Molecular Electronic Structure System Research Articles

A two-step Rayleigh-Schrödinger Brillouin-Wigner approach to transition energies

Perturbative methods are attractive to describe the electronic structure of molecular systems because of their low-computational cost and systematically improvable character. In this work, a two-step perturbative approach is introduced combining multi-state Rayleigh-Schrödinger (effective Hamiltonian theory) and state-specific Brillouin-Wigner schemes to treat degenerate configurations and yield an efficient evaluation of multiple energies. The first step produces model functions and an updated definition of the perturbative partitioning of the Hamiltonian. The second step inherits the improved starting point provided in the first step, enabling then faster processing of the perturbative corrections for each individual state. The here-proposed two-step method is exemplified on a model-Hamiltonian of increasing complexity.

Physicochemical properties as a function of lomefloxacin biological activity.

Aim: The goal is to discover QSAR of Lomefloxacin as antibacterial activity. Materials and Methods: A number of lomefloxacins analogs activities were studied by program Windows Chem SW. The analogues were obtained and energy minimization was carried out through Molecular Modeling Program, the calculations were performed using General Atomic and Molecular Electronic Structure System (GAMESS) software. Results: There were six descriptions (N-quinoline more (-) ev charge, Kinetic Energy, Potential Energy, Log p, Log S, F6 charge) results have highly compatible of physicochemical properties with lomefloxacin analogs activities. It can be used to estimate the activities depending on QSAR equation of lomefloxacin analogs. Conclusions: The parameters used for calculation were depending on the quantum chemical was employed in deriving from computational study of properties and can used to predict the activities of certain analogs of Lomefloxacins as antibacterial compounds.

The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures.

The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Best practices for the maintenance and distribution of GAMESS are also discussed.

Toward an extreme-scale electronic structure system.

Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery to material science and catalysis. However, a predictive physicochemical characterization of these processes often requires accurate quantum chemical modeling of complex molecular systems with hundreds to thousands of atoms. Due to the computationally demanding nature of electronic structure calculations and the complexity of modern high-performance computing hardware, quantum chemistry software has historically failed to operate at such large molecular scales with accuracy and speed that are useful in practice. In this paper, novel algorithms and software are presented that enable extreme-scale quantum chemistry capabilities with particular emphasis on exascale calculations. This includes the development and application of the multi-Graphics Processing Unit (GPU) library LibCChem 2.0 as part of the General Atomic and Molecular Electronic Structure System package and of the standalone Extreme-scale Electronic Structure System (EXESS), designed from the ground up for scaling on thousands of GPUs to perform high-performance accurate quantum chemistry calculations at unprecedented speed and molecular scales. Among various results, we report that the EXESS implementation enables Hartree-Fock/cc-pVDZ plus RI-MP2/cc-pVDZ/cc-pVDZ-RIFIT calculations on an ionic liquid system with 623 016 electrons and 146 592 atoms in less than 45minusing 27 600 GPUs on the Summit supercomputer with a 94.6% parallel efficiency.

Observation of Core-Excited Dipole-Bound States.

Polar molecules can bind an electron in a diffuse orbital due to the charge-dipole interaction. Electronic excited states of polar molecules can also bind an electron to form core-excited dipole-bound states (DBSs), analogous to core-excited Rydberg states. However, core-excited DBSs have not been observed because of the complicated electronic structure of molecular systems. Here, we report the observation of a core-excited DBS in the pyrazolide anion as a result of the favorable electronic structure of the neutral pyrazolyl core, which has a low-lying excited state (Ã2B1) only 266 cm-1 above its ground state (X̃2A2). The binding energy of the DBS associated with the ground state is measured to be 221 cm-1, while that of the core-excited DBS is 276 cm-1, which is still a bound state relative to the detachment threshold. Vibrational Feshbach resonances are observed for both DBSs, and their autodetachment behaviors are studied by resonant photoelectron imaging.

Intramolecular interactions in a target specific anti-tumor nanodrug: a theoretical study

Through this authoritative report, an application of fragment molecular orbital (FMO) method on a functionalized carbon nanotube (CNT) has been proposed. A targeted anti-tumor nanodrug, based on CNT that converges towards cancerous cells, has been innovated in this regard. The anticancer drug cisplatin and the target selector arginine-aspartate-glycine acid (RGD) have been attached via poly ethylene glycol (PEG) on CNT. This nanodrug has been divided into 12 fragments including CNT as one of them. General atomic molecular electronic structure system (GAMESS), an ab initio package, has been used for calculations. The contributions of various fragments have been discussed in terms of inter-fragment interactions. Results indicate that the CNT shares the important role in stabilizing the different parts of its derivatives. In addition, this report proves CNT as a fragment for FMO method.

