Quantum Chemistry Program Research Articles

SpectroIBIS: Automated Data Processing for Multiconformer Quantum Chemical Spectroscopic Calculations.

Quantum chemical spectroscopic calculations have grown increasingly popular in natural products research for aiding the elucidation of chemical structures, especially their stereochemical configurations. These calculations have become faster with modern computational speeds, but subsequent data handling, inspection, and presentation remain key bottlenecks for many researchers. In this article, we introduce the SpectroIBIS computer program as a user-friendly tool to automate tedious tasks commonly encountered in this workflow. Through a simple graphical user interface, researchers can drag and drop Gaussian or ORCA output files to produce Boltzmann-averaged ECD, VCD, UV-vis and IR data, optical rotations, and/or 1H and 13C NMR chemical shifts in seconds. Also produced are formatted, publication-quality supplementary data tables containing conformer energies and atomic coordinates, saved to a DOCX file compatible with Microsoft Word and LibreOffice. Importantly, SpectroIBIS can assist researchers in finding common calculation issues by automatically checking for redundant conformers and imaginary frequencies. Additional useful features include recognition of conformer energy recalculations at a higher theory level, and automated generation of input files for quantum chemistry programs with optional exclusion of high-energy conformers. Lastly, we demonstrate the applicability of SpectroIBIS with spectroscopic calculations for five natural products. SpectroIBIS is open-source software available as a free desktop application (https://github.com/bbulcock/SpectroIBIS).

PyVPT2: Interoperable software for anharmonic vibrational frequency calculations.

We present pyVPT2, a program to perform second-order vibrational perturbation theory (VPT2) computations to obtain anharmonic vibrational frequencies. This program is written in Python and can utilize any of the several quantum chemistry programs that have been interfaced to the QCEngine project of the Molecular Sciences Software Institute (MolSSI). The requisite single point energy, gradient, or Hessian computations can be automatically performed in a distributed-parallel fashion by optionally using the MolSSI's QCFractal software. With pyVPT2, VPT2 anharmonic frequencies can now be computed using quantum chemistry programs that lack their own VPT2 capabilities.

Fourth-Order Algebraic Diagrammatic Construction for Electron Detachment and Attachment: The IP- and EA-ADC(4) Methods.

We present a non-Dyson fourth-order algebraic diagrammatic construction formulation of the electron propagator, featuring the distinct IP- and EA-ADC(4) schemes for the treatment of ionization and electron attachment processes. The algebraic expressions have been derived automatically using the intermediate state representation approach and implemented in the Q-Chem quantum-chemical program package. The performance of the novel methods is assessed with respect to high-level reference data for ionization potentials and electron affinities of closed- and open-shell systems. While only minor improvements over the corresponding third-order methods are observed for one-hole ionization and one-particle electron attachment processes from closed-shell systems (MAEIP-ADC(4) = 0.27 eV and MAEEA-ADC(4) = 0.05 eV), a significantly enhanced performance is found in case of open-shell reference states (MAEIP-ADC(4) = 0.11 eV and MAEEA-ADC(4) = 0.02 eV). A particularly appealing feature of the novel methods is their accurate treatment of satellite transitions. For closed-shell reference states, we obtain accuracies of MAEIP-ADC(4) = 0.81 eV and MAEEA-ADC(4) = 0.27 eV, while in case of open-shell reference states, mean absolute errors of MAEIP-ADC(4) = 0.15 eV and MAEEA-ADC(4) = 0.27 eV are found.

Cclib 2.0: An updated architecture for interoperable computational chemistry.

Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots-the formalization of cclib's intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects.

The updates in Libcint 6: More integrals, API refinements, and SIMD optimization techniques.

Libcint is a library designed for the evaluation of analytical integrals for Gaussian type orbitals. It prioritizes simplicity, ease of use, and efficiency for the development of quantum chemistry programs. In the release of version 6.0, Libcint supports the computation of integrals for various operators, such as overlap, Coulomb, Gaunt, Breit, attenuated Coulomb, Slater-type geminals, and Yukawa potential, as well as arbitrary orders of derivatives for these operators. To enhance the usability of the library, Libcint provides a uniform function signature for all integral functions. A code generator is included to automate the implementation of new integrals. To achieve better performance on modern central processing unit architectures, the library employs explicit single instruction multiple data parallelization in the code implementation.

