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All sources NASA NTRS DOE OSTI

DOE OSTI2022

An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts

The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13 >C and 1 H NMR spectra with respect to experimentally measured values. This leads us to the question–what accuracy is required in predicted 13 C and 1 H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1 H and 13 C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations

We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempirical OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.

Dral, Pavlo O.↗

NASA NTRS1989

Accurate quantum chemical calculations

An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

Bauschlicher, Charles W., Jr.↗

NASA NTRS1997

Quantum Chemical Calculations

The current methods of quantum chemical calculations will be reviewed. The accent will be on the accuracy that can be achieved with these methods. The basis set requirements and computer resources for the various methods will be discussed. The utility of the methods will be illustrated with some examples, which include the calculation of accurate bond energies for SiF$_n$ and SiF$_n^+$ and the modeling of chemical data storage.

Bauschlicher, Charles W.↗

DOE OSTI2018

A new approach for the acceleration of large-scale serial quantum chemical calculations of docking complexes

A new approach to radical accelerate large-scale quantum chemical calculations of docking complexes, which require large computational times, is proposed. It takes into account the local nature of protein interaction with ligands and is based on a formation of special groups of atoms, which include the compactly located ligands and the protein atoms surrounding them. The procedure based on this approach allowed more than twice to reduce the time of a very resource-consuming calculation with respect to our previous high-speed semi-empirical method without a noticeable decrease in accuracy and provided a level of the time consumption appropriate for the large-scale serial calculations of such complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Chemical expansion affected oxygen vacancy stability in different oxide structures from first principles calculations

We study the chemical expansion for neutral and charged oxygen vacancies in fluorite, rocksalt, perovskite and pyrochlores materials using first principles calculations. We show that the neutral oxygen vacancy leads to lattice expansion whereas the charged vacancy leads to lattice contraction. In addition, we show that there is a window of strain within which an oxygen vacancy is stable; beyond that range, the vacancy can become unstable. Using CeO2|ZrO2 interface structure as an example, we show that the concentration of oxygen vacancies can be manipulated via strain, and the vacancies can be preferentially stabilized. These results could serve as guiding principles in predicting oxygen vacancy stability in strained systems and in the design of vacancy stabilized materials.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2024

Scaling Ensembles of Data-Intensive Quantum Chemical Calculations for Millions of Molecules

Deep learning models are efficient computational tools that can accelerate the inverse design of molecules with desired functional properties by generating predictions at a fraction of the time required by traditional quantum chemical approaches. To ensure that a model maintains accuracy and transferability across broad regions of the chemical space explored during the inverse design, it must be trained on massively large volumes of simulation data. This requires running large-scale ensemble quantum chemical calculations on high-performance computing (HPC) systems for data collection. However, the efficient execution of such large ensemble calculations and the management of large volumes of output data require tools that can judiciously utilize computational resources and manage metadata overhead on the file system. Therefore, we present a high-performance, scalable, ensemble management framework for performing data-intensive quantum chemical electronic structure calculations for organic molecules. This framework provides abstractions to plug different ab initio, first principles, and first principles-based semi-empirical methods and executes them efficiently at large scale on HPC systems. It dynamically distributes tasks to resources and uses tiered storage for managing large collections of files. We employed this framework to process over ten million organic molecules and generate open-source datasets that provide UV-vis absorption spectra by running time-dependent density-functional tight-binding calculations. It is the largest database containing molecular optical spectra that were simulated with quantum chemical methods in a consistent manner.

