Anuja P. Rahalkar

Enabling ab initio Hessian and frequency calculations of large molecules

A linear scaling method, termed as cardinality guided molecular tailoring approach, is applied for the estimation of the Hessian matrix and frequency calculations of spatially extended molecules. The method is put to test on a number of molecular systems largely employing the Hartree-Fock and density functional theory for a variety of basis sets. To demonstrate its ability for correlated methods, we have also performed a few test calculations at the Moller-Plesset second order perturbation theory. A comparison of central processing unit and memory requirements for medium-sized systems with those for the corresponding full ab initio computation reveals substantial gains with negligible loss of accuracy. The technique is further employed for a set of larger molecules, Hessian and frequency calculations of which are not possible on commonly available personal-computer-type hardware.

Ab initio investigation of benzene clusters: molecular tailoring approach.

An exhaustive study on the clusters of benzene (Bz)(n), n = 2-8, at MP2/6-31++G(∗∗) level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (∼0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n-1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.

Molecular tailoring approach in conjunction with MP2 and Ri‐MP2 codes: A comparison with fragment molecular orbital method

Many Divide‐and‐Conquer based approaches are being developed to overcome the high scaling problem of the ab initio methods. In this work, one such method, Molecular Tailoring Approach (MTA) has been interfaced with recently developed efficient Møller‐Plesset second order perturbation theory (MP2) codes viz. IMS‐MP2 and RI‐MP2 to reap the advantage of both. An external driver script is developed for implementing MTA at the front‐end and the MP2 codes at the back‐end. The present version of the driver script is written only for a single point energy evaluation of a molecular system at a fixed geometry. The performance of these newly developed MTA‐IMS‐MP2 and MTA‐RI‐MP2 codes is extensively benchmarked for a variety of molecular systems vis‐à‐vis the corresponding actual runs. In addition to this, the performance of these programs is also critically compared with Fragment Molecular Orbital (FMO), another popular fragment‐based method. It is observed that FMO2/2 is superior to FMO3/2 and MTA with respect to time advantage; however, the errors of FMO2 are much beyond chemical accuracy. However, FMO3/2 is a highly accurate method for biological systems but is unsuccessful in case of water clusters. MTA produces estimates with errors within 1 kcal/mol uniformly for all systems with reasonable time advantage. Analysis carried out employing various basis sets shows that FMO gives its optimum performance only for basis sets, which does not include diffuse functions. On the contrary, MTA performance is found to be similar for any basis set used.

Facilitating Minima Search for Large Water Clusters at the MP2 Level via Molecular Tailoring

Water clusters (H2O)20 and (H2O)25 are explored at the Møller-Plesset second-order perturbation (MP2) level of theory. Geometry optimization is carried out on favorable structures, initially generated by the temperature basin paving (TBP) method, utilizing the fragment-based molecular tailoring approach (MTA). MTA-based stabilization energies at the complete basis set limit are accurately estimated by grafting the energy correction using a smaller basis set. For prototypical cases, the minima are established via MTA-based vibrational frequency calculations at the MP2/aug-cc-pVDZ level. The potential of MTA in tackling large clusters is further demonstrated by performing geometry optimization at MP2/aug-cc-pVDZ starting with the global minimum of (H2O)30 reported by Monte Carlo (MC) and molecular dynamics (MD) investigations. The present study brings out the efficacy of MTA in performing computationally expensive ab initio calculations with minimal off-the-shelf hardware without significant loss of accuracy.

Structure, energetics, and reactivity of boric acid nanotubes: a molecular tailoring approach.

Cardinality guided molecular tailoring approach (CG-MTA) [Ganesh et al. J. Chem. Phys. 2006, 125, 104019] has been effectively employed to perform ab initio calculations for large molecular clusters of boric acid. It is evident from the results that boric acid forms nanotubes, structurally similar to carbon nanotubes, with the help of an extensive hydrogen-bonding (H-bonding) network. Planar rosette-shaped hexamer of boric acid is the smallest repeating unit in such nanotubes. The stability of these tubes increases due to enhancement in the number of H-bonding interactions as the diameter increases. An analysis of molecular electrostatic potential (MESP) of these systems provides interesting features regarding the reactivity of these tubes. It is predicted that due to alternate negative and positive potentials on O and B atoms, respectively, boric acid nanotubes will interact favorably with polar systems such as water and can also form multiwalled tubes.

WebMTA: a web-interface for ab initio geometry optimization of large molecules using molecular tailoring approach.

