Molecular tailoring approach for geometry optimization of large molecules: Energy evaluation and parallelization strategies

A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including alpha-tocopherol, taxol, gamma-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.The authors thank C-DAC, UGC (CAS program to the University of Pune) and the Council of Scientific and Industrial Research (CSIR), New Delhi for financial assistance

An ab initio and force field study on the conformation and chain flexibility of the dichlorophosphazene trimer

Ab initio molecular orbital calculations have been used to study the conformation, valence electron charge density, and chain flexibility of a dichlorophosphazene trimer (CH3[NP(Cl2)]3CH3). The calculations were carried out at the restricted Hartree-Fock level with the 6-31 G* basis set. The dichlorophosphazene trimer adopts a planar transcis conformation. The valence electron charge distribution indicates strong charge separations along the backbone of the molecule, and is in agreement with Dewar's island delocalization model for bonding in linear and cyclic phosphazenes. In order to determine the height of the torsional barrier (2,5 kcal/mol), the torsional potential of a central P-N bond of the trimer was studied with a rigid rotor scan and geometry optimizations of selected rotamers. The flexibility of the P-N-P bond angle contributes significantly to the chain flexibility. Based on the results of the ab initio calculations, an empirical force field for the dichlorophosphazene trimer was developed. The energy expression includes bond stretch, angle bend, electrostatic, van der Waals, and torsional potential terms. A relaxed scan with the force field achieves good agreement with the ab initio results for the torsional potential in the vicinity of the stable conformation, and an excellent agreement with the ab initio results on changes in the P2N2P3 bond angle and the N1P2 - N2P3 dihedral angle during a full rotation around the N2 - P3 bond

Ab initio lattice dynamics of nonconducting crystals by systematic fragmentation

A systematic method for approximating the ab initio electronic energy of crystal lattices has been improved by the incorporation of long range electrostatic and dispersion interactions. The effect of these long range interactions on the optimization of the crystal structure is reported. The harmonic lattice dynamics have been evaluated to give phonon frequencies and neutron scattering intensities. Exemplary results are reported for diamond, silicon, and α-quartz using Hartree-Fock, Möller-Plesset perturbation, and coupled-cluster levels of ab initio theory

The Hessian biased singular value decomposition method for optimization and analysis of force fields

We present methodology (HBFF/SVD) for optimizing the form and parameters of force fields (FF) for molecular dynamics simulations through utilizing information about properties such as the geometry, Hessian, polarizability, stress (crystals), and elastic constants (crystals). This method is based on singular value decomposition (SVD) of the Jacobian describing the partial derivatives in various properties with respect to FF parameters. HBFF/SVD is effective for optimizing the parameters for accurate FFs of organic, inorganic, and transition metal compounds. In addition it provides information on the validity of the functional form of the FF for describing the properties of interest. This method is illustrated by application to organic molecules (CH2O, C2H4, C4H6, C6H8, C6H6, and naphthalene) and inorganic molecules (Cl2CrO2 and Cl2MoO2)

Ab initio energies of nonconducting crystals by systematic fragmentation

A systematic method for approximating the ab initio electronic energy of molecules from the energies of molecular fragments has been adapted to estimate the total electronic energy of crystal lattices. The fragmentation method can be employed with any ab initio electronic structure method and allows optimization of the crystal structure based on ab initio gradients. The method is demonstrated on SiO₂ polymorphs using the Hartree-Fock approximation, second order Moller-Plesset perturbation theory, and the quadratic configuration interaction method with single and double excitations and triple excitations added perturbatively