Biomedical subjects

J Liévin

Publications and source records attributed to J Liévin.

3 recordsLinked to original sources

PubMed2006

The VMFCI method: a flexible tool for solving the molecular vibration problem.

The present article introduces a general variational scheme to find approximate solutions of the spectral problem for the molecular vibration Hamiltonian. It is called the "vibrational mean field configuration interaction" (VMFCI) method, and consists in performing vibrational configuration interactions (VCI) for selected modes in the mean field of the others. The same partition of modes can be iterated until self-consistency, generalizing the vibrational self-consistent field (VSCF) method. As in contracted-mode methods, a hierarchy of partitions can be built to ultimately contract all the modes together. So, the VMFCI method extends the traditional variational approaches and can be included in existing vibrational codes based on the latter approaches. The flexibility and efficiency of this new method are demonstrated on several molecules of atmospheric interest.

Computer Simulation↗

PubMed2000

Contribution of cation-pi interactions to the stability of protein-DNA complexes.

Cation-pi interactions between an aromatic ring and a positive charge located above it have proven to be important in protein structures and biomolecule associations. Here, the role of these interactions at the interface of protein-DNA complexes is investigated, by means of ab initio quantum mechanics energy calculations and X-ray structure analyses. Ab initio energy calculations indicate that Na ions and DNA bases can form stable cation-pi complexes, whose binding strength strongly depends on the type of base, on the position of the Na ion, and whether the base is isolated or included in a double-stranded B-DNA. A survey of protein-DNA complex structures using appropriate geometrical criteria revealed cation-pi interactions in 71% of the complexes. More than half of the cation-pi pairs involve arginine residues, about one-third asparagine or glutamine residues that only carry a partial charge, and one-seventh lysine residues. The most frequently observed pair, which is also the most stable as monitored by ab initio energy calculations, is arginine- guanine. Arginine-adenine interactions are also favorable in general, although to a lesser extent, whereas those with thymine and cytosine are not. Our calculations show that the major contribution to cation-pi interactions with DNA bases is of electrostatic nature. These interactions often occur concomitantly with hydrogen bonds with adjacent bases; their strength is estimated to be from three to four times lower than that of hydrogen bonds. Finally, the role of cation-pi interactions in the stability and specificity of protein-DNA complexes is discussed.

Arginine↗

PubMed1999

Emission Spectroscopy and Ab Initio Calculations on IrN.

The emission spectrum of IrN was recorded in the near infrared using a Fourier transform spectrometer. The IrN molecules were excited in an Ir hollow cathode lamp operated with a mixture of Ne and a trace of N(2). Numerous IrN bands observed in the 7500-9200 cm(-1) region were assigned to a new a(3)Pi-X(1)Sigma(+) electronic transition with the 0-0 bands of the a(3)Pi(0)-X(1)Sigma(+) and a(3)Pi(1)-X(1)Sigma(+) subbands near 9175 and 8841 cm(-1), respectively. A rotational analysis of several bands of the 0-0 and 0-1 sequences was obtained and molecular constants were extracted. The effective Hund's case (a) constants for the new a(3)Pi state are: T(00) = 8840.31747(88) cm(-1), A(0) = -340.53329(93) cm(-1), DeltaG(1/2) = 984.3629(23) cm(-1), B(e) = 0.4699116(27) cm(-1), alpha(e) = 0.0030058(50) cm(-1), and r(e)= 1.6576432(47) Å. The spectroscopic properties of the ground state and several low-lying electronic states of IrN were also predicted by ab initio calculations. These calculations are consistent with our assignment of the a(3)Pi-X(1)Sigma(+) transition and also support our previous assignments of the A' (1)Pi and A(1)Pi electronic states [R. S. Ram and P. F. Bernath, J. Mol. Spectrosc. 193, 363 (1999)]. The excited a(3)Pi state of IrN has an 1varsigma(2)2varsigma(2)1pi(4)3varsigma(1)1delta(4)2pi(1) electron configuration and the configurations of the other low-lying electronic states are also discussed. Copyright 1999 Academic Press.

Journal Article↗