Jahn-Teller induced microwave spectra of the C70 + fullerene cation.

The C70 molecule is apolar. Upon ionization Jahn-Teller effects occur that distort the D5h neutral symmetry to Cs. This point group is polar thus ionization induces a permanent electric dipole moment in C70. The goal of the present calculations is to compute the equilibrium geometry and dipole moment of the C70 + cation by various DFT methods and to simulate microwave spectra. Using the Gaussian16 quantum chemistry program rotational constants, Cartesian dipole moment components, and the resultant dipole, as well as the Jahn-Teller stabilization energy and the HOMO-LUMO gaps were obtained. The microwave rotational spectra at gas phase temperatures 2.73 K and 10K were simulated using the Pgopher software. These spectra may serve as starting point for laboratory microwave measurements and as screening guide in radio astronomical searches. The static Jahn-Teller effect in C70 + is the consequence of the mixing of the two highest ground state occupied orbitals, thus it is a pseudo Jahn-Teller effect.

Interoperable workflows by exchanging grid-based data between quantum-chemical program packages.

Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that go beyond simple quantities, such as molecular structures and energies. Here, we describe our approach for addressing this interoperability challenge by exchanging electron densities and embedding potentials as grid-based data. We describe the approach that we have implemented to this end in a dedicated code, PyEmbed, currently part of a Python scripting framework. We discuss how it has facilitated the development of quantum-chemical subsystem and embedding methods and highlight several applications that have been enabled by PyEmbed, including wave-function theory (WFT) in density-functional theory (DFT) embedding schemes mixing non-relativistic and relativistic electronic structure methods, real-time time-dependent DFT-in-DFT approaches, the density-based many-body expansion, and workflows including real-space data analysis and visualization. Our approach demonstrates, in particular, the merits of exchanging (complex) grid-based data and, in general, the potential of modular software development in quantum chemistry, which hinges upon libraries that facilitate interoperability.

Two-component transformation inclusive contraction scheme in the relativistic molecular orbital theory

The incorporation of a two-component transformation into the contraction coefficients of basis functions is suggested. Such a contraction, referred to as “two-component transformation inclusive contraction (TIC)”, effectively eliminates the computational cost associated with the two-component transformation and can be readily implemented into conventional quantum chemistry programs. TIC was verified through numerical calculations using the second- and third-order unitarized Douglas–Kroll method, which is newly derived for the validation of TIC, and the infinite-order two-component method. The numerical validation results suggested that TIC could sufficiently reproduce the results of primitive basis sets for both atoms and molecules.

A perspective on the future of quantum chemical software: the example of the ORCA program package.

The field of computational chemistry has made an impressive impact on contemporary chemical research. In order to carry out computational studies on actual systems, sophisticated software is required in form of large-scale quantum chemical program packages. Given the enormous diversity and complexity of the methods that need to be implementation in such packages, it is evident that these software pieces are very large (millions of code lines) and extremely complex. Most of the packages in widespread use by the computational chemistry community have had a development history of decades. Given the rapid progress in the hardware and a lack of resources (time, workforce, money), it is not possible to keep redesigning these program packages from scratch in order to keep up with the ever more quickly shifting hardware landscape. In this perspective, some aspects of the multitude of challenges that the developer community faces are discussed. While the task at hand - to ensure that quantum chemical program packages can keep evolving and make best use of the available hardware - is daunting, there are also new evolving opportunities. The problems and potential cures are discussed with the example of the ORCA package that has been developed in our research group.

Tools to Simulate Resonance Raman Spectra for in-Situ Studies of Electron Transport Mediators and Bioelectrocatalysts

