Improved Algorithms For Subsystem Construction In The Generalized Energy-Based Fragmentation Approach And Their Applications

Fragment-based quantum chemistry methods have become important tools in investigating the energy,structure,and properties of large molecules and condensedphase systems.The core idea of fragment-based methods is to evaluate the total energy(or properties)of a target system through a linear combination of energies(or properties)of a series of small"electrostatically embedded"subsystems constructed according to some fragmentation schemes.Many fragment-based methods have been proposed by different groups and they differ from each other in the way of constructing subsystems.It is well established that these fragment-based methods can provide similar descriptions as conventional full-system calculations.The thesis is mainly to evaluate and improve the computational efficiency and applicability of the generalized energybased fragmentation(GEBF)method for large molecules and condensed-phase systems.The main contributions are summarized as follows.In Chapter 3,we have implemented an algorithm for constructing subsystems in EE-MB(electrostatically embedded many body)method and systematically compared the performance of GEBF and EE-MB in describing medium-sized water clusters(H20)n(Tn= 10,20,30)at large basis sets.We have revealed that at various levels of theory,GEBF can provide accurate descriptions on water clusters.When the basis set has diffuse functions,EE-MB shows a poor performance of convergence for(H2O)20(without a distance cutoff and each water molecule is taken as a fragment).For large basis sets with diffuse functions,EE-MB suffers from the BSSE(basis set superstition error)problem,while GEBF does not.A possible reason for the good performance of GEBF is that the BSSEs of subsystems are almost cancelled.With comparable computational cost,the overall performance of EE-MB(?)(even with two water molecules as a fragment)is inferior to GEBF.Accordingly,for large systems,GEBF is a cost-effective and reliable fragment-based quantum chemistry method.In Chapter 4,we have proposed an efficient and faster way of generating subsystems in GEBF and PBC-GEBF so that GEBF and PBC-GEBF calculations can be done for more complicated systems.Then,this newly implemented PBC-GEBF method is applied to evaluate the J-couplings of condensed-phase systems,such as liquid water.Our calculations show that PBC-GEBF calculations on a snapshot of molecular dynamic simulation can give descriptions,in good agreement with the experimental result.But the results based upon the cluster model substantially deviate from the experiment.The possible reason for this large discrepancy originates from the artificial boundary effect of the cluster model.In PBC-GEBF calculations on Jcouplings of liquid water,every water molecule within a unit cell is treated equally to obtain the ensemble-averaged molecular properties.Finally,we have also calculated the J-couplings of liquid CH3CH2COOH.In Chapter 5,we proposed a "fragment-based"subsystem construction scheme for PBC-GEBF to compute energies,structures,and properties of condensed-phased systems with large molecules in a unit cell.In this new scheme,a large molecule is first divided into several fragments,and a subsystem in PBC-GEBF is constructed as a union of several fragments,and thus the size of subsystems is much less than that of subsystems constructed previously that are a union of several molecules.Our calculations show that this fragment-based subsystem construction strategy is much faster than the old"molecule-based"strategy,when the basis set is relatively large.We then applied this newly implemented PBC-GEBF method to optimize the crystal structure of a medium-sized molecular crystal of peptide,and calculate the chemical shifts of all nuclei for this system.Our results reveal that the new fragmentation scheme can provide similar results as the original fragmentation scheme,with much less computational cost.Our work here provides a solid foundation for applications of PBC-GEBF in more complex crystals of biomacromolecules.Finally,at the end of this thesis,I summarized the main works I have accomplished and offered an outlook for further developments of fragment-based quantum chemistry methods and their applications.