Molecular Electronic Structure System Research Articles

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.

Mechanistic study on lowering the sensitivity of positive atmospheric pressure photoionization mass spectrometric analyses: size-dependent reactivity of solvent clusters.

Understanding the mechanism of atmospheric pressure photoionization (APPI) is important for studies employing APPI liquid chromatography/mass spectrometry (LC/MS). In this study, the APPI mechanism for polyaromatic hydrocarbon (PAH) compounds dissolved in toluene and methanol or water mixture was investigated by use of MS analysis and quantum mechanical simulation. In particular, four different mechanisms that could contribute to the signal reduction were considered based on a combination of MS data and quantum mechanical calculations. The APPI mechanism is clarified by combining MS data and density functional theory (DFT) calculations. To obtain MS data, a positive-mode (+) APPI Q Exactive Orbitrap mass spectrometer was used to analyze each solution. DFT calculations were performed using the general atomic and molecular electronic structure system (GAMESS). The experimental results indicated that methanol significantly reduced the signal in (+) APPI, but no significative signal reduction was observed when water was used as a co-solvent with toluene. The signal reduction is more significant especially for molecular ions than for protonated ions. Therefore, important information about the mechanism of methanol-induced signal reduction in (+) APPI-MS can be gained due its negative impact on APPI efficiency. The size-dependent reactivity of methanol clusters ((CH3 OH)n , n = 1-8) is an important factor in determining the sensitivity of (+) APPI-MS analyses. Clusters can compete with toluene radical ions for electrons. The reactivity increases as the sizes of the methanol clusters increase and this effect can be caused by the size-dependent ionization energy of the solvent clusters. The resulting increase in cluster reactivity explains the flow rate and temperature-dependent signal reduction observed in the analytes. Based on the results presented here, minimizing the sizes of methanol clusters can improve the sensitivity of LC/(+)-APPI-MS.

Spectroscopic studies and molecular orbital calculations of charge transfer complexation between 3,5-dimethylpyrazole with DDQ in acetonitrile

Charge transfer (CT) interaction between 3,5-dimethylpyrazole (DMP) with the π-acceptor 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ) has been investigated spectrophotometrically in acetonitrile (AN). Simultaneous reddish brown color has been observed upon mixing donor with acceptor solutions attributing to CT complex formation. The electronic spectra of the formed complex exhibited multi-charge transfer bands at 429, 447, 506, 542 and 589nm, respectively. Job’s method of continuous variations and spectrophotometric titration methods confirmed the formation of the studied complex in 1:2 ratio between DMP and DDQ. Benesi–Hildebrand equation has been applied to calculate the stability constant of the formed complex where it recorded high value supporting formation of stable complex. Molecular orbital calculations using MM2 method and GAMESS (General Atomic and Molecular Electronic Structure System) interface computations as a package of ChemBio3D Ultra12 software were carried out for more analysis of the formed complex in the gas phase. The computational analysis included energy minimisation, stabilisation energy, molecular geometry, Mullikan charges, molecular electrostatic potential (MEP) surfaces of reactants and complex as well as characterization of the higher occupied molecular orbitals (HOMO) and lower unoccupied molecular orbitals (LUMO) surfaces of the complex. A good consistency between experimental and theoretical results has been recorded.

Interfacing the Ab initio multiple spawning method with electronic structure methods in GAMESS: Photodecay of trans-azomethane.

This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitation on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ∼60-200 fs. These short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.

Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program

A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.

Efficient and accurate fragmentation methods.

Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment-fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method.

Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab As Implemented Using Three-Dimensional Modeling Software

In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel calculations were also performed using ChemBio3D, and the results were then used to develop molecular orbital theory descriptions of the bonding. Both quantitative (posttest results) and qualitative (online student evaluations) data were used in the assessment of student learning.

Recent performance improvements to the DFT and TDDFT in GAMESS

The general atomic and molecular electronic structure system (GAMESS) is a quantum chemistry package used in the first-principles modeling of complex molecular systems using density functional theory (DFT) as well as a number of other post-Hartree-Fock methods. Both DFT and time-dependent DFT (TDDFT) are of particular interest to the materials modeling community. Millions of CPU hours per year are expended by GAMESS calculations on high-performance computing systems; any substantial reduction in the time-to-solution for these calculations represents a significant saving in CPU hours. As part of this work, three areas for improvement were identified: (1) the exchange-correlation (XC) integration grid, (2) profiling and optimization of the DFT code, and (3) TDDFT parallelization. We summarize the work performed in these task areas and present the resulting performance improvement. These software enhancements are available in 12JAN2009R3 or later versions of GAMESS.

