6 research outputs found
Valence isomerization of 2-phospha-4-silabicyclo[1.1.0]butane: a high-level ab initio study
The rearrangements for 2-phospha-4-silabicyclo[1.1.0]butane, analogous to the valence isomerization of the hydrocarbons bicyclobutane, 1,3-butadiene, and cyclobutene, were studied at the (U)QCISD(T)/6-311+G**//(U)QCISD/6-31G* level of theory. The monocyclic 1,2-dihydro-1,2-phosphasiletes are shown to be the thermodynamically preferred product, in contrast to the isomerization of the hydrocarbons, which favors the 1,3-butadiene structure. Furthermore, an unprecedented direct isomerization pathway to the 1,2-dihydro-1,2-phosphasiletes was identified. This pathway is competitive with the isomerization via the open-chain butadienes and becomes favorable when electron-donating substituents are present on silicon
A Self-Organizing Algorithm for Modeling Protein Loops
Protein loops, the flexible short segments connecting two stable secondary
structural units in proteins, play a critical role in protein structure and
function. Constructing chemically sensible conformations of protein loops that
seamlessly bridge the gap between the anchor points without introducing any
steric collisions remains an open challenge. A variety of algorithms have been
developed to tackle the loop closure problem, ranging from inverse kinematics to
knowledge-based approaches that utilize pre-existing fragments extracted from
known protein structures. However, many of these approaches focus on the
generation of conformations that mainly satisfy the fixed end point condition,
leaving the steric constraints to be resolved in subsequent post-processing
steps. In the present work, we describe a simple solution that simultaneously
satisfies not only the end point and steric conditions, but also chirality and
planarity constraints. Starting from random initial atomic coordinates, each
individual conformation is generated independently by using a simple alternating
scheme of pairwise distance adjustments of randomly chosen atoms, followed by
fast geometric matching of the conformationally rigid components of the
constituent amino acids. The method is conceptually simple, numerically stable
and computationally efficient. Very importantly, additional constraints, such as
those derived from NMR experiments, hydrogen bonds or salt bridges, can be
incorporated into the algorithm in a straightforward and inexpensive way, making
the method ideal for solving more complex multi-loop problems. The remarkable
performance and robustness of the algorithm are demonstrated on a set of protein
loops of length 4, 8, and 12 that have been used in previous studies