A web‐interface for geometry optimization of large molecules using a linear scaling method, i.e., cardinality guided molecular tailoring approach (CG‐MTA), is presented. CG‐MTA is a cut‐and‐stitch, fragmentation‐based method developed in our laboratory, for linear scaling of conventional ab initio techniques. This interface provides limited access to CG‐MTA‐enabled GAMESS. It can be used to obtain fragmentation schemes for a given spatially extended molecule depending on the maximum allowed fragment size and minimum cut radius values provided by the user. Currently, we support submission of single point or geometry optimization jobs at Hartree‐Fock and density functional theory levels of theory for systems containing between 80 to 200 first row atoms and comprising up to 1000 basis functions. The graphical user interface is built using HTML and Python at the back end. The back end farms out the jobs on an in‐house Linux‐based cluster running on Pentium‐4 Class or higher machines using an @Home‐based parallelization scheme (http://chem.unipune.ernet.in/∼tcg/mtaweb/).

WebProp: Web interface for ab initio calculation of molecular one‐electron properties

This note describes the features and implementation issues of WebProp, a web‐based interface for evaluating ab initio quality one‐electron properties. The interface code is written in HTML and Python, while the backend is handled using Python and our indigenously developed code INDPROP for property evaluation. A novel feature of this setup is that it provides a simple interface for computing first principle one‐electron properties of small to medium sized molecules. To facilitate computation of otherwise expensive calculations on large molecular systems, we employ the Molecular Tailoring Approach (MTA) developed in our laboratory to obtain the density matrix (DM). This DM is then employed for computing the one‐electron properties of these systems. The backend transparently handles jobs submitted by the user and runs them either on a single machine or over a grid of compute nodes. The results of the calculations, which include the summary and the files necessary for visualization of one‐electron properties, are e‐mailed to the user. The user can either directly use the data or visualize it using visualization tools such as UNIVIS‐2000 or Drishti.

Molecular Tailoring: An Art of the Possible for Ab Initio Treatment of Large Molecules and Molecular Clusters

Divide-and-conquer (DC) type methods are being actively developed in order to break the bottleneck of high scaling order of ab initio calculations of large molecules. Molecular Tailoring Approach (MTA) is one of such early attempts, which scissors the parent molecular system into subsystems (fragments). The properties of these subsystems are stitched back in order to estimate those for the parent system. Inclusion-exclusion principle from set theory is incorporated into MTA, which allows accurate estimation of electronic energy, energy-gradients and Hessian. This Chapter summarizes the algorithm, equations as well as basic parameters for obtaining an optimal fragmentation for a given molecule. The fragmentation in MTA is exclusively based on distance-criterion allowing its application to a general class of molecules. Further, the versatility of this method with respect to the level of theory [Hartree-Fock (HF) method, Moller-Plesset second order perturbation theory (MP2) and Density Functional Theory (DFT)] as well as the basis set is illustrated. Apart from earlier benchmarks, a few new test cases including geometry optimization of variety of molecules, benzene clusters, polyaromatic hydrocarbons, metal cluster and a protein with charged centers are presented in this Chapter.

Tailoring approach for obtaining molecular orbitals of large systems

AbstractMolecular orbitals (MO’s) within Hartree-Fock (HF) theory are of vital importance as they provide preliminary information of bonding and features such as electron localization and chemical reactivity. The contemporary literature treats the Kohn–Sham orbitals within density functional theory (DFT) equivalently to the MO’s obtained within HF framework. The high scaling order of ab initio methods is the main hurdle in obtaining the MO’s for large molecular systems. With this view, an attempt is made in the present work to employ molecular tailoring approach (MTA) for obtaining the complete set of MO’s including occupied and virtual orbitals, for large molecules at HF and B3LYP levels of theory. The energies of highest occupied and lowest unoccupied molecular orbitals, and hence the band gaps, are accurately estimated by MTA for most of the test cases benchmarked in this study, which include π-conjugated molecules. Typically, the root mean square errors of valence MO’s are in range of 0.001 to 0.010 a.u. for all the test cases examined. MTA shows a time advantage factor of 2 to 3 over the corresponding actual calculation, for many of the systems reported. Graphical AbstractMolecular tailoring approach, a fragment-based method, is employed for obtaining the complete set of MOs, for large molecular systems, without performing the calculation on the whole system. The benchmarks are performed on the diverse molecules including π-conjugated systems at HF and DFT levels of theory.