Application of GAMESS/NEO to quantum calculations of muonic molecules

The General Atomic and Molecular Electronic Structure System (GAMESS) has been modified to perform studies involving negative muons. This system, coupled with the Nuclear-Electronic Orbital (NEO) method enables the ab-initio study of muonic atoms where both the negative muon and the positive nuclei are modeled as quantum particles. This is of particular usefulness in the study light nuclei, muonic atoms, such as is encountered in muon-catalyzed fusion. NEO was also modified to allow the inclusion of positive exotic-particles to be studied using open and closed shell Hartree-Fock and Configuration Interaction. Capitalizing on these modified methods, the muon density and vibrational dynamics of some light muonic molecules have been analyzed.

Open-Shell Formulation of the Fragment Molecular Orbital Method.

Performing accurate calculations on large molecular systems is desirable for closed- and open-shell systems. In this work, the fragment molecular orbital method is extended to open-shell systems and implemented in the GAMESS (General Atomic and Molecular Electronic Structure System) program package. The accuracy of the method is tested, and the ability to reproduce reaction enthalpies is demonstrated. These tests also demonstrate its utility in providing an efficient means to model large open-shell systems.

Robust and Reliable Multilevel Minimization of the Kohn-Sham Energy.

Kohn-Sham density-functional calculations are used in many branches of science to obtain information about the electronic structure of molecular systems and materials. Conventional algorithms for minimization of the Kohn-Sham energy have certain deficiencies, however, that may cause divergence or, worse, convergence to unphysical saddle points. We here present a three-level hierarchical minimization strategy which is both more efficient and robust than the conventional algorithms and which does not suffer from the flaws of these algorithms. Using the three-level minimization strategy, the molecular density is built up in a hierarchical fashion in accordance with chemical insight: First, the molecular density is composed by a superposition of atomic densities; next, bonds are formed by performing a simple valence-shell optimization; finally, the molecular description is refined by an optimization in the full molecular basis. Importantly, the density matrix generated at each of the two lower levels in this hierarchy is transferred to the next without loss of information. Examples demonstrate the efficacy and robustness of the proposed scheme.

A ground-state-directed optimization scheme for the Kohn–Sham energy

Kohn-Sham density-functional calculations are used in many branches of science to obtain information about the electronic structure of molecular systems and materials. Unfortunately, the traditional method for optimizing the Kohn-Sham energy suffers from fundamental problems that may lead to divergence or, even worse, convergence to an energy saddle point rather than to the ground-state minimum--in particular, for the larger and more complicated electronic systems that are often studied by Kohn-Sham theory nowadays. We here present a novel method for Kohn-Sham energy minimization that does not suffer from the flaws of the conventional approach, combining reliability and efficiency with linear complexity. In particular, the proposed method converges by design to a minimum, avoiding the sometimes spurious solutions of the traditional method and bypassing the need to examine the structure of the provided solution.

Coupled cluster algorithms for networks of shared memory parallel processors

Abstract As the popularity of using SMP systems as the building blocks for high performance supercomputers increases, so too increases the need for applications that can utilize the multiple levels of parallelism available in clusters of SMPs. This paper presents a dual-layer distributed algorithm, using both shared-memory and distributed-memory techniques to parallelize a very important algorithm (often called the “gold standard”) used in computational chemistry, the single and double excitation coupled cluster method with perturbative triples, i.e. CCSD(T). The algorithm is presented within the framework of the GAMESS [M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.J. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S. Su, T.L. Windus, M. Dupuis, J.A. Montgomery, General atomic and molecular electronic structure system, J. Comput. Chem. 14 (1993) 1347–1363]. (General Atomic and Molecular Electronic Structure System) program suite and the Distributed Data Interface [M.W. Schmidt, G.D. Fletcher, B.M. Bode, M.S. Gordon, The distributed data interface in GAMESS, Comput. Phys. Comm. 128 (2000) 190]. (DDI), however, the essential features of the algorithm (data distribution, load-balancing and communication overhead) can be applied to more general computational problems. Timing and performance data for our dual-level algorithm is presented on several large-scale clusters of SMPs.

Molecular basic data calculation for radiation transport in chromatin

Differential and integral electron impact ionisation cross sections were calculated using the binary-encounter-Bethe theoretical model for each core particle molecules: the four DNA bases, the backbone (sugar phosphate), and the 19 amino acids constituent of histone proteins. The binding energies and populations of molecular orbitals were computed using General Atomic Molecular Electronic Structure System. At present, there are neither experimental nor other theoretical results on amino acid electron impact ionisation cross sections. Regarding DNA bases and backbone, our results show good agreement with those published in journals.

