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Molecules atoms

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. [Pg.78]

As an example for an efficient yet quite accurate approximation, in the first part of our contribution we describe a combination of a structure adapted multipole method with a multiple time step scheme (FAMUSAMM — fast multistep structure adapted multipole method) and evaluate its performance. In the second part we present, as a recent application of this method, an MD study of a ligand-receptor unbinding process enforced by single molecule atomic force microscopy. Through comparison of computed unbinding forces with experimental data we evaluate the quality of the simulations. The third part sketches, as a perspective, one way to drastically extend accessible time scales if one restricts oneself to the study of conformational transitions, which arc ubiquitous in proteins and are the elementary steps of many functional conformational motions. [Pg.79]

That simulation study [49] aimed at a microscopic interpretation of single molecule atomic force microscope (AFM) experiments [50], in which unbinding forces between individual protein-ligand complexes have been m( asured... [Pg.84]

Electronic spectroscopy is the study of transitions, in absorption or emission, between electronic states of an atom or molecule. Atoms are unique in this respect as they have only electronic degrees of freedom, apart from translation and nuclear spin, whereas molecules have, in addition, vibrational and rotational degrees of freedom. One result is that electronic spectra of atoms are very much simpler in appearance than those of molecules. [Pg.199]

In addition to these molecules, atoms are present, as shown by absorptions of Ca, Na, K, Fe, and other atoms. There are some absorptions that have not been identified but these may be due to small solid particles. How these particular molecules and atoms happen to be present in these almost nonexistent clouds and what other molecules and atoms are there, yet to be detected, is a matter for wondering. But wondering is at once the pleasure and the driving force of science. [Pg.448]

Single-step nucleation, (ii) above, requires the unsatisfactory assumption that the generation of a single molecule (atom, ion-pair, etc.) of product constitutes the establishment of a nucleus. (It would seem to be more realistic to regard this as the outcome of several distinct chemical steps.) The mathematical treatment expressing the probability of the occurrence of this unimolecular process is... [Pg.45]

The difference can be traced to the weaker London forces that exist in branched molecules. Atoms in neighboring branched molecules cannot lie as close together as they can in un branched isomers. [Pg.1021]

Molecule Atom Equation 1-1 Inclusion of doublebond character Electronegativity equalization... [Pg.338]

It is probably true that almost every coneeivable molecule, atom or ion could act as a ligand under some circumstance or other. However, certain types of ligands are commonly encountered, and it is these, together with the vocabulary which they generate, that we introduce at this stage. [Pg.5]

Jorgensen CK (1981) The Conditions for Total Symmetry Stabilizing Molecules, Atoms, Nuclei and Hadrons. 43 1-36... [Pg.248]

The chemical formula for water shows how formulas are constructed. The formula lists the symbols of all elements found in the compound, in this case H (hydrogen) and O (oxygen). A subscript number after an element s symbol denotes how many atoms of that element are present in the molecule. The subscript 2 in the formula for water indicates that each molecule contains two hydrogen atoms. No subscript is used when only one atom is present, as is the case for the oxygen atom in a water molecule. Atoms are indivisible, so molecules always contain whole numbers of atoms. Consequently, the subscripts in chemical formulas of molecular substances are always integers. We explore chemical formulas in greater detail in Chapter 3. [Pg.15]

C05-0013. Suppose that Sample A is used and that the second gas is helium instead of neon. Sketch a graph showing the number of molecules/atoms vs. time. [Pg.296]

The most common type of elementary process is a bimolecular reaction that results from the collision of two molecules, atoms, or ions. The collision of two NO2 molecules to give N2 O4 is a bimolecular reaction. Here is another example ... [Pg.1049]

Scale Atom Atom-Atom Molecule Molecule Molecule Molecule Atom-Atom OO OO Atom... [Pg.775]

Arbitrary the book can be divided into two complementary parts. The first one describes the physical and chemical basics leading to description of the method of semiconductor sensors. The mechanisms of underlying processes are given. These processes involve interaction of gas with the surface of semiconductor adsorbent which brings about tiie change of electric and physics characteristics of the latter. Various models of absorption-induced response of electric and physics characteristics of semiconductor adsorbent are considered. Results of numerous physical and chemical experiments carried out by the authors of this book and by other scientists underlying the method of semiconductor sensors are scrupulously discussed. The possibility of qualitative measurements of ultra-small concentrations of molecules, atoms, radicals as well as excited particles in gases, liquids and on surfaces of solids (adsorbents and catalysts) is demonstrated. [Pg.1]

