Search NASA⌕ Search

SEARCH · Search NASA

Results for “molecules potential energy”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Advancing density functional tight-binding method for large organic molecules through equivariant neural networks

Semi-empirical quantum-mechanical (QM) methods have become valuable tools for studying complex (bio)molecular systems due to their balance between computational efficiency and accuracy. A key aspect of these methods is their parameterization, which not only governs the reliability of the results but also provides an opportunity to enhance their overall performance. In our previous work [J. Phys. Chem. Lett., 2021, 11, 16], we advanced the third-order semi-empirical density functional tight-binding (DFTB3) method for computing multiple properties of small molecules by developing the machine learning (ML) potential NN rep to bridge the gap between DFTB3 electronic components and those of the hybrid DFT-PBE0 functional. To overcome the limitations of NN rep , we introduce the EquiDTB framework, which leverages physics-inspired equivariant neural networks (NN) to parameterize scalable and transferable many-body Δ TB potentials, replacing the standard pairwise DFTB repulsive potential. This advancement extends the applicability of our ML-corrected DFTB approach to larger molecules and non-covalent systems (including only C, N, O, and H atoms), going beyond the chemical space represented in the training QM datasets. The enhanced performance of EquiDTB over the standard TB methods is demonstrated by the accurate computation of the atomic forces of S66x8 molecular dimers, as well as their interaction energies. Moreover, EquiDTB can be effectively employed to explore the potential energy surfaces of large and flexible drug-like molecules—for example, to determine the minimum energy path between isomers, analyze structural transitions during dynamical simulations, compute vibrational modes, and investigate energetic rankings. The performance for single molecules slightly decreases when the DFTB electronic energy is reduced to first-order but remains superior to standard TB methods. Our work thus demonstrates that an optimal integration of an equivariant NN with QM datasets can advance the DFTB method while maintaining high efficiency, paving the way for reliable (bio)molecular simulations.

Medrano Sandonas, Leonardo [Technische Universität↗
DOE OSTI2020

Li-Metal Anode in Dilute Electrolyte LiFSI/TMP: Electrochemical Stability Using Ab Initio Molecular Dynamics

Ab initio molecular dynamics simulations were performed for Li + conducting electrolytes based on trimethyl phosphates (TMP) and lithium bis(fluorosulfonyl)imide (Li + FSI – ) salt in contact with a Li-metal electrode. We focused on the transient-state behavior at the electrolyte, interfacial electrolyte–Li-metal electrode, and lithium reference electrode–electrolyte–Li-metal electrode to study dynamics and activation energy barriers of the Li + ion, electrochemical and thermal stability of the interface electrode-electrolyte, and potential behavior of the Li-metal electrode, respectively. Our results show that in the most stable state, Li + ions are tetrahedrally coordinated to three TMPs and one FSI – . The inner solvation shell of a Li-ion is composed of three TMP and one FSI – in one contact ion-pair and four TMPs in a solvent-separated ion-pair. On the other hand, Li-ions transport through electrolyte cages takes place when they are coordinated with three or less molecules that could be a combination of TMPs and FSI – . The decomposition pathway of the LiFSI salt when in direct contact with the Li-metal anode starts with defluorination of FSI – , rapidly losing F– to the lithium surface, forming LiF species. The remaining FSO 2 NSO 2 –2 with the addition of 2e – from the Li-metal decomposes into SO 2 –2 and NFSO 2 –2 . SO 2 –2 deposits on the Li-surface and decomposes into Li 2 O and Li 2 S. The remaining NFSO 2 –2 defluorinates, losing F – ion to the lithium surface, resulting in LiF and the remaining NSO 2 –1 deposits on the lithium surface and decomposes in the following picoseconds, forming several binary compounds such as Li 3 N, Li 2 S and Li 2 O. In contrast, when the salt is solvated by the TMP molecules, avoiding a direct contact with the Li metal electrode, only one defluorination occurs, decomposing the FSI – into FSO 2 NSO 2 –2 and a F – . The two anions remain stable as they are solvated by the TMP molecules. Furthermore, we also analyzed the open circuit potential energy (OCPE) of the Li-metal electrode during the SEI formation. OCPE is calculated from the average local potential profile difference within the Li-metal electrode and a pristine Li-crystal reference electrode (LRE). When no SEI is formed, the Li-metal electrode has an average OCPE of +0.36 eV vs LRE. Due to the formation of a SEI, the Li-metal electrode has an average OCPE between -0.07 and -0.21 eV vs LRE. The OCPE of the Li-metal electrode decreases by ~0.42 eV when a SEI is formed.