Mehta, Kshitij↗

DOE OSTI2023

Refining the thermochemical properties of CF, SiF, and their cations by combining photoelectron spectroscopy, quantum chemical calculations, and the Active Thermochemical Tables approach

Fluorinated species have a pivotal role in semiconductor material chemistry and some of them have been detected beyond the Earth's atmosphere. Achieving good energy accuracy on fluorinated species using quantum chemical calculations has long been a challenge. In addition, obtaining direct experimental thermochemical quantities has also proved difficult. Here, we report the threshold photoelectron and photoion yield spectra of SiF and CF radicals generated with a fluorine reactor. The spectra were analysed with the support of ab initio calculations, resulting in new experimental values for the adiabatic ionisation energies of both CF (9.128 ± 0.006 eV) and SiF (7.379 ± 0.009 eV). Using these values, the underlying thermochemical network of Active Thermochemical Tables was updated, providing further refined enthalpies of formation and dissociation energies of CF, SiF, and their cationic counterparts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Quantum Chemical Calculations of the Spectroscopic Properties and Nonlinear Optical Activity of 2,6-Dibromo-3-Chloro-4-Fluoroaniline

The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 2,6-dibromo-3-chloro-4-fluoroaniline in the solid phase were recorded and analyzed. Quantum chemical calculations of the optimized molecular structure, energies, nonlinear optical (NLO) analysis, molecular surfaces, and vibrational analysis of this substance were performed. The obtained results on the geometric structure and vibrational frequencies were compared with the observed data. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies also confirm that charge transfer occurs within the molecule. The detailed vibrational assignments were performed using the HF and DFT calculations, and the potential energy distribution (PED) was obtained by the vibrational energy distribution analysis (VEDA4) program. Finally, the effects of the amino, bromo, chloro, and fluoro substituents on the vibrational frequencies were investigated.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Error detection on quantum computers improving the accuracy of chemical calculations

The ultimate goal of quantum error correction is to achieve the fault-tolerance threshold beyond which quantum computers can be made arbitrarily accurate. This requires extraordinary resources and engineering efforts. We show that even without achieving full fault-tolerance, quantum error detection is already useful on the current generation of quantum hardware. We demonstrate this by executing an end-to-end chemical calculation for the hydrogen molecule encoded in the [[4, 2, 2]] quantum error-detecting code. The encoded calculation with logical qubits significantly improves the accuracy of the molecular ground-state energy.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Quantum chemical calculations to determine partitioning coefficients for HgCl 2 on iron-oxide aerosols

Gas-to-particle phase partitioning controls the pathways for oxidized mercury deposition from the atmosphere to the Earth's surface. The propensity of oxidized mercury species to transition between these two phases is described by the partitioning coefficient (K p ). Experimental measurements of K p values for HgCl 2 in the presence of atmospheric aerosols are difficult and time-consuming. Quantum chemical calculations, therefore, offer a promising opportunity to efficiently estimate partitioning coefficients for HgCl 2 on relevant aerosols. In this study, density functional theory (DFT) calculations are used to predict K p values for HgCl 2 on relevant iron-oxide surfaces. The model is first verified using a NaCl(100) surface, showing good agreement between the calculated (2.8) and experimental (29–43) dimensionless partitioning coefficients at room temperature. Then, the methodology is applied to six atmospherically relevant terminations of α-Fe 2 O 3 (0001): OH-Fe-R, (OH) 3 -Fe-R, (OH) 3 -R, O-Fe-R, Fe-O 3 -R, and O 3 -R (where R denotes bulk ordering). The OH-Fe-R termination is predicted to be the most stable under typical atmospheric conditions, and on this surface termination, a dimensionless HgCl 2 K p value of 5.2 x 10 3 at 295 K indicates a strong preference for the particle phase. Here this work demonstrates DFT as a promising approach to obtain partitioning coefficients, which can lead to improved models for the transport of mercury, as well as for other atmospheric pollutant species, through and between the anthroposphere and troposphere.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Quantum chemically calculated Abraham parameters for quantifying and predicting polymer hydrophobicity

