MeTA studio: a cross platform, programmable IDE for computational chemist

Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins

Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5-10 millihartrees and 5 cm-1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.

Constructing Potential Energy Surface with Correlated Theory for Dipeptides Using Molecular Tailoring Approach

We demonstrate a cost-effective alternative employing the fragment-based molecular tailoring approach (MTA) for building the potential energy surface (PES) for two dipeptides viz. alanine-alanine and alanine-proline employing correlated theory, with augmented Dunning basis sets. About 1369 geometries are generated for each test dipeptide by systematically varying the dihedral angles Φ ${{\rm{\Phi }}}$ and Ψ ${{{\Psi }}}$ . These conformational geometries are partially optimized by relaxing all the other Z-matrix parameters, fixing the values of Φ ${{\rm{\Phi }}}$ and Ψ ${{{\Psi }}}$ . The MP2 level PES is constructed from the MTA-energies of chemically intact geometries using minimal hardware. The fidelity of MP2/aug-cc-pVDZ level PES is brought out by comparing it with its full calculation counterpart. Further, we bring out the power of the method by reporting the MTA-based CCSD/aug-cc-pVDZ level PES for these two dipeptides containing 498 and 562 basis functions respectively.

DJMol: An open-source modeling platform for computational chemistry and materials science with a Python interpreter

We present a modular and extendable software suite, DJMol, for performing molecular simulations and it is demonstrated with DFTB+, Siesta, Atomic Simulation Environment, and OpenMD codes. It supports many of the standard features of an integrated development environment and consists of a structure builder and viewer, which could be connected with these electronic structure codes along with a set of data analyzers. This program comprises Java and Python modules and its libraries to carry out a different set of modeling tasks in materials science and chemistry. By adopting a Python interpreter into the software, a range of scriptable Python codes, such as Pymatgen can be incorporated into this programmable modeling platform. DJMol, through its common application programming interface (API), supports multiple modeling codes in the backend and several post-processing tools. It benefits an experienced user by increasing efficiency, while a nonexpert user by easy to use API.

Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity

Following the pioneering investigations of Bader on the topology of molecular electron density, the topology analysis of its sister field viz. molecular electrostatic potential (MESP) was taken up by the authors’ groups. Through these studies, MESP topology emerged as a powerful tool for exploring molecular bonding and reactivity patterns. The MESP topology features are mapped in terms of its critical points (CPs), such as bond critical points (BCPs), while the minima identify electron-rich locations, such as lone pairs and π-bonds. The gradient paths of MESP vividly bring out the atoms-in-molecule picture of neutral molecules and anions. The MESP-based characterization of a molecule in terms of electron-rich and -deficient regions provides a robust prediction about its interaction with other molecules. This leads to a clear picture of molecular aggregation, hydrogen bonding, lone pair–π interactions, π-conjugation, aromaticity and reaction mechanisms. This review summarizes the contributions of the authors’ groups over the last three decades and those of the other active groups towards understanding chemical bonding, molecular recognition, and reactivity through topology analysis of MESP.

Molecular Hydration of Carbonic Acid: Ab Initio Quantum Chemical and Density Functional Theory Investigation

Molecular hydration of carbonic acid (H₂CO₃) is investigated in terms of bonding patterns in H₂CO₃···(H₂O) _n [ n = 1-4] hydrogen-bonded clusters within ab initio quantum chemical and density functional theory (DFT) frameworks. Successive addition of water molecules to H₂CO₃···H₂O entails elongation of O-H (hydroxyl) bond as well as contraction of specific intermolecular hydrogen bonds signifying hydration of carbonic acid; these structural features get markedly enhanced under the continuum solvation framework. A comparison between the structurally similar clusters H₂CO₃···(H₂O) _n and HCOOH···(H₂O) _n [ n = 1-3] brings out the structural stability of the former. The present investigation in conjunction with the binding energy behavior of approaching water molecule(s) should serve as a precursor for pathways exploring aqueous dissociation of H₂CO₃ for larger clusters, as well as development of force-field potentials for acid dissociation process.