Raman spectroscopy is widely applied as an in-situ probe of electrochemical processes. When the excitation light is resonant with an electronic transition, the detected signal can be enhanced by more than 1,000-fold. Resonance Raman (RR) spectroscopy has broad application in the study of common organic electron transport mediators (i.e., viologens, phenazines, photosynthetic pigments) and active sites of redox proteins (i.e., laccases, peroxidases, flavin-containing enzymes). To support investigations of bioelectrocatalytic membranes, we have been adapting RR spectroscopy to gain insights into the properties of immobilized redox mediators and biocatalyst active sites.1,2 Computational methods can be useful for guiding spectral interpretation. This poster reports on applications of recently advanced time-dependent density functional theory (TDDFT) codes that enable the simulation of RR spectra for small electron transport mediators (e.g., methyl viologen radical anion) and redox protein active site models (e.g., laccase T1 site mimics). The ORCA program suite3 was adapted. A series of Cu-centered compounds that model the T1 active site in laccases was studied along with the methyl viologen radical cation. The T1 site in laccases facilitates direct electron transport to an electrode and is a target for in-situ RR measurements. The reported work demonstrates careful selection of the functional (B3-LYP versus the long-range corrected hybrid exchange functional, ωB97X-D3) results in TDDFT-calculated electronic absorption and RR spectra that have features in excellent agreement with experiment. The results provide a foundation to build from in advancing models of small redox mediators and laccase catalytic active sites in support of sustainable technologies. Ozuguzel, U.; Aquino, A.J.A.; Nieman, R.; Minteer, S.D.; Korzeniewski, C. “Calculation of Resonance Raman Spectra and Excited State Properties for Blue Copper Protein Model Complexes” ACS Sustainable Chem. Eng. 2022, 10, 14614. Xu, J.; Koh, M.; Minteer, S. D.; Korzeniewski, C. “In Situ Confocal Raman Microscopy of Redox Polymer Films on Bulk Electrode Supports” ACS Measurement Science Au 2023 (DOI: 10.1021/acsmeasuresciau.2c00064). Neese, F.; Wennmohs, F.; Becker, U.; Riplinger, C. “ORCA Quantum Chemistry Program Package” J. Chem. Phys. 2020, 152, 224108.

Cluster-Based Approach Utilizing Optimally Tuned TD-DFT to Calculate Absorption Spectra of Organic Semiconductor Thin Films.

The photophysics of organic semiconductor (OSC) thin films or crystals has garnered significant attention in recent years since a comprehensive theoretical understanding of the various processes occurring upon photoexcitation is crucial for assessing the efficiency of OSC materials. To date, research in this area has relied on methods using Frenkel-Holstein Hamiltonians, calculations of the GW-Bethe-Salpeter equation with periodic boundaries, or cluster-based approaches using quantum chemical methods, with each of the three approaches having distinct advantages and disadvantages. In this work, we introduce an optimally tuned, range-separated time-dependent density functional theory approach to accurately reproduce the total and polarization-resolved absorption spectra of pentacene, tetracene, and perylene thin films, all representative OSC materials. Our approach achieves excellent agreement with experimental data (mostly ≤0.1 eV) when combined with the utilization of clusters comprising multiple monomers and a standard polarizable continuum model to simulate the thin-film environment. Our protocol therefore addresses a major drawback of cluster-based approaches and makes them attractive tools for OSC investigations. Its key advantages include its independence from external, system-specific fitting parameters and its straightforward application with well-known quantum chemical program codes. It demonstrates how chemical intuition can help to reduce computational cost and still arrive at chemically meaningful and almost quantitative results.

PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules Using B3LYP/6-31G* Calculations.

The presented "PubChemQC B3LYP/6-31G*//PM6" data set is composed of the electronic properties of 85,938,443 molecules, encompassing a broad spectrum of molecules from essential compounds to biomolecules with a molecular weight up to 1000. These molecules account for 94.0% of the original PubChem Compound catalog as of August 29, 2016. The electronic properties, including orbitals, orbital energies, total energies, dipole moments, and other pertinent properties, were computed by using the B3LYP/6-31G* and PM6 methods. The data set, available in three formats, namely, GAMESS quantum chemistry program files, selected JSON output files, and a PostgreSQL database, provides researchers with the ability to query molecular properties. It is further subdivided into five subdata sets for more specific data. The first two subsets encompass molecules with carbon, hydrogen, oxygen, and nitrogen with molecular weights under 300 and 500, respectively. The third and fourth subsets incorporate molecules with carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, fluorine, and chlorine, with molecular weights under 300 and 500, respectively. The fifth subset comprises molecules with carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, fluorine, chlorine, sodium, potassium, magnesium, and calcium, with a molecular weight of under 500. The coefficients of determination for the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap range from 0.892 (for CHON500) to 0.803 (for the whole data set). These comprehensive results pave the way for applications in drug discovery and materials science, among others. The data sets can be accessed under the Creative Commons Attribution 4.0 International license at the following web address: https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html.

