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Atomic Properties of Selected Biomolecules: Quantum Topological Atom Types of Hydrogen, Oxygen, Nitrogen and Sulfur Occurring in Natural Amino Acids and Their Derivatives
Author(s) -
Popelier Paul L. A.,
Aicken Fiòna M.
Publication year - 2003
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.200390138
Subject(s) - chemistry , molecule , atoms in molecules , topology (electrical circuits) , sulfur , nitrogen , atom (system on chip) , biomolecule , dipole , hydrogen atom , quadrupole , hydrogen , crystallography , atomic physics , computational chemistry , group (periodic table) , physics , organic chemistry , biochemistry , mathematics , combinatorics , computer science , embedded system
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.