Density Functional Treatment on Alkylation of a Functionalized Deltahedral Zintl Cluster.

Density functional theory (DFT) is one of the popular methods to understand the electronic structure of molecular systems based on electronic density. On the basis of this theory, several conceptual DFT descriptors have been developed which can deal with the stability, reactivity, and several other physicochemical properties of molecules. Here, we have taken a nine-atom-functionalized deltahedral Zintl cluster of germanium (Ge) to examine the alkylation reaction mechanism. The study showed that the Zintl cluster having a methyl group as a ligand, [Ge9(CH3)3-], acts as a better nucleophile than the cyanide (-CN)-substituted cluster [Ge9(CN)3-] in terms of different thermodynamic parameters like free energy, enthalpy of activation, reaction energy, etc. A detailed reaction electronic flux analysis reveals the nature of the electronic activity throughout the reaction pathway. The reaction force, Wiberg bond indices, and dual descriptor lend additional support to the reaction mechanism. It has been found that the alkylation reaction between the Zintl ion and the alkyl halide follows a SN2-like mechanism.

Analysis of Ibuprofen and Naproxen Based Two NSAID Candidates with Theoretical DFT Calculations

Theoretical quantum calculations have been carried out for two new ibuprofen and naproxen based Non Steroid Anti inflammatory Drug candidates. DFT (Density Functional Theory) calculations of molecules have been carried out with a general quantum chemistry software package GAMESS (the General Atomic and Molecular Electronic Structure System). Both molecules have been optimised successfully, and IR (Infra Red) spectra have been obtained via vibrational HESSIAN analyses. The frontier orbitals, HOMO (the Highest Occupied Molecular Orbital) and LUMO (the Lowest Unoccupied Molecular Orbital) have been obtained, and also molecular dynamic descriptors, such as chemical hardness, electronegativity and electrophilicity have been calculated for both molecules. Electrostatic potentials, total molecular electron densities also have been calculated for optimised molecules. All the result has been represented comparatively for both molecules. Keywords : Ibuprofen, Naproxen, DFT, GAMESS. DOI : 10.7176/JHMN/78-03

Recent developments in the general atomic and molecular electronic structure system.

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.

Accurate Prediction of Gas Chromatographic Retention Times via Density Functional Theory Calculations: A Case Study Using Brominated Flame Retardants

AbstractIdentification of structurally similar congeners of polybrominated diphenyl ether (PBDE) can be challenging without the use of analytical standards. Density Functional Theory (DFT) calculations paired with gas chromatographic (GC) retention times of reference standards were used to predict the retention times of PBDE congeners. This was accomplished by calculating polarizability of 31 PBDEs using the open‐sourced software package General Atomic and Molecular Electronic Structure System (GAMESS). Three PBDEs were randomly chosen from a training set of PBDEs and were treated as “unknowns” to test the accuracy of linear regressions constructed from calculated polarizabilities versus experimentally determined retention times. The top performing functionals predicted retention times of these “unknown” congeners to be within 1.3% and 3% for the DB‐5HT GC column and the ZB‐SemiVolatiles GC column, respectively. This study demonstrates that DFT calculations combined with experimental retention times can be used to aid in the identification of unknown analytes or, at the very least, reduce the number of plausible identities of analytes.

Theoretical evaluation of valeraldehyde

The aim of this study was to compute the theoretical (software-based) spectroscopic properties of valeraldehyde as a member of the aldehyde family. The structural, thermochemical, electrical and spectroscopic properties of valeraldehyde were investigated using a quantum calculation approach. The infrared, ultraviolet-visible, Raman, and vibrational self-consistent field calculations and thermochemistry were calculated using the computational software GAMESS (General Atomic and Molecular Electronic Structure System) and the nuclear magnetic resonance predictions were calculated. The calculated energy gap between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) was 164.892.eV, which means valeraldehyde is a poor electrical conductor. The band gap is a non-neglected parameter for optical material. Results of the current computational analysis are useful to predict even a complex aldehyde precursor.
 Significance:
 
 The computational strategy used successfully here could also be useful for investigation of other aldehyde polymers.