Numerous studies of broadband oxide semiconductors made in tiie form of a relatively thin monocrystal or a thin film sintered on a dielectric substrate revealed that if oxides ZnO, Ti02, SnC>2, CdO, or similar ones are used, it is possible to determine with sufficient accuracy trace concentrations of such active molecules, atoms and radicals as O2, CI2, Br2, J2, H2, H, N, O, OH, Cl, OH, Cl, CH3, CjHj, C3H7, NHj, NH as well as atoms of many metals (Na, Ag, Zn, Cd, Pb, Fe, Pd, Pt, etc.) without the need of prior activating adsorbates. [Pg.171]

Excited particles (molecules, atoms, and ions) also play an important role in plasma and radiation chemical reactions. These particles interact actively with components of a gas (liquid) phase and with the adsorbed layer. These processes are discussed in detail in the next Chapter. [Pg.276]

Molecules Atoms of the same element or of different elements combine with each other into more complicated systems called molecules molecules are the smallest units of chemical compounds, the basic components of the countless inorganic and organic compounds. A few molecules, such as, those of the chemical elements hydrogen, oxygen, and nitrogen, are com-... [Pg.32]

Chemical hardness is an energy parameter that measures the stabilities of molecules—atoms (Pearson, 1997).This is fine for measuring molecular stability, but energy alone is inadequate for solids because they have two types of stability size and shape. The elastic bulk modulus measures the size stability, while the elastic shear modulus measures the shape stability. The less symmetric solids require the full set of elastic tensor coefficients to describe their stabilities. Therefore, solid structures of high symmetry require at least two parameters to describe their stability. [Pg.189]

A methyl radical abstracts a This step produces a molecule of methyl chlorine atom from a chloride and a cholrine atom. The chlorine chlorine molecule. atom can now cause a repetition of Step 2. [Pg.374]

As a phase transition occurs, there is a change of some type in the lattice. The units (molecules, atoms, or ions) become more mobile. If the solid is reacting in some way and the temperature is at or very near that at which the solid undergoes a phase transition, there may be a rapid increase in the rate of the reaction with a slight increase in temperature because lattice reorganization enhances the ability of the solid to react. A similar situation can occur in cases in which two solids are reacting if the temperature is at or near the temperature corresponding to a phase transition in one of the solids. This phenomenon is sometimes referred to as the Hedvall effect. [Pg.276]

Boltzmann distribution The law describing the partitioning of the available energy from the local environment among the available levels of a molecule, atom or, in general, a system. [Pg.308]

Flytzanis, C. French patent "Nonlinear Behaviour of molecules Atoms and Ions in Electric, Magnetic or Electromagnetic 22. [Pg.106]

C. Flytzanis, in Nonlinear Behaviour of Molecules Atoms and Ions in Electrics, Magnetics or Electromagnetic Fields... [Pg.184]

The collision theory of reaction rates states that molecules, atoms or ions must collide effectively in order to react. For an effective collision to occur, the reacting species must have (1) at least a minimum amount of energy in order to break old bonds and make new ones, and (2) the proper orientation toward each other. [Pg.259]


See other pages where Molecules atoms is mentioned: [Pg.144]    [Pg.261]    [Pg.98]    [Pg.81]    [Pg.91]    [Pg.912]    [Pg.1280]    [Pg.241]    [Pg.942]    [Pg.958]    [Pg.284]    [Pg.98]    [Pg.124]    [Pg.17]    [Pg.7]    [Pg.171]    [Pg.90]    [Pg.726]    [Pg.728]    [Pg.502]    [Pg.37]    [Pg.76]    [Pg.78]    [Pg.366]   
See also in sourсe #XX -- [ Pg.260 ]




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A Computer-Algebraic Approach to the Derivation of Feynman-Goldstone Perturbation Expansions for Open-Shell Atoms and Molecules