Surface-Stabilized Amorphous Germanium Nanoparticles for Lithium-Storage Material

Amorphous Ge nanoparticles with the particle size of approximately 10 nm were prepared by capping butyl groups and were characterized using XAS, TEM, FT-IR reflectance, and electrochemical cycling. The XAS results for the first-cycle Ge nanoparticles exhibited either a little particle aggregation after reformation of the Ge-Ge metallic bond or reformation of Ge-Ge metallic bond followed by a little particle aggregation. More interestingly, butyl groups, being electrochemically stable, remained after cycling, and the quantum mechanical calculation of the thermodynamic energy of the reaction using the GAMESS (General Atomic and Molecular Electronic Structure System) program suggested the formation of a very stable surface Ge-C bond that cannot be easily subjected to the subsequent chemical reactions. Initial charge capacity is 1470 mAh/g with an irreversible capacity ratio of 12%; no capacity fading was observed out to 30 cycles. Even at 5 C rate discharging, capacity retention was 98%, compared to that at 0.2 C rate discharging. In addition, the capacity was fully recovered at 0.2 C rate cycling.

The structure and spin-states of some Fe(III) mimics of nitrile hydratase, studied by DFT and ONIOM(DFT:PM3) calculations

Density functional methods have been successful in studying the electronic structure of molecular systems containing transition metal atoms, such as metalloenzymes. However, the treatment of large systems is still very computationally demanding, and is definitely not practical for many systems of interest, due to their size. In this paper we assess the use of these methods both alone, and when combined with the semi-empirical PM3 method within an ONIOM scheme, for determining the structure and spin-dependent energetics of a series of Fe(III) model complexes that have been synthesized to mimic the active site of nitrile hydratase, a metalloenzyme that catalyses the conversion of a wide variety of nitriles to their corresponding amides. We have found that geometry optimizations employing B3LYP generally give a good description of the structure and spin-states of these complexes and that when combined with PM3 in the framework of ONIOM, the multilevel method also performs well for some of them, suggesting that the ONIOM(B3LYP:PM3) approach offers the possibility for improvement in future calibration studies. We also find that DFT and ONIOM(DFT:PM3) calculations at the experimental geometries using the BP86, PW91PW91 and B3LYP functionals can also describe the spin-state energetics of these model complexes, with DFT performing the best.

Synthesis, characterization and theoretical study of the structure and second-order nonlinear optical properties of two new Monoazo Schiff-base compounds

We describe the syntheses, characterization and theoretical investigation of two new monoazo Schiff-base ligands 5-[(4-methylphenyl)azo]-N-(2′-hydroxyphenyl)salicylaldimine (SB1) and 5-[(4-nitrophenyl)azo]-N-(2′-hydroxyphenyl)salicylaldimine (SB2). AM1 semiempirical calculations were used to study the structures, electronic properties and second-order nonlinearity of these compounds. Theoretical calculations are useful for describing the relationship between the electronic structure of molecular systems and their nonlinear optical (NLO) response. Second-order NLO calculations and comparison of the NLO properties of these ligands with others reveal that the presence of an NO2 group enhances the second-order NLO properties of the ligands.

Block-correlated coupled cluster theory: the general formulation and its application to the antiferromagnetic Heisenberg model.

The general formalism of the block-correlated coupled cluster (BCCC) method, an alternative multireference coupled cluster method for calculating the ground-state electronic structures of molecular systems, has been presented. The BCCC theory is constructed in terms of a complete set of many-electron states of individual blocks, assumed that the whole system could be partitioned into a set of blocks. The reference state in the BCCC is selected as a tensor product of the most important many-electron state of each system block. By truncating the cluster operator to a certain n-block correlation level, an approximate but size-extensive BCCC method, denoted as BCCCn, is defined. For reducing the computational effort but without much loss of accuracy, the reduced density matrix is introduced to generate an optimal subset of many-electron states for each block. I have implemented the BCCCn (n=2,3) methods within the S=1/2 Heisenberg Hamiltonian, and applied them to calculate the ground-state energies of one-dimensional spin chains and quasi-one-dimensional two-leg spin ladders. The calculated results show that with the appropriate partition of the studied systems the BCCC3 method can yield quite satisfactory ground-state energies for these spin systems.

The use of methods involving semi-empirical molecular orbital theory to study the structure and reactivity of transition metal complexes.

The electronic structure of molecular systems containing transition metal atoms is traditionally studied using methods based on density functional theory (DFT). Although such an approach has been quite successful, the treatment of large systems, be they transition metal complexes, bioinorganic molecules or the solid state, is still extremely computationally demanding at this level, and may not be practical for many systems of interest. In this paper we describe how semi-empirical MO methods can be used to overcome these computational bottlenecks, yet still provide predictions of the necessary accuracy. We describe strategies to achieve this by focussing on: (i) obtaining appropriate parameters for transition metal atoms via a genetic algorithm, to be used within a parallelised implementation of neglect of differential diatomic overlap (NDDO) methods, and (ii) the use of multilevel treatments which involve DFT and semi-empirical methods to describe different regions of the molecule. Here we show by reference to histidine and porphyrin complexes, the importance of a correct partitioning of the organic substrate. We illustrate the potential of such a dual level approach by reporting preliminary results showing the catalytic role of the enzyme, dimethyl sulfoxide reductase.