Anharmonic vibrational computations with a quartic force field for curvilinear coordinates

The direct vibrational self-consistent field (VSCF) method, which combines anharmonic vibrational theory with electronic structure calculations, is a sophisticated theoretical approach to calculate the vibrational spectra of molecules from first principles. Combining the VSCF approach with the quartic force field (QFF) is a good alternative to direct VSCF, with a lower computational cost. QFF is a 4th-order Taylor expansion of the potential energy surface near an equilibrium geometry. In this study, a new strategy is proposed to derive the QFF in terms of normal coordinates; the QFF coefficients are determined through numerical differentiations of the energy by representing the normal coordinates in internal rather than Cartesian coordinates. The VSCF/QFF-internal method was implemented in the General Atomic and Molecular Electronic Structure System electronic structure program and applied to the evaluations of the fundamental vibrational frequencies of HNO2, HNO3, H2O dimer, and H2O trimer, using Møller-Plesset second order perturbation theory and the aug-cc-pVDZ and aug-cc-pVTZ basis sets. The results are much improved, especially for the intermolecular vibrational modes, compared with the Cartesian coordinate representation of the normal coordinates in the VSCF/QFF approach.

Ab initio computations of molecular systems by the auxiliary‐field quantum Monte Carlo method

The auxiliary‐field quantum Monte Carlo (AFQMC) method provides a computational framework for solving the time‐independent Schrödinger equation in atoms, molecules, solids, and a variety of model systems. AFQMC has recently witnessed remarkable growth, especially as a tool for electronic structure computations in real materials. The method has demonstrated excellent accuracy across a variety of correlated electron systems. Taking the form of stochastic evolution in a manifold of nonorthogonal Slater determinants, the method resembles an ensemble of density‐functional theory (DFT) calculations in the presence of fluctuating external potentials. Its computational cost scales as a low‐power of system size, similar to the corresponding independent‐electron calculations. Highly efficient and intrinsically parallel, AFQMC is able to take full advantage of contemporary high‐performance computing platforms and numerical libraries. In this review, we provide a self‐contained introduction to the exact and constrained variants of AFQMC, with emphasis on its applications to the electronic structure of molecular systems. Representative results are presented, and theoretical foundations and implementation details of the method are discussed.This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Structure and Mechanism > Computational Materials Science Computer and Information Science > Computer Algorithms and Programming

PAREMD: A parallel program for the evaluation of momentum space properties of atoms and molecules

The present work describes a code for evaluating the electron momentum density (EMD), its moments and the associated Shannon information entropy for a multi-electron molecular system. The code works specifically for electronic wave functions obtained from traditional electronic structure packages such as GAMESS and GAUSSIAN. For the momentum space orbitals, the general expression for Gaussian basis sets in position space is analytically Fourier transformed to momentum space Gaussian basis functions. The molecular orbital coefficients of the wave function are taken as an input from the output file of the electronic structure calculation. The analytic expressions of EMD are evaluated over a fine grid and the accuracy of the code is verified by a normalization check and a numerical kinetic energy evaluation which is compared with the analytic kinetic energy given by the electronic structure package. Apart from electron momentum density, electron density in position space has also been integrated into this package. The program is written in C++ and is executed through a Shell script. It is also tuned for multicore machines with shared memory through OpenMP. The program has been tested for a variety of molecules and correlated methods such as CISD, Møller–Plesset second order (MP2) theory and density functional methods. For correlated methods, the PAREMD program uses natural spin orbitals as an input. The program has been benchmarked for a variety of Gaussian basis sets for different molecules showing a linear speedup on a parallel architecture. Program summaryProgram Title: PAREMDProgram Files doi:http://dx.doi.org/10.17632/gcr9gmh6zv.1Licensing provisions: GPLv3Programming language: C, CshExternal routines/libraries: GSL[1], BLAS[2,3], OpenMP[4], GAMESS[5,6] and GAUSSIAN[7].Nature of problem: Momentum space properties for a multi-electron system.Solution method: Analytic Fourier transformation of Gaussian basis in position space to get momentum space basis followed by EMD evaluation on spherical or Cartesian grids. A numerical integration procedure is implemented for evaluating moments of EMD and Shannon information entropy on a polar grid.[1] Galassi et al, GNU Scientific Library Reference Manual (3rd Ed.), ISBN 0954612078.[2] L. S. Blackford, J. Demmel, J. Dongarra, I. Duff, S. Hammarling, G. Henry, M. Heroux, L. Kaufman, A. Lumsdaine, A. Petitet, R. Pozo, K. Remington, R. C. Whaley, An Updated Set of Basic Linear Algebra Subprograms (BLAS), ACM Trans. Math. Soft., 28-2 (2002), pp. 135–151.[3] J. Dongarra, Basic Linear Algebra Subprograms Technical Forum Standard, International Journal of High Performance Applications and Supercomputing, 16(1) (2002), pp. 1–111, and International Journal of High Performance Applications and Supercomputing, 16(2) (2002), pp. 115–199.[4] OpenMP Architecture Review Board, ”OpenMP Application Program Interface, Version 4.5”, November 2015.[5] ”General Atomic and Molecular Electronic Structure System” M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.H. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S.J. Su, T.L. Windus, M. Dupuis, J.A. MontgomeryJ. Comput. Chem. 14 1347–1363, 1993.[6] “Advances in electronic structure theory: GAMESS a decade later M.S. Gordon, M.W. Schmidt pp. 1167–1189, in Theory and Applications of Computational Chemistry: the first forty years C.E. Dykstra, G. Frenking, K.S. Kim, G.E. Scuseria (editors), Elsevier, Amsterdam, 2005.[7] Gaussian 09, Revision C.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.