Harmonizing accuracy and efficiency: A pragmatic approach to fragmentation of large molecules

Fragmentation methods offer an attractive alternative for ab initio treatment of large molecules and molecular clusters. However, balancing the accuracy and efficiency of these methods is a tight-rope-act. With this in view, we present an algorithm for automatic molecular fragmentation within Molecular Tailoring Approach (MTA) achieving this delicate balance. The automated code is tested out on a variety of molecules and clusters at the Hartree-Fock (HF)- and Møller-Plesset second order perturbation theory as well as density functional theory employing augmented Dunning basis sets. The results show remarkable accuracy and efficiency vis-à-vis the respective full calculations. Thus the present work forms an important step toward the development of an MTA-based black box code for implementation of HF as well as correlated quantum chemical calculations on large molecular systems.

Vibrational infrared and Raman spectra of polypeptides: Fragments-in-fragments within molecular tailoring approach

The present work reports the calculation of vibrational infrared (IR) and Raman spectra of large molecular systems employing molecular tailoring approach (MTA). Further, it extends the grafting procedure for the accurate evaluation of IR and Raman spectra of large molecular systems, employing a new methodology termed as Fragments-in-Fragments (FIF), within MTA. Unlike the previous MTA-based studies, the accurate estimation of the requisite molecular properties is achieved without performing any full calculations (FC). The basic idea of the grafting procedure is implemented by invoking the nearly basis-set-independent nature of the MTA-based error vis-à-vis the respective FCs. FIF has been tested out for the estimation of the above molecular properties for three isomers, viz., β-strand, 310- and α-helix of acetyl(alanine)nNH2 (n = 10, 15) polypeptides, three conformers of doubly protonated gramicidin S decapeptide and trpzip2 protein (PDB id: 1LE1), respectively, employing BP86/TZVP, M06/6-311G**, and M05-2X/6-31G** levels of theory. For most of the cases, a maximum difference of 3 cm(-1) is achieved between the grafted-MTA frequencies and the corresponding FC values. Further, a comparison of the BP86/TZVP level IR and Raman spectra of α-helical (alanine)20 and its N-deuterated derivative shows an excellent agreement with the existing experimental spectra. In view of the requirement of only MTA-based calculations and the ability of FIF to work at any level of theory, the current methodology provides a cost-effective solution for obtaining accurate spectra of large molecular systems.

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules

DAMQT-2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP-based atomic basin is a new and exclusive feature introduced in DAMQT-2.1.0. The GUI in DAMQT provides a user-friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.

Accurate vibrational spectra via molecular tailoring approach: a case study of water clusters at MP2 level

In spite of the recent advents in parallel algorithms and computer hardware, high-level calculation of vibrational spectra of large molecules is still an uphill task. To overcome this, significant effort has been devoted to the development of new algorithms based on fragmentation methods. The present work provides the details of an efficient and accurate procedure for computing the vibrational spectra of large clusters employing molecular tailoring approach (MTA). The errors in the Hessian matrix elements and dipole derivatives arising due to the approximation nature of MTA are reduced by grafting the corrections from a smaller basis set. The algorithm has been tested out for obtaining vibrational spectra of neutral and charged water clusters at Møller-Plesset second order level of theory, and benchmarking them against the respective full calculation (FC) and/or experimental results. For (H2O)16 clusters, the estimated vibrational frequencies are found to differ by a maximum of 2 cm(-1) with reference to the corresponding FC values. Unlike the FC, the MTA-based calculations including grafting procedure can be performed on a limited hardware, yet take a fraction of the FC time. The present methodology, thus, opens a possibility of the accurate estimation of the vibrational spectra of large molecular systems, which is otherwise impossible or formidable.

