Dynamic molecules

Calling hydrogen the "comet" of the chemical universe 13 was laden with levels of meaning for a new mechanistic chemistry. The metaphor expressed a hypothesis that hydrogen is a finite particle, that it is in continuous and repetitive motion within a dynamic molecule, and that the gravitational analogy for chemical affinity is an apt one. 

Applying this idea to our history, we remember that physical chemistry has employed disciplinary methods and aims taken from both physics and chemistry and that its practice has been one of striking epistemological pluralism. Laboratory investigations aimed at understanding chemical reaction mechanisms profited from the selection of mechanical and kinetic hypotheses from physics that transformed the static molecule of classical organic chemistry into the dynamic molecule of physical organic chemistry. 

Knowing the three-dimensional structure of a protein is an important part of understanding how the protein functions. However, the structure shown in two dimensions on a page is deceptively static. Proteins are dynamic molecules whose functions almost invariably depend on interactions with other molecules, and these interactions are affected in physiologically important ways by sometimes subtle, sometimes striking changes in protein conformation. In this chapter, we explore how... 

Indirect methods for obtaining information on the kinetics of the associa-tion/dissociation equilibrium include sedimentation velocity and GPC experiments. The application of these techniques is based on comparison of sedimentation or GPC elution curves with model curves based on theories for separation of unimers and micelles during a sedimentation velocity (Gilbert 1955) or GPC (Ackers and Thompson 1965 Coll 1971 Prochazka et at. 1988, 1989) experiment. Experiments have been performed that demonstrate several of the qualitative model predictions (Prochazka et at. 1989). The main conclusions were that GPC curves with two well-separated peaks can only result from a slow dynamic molecule micelle equilibrium, and that no simple interpretation of elution curves in terms of relative concentrations of unimer and micelles is possible (Prochazka et at. 1989). Thus no quantitative information on the kinetics of the molecule micelle equilibrium can be obtained from sedimentation velocity or GPC data. 

The chair conformer can undergo conformational isomerism to a second chair conformer which is degenerate in energy with the first. Cyclohexane is thus a dynamic molecule which exists largely in one of two chair isomers. These are the lowest energy conformations. Other higher energy conformations of cyclohexane include the boat form, which is 10.1 kcal/mol (42.3 kJ/mol) above the chair form, and the twist boat form, which lies 3.8 kcal/mol (15.9 kJ/mol) above the chair form. 

Fig. 1.1. Schematic view of the Coulomb explosion imaging of nuclear dynamics. Molecules exposed to an intense laser field undergo structural deformation in response to the formation of light-dressed potential energy surfaces, and decompose into fragment ions after multiple ionization. Since the momentum vectors of fragment ions sensitively reflect the geometrical structure just before the Coulomb explosion, the ultrafast nuclear dynamics of a molecule in an intense laser field can be elucidated through measurements of the momenta of fragment ions...

Proteins are dynamic molecules with respect to structure. The preferred folded structure for a given set of environmental conditions is that which has the minimum free energy. The driving force to assume a given folded structure is a thermodynamic force. In aqueous systems, the hydrophobic side-chains will endeavour to orient away from the surrounding water and towards the core of the molecule. However, for high surface activity, it is essential that the protein molecule should unfold and orient its hydrophobic side-chains towards the oil phase. A lack of hydrophilic residues usually does not restrict protein functionality at interfaces. Thus, flexible proteins can create a highly hydrated, mobile layer to stabilize an emulsion particle. 

Much less is known about the first interaction between ligand and receptor. It seems to become clearer and clearer that the productive lock and key theory needs some adjustment. Receptors are dynamic molecules, being able to adapt several conformations. 

S. A. Superti-Furga, G. Wierenga, R.K. The 2.35 A crystal structure of the inactivated form of chicken Src a dynamic molecule with multiple regulatory interactions. J. Mol. Biol., 274, 757-775 (1997)... 

Fluorescence anisotropy can be used to study complex fonnation between two interacting molecules. Anisotropy allows obtaining an idea on the motion of a molecule. A highly dynamic molecule yields a low anisotropy value. 

The double helix is not symmetrical it has a broad and a narrow groove between the chains. These provide steric orientation for the processes of replication and transcription (Fig. 1). This right-handed double helix with 10 base pairs per helical turn is called B-DNA. It probably approximates closely the structure of relaxed (unstrained) DNA. It is generally accepted, however, that DNA is a dynamic molecule, with different conformations in equilibrium with one another. This equilibrium is affected by nucleotide sequence, ionic strength of the environment, presence of proteins [e. g. Histones (see) and other DNA binding proteins (see)] and the extent to which the molecule is under topological strain. 

Equation (1) refers to a crystal of m dynamic chains of 100 CHj-groups each. The second brackets represent the nonbonded interactions among all dynamic molecules i with j, where the latter are the dynamic atoms not considered in Eqs. (2,4, and 5) for the given /. The last term, summing over the interactions of the atoms i with k, is only needed if the crystal is enclosed with I chains of rigid (nondynamic) atoms to keep the volume constant The potential fimctions for the adjacent bonded atoms (i and i + 1) are ... 

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