Electronic structure and vibrational spectra of 1OCB liquid crystal: a DFT study

The molecular and thermodynamical properties of 4-n-methoxy-4′-cyanobiphenyl (1OCB), which is the first homologue of the 4-n-alkoxy-4′-cyanobiphenyl liquid crystal series, have been investigated. 4-n-methoxy-4′-cyanobiphenyl is a nematic liquid crystal which transforms from crystal to isotropic phase at 104°C and from isotropic to nematic phase at 85·5°C.The molecular geometry has been optimized by first-principles Hartree–Fock (HF)/6-31G(d,p) and density functional theory (DFT) Becke, three-parameter, Lee–Yang–Parr (B3LYP)/6-31G(d,p) methods using the General Atomic and Molecular Electronic Structure System program. The molecular electrostatic potential surface has been scanned with a 0·001 electrons/b3 isodensity surface. The highest occupied molecular orbital and lowest unoccupied molecular orbital energies and thermodynamic properties of the molecule such as internal energy, entropy, enthalpy and Gibbs free energy have been reported. Further, vibrational assignments of the molecule, carried out using first-principles HF/6-31G(d,p) as well as DFT B3LYP/6-31G(d,p) techniques, have been compared and discussed. Efforts have been made to understand the liquid crystalline behavior of the system.

Applying EMD/HHT analysis to power traces of applications executed on systems with Intel Xeon Phi

Power draw is a complex physical response to the workload of a given application on the hardware, which is difficult to model, in part, due to its variability. The empirical mode decomposition and Hilbert–Huang transform (EMD/HHT) is a method commonly applied to physical systems varying with time to analyze their complex behavior. In authors’ work, the EMD/HHT is considered for the first time to study power usage of high-performance applications. Here, this method is applied to the power measurement sequences (called here power traces) collected on three different computing platforms featuring two generations of Intel Xeon Phi, which are an attractive solution under the power budget constraints. The high-performance applications explored in this work are codesign molecular synamics and general atomic and molecular electronic structure system—which exhibit different power draw characteristics—to showcase strengths and limitations of the EMD/HHT analysis. Specifically, EMD/HHT measures intensity of an execution, which shows the concentration of power draw with respect to execution time and provides insights into performance bottlenecks. This article compares intensity among executions, noting on a relationship between intensity and execution characteristics, such as computation amount and data movement. In general, this article concludes that the EMD/HHT method is a viable tool to compare application power usage and performance over the entire execution and that it has much potential in selecting most appropriate execution configurations.

Dissociative ionization of acetonitrile in intense femtosecond laser fields

We investigate the formation of positively charged fragments of acetonitrile (CH3CN) in intense 800 nm, 50 fs pulses of radiation using a reflectron time-of-flight (TOF) ion mass spectrometer. Singly-charged ions of CHnCN+ HCN+, CN+, CH+, C+ and H+; and the multiply charged ions of C2+, C3+, and were observed in the mass spectra. Quantum chemical calculations with GAMESS (General Atomic and Molecular Electronic Structure System) of appearance energies for the parent molecule and daughter fragments have been carried out. Intensity dependent ion yields were measured for intensities between and Angular distributions of most fragment ions were found to peak when the laser radiation was polarized parallel to the TOF axis, while the carbon ions, C+ and C2+, were found to have maxima for both polarizations parallel and perpendicular to this axis. Kinetic energies of H+ fragments were experimentally measured and three different photo dissociation mechanisms were identified.