Molecular dynamic study of abrasive wear, viscosity and moduli of UDMA: A component of dental composite

Among the dental composites, Urethane Dimethacrylate (UDMA) is commonly used as a component in treating oral complications. Many molecular dynamics approaches are used to understand the behaviour of the material at room temperature as well as at higher temperatures to get a better insight after comparison with experimental values at the atomic level. There are three critical physical properties associated with these components, like abrasive wear, viscosity, and moduli, which play an essential role in determining the treatment and can be computed using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), the general-purpose quantum chemistry program package (ORCA), and the General Utility Lattice Program (GULP) molecular dynamics methods. A radial distribution function plot is generated using visual molecular dynamics (VMD) for UDMA and BisGMA. A comparison of these parameters with BisGMA, another component of dental composites, along with experimental results, is carried out in the present investigation. Further, since radiation also matters for settling the materials in dental treatment, we have computed absorption spectra from 200 nm to 800 nm using LAMMPS/ORCA.

Simple, Efficient, and Universal Energy Decomposition Analysis Method Based on Dispersion-Corrected Density Functional Theory.

Energy decomposition analysis (EDA) is an important class of methods to explore the nature of interaction between fragments in a chemical system. It can decompose the interaction energy into different physical components to understand the factors that play key roles in the interaction. This work proposes an EDA strategy based on dispersion-corrected density functional theory (DFT), called sobEDA. This method is fairly easy to implement and very universal. It can be used to study weak interactions, chemical bond interactions, open-shell systems, and interactions between multiple fragments. The total time consumption of sobEDA is only about twice that of conventional DFT single-point calculation for the entire system. This work also proposes a variant of the sobEDA method named sobEDAw, which is designed specifically for decomposing weak interaction energies. Through a proper combination of DFT correlation energy and dispersion correction term, sobEDAw gives a ratio between dispersion energy and electrostatic energy that is highly consistent with the symmetry-adapted perturbation theory, which is quite popular and robust in studying weak interactions but expensive. We present a shell script sobEDA.sh to implement the methods proposed in this work based on the very popular Gaussian quantum chemistry program and Multiwfn wavefunction analysis code. Via the script, theoretical chemists can use the sobEDA and sobEDAw methods very conveniently in their study. Through a series of examples, the rationality of the new methods and their implementation are verified, and their great practical values in the study of various chemical systems are demonstrated.

Algebraic Diagrammatic Construction Schemes Employing the Intermediate State Formalism: Theory, Capabilities, and Interpretation.

Algebraic diagrammatic construction (ADC) schemes represent a family of ab initio methods for the calculation of excited electronic states and electron-detached and -attached states. All ADC methods have been demonstrated to possess great potential for molecular applications, e.g., for the calculation of absorption or photoelectron spectra or electron attachment processes. ADC originates from Green's function or propagator theory; however, most recent ADC developments heavily rely on the intermediate state representation or effective Liouvillian formalisms, which comprise new ADC methods and computational schemes for high-order properties. The different approaches for the calculation of excitation energies, ionization potentials, and electron affinities are intimately related, and they provide a coherent description of these quantities at equivalent levels of theory and with comparable errors. Most quantum chemical program packages contain ADC methods; however, the most complete ADC suite of methods can be found in the recent release of Q-Chem.

BasisOpt: A Python package for quantum chemistry basis set optimization.

The accuracy and efficiency of molecular quantum chemical calculations depend critically on the basis set used. However, the development of novel basis sets is hindered because much of the literature relies on the use of opaque processes and tools that are not publicly available. We present here BasisOpt, a tool for the automated optimization of basis sets with an easy-to-use framework. It features an open and accessible workflow for basis set optimization that can be easily adapted to almost any quantum chemistry program, a standardized approach to testing basis sets, and visualization of both the optimized basis sets and the optimization process. We provide examples of usage in realistic basis set optimization scenarios where: (i) a density fitting basis set is optimized for He, Ne, and Ar; (ii) the exponents of the def2-SVP basis are re-optimized for a set of molecules rather than atoms; and (iii) a large, almost saturated basis of sp primitives is automatically reduced to (10s5p) while achieving the lowest energy for such a basis set composition.

