We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The ...

Two softwares used for sequence alignment and searches are BioJava and BioPerl Comparison between these two tolls is shown. There are several software engineering issues such as software reuse, component-based software engineering, cleanroom engineering. We are discussing here software reuse (reusable objects). What kind and amount of bimolecular data is available and how to encode that data an...

In this study, acetylcholinesterases (AChEs)were extracted from twoMexicanBoophilusmicroplus strains thatdemonstrated resistance to theorganophosphate(OP)acaricide, coumaphos, in bioassay. The rate of inhibition of the extractedAChEs by the diethyl-OPparaoxonwas determined for two resistant strains and two susceptible strains ofB.microplus. The time to inhibition of 50%AChE activity was approxi...

From a rigorous multichannel quantum-defect formulation of bimolecular processes, we derive a fully quantal and analytic model for the total rate of exoergic bimolecular reactions or inelastic processes that is applicable over a wide range of temperatures including the ultracold regime. The theory establishes a connection between the ultracold chemistry and the regular chemistry by showing that...

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereosel...

A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This "deoxyribozyme" can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas th...

A combined multivariate and theoretical analysis of coupled XAS/UV–Vis data was proven to be an innovative method obtain direct structural mechanistic evidence for bimolecular reactions in solution involving organic substrates.

The tetramolecular PNA quadruplex motif has been probed using a dynamic covalent chemistry (DCC) approach to create and characterize a bimolecular PNA quadruplex.