The leakage and accumulation of plastic in the environment is a significant and growing problem with numerous detrimental impacts and has led to a push toward the design and development of more environmentally benign materials. To this end, we have developed a quantum chemistry-based model for predicting the mobility of polymer materials from molecular structure. Hydrophobicity is used as a surrogate for mobility given that hydrophobic interactions drive much of the partitioning of contaminants in and out of various environmentally relevant compartments. To model polymer hydrophobicity, we adjusted a previously developed Quantum Chemically Calculated Abraham Parameter model to calculate Abraham parameters of small molecules from molecular structure information. The resulting model predicted the octanol-water partition coefficient (K OW ) of polymer repeating units with a root mean square error (RMSE) of 0.48 (log scale). Additionally, the hydrophobicity of high molecular weight polymer materials was captured through solubility parameters and Nile red staining experiments from the literature and predicted with RMSEs of 1.21 (J/cc) 0.5 and 3.42 nm, respectively. Finally, to test the environmental applicability of the model, the relative adsorption capacity of three polymers was predicted and used to unify sorption isotherms across multiple sorbates and polymer sorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Octafluorodirhenate(III) Revisited: Solid-State Preparation, Characterization, and Multiconfigurational Quantum Chemical Calculations

A simple method for the high-yield preparation of (NH 4 ) 2 [Re 2 F 8 ]· 2H 2 O has been developed that involves the reaction of (n-Bu 4 N)2[Re 2 Cl 8 ] with molten ammonium bifluoride (NH 4 HF 2 ). Using this method, the new salt [NH 4 ] 2 [Re 2 F 8 ]·2H 2 O was prepared in ~90% yield. The product was characterized in solution by ultraviolet-visible light (UV-vis) and 19 F nuclear magnetic resonance (19F NMR) spectroscopies and in the solid-state by elemental analysis, powder X-ray diffraction (XRD), and infrared (IR) spectroscopy. Multiconfigurational CASSCF/CASPT2 quantum chemical calculations were performed to investigate the molecular and electronic structure, as well as the electronic absorption spectrum of the [Re 2 F 8 ] 2- anion. The metal-metal bonding in the Re 2 6+ unit was quantified in terms of effective bond order (EBO) and compared to that of its [Re 2 Cl 8 ] 2- and [Re 2 Br 8 ] 2- analogues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Reactions of Th + + H 2 , D 2 , and HD Studied by Guided Ion Beam Tandem Mass Spectrometry and Quantum Chemical Calculations

Kinetic energy dependent reactions of Th + with H 2 , D 2 , and HD were studied using a guided ion beam tandem mass spectrometer. Formation of ThH + and ThD + is endothermic in all cases with similar thresholds. Branching ratio results for the reaction with HD indicate that Th + reacts via a statistical mechanism, similar to Hf + . The kinetic energy dependent cross sections for formation of ThH + and ThD + were evaluated to determine a 0 K bond dissociation energy (BDE) of D 0 (Th + –H) = 2.45 ± 0.07 eV. This value is in good agreement with a previous result obtained from analysis of the Th + + CH 4 reaction. D 0 (Th + –H) is observed to be larger than its transition metal congeners, TiH + , ZrH + , and HfH + , believed to be a result of lanthanide contraction. The reactions with H 2 were also explored using quantum chemical calculations that include a semiempirical estimation and explicit calculation of spin–orbit contributions. These calculations agree nicely and indicate that ThH + most likely has a 3 Δ 1 ground level with a low-lying 1 Σ + excited state. As a result, theory also provides the reaction potential energy surfaces and BDEs that are in reasonable agreement with experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Absorption and Fluorescence Features of an Amphiphilic meso -Pyrimidinylcorrole: Experimental Study and Quantum Chemical Calculations