Friedel-Crafts Reaction of Vinyltrimethoxysilane with Styrene and Composite Materials on Their Base

Friedel-Crafts alkylation reaction of vinyltri-methoxysilane with styrene was performed in the pres-ence of anhydrous AlCl3. Alkoxy(4-vinylphenethyl)silane has been obtained. The synthesized products were identified by 1H, 13C, COSY NMR, and FTIR spectroscopy. Calculations using the quantum-chemical non-empirical density functional theory (DFT) method for the reaction between vinyltrimethoxysilane and styrene performed for ortho-, meta- and para-positions were discussed. For the theoretical modeling an online prediction program "Priroda 04: A quantum-chemical program suite" was used. Composite materials based on wood sawdust with various dispersion qualities and synthesized trimethoxysilylated styrene as a binding and reinforcing agent with degrees of silylation (5 %), in the presence of various organic/inorganic additives, fire retardants, and antioxidants, have been developed at different temperatures and pressures via hot press method or extrusion. The physico-mechanical properties of composites have been investigated.

Massively parallel fragment-based quantum chemistry for large molecular systems: the serestipy software

We present the Serestipy software as an add-on to the quantum-chemistry program Serenity. Serestipy is a representational-state transfer-oriented application programming interface written in the Python programming language enabling parallel subsystem density-functional theory calculations. We introduce approximate strategies in the context of frozen-density embedding time-dependent density-functional theory to make parallel large-scale excited-state calculations feasible. Their accuracy is carefully benchmarked with calculations for a model system consisting of porphine rings. We apply this framework to a nanotube made up of those porphine rings consisting of 12 160 atoms (or 264 960 basis functions) and obtain its electronic structure and absorption spectrum in less than a day of computational time.

Enabling large-scale quantum path integral molecular dynamics simulations through the integration of Dcdftbmd and i-PI codes.

A large-scale quantum chemical calculation program, Dcdftbmd, was integrated with a Python-based advanced atomistic simulation program, i-PI. The implementation of a client-server model enabled hierarchical parallelization with respect to replicas and force evaluations. The established framework demonstrated that quantum path integral molecular dynamics simulations can be executed with high efficiency for systems consisting of a few tens of replicas and containing thousands of atoms. The application of the framework to bulk water systems, with and without an excess proton, demonstrated that nuclear quantum effects are significant for intra- and inter-molecular structural properties, including oxygen-hydrogen bond distance and radial distribution function around the hydrated excess proton.

Adsorption Capacity of Silica SBA-15 and Titanosilicate ETS-10 toward Indium Ions.

Indium is an extremely important element for industry that is distributed in the Earth's crust at very low concentrations. The recovery of indium by silica SBA-15 and titanosilicate ETS-10 was investigated at different pH levels, temperatures, times of contact and indium concentrations. A maximum removal of indium by ETS-10 was achieved at pH 3.0, while by SBA-15 it was within the pH range of 5.0-6.0. By studying kinetics, the applicability of the Elovich model for the description of indium adsorption on silica SBA-15 was shown, while its sorption on titanosilicate ETS-10 fitted well with the pseudo-first-order model. Langmuir and Freundlich adsorption isotherms were used to explain the equanimity of the sorption process. The Langmuir model showed its applicability for the explanation of the equilibrium data obtained for both sorbents, the maximum sorption capacity obtained using the model constituted 366 mg/g for titanosilicate ETS-10 at pH 3.0, temperature 22 °C and contact time 60 min, and 2036 mg/g for silica SBA-15 at pH 6.0, temperature 22 °C and contact time 60 min. Indium recovery was not dependent on the temperature and the sorption process was spontaneous in nature. The interactions between the indium sulfate structure and surfaces of adsorbents were investigated theoretically using the ORCA quantum chemistry program package. The spent SBA-15 and ETS-10 could be easily regenerated by using 0.01 M HCl and reused with up to 6 cycles of adsorption/desorption with a decrease in the removal efficiency between 4% and 10% for SBA-15 and 5% and 10% for ETS-10, respectively.