Appraisal of molecular tailoring approach for large clusters

High level ab initio investigations on molecular clusters are generally restricted to those of small size essentially due to the nonlinear scaling of corresponding computational cost. Molecular tailoring approach (MTA) is a fragmentation-based method, which offers an economical and efficient route for studying larger clusters. However, due to its approximate nature, the MTA-energies carry some errors vis-à-vis their full calculation counterparts. These errors in the MTA-energies are reduced by grafting the correction at a lower basis set (e.g., 6-31+G(d)) onto a higher basis set (e.g., aug-cc-pvdz or aug-cc-pvtz) calculation at MP2 level of theory. Further, better estimates of energies are obtained by making use of many-body interaction analysis. For this purpose, R-goodness (Rg) parameters for the three- and four-body interactions in a fragmentation scheme are proposed. The procedure employing grafting and many-body analysis has been tested out on molecular clusters of water, benzene, acetylene and carbon dioxide. It is found that for the fragmentation scheme having higher three- and four-body Rg-values, the errors in MTA-grafted energies are reduced typically to ~0.2 mH at MP2 level calculation. Coupled with the advantage in terms of computational resources and CPU time, the present method opens a possibility of accurate treatment of large molecular clusters.

Rapid topography mapping of scalar fields: large molecular clusters

An efficient and rapid algorithm for topography mapping of scalar fields, molecular electron density (MED) and molecular electrostatic potential (MESP) is presented. The highlight of the work is the use of fast function evaluation by Deformed-atoms-in-molecules (DAM) method. The DAM method provides very rapid as well as sufficiently accurate function and gradient evaluation. For mapping the topography of large systems, the molecular tailoring approach (MTA) is invoked. This new code is tested out for mapping the MED and MESP critical points (CP's) of small systems. It is further applied to large molecular clusters viz. (H(2)O)(25), (C(6)H(6))(8) and also to a unit cell of valine crystal at MP2/6-31+G(d) level of theory. The completeness of the topography is checked by extensive search as well as applying the Poincaré-Hopf relation. The results obtained show that the DAM method in combination with MTA provides a rapid and efficient route for mapping the topography of large molecular systems.

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.

Topography of scalar fields: molecular clusters and π-conjugated systems

The pioneering works due to Bader and co-workers have generated widespread interest in the study of the topography of molecular scalar fields, the first step of which is the identification and characterization of the corresponding critical points (CPs). The topography of a molecular system becomes successively richer in going from the bare nuclear potential (BNP) to the molecular electrostatic potential (MESP) through the molecular electron density (MED). The present work clearly demonstrates, through the study of some π-conjugated test molecules as well as molecular clusters, that the CPs could be economically located by following this path within ab initio level theory. Further, the topography mapping of large molecules, especially at a higher level of theory, is known to be a demanding task. However, it is rendered possible by following the above sequential mapping assisted by a divide-and-conquer-type method termed as the molecular tailoring approach (MTA). This is demonstrated with the topography mapping of β-carotene and benzene nonamer at MP2 and a (H(2)O)(32) cluster at the HF level of theory, which are rather challenging problems with contemporary off-the-shelf computer hardware.

Molecular cluster building algorithm: electrostatic guidelines and molecular tailoring approach

Nano-sized clusters of various materials are recent experimental targets, since they exhibit size-dependent physico-chemical properties. A vast amount of literature is available on the study of molecular clusters but general methods for systematic evolution of their growth are rather scarce. The present work reports a molecular cluster building algorithm based on the electrostatic guidelines, followed by ab initio investigations, enabled by the application of molecular tailoring approach. Applications of the algorithm for generating geometries and interaction energies of large molecular clusters of zinc sulfide, benzene, and water are presented.

Estimation of N-H...O=C intramolecular hydrogen bond energy in polypeptides

The previously proposed molecular tailoring approached (MTA) [Deshmukh, M. M.; Gadre, S. R.; Bartolotti, L. J. J. Phys. Chem. A 2006, 110, 12519] for the estimation of intramolecular O-H...O hydrogen bond energy is extended to that for the N-H...O=C bond within polypeptides. The methodology is initially tested on a tetrapeptide containing two types of N-H...O=C hydrogen bonds and is found to distinguish between them. The estimated values are in good agreement with the trends predicted by the geometrical parameters. Furthermore, this methodology is applied to partially as well as fully substituted, capped polyglycines that contain five glycine residues (acetyl-(gly)(5)-NH(2)) to check the effect of substituents on the energetics of hydrogen bonds. The estimated N-H...O=C bond energy values lie in the range of 4-6 kcal/mol. These estimated values are not only in concurrence with the geometric parameters but also able to reflect the subtle effects of substituents for the substituted polypeptides studied in the present work.