Structural and electronic characteristics of intercalated monopotassium–rubrene: Simulation on a commodity computing cluster

The structural and electronic characteristics of the intercalated monopotassium–rubrene (K1Rub) are studied. In the intercalated K1Rub, one of the two pairs of phenyl groups of rubrene is intercalated by potassium, whereas the other pair remains pristine. This structural feature facilitates the comparison of the electronic structures of the intercalated and pristine pairs of phenyl groups. It is found that, in contrast to potassium adsorption to rubrene, the potassium intercalation promotes the carbon [Formula: see text] orbitals of the intercalated pair of phenyls to participate in the electronic structures of HOMO. Additionally, this intercalated K1Rub is used as a testing vehicle to study the performance of a commodity computing cluster built to run the General Atomic and Molecular Electronic Structure System (GAMESS) simulation package. It is shown that, for many frequently encountered simulation tasks, the performance of the commodity computing cluster is comparable with a massive computing cluster. The high performance-cost-ratio of the computing clusters constructed with commodity hardware suggests a feasible alternative for research institutes to establish their computing facilities.

On the dispersion of lithium-sulfur battery cathode materials effected by electrostatic and stereo-chemical factors of binders

Sodium carboxymethyl cellulose-styrene butadiene rubber (CMC-SBR), sodium alginate (SA) and LA132 are utilized as the polymer binders for the cathodes of Li-S batteries to study their dispersion mechanism on the cathode materials and the consequent influence on the performance of Li-S batteries. Zeta potential tests, differential scanning calorimetry analysis and calculations of the rotational barriers of the links of the polymer chains by General Atomic and Molecular Electronic Structure System (GAMESS) reveal that higher charge densities and better chain flexibility of the binders promise the dispersion of the downsized cathode materials. LA132 is found to have optimal characteristic for dispersing and stabilizing the cathode materials in aqueous environment. The cycling performance and SEM images of the cathodes demonstrate that cathodes with higher dispersion degree achieve higher discharge capacities. The electrochemical impedance spectroscopy (EIS) results further support that better dispersed cathodes have lower impedance resulting from their well established conducting frameworks.

Ferrocene Orientation Determined Intramolecular Interactions Using Energy Decomposition Analysis.

Two very different quantum mechanically based energy decomposition analyses (EDA) schemes are employed to study the dominant energy differences between the eclipsed and staggered ferrocene conformers. One is the extended transition state (ETS) based on the Amsterdam Density Functional (ADF) package and the other is natural EDA (NEDA) based in the General Atomic and Molecular Electronic Structure System (GAMESS) package. It reveals that in addition to the model (theory and basis set), the fragmentation channels more significantly affect the interaction energy terms (ΔE) between the conformers. It is discovered that such an interaction energy can be absorbed into the pre-partitioned fragment channels so that to affect the interaction energies in a particular conformer of Fc. To avoid this, the present study employs a complete fragment channel—the fragments of ferrocene are individual neutral atoms. It therefore discovers that the major difference between the ferrocene conformers is due to the quantum mechanical Pauli repulsive energy and orbital attractive energy, leading to the eclipsed ferrocene the energy preferred structure. The NEDA scheme further indicates that the sum of attractive (negative) polarization (POL) and charge transfer (CL) energies prefers the eclipsed ferrocene. The repulsive (positive) deformation (DEF) energy, which is dominated by the cyclopentadienyle (Cp) rings, prefers the staggered ferrocene. Again, the cancellation results in a small energy residue in favour of the eclipsed ferrocene, in agreement with the ETS scheme. Further Natural Bond Orbital (NBO) analysis indicates that all NBO energies, total Lewis (no Fe) and lone pair (LP) deletion all prefer the eclipsed Fc conformer. The most significant energy preferring the eclipsed ferrocene without cancellation is the interactions between the donor lone pairs (LP) of the Fe atom and the acceptor antibond (BD*) NBOs of all C–C and C–H bonds in the ligand, LP(Fe)-BD*(C–C & C–H), which strongly stabilizes the eclipsed (D5h) conformation by −457.6 kcal·mol−1.