Here corroles are emerging as an important class of macrocycles with numerous applications because of their peculiar photophysical and metal chelating properties. meso -Pyrimidinylcorroles are easily deprotonated in certain solvents, which changes their absorption and emission spectra as well as their accessible supramolecular structures. To enable control over the formation of supramolecular structures, the dominant corrole species, i.e., the deprotonated form or one of the two NH-tautomers, needs to be identified. Therefore, we focus in the present article on the determination of the UV–vis spectroscopic properties of the free-base NH-tautomers and the deprotonated form of a new amphiphilic meso -pyrimidinylcorrole that can assemble to supramolecular structures at heterointerfaces as utilized in the Langmuir–Blodgett and liquid–liquid interface precipitation techniques. After quantification of the polarities of the free-base NH-tautomers and the deprotonated form by means of quantum chemically derived electrostatic potential distributions at the corroles’ van der Waals surfaces, the preferential stabilization of (some of) the considered species in solvents of different polarity is identified by means of absorption spectroscopy. For the solutions with complex mixtures of species, we applied fluorescence excitation spectroscopy to estimate the relative weights of the individual corrole species. This technique might also be applied to identify dominating species in molecularly thin films directly on the subphase’ surface of Langmuir–Blodgett troughs. Supported by quantum chemical calculations we were able to differentiate between the spectral signatures of the individual NH-tautomers by means of fluorescence excitation spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Quantum Chemical Calculation of p K a s of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines, and Thiols in Aqueous Solution

Developing accurate quantum chemical approaches for calculating p K a s is of broad interest. Useful accuracy can be obtained by using density functional theory (DFT) in combination with a polarizable continuum solvent model. However, some classes of molecules present problems for this approach, yielding errors greater than 5 p K units. Various methods have been developed to improve the accuracy of the combined strategy. These methods perform well but either do not generalize or introduce additional degrees of freedom, increasing the computational cost. The Solvation Model based on Density (SMD) has emerged as one of the most commonly used continuum solvent models. Nevertheless, for some classes of organic compounds, e.g., thiols, the p K a s calculated with the original SMD model show errors of 6–10 p K units, and we traced these errors to inaccuracies in the solvation free energies of the anions. To improve the accuracy of p K a s calculated with DFT and the SMD model, we developed a scaled solvent-accessible surface approach for constructing the solute–solvent boundary. By using a “direct” approach, in which all quantities are computed in the presence of the continuum solvent, the use of thermodynamic cycles is avoided. Furthermore, no explicit water molecules are required. Three benchmark data sets of experimentally measured p K a values, including 28 carboxylic acids, 10 aliphatic amines, and 45 thiols, were used to assess the optimized SMD model, which we call SMD with a scaled solvent-accessible surface (SMD sSAS ). Of the methods tested, the M06-2X density functional approximation, 6-31+G(d,p) basis set, and SMD sSAS solvent model provided the most accurate p K a s for each set, yielding mean unsigned errors of 0.9, 0.4, and 0.5 p K units, respectively, for carboxylic acids, aliphatic amines, and thiols. As a result, this approach is therefore useful for efficiently calculating the p K a s of environmentally relevant functional groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1991

An approximate viscous shock layer technique for calculating chemically reacting hypersonic flows about blunt-nosed bodies

An approximate axisymmetric method was developed which can reliably calculate fully viscous hypersonic flows over blunt nosed bodies. By substituting Maslen's second order pressure expression for the normal momentum equation, a simplified form of the viscous shock layer (VSL) equations is obtained. This approach can solve both the subsonic and supersonic regions of the shock layer without a starting solution for the shock shape. The approach is applicable to perfect gas, equilibrium, and nonequilibrium flowfields. Since the method is fully viscous, the problems associated with a boundary layer solution with an inviscid layer solution are avoided. This procedure is significantly faster than the parabolized Navier-Stokes (PNS) or VSL solvers and would be useful in a preliminary design environment. Problems associated with a previously developed approximate VSL technique are addressed before extending the method to nonequilibrium calculations. Perfect gas (laminar and turbulent), equilibrium, and nonequilibrium solutions were generated for airflows over several analytic body shapes. Surface heat transfer, skin friction, and pressure predictions are comparable to VSL results. In addition, computed heating rates are in good agreement with experimental data. The present technique generates its own shock shape as part of its solution, and therefore could be used to provide more accurate initial shock shapes for higher order procedures which require starting solutions.

Cheatwood, F. Mcneil↗

NASA NTRS1981

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

Kahn, L. R.↗