Random diffusion is supposed to be mostly responsible for the meeting of molecules before they are able to recognize. However, this mechanism is only efficient at short distances. The transmission of information between molecules can be explained in terms of their electromagnetic properties. According to the Shannon paradigm, a message is emitted by a source and then transmitted to an addressee via a channel, where eventually perturbations can take place. In the present scheme the source is equipped with an apparatus of emission and the addressee contains a reception set. It is shown that some charged and flexible aminoacid side chains can behave as aerials with specific power and directivity properties and therefore are able to emit and/or receive electromagnetic power containing structural and dynamical information. Several molecular systems ( in vacuo and in water for the blocked aminoacids ) have been investigated to demonstrate these findings: arginine, glutamic acid, arginine in presence of glutamic acid and glutamic acid in presence of arginine.
Results and discussion:
In order to obtain the scalar and vector potentials the Maxwell equations are solved using atomic point charges as deduced from high level quantum mechanical calculations (Mulliken and HF/6-31G*) and atomic accelerations given by long time (several nanoseconds) molecular dynamics simulations. In this latter case, the use of the SPASIBA force field  is essential since a precise knowledge of low vibrational frequencies is required. It was first demonstrated that electrostatic charges do not depend upon conformational changes as previously found . The electrostatic potential was calculated on several spheres centered on the center of gravity of the molecule and with diameters of 3, 6 and 12 angstroems. It was found to be also insensitive to conformational changes.
The Poynting vector is obtained as the vector product of the electric field vector and the magnetic field vector. Integration of the Poynting vector over a closed surface corresponds to the radiated energy per time unit. The mean emitted power P is equal to the Poynting vector flux through a closed surface. The directivity D is the energy density in a certain direction of space divided by the density when the radiation is uniform in all directions. From a Fourier transform of the molecular dynamics (3.3 nanoseconds) trajectory performed in the present case in vacuo, oscillation frequencies (or wavenumbers) of the dipole moment were obtained. Table 1 gives some low wavenumbers for the blocked aminoacids N-acetyl-L-arginine-N-methylamide and N-acetyl-L-glutamic acid-N-methylamide .
Table 1: some low wavenumbers (cm-1) (and amplitudes (Debye) in parenthesis) for the blocked aminoacids Arg and Glu
Table 2 gives the mean emitted power (kcal.mol-1.s-1) and the directivity (no unit) for the blocked arginine and glutamic acid.
Table 2: Mean power of emission P (kcak.mol-1.s-1) and directivity D of the two blocked aminoacids in vacuo
It should be noted that a directivity of 1 corresponds to an isotropic emission (no preferred direction). From Table 2 it is found that arginine displays a high power of emission with a high directivity. Arginine and glutamic acid exhibit a common very low wavenumber (27 cm-1). This result indicates that a resonance phenomenon can occur between the two molecules. For checking these findings, a molecular dynamics simulation of the two compounds in presence has been performed both in vacuo and in a water box. In this case arginine is found to transmit electromagnetic power to glutamic acid with a high directivity. These computer experiments give a new insight on the molecular rendez-vous which take place before molecular recognition.
Derreumaux, P., Vergoten, G., J. Chem. Phys., 102 (1995) 8586
Dinur U., Hagler, A.T., J. Comp. Chem., 16 (1995) 154
Prof. G. VERGOTEN
CRESIMM, Université des Sciences et Technologies de Lille,
Bât C8 59655 Villeneuve d'Ascq cedex, France