Biomedical subjects

Paul L A Popelier

Publications and source records attributed to Paul L A Popelier.

9 recordsLinked to original sources

PubMed2007

Long range behavior of high-rank topological multipole moments.

The construction of a high-rank multipolar force field (for peptides) is a complex task, leading to several intermediate questions in need of a clear answer. Here we focus on the convergence of the (electrostatic) multipolar expansion at medium and long range. Using molecular electron densities, quantum chemical topology (QCT) defines the atoms as finite volumes, each endowed with multipole moments. The terms in the multipole expansion are grouped according to powers of the internuclear distance, R(-L). Given two atom types at a given distance, we determine which rank (L) is necessary for the electrostatic energy to converge to the exact interaction energy within a certain error. With this information, the rank of the expansion for each interaction can be adapted to the required accuracy and the available computing power.

Carbon Monoxide↗

PubMed2006

Transferability of quantum topological atoms in terms of electrostatic interaction energy.

Understanding atomic transferability is important to guide the design of a force field. Atoms in molecules are defined and computed according to the theory of quantum chemical topology (QCT). The electron density associated with such topological atoms is conveniently described by high-rank multipole moments. Here, we assess the transferability of atoms by means of their electrostatic interaction energy, using a convergent multipole expansion. The test systems are (H2O)3 and serine...(H2O)5. The effect of a varying electron density cutoff (i.e., truncating the atoms) is discussed and the effect of polarization is quantified.

Journal Article↗

PubMed2006

Computation of relative bond dissociation enthalpies (DeltaBDE) of phenolic antioxidants from quantum topological molecular similarity (QTMS).

A recently proposed method called quantitative topological molecular similarity (QTMS) generated a model for the computation of the relative substituent effects on the bond dissociation enthalpies (DeltaBDEs) for a set of 39 phenols. The data set includes a diverse set of substituents with monosubstituted and poly-substituted derivatives that exhibit different electronic and steric effects. Many share common structural features with already well-established antioxidants. QTMS reveals the active region of the substituted phenols and identifies the electronic descriptors that best explain the range of DeltaBDEs observed. For substituents in the 4-X position (para) we find that our model requires a correction for radical stabilization enthalpy (RSE). Application of the QTMS methodology yields an unrivalled QSAR with r(2) = 0.98 and q(2) = 0.85 for the bond dissociation enthalpies of this phenolic antioxidant data set.

Journal Article↗

PubMed2003

An algorithm to delineate and integrate topological basins in a three-dimensional quantum mechanical density function.

The growing activity in the area of Quantum Chemical Topology warrants a new algorithm to delineate topological basins in 3D scalar fields other than the electron density. A method based on the "octal tree search algorithm" of computer graphics is proposed to reach this goal. We illustrate the algorithm on the L(r) function, which is the negative of the Laplacian of the electron density. Because of its complicated topology, even in a simple test molecule such as water, it benefits from the octal tree algorithm as a robust, compact, and general technique to find the boundaries of topological basins. For the first time, we are able to compute the population and volume of the core and valence (bonding and nonbonding, i.e., lone pair) basins given by L(r)'s topology.

Journal Article↗

PubMed2003

Atomic properties of selected biomolecules: quantum topological atom types of hydrogen, oxygen, nitrogen and sulfur occurring in natural amino acids and their derivatives.

Molecular electron densities are generated at B3LYP/6-311+G(2d,p)//HF/6-31G(d) level for 57 molecules, including one conformation of each naturally occurring amino acid and smaller derived molecules. The electron densities are partitioned into atomic fragments according to the approach of quantum chemical topology (QCT). A set of 547 unique topological atoms is obtained, containing 421 hydrogens, 63 oxygens, 57 nitrogens and 6 sulfurs. Each atom is described by seven properties: volume, kinetic energy, monopole, dipole, quadrupole, octupole and hexadecapole moment. Cluster analysis groups atoms into atom types based on their similarity expressed in the discrete 7D space of atomic properties. Using a separation criterion we distinguish seven hydrogen, six oxygen, two nitrogen and six sulfur atom types.

Amino Acids↗

PubMed2003

An improved algorithm to locate critical points in a 3D scalar field as implemented in the program MORPHY.

A new algorithm for location of the critical points in general scalar fields is described. The new method has been developed as part of an on-going process to exploit the topologic analysis of general 3D scalar fields. Part of this process involves the use of topologic information to seed the critical point search algorithm. The continuing move away from topologic studies of just the electron density requires more general algorithms and the ability to easily "plug in" new functions, for example, the Laplacian of the electron density ( triangle down (2)rho), the Electron Localisation Function (ELF), the Localised Orbital Locator (LOL), the Lennard-Jones function (LJF), as well as any new functions that may be proposed in the future. Another important aspect of the current algorithm is the retention of all possible intermediate information, for example, the paths describing the connectivity of critical points, as well as an ability to restart searches, something that becomes increasingly important when analysing larger systems. This new algorithm represents a core part of a new local version of the MORPHY code. We distinguish nine universal types of gradient paths.

Journal Article↗

PubMed2003

The full topology of the Laplacian of the electron density: scrutinising a physical basis for the VSEPR model.

Within the framework of quantum chemical topology (QCT) the function L(r), which equals the negative of the Laplacian of the electron density, has been proposed before as a physical basis for the valence shell electron pair repulsion (VSEPR) model. The availability of a new algorithm to integrate property densities over the basins of L(r) enabled a re-evaluation of this physical basis. We optimised a set of nine molecules at B3LYP/6-311+G(2d,p) level and partitioned the corresponding L(r) function for each molecule into basins. For the first time we visualise these basins in L(r), by directly showing their boundaries. We identify the basins in L(r) with the domains of the VSEPR model. Observations drawn from the populations and volumes of L-basins are contrasted with the three subsidiary VSEPR postulates. We find unexpectedly small populations, nearer to one than to two, for non-hydrogen cores and bonding domains, and populations much larger than two for non-bonding domains. We conclude that non-bonding or lone pairs have larger domains than bonding pairs in the same valence shell, in accordance with VSEPR. We also confirm that double and triple bond domains are larger than single-bond domains. However we cannot substantiate the effect of the electronegativity of central atom or ligand on the volume of bonding domains. In summary, the full topology of L(r) supports two out of three subsidiary VSEPR postulates.

Journal Article↗

PubMed2002

The elusive atomic rationale for DNA base pair stability.

A systematic analysis of the electrostatic interaction between 27 natural DNA base pairs was carried out, based on ab initio correlated wave functions and the topology of the electron density. Using high rank multipole moments we show that the atomic partitioning of the interaction energy contains many substantial contributions between distant atoms. Profiles of cumulative energy versus internuclear distance show large fluctuations and provide an electrostatic fingerprint of the partitioning of interaction energy in a complex. A quantified comparison between each pair of energy profiles, one for each base pair, makes clear that there is no correlation between the total base pair interaction energy and the shape of the profile. In other words, base pairs with similar interaction energy are not stable for the same reasons in terms of atomic partitioning. In summary, simple rules to rationalize the pattern of energetic stability of naturally occurring base pairs in terms of subsets of atoms are elusive. Our work cautions against inappropriate use of Jorgensen's secondary interaction hypothesis.

Base Pairing↗

PubMed2002

Distributed response analysis of conductive behavior in single molecules.

The ab initio computational approach of distributed response analysis is used to quantify how electrons move across conjugated molecules in an electric field, in analogy to conduction. The method promises to be valuable for characterizing the conductive behavior of single molecules in electronic devices.

Journal Article↗