroscopic Characteristics of Neutral Atoms.- 7.1 Low-Lying Atomic Terms.- 7.2 Diagrams of Atomic Energy Levels and Grotrian Diagrams.- 7.3 Atomic Oscillator Strengths in Absorption.- 7.4 Lifetimes of Resonant Excited States in Atoms.- 7.5 Energy Levels and Lifetimes for Metastable States in Atoms.- 7.6 Lifetimes of Atomic Rydberg States.- 8. Spectroscopic Characteristics of Atomic Positive Ions.- 8.1 Low-Lying Terms of Singly Ionized Atoms.- 8.2 Lifetimes of Resonant Excited States in Atomic Ions.- 8.3 Energy Levels and Lifetimes for Metastable States in Singly Ionized Atoms.- 8.4 Optical Parameters of Multiply Charged Atomic Ions.- II Molecules and Molecular Ions.- 9. Interaction Potentials Between Atomic and Molecular Species.- 9.1 Van der Waals Coefficients for Interatomic Multipole Interactions.- 9.2 Long-Range Exchange Interactions of Atoms.- 9.3 Short-Range Repulsive Interactions Between Atomic and Molecular Species.- 10. Diatomic Molecules.- 10.1 Electron Configurations of Diatomic Molecules.- 10.2 Asymptotic Parameters of Wavefunctions for Valence Electrons in Diatomic Molecules.- 10.3 Spectroscopic Constants of Diatomic Molecules.- 10.4 Potential Energy Curves.- 10.5 Ionization Potentials of Diatomic Molecules.- 10.6 Dissociation Energies of Diatomic Molecules.- 10.7 Lifetimes of Excited Electron States in Diatomic Molecules.- 10.8 Parameters of Excimer Molecules.- 10.9 Einstein Coefficients for Spontaneous Emission from Vibrationally Excited Diatomic Molecules.- 11. Diatomic Molecular Ions.- 11.1 Electron Configurations and Asymptotic Parameters of Wavefunctions for Valence Electrons in Diatomic Molecular Ions.- 11.2 Spectroscopic Constants of Diatomic Molecular Ions.- 11.3 Dissociation Energies of Diatomic Molecular Ions.- 11.4 Electron Affinities of Diatomic Molecules.- 11.5 Proton Affinities of Atoms.- 11.6 Lifetimes of Excited Electron States in Diatomic Molecular Ions.- 12. Van der Waals Molecules.- 12.1 Potential Well Parameters of Van der Waals Molecules.- 12.2 Potential Well Parameters of Van der Waals Molecular Ions.- 12.3 Ionization Potentials of Van der Waals Molecules.- 13. Polyatomic Molecules.- 13.1 Constants of Triatomic Molecules.- 13.2 Ionization Potentials of Polyatomic Molecules.- 13.3 Bond Dissociation Energies of Polyatomic Molecules.- 13.4 Lifetimes of Vibrationally Excited Polyatomic Molecules.- 14. Polyatomic Molecular Ions.- 14.1 Bond Dissociation Energies of Complex Positive Ions.- 14.2 Bond Dissociation Energies of Complex Negative Ions.- 14.3 Electron Affinities of Polyatomic Molecules.- 14.4 Proton Affinities of Molecules.- 15. Electrical Properties of Molecules.- 15.1 Dipole Moments of Molecules.- 15.2 Molecular Polarizabilities.- 15.3 Quadrupole Moments of Molecules.- Mathematical Appendices.- A. Coefficients of Fractional Parentage.- B. Clebsch-Gordan Coefficients.

The atom, the molecule, and the covalent organic framework

Abstract: Just over a century ago, Lewis published his seminal work on what became known as the covalent bond, which has since occupied a central role in the theory of making organic molecules. With the advent of covalent organic frameworks (COFs), the chemistry of the covalent bond was extended to two- and three-dimensional frameworks. Here, organic molecules are linked by covalent bonds to yield crystalline, porous COFs from light elements (boron, carbon, nitrogen, oxygen, and silicon) that are characterized by high architectural and chemical robustness. This discovery paved the way for carrying out chemistry on frameworks without losing their porosity or crystallinity, and in turn achieving designed properties in materials. The recent union of the covalent and the mechanical bond in the COF provides the opportunity for making woven structures that incorporate flexibility and dynamics into frameworks.

Hydrogen-bond kinetics in liquid water

Abstract: HYDROGEN bonds play a crucial role in the behaviour of water1–4; their spatial patterns and fluctuations characterize the structure and dynamics of the liquid5–7. The processes of breaking and making hydrogen bonds in the condensed phase can be probed indirectly by a variety of experimental techniques8, and more quantitative information can be obtained from computer simulations9. In particular, simulations have revealed that on long timescales the relaxation behaviour of hydrogen bonds in liquid water exhibit non-exponential kinetics7,10–13, suggesting that bond making and breaking are not simple processes characterized by well defined rate constants. Here we show that these kinetics can be understood in terms of an interplay between diffusion and hydrogen-bond dynamics. In our model, which can be extended to other hydrogen-bonded liquids, diffusion governs whether a specific pair of water molecules are near neighbours, and hydrogen bonds between such pairs form and persist at random with average lifetimes determined by rate constants for bond making and breaking.

Infrared spectra of inorganic compounds

Abstract: This chapter discusses the experimental, theoretical, and empirical correlations between functional organic groups and the infrared spectrum. The application of infrared spectroscopy to the identification of inorganic compounds is less successful. In obtaining infrared spectra of inorganic solids, an experimental complication arises from possible chemical reaction between the inorganic compound and the infrared window material or support medium. The chapter presents many examples of spectra of inorganic compounds in the solid phase. The majority of these compounds are crystalline solids in which the crystallographic unit cell contains several polyatomic ions or molecules. Optical modes called lattice modes of vibration result from the motion of one polyatomic group relative to another within the unit cell. Lattice modes occur in the region 400–10 cm −1 and are characteristic of specific crystal geometry. They are used as fingerprints for an inorganic compound in much the same way as the internal modes of vibration of organic compounds are used in the region 4000–400 cm −1 .