AIM (“atoms in molecules

ATOMS, MOLECULES, AND IONS

Ab Initio Calculations on Molecules containing Five or Six Atoms

Absorption, atoms/molecules

Accurate Determination of Electric Field Gradients for Heavy Atoms and Molecules

Adsorbed atoms and molecules

All Things Are Made of Atoms and Molecules

All atoms-in-molecules

Applications of Cooled Atoms and Molecules

Asymmetric molecules hydrogen atom

Atom 4 Molecule Bimolecular Transfer Reactions

Atom and Molecule Probes

Atom in the molecule

Atom-Linear Molecule Dispersion

Atom-in-molecule model

Atom-in-molecule polarizability

Atom-in-molecule similarity

Atom-molecule complex mechanism

Atom-molecule complexes

Atom-molecule complexes anisotropic interactions

Atom-molecule reaction

Atom-molecule reactions studied in flow systems the hydrogen halide system

Atom-molecule scattering

Atom-water molecule adducts

Atom/ion/molecule reaction

Atomic force microscopy dendrimer molecules

Atomic force microscopy molecule types

Atomic force microscopy single-molecule studies

Atomic orbitals heteronuclear diatomic molecules

Atomic orbitals homonuclear diatomic molecules

Atomic orbitals in molecules

Atomic reactions with diatomic molecules

Atomic single molecule biopolymers

Atomic substrate-molecule-particle

Atoms and Molecules A Momentum Space Perspective

Atoms and Molecules Have Energies

Atoms and Molecules in Optical Lattices

Atoms and Molecules in Space

Atoms and Molecules in Strong Laser Fields

Atoms and Molecules of the Elements

Atoms and Other Molecules Sorbed onto Solids

Atoms and molecules

Atoms and molecules of simple gases

Atoms in a Molecule Are Held Together by Chemical Bonds

Atoms in a molecule

Atoms in molecules and structural formulae

Atoms in molecules theory

Atoms in molecules, electronegativity and

Atoms in open-shell molecules

Atoms into Molecules

Atoms molecules containing

Atoms vs. Molecules and Complex Ions

Atoms, elements, molecules

Atoms-In-Molecules

Atoms-in-Molecules Discretization

Atoms-in-molecules analysis

Atoms-in-molecules approach

Atoms-in-molecules methods

Bader’s theory of atoms in molecules

Benzonitrile and some molecules containing eight carbon atoms

Bonds between atoms and molecules

CHEMISTS USE RELATIVE MASSES TO COUNT ATOMS AND MOLECULES

Central atom concepts designer molecules

Charges on atoms in molecules

Chemical Composition Atoms, Molecules, and Ions

Chiral recognition molecule net atomic partial

Compound atom molecules

Consecutive atom reactions with molecules

Coordinates, atomic molecule centered

Diatomic Molecules with Different Atomic Nuclei

Diatomic molecules, atomic pressures

Diatomic molecules, atomization

Diatomic molecules, atomization metals

Diffraction atoms, molecules

Effects in heavy-atom molecules

Electron Density Description of Atoms and Molecules

Electron Density Integrals and Atoms-in-Molecules Methods

Electron-deficient atoms/molecules

Electron-excited state of atoms and molecules

Electronegativity The tendency of an atom in a molecule to attract shared electrons

Electronegativity as Connectivity of Atoms in Molecules

Electronegativity of Atoms-in-Molecules

Electronic Motion in the Mean Field Atoms and Molecules

Electronic Structure of Atoms and Molecules

Elements, Atoms and Molecules

Elements, atoms, molecules and substances

Encaged atoms molecules

Energy of an atom in a molecule

Energy of atoms and molecules

Excitation of atoms and molecules

Excited Rare Gas Atoms by Molecules Containing Group IV elements

Excited atoms (or molecules)

