Abstract:In this paper, an evolutionary approach, improved CAMD based on the hybrid gene algorithm and simulated annealing algorithm (GASA), is developed. The new approach combines the feature of GA and SA, avoiding the problem of prematurity. With a new category strategy of candidate groups from the Mod UNIFAC group database adopted, a repair operator is introduced to guarantee the integrity of randomly generated molecules and thus the search of straight chain alkane as well as cyclane solutions can be performed toget… Show more
“…The reverse problem is a mixed-integer nonlinear programming problem aimed at finding the correct molecular structures that would produce the desired material properties. Commonly used optimization algorithms include the genetic algorithm (GA), − simulated annealing (SA), ,, GASA, , ant colony optimization, , tabu search, ,, outer approximation, − branch-and-reduce algorithm, − exhaustive search with problem decomposition, − etc. A key component hidden in CAMD algorithms is the representation of the three-dimensional molecular structure of a molecule using digital data based on which different operations can be applied to alter the chemical structure of the existing molecules or to generate new ones.…”
A new
molecular data structure and molecular structure operation
algorithms are proposed for general purpose molecular design. The
data structure allows for a variety of molecular operations for creating
new molecules. Two types of molecular operations were developed, unimolecular
and bimolecular operations. In unimolecular operations, a child molecule
can be created from a parent via addition of a functional group, deletion
of a fragment, mutation of an atom, etc. In bimolecular operations,
children molecules are generated from two parent molecules through
combination or crossover (hybridization). These molecular operations
are essential for the creation and modification of molecules for the
purpose of molecular design. The data structure is capable of representing
linear, branched, multifunctional, and multivalent compounds. Algorithms
are developed for deriving the molecular data structure of a molecule
from its atomic coordinates and vice versa. We show that this new
molecular data structure and the developed algorithms, referred to
as Molecular Assembling and Representation Suite, allow one to generate
a comprehensive library of new molecules via performing every possible
molecular structure modification.
“…The reverse problem is a mixed-integer nonlinear programming problem aimed at finding the correct molecular structures that would produce the desired material properties. Commonly used optimization algorithms include the genetic algorithm (GA), − simulated annealing (SA), ,, GASA, , ant colony optimization, , tabu search, ,, outer approximation, − branch-and-reduce algorithm, − exhaustive search with problem decomposition, − etc. A key component hidden in CAMD algorithms is the representation of the three-dimensional molecular structure of a molecule using digital data based on which different operations can be applied to alter the chemical structure of the existing molecules or to generate new ones.…”
A new
molecular data structure and molecular structure operation
algorithms are proposed for general purpose molecular design. The
data structure allows for a variety of molecular operations for creating
new molecules. Two types of molecular operations were developed, unimolecular
and bimolecular operations. In unimolecular operations, a child molecule
can be created from a parent via addition of a functional group, deletion
of a fragment, mutation of an atom, etc. In bimolecular operations,
children molecules are generated from two parent molecules through
combination or crossover (hybridization). These molecular operations
are essential for the creation and modification of molecules for the
purpose of molecular design. The data structure is capable of representing
linear, branched, multifunctional, and multivalent compounds. Algorithms
are developed for deriving the molecular data structure of a molecule
from its atomic coordinates and vice versa. We show that this new
molecular data structure and the developed algorithms, referred to
as Molecular Assembling and Representation Suite, allow one to generate
a comprehensive library of new molecules via performing every possible
molecular structure modification.
“…The GC approach was later developed into a multilevel CAMD method where the connectivity of functional groups and three-dimensional structure are taken into account after the initial functional group search . Since then, GC based CAMD has been applied toward the search for alternative refrigerants and gas absorbents, in addition to the design of extraction solvents. − …”
The value of fine and specialty chemicals is often determined by the specific requirements in their physical and chemical properties. Therefore, it is most desirable to design the structure of chemicals to meet some targeted material properties. In the past, the design of specialty chemicals has been based largely on experience and trial-and-error. However, recent advances in computational chemistry and machine learning can offer a new path to this problem. In this presentation, we demonstrate a successful example where the structure of a chemical of specified value of octanol−water partition coefficient (K ow ) can be predicted by computers. This method consists of two parts, the first being a robust method, the COSMO-SAC activity coefficient model, that predicts the activity coefficient with input of only the molecular structure. The second component of this method is a derivative-free optimization algorithm that searches in the multidimensional structure space for the desired value of K ow . In particular, the genetic algorithm (GA), based on the Darwinian theory of evolution and natural selection, combined with simulated annealing (SA) is adopted for this purpose. Compared to other optimization algorithms, GA can overcome the problem of being trapped in local minima and SA can help improve the convergence. Therefore, the GA−SA combination has been found to be very suitable for molecular design. We show that the value of K ow can be achieved within 1% of the target in 30 generations with a proper set of evolution parameters (including the size of the population, the probability of selection, the rate of temperature annealing, etc.). The same method can be applied to the search for chemicals with other desired properties, such as vapor pressure and solubility.
“…The task of selecting a solvent or solvent mixture with a desirable combination of physical properties to meet the needs of specific applications has largely been tackled using a combination of heuristics and experimental studies. − Models have been proposed to make use of the different existing predictive polymer miscibility concepts in performing a computer aided molecular design, thereby transferring the solvent search from the laboratory to the desktop. − However, in this context of solvent selection, we would like to highlight it was not our intention to use computer aided molecular design because we consider our selection not as completely unlimited. There is considerable guidance existing from industry and regulatory bodies in the food contact and pharmaceutical area.…”
Regulatory authorities require the
biopharmaceutical industry to
demonstrate that extractables that may migrate from production systems
do not alter the safety, efficacy, potency, or purity of drug products.
Extractables studies of polymeric materials used in production systems
and in particular single-use systems are designed to show material
safety and should support the users to perform risk-based toxicological
assessment of leachables that could potentially enter into the final
product under process conditions. In this paper, we intend to improve
the understanding of solvent–polymer interactions and thereby
allow the prediction of extractables from a range of fluids based
on their chemical properties. The possibility to predict solvent–polymer
interactions and polymer swelling in biopharmaceutical applications
based on solubility parameters is introduced.
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