Excited atoms and molecules

Excited states, of atoms and molecules

FATO molecular mechanics of nitrogen atom. Model ammonia molecule

FATO molecular mechanics of oxygen atom. Model water molecule

Fluorescence Spectroscopy of Adsorbed Atoms and Molecules

Fluorine atoms, in molecules

Forces between Atoms and Molecules

Geometry of Molecules with More Than One Central Atom

Ground state, of atoms and molecules

H. Stoll, Electronic structure calculations for molecules containing lanthanide atoms

Heavy-atom molecules

Heavy-atom molecules Dirac-Coulomb

Heavy-atom molecules Dirac-Coulomb-Breit

Heavy-atom molecules Dirac-Fock

Heavy-atom molecules Hamiltonians

Heavy-atom molecules collisions

Heavy-atom molecules, relativistic

Heavy-atom molecules, relativistic effects

Homonuclear diatomic molecule first-period atoms

Homonuclear diatomic molecule second-period atoms

Homonuclear diatomic molecules atomic / -orbital combinations

Hydrogen atom deficient molecules

Hydrogen atoms, in molecules

Hypervalent molecules atomic charges

INDEX OF ATOMS AND MOLECULES

Imaging Atoms, Molecules, and Chemical Reactions

Implications for the Description of Atoms and Molecules

Individual gauges for atoms in molecules

Intermetallic molecules, atomic cell

Interstellar molecules, carbon atom reactions

Isomerism some different arrangements of atoms within a molecule

Light from atom-molecule

MANY-BODY THEORIES FOR ATOMS AND MOLECULES

Magnetic Moments of Atoms and Molecules

Manipulating Atoms and Molecules with STM

Manipulation of atoms and molecules

Many atoms in contact The solid state as a giant molecule

Matter Consists of Atoms and Molecules

Metal atoms molecules

Metal atoms reactions with small-molecule organic

Molecular structure The three-dimensional arrangement of atoms in a molecule

Molecule numbering atoms

Molecules atomizing

Molecules atomizing

Molecules containing four carbon atoms

Molecules containing hetero atom

Molecules containing one carbon atom

Molecules containing three carbon atoms

Molecules containing two carbon atoms

Molecules containing very heavy atoms

Molecules counting atoms

Molecules five-atom

Molecules four-atom

Molecules made from Hydrogen Atoms

Molecules many-electron atom

Molecules with Lone Pairs on the Central Atom

Multielectron Atoms and Molecules

Nature of Atoms and Molecules

Numbering the atoms of a molecule

Observable transitions in atoms and molecules

Other Four-Atom Molecules

Oxidation state, of atoms in a molecule

Oxygen atom, electron affinity molecule

Packing of atoms and molecules

Partition Functions of Atoms and Molecules

Phenyl group The benzene molecule minus one hydrogen atom

Photodissociation Dynamics of Hydride Molecules H Atom Photofragment Translational Spectroscopy (Ashfold, Mordaunt, and Wilson)

Planar four-atom molecules

Polarizability free atoms and molecules

Polarizability of atoms and molecules

Polyelectronic atoms and molecules

Potential parameters atom/molecule

Principles Atoms and Molecules

Probability Distributions for Atoms and Molecules

Properties of Atoms, Ions, Molecules, and Solids

Properties of atoms in molecules

Pyramidal Four-Atom Molecules

Pyridine and other molecules containing five carbon atoms

Quantum Atoms-in-Molecules Similarity

Quantum theory of atoms in molecules

Quantum theory of atoms in molecules QTAIM)

Quantum theory of atoms molecules

Radii of Atoms in Molecules and Crystals

Reaction Cross Section Atom-Molecule Systems

Reaction of Atoms and Molecules

Reactions From Unsaturated Molecules by F or Cl Atoms

Reactions between Atoms, Radicals and Unsaturated Molecules

Reactive hydrogen atoms-halogen molecule

Reduced-Density-Matrix Mechanics . With Application to Many-Electron Atoms and Molecules

Refraction, atomic organic molecules

Relative Masses of Atoms and Molecules

Relaxation of Electronically Excited Atoms and Molecules

Release of Hydrogen Atoms and Molecules from Recycling Processes

Rovibrational spectra - an example of accurate calculations atom - diatomic molecule

Scattering by Molecules Independent Atom Approximation

Selected Molecules with Four or More Atoms

Selection Rules in Atoms and Molecules

Sensitivity of Atoms-in-Molecules

Shape Resonances in Atom and Molecule Scattering

Shielding of Nuclei in Atoms and Molecules

Short-lived Elementary Particles in Atoms and Molecules

Silicon cations, atomic, reactions with neutral molecules

Single-molecule methods atomic force microscope

Skill 12.1c-Differentiate between atoms, molecules, elements, and compounds

Spectrometry Measuring the Mass of Atoms and Molecules

Square-planar five-atom molecules

Strategies for Assigning Resonance to Atoms Within a Molecule

Surfaces atom-molecule interaction

Temperature Random Motion of Molecules and Atoms

Testing Simple Atoms and Molecules

Tetra-atomic Molecules

Tetrahedral and Square-Planar Five-Atom Molecules

Tetrahedral five-atom molecules

The Building of Atoms and Molecules

The Electric Nature of Atoms and Molecules

The Structure of Matter Atoms and Molecules

The Virial Theorem for Atoms and Diatomic Molecules

The Wonderful World of Atoms and Molecules

The many-body problem in atoms and molecules

The theory of atoms in molecules

Theory of atoms in molecules

Thermal motion of atoms and molecules

Transfer of the Tellurium Atom to other Molecules

Trigonal molecules diastereotopic atoms

Trigonal molecules enantiotopic atoms

Valence-shell electron-pair repulsion molecules with multiple central atoms

Vibrations of Adsorbed Atoms and Molecules

Weights of atoms and molecules

What Happens When Individual Atoms and Molecules Collide

World of Atoms and Molecules

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