25 ENERGY STORAGE↗
DOE OSTI2025

Conjugation effect of amine molecules in non-aqueous Mg redox flow batteries

Nonaqueous magnesium redox flow batteries (Mg RFBs) are attractive for low-cost, high-energy-density and long-cycle-life stationary energy storage applications. However, state-of-the-art cathode redox-active molecules suffer from low solubility and low redox potential. Herein, we screened a range of cathode redox-active molecules and identified amine molecules as optimal to couple with the Mg anode. The properties of amine derivatives and their performances were collected to establish the correlation between molecular structures and electrochemical performances. The redox potential and solubility of these amine molecules were influenced by the π-conjugated and non-conjugated structures of amine derivatives. Density functional theory (DFT) simulations and the inverse aromatic fluctuation index (FLU −1 ) verified that conjugation had an important role in stabilizing the molecule and increasing its redox potential. Notably, tris[4-(diethylamino)phenyl]amine (TDPA) achieved the highest theoretical energy density (∼120 Wh L −1 ) due to its high solubility (∼0.9 M) and voltage (∼2.5 V vs. Mg/Mg 2+ ). We also demonstrated that ether solvents were crucial for stable, high-solubility catholytes, while bulk anions did not affect the redox potential of these p-type molecules. In a Mg-amine RFB configuration, the battery delivered 2.50 V, a specific discharge capacity of 106.5 mAh g −1 , an initial coulombic efficiency of 90.74%, and a capacity retention of 93.88% after 150 cycles.

Qin, Yunan [University of Utah, Salt Lake City, UT↗
DOE OSTI2023

Probing the Potential Energy Profile of the I + (H 2 O) 3 → HI + (H 2 O) 2 OH Forward and Reverse Reactions: High Level CCSD(T) Studies with Spin-Orbit Coupling Included

Three different pathways for the atomic iodine plus water trimer reaction I + (H 2 O) 3 → HI + (H 2 O) 2 OH were preliminarily examined by the DFT-MPW1K method. Related to previous predictions for the F/Cl/Br + (H 2 O) 3 reactions, three pathways for the I + (H 2 O) 3 reaction are linked in terms of geometry and energetics. To legitimize the results, the “gold standard” CCSD(T) method was employed to investigate the lowest-lying pathway with the correlation-consistent polarized valence basis set up to cc-pVQZ(-PP). According to the CCSD(T)/cc-pVQZ(-PP)//CCSD(T)/cc-pVTZ(-PP) results, the I + (H 2 O) 3 → HI + (H 2 O) 2 OH reaction is predicted to be endothermic by 47.0 kcal mol -1 . The submerged transition state is predicted to lie 43.7 kcal mol -1 above the separated reactants. The I···(H 2 O) 3 entrance complex lies below the separated reactants by 4.1 kcal mol -1 , and spin-orbit coupling has a significant impact on this dissociation energy. The HI···(H 2 O) 2 OH exit complex is bound by 4.3 kcal mol -1 in relation to the separated products. Compared with simpler I + (H 2 O) 2 and I + H 2 O reactions, the I + (H 2 O) 3 reaction is energetically between them in general. It is speculated that the reaction between the iodine atom and the larger water clusters may be energetically analogous to the I + (H 2 O) 3 reaction. The iodine reaction I + (H 2 O) 3 is connected with the analogous valence isoelectronic bromine/chlorine reactions Br/Cl + (H 2 O) 3 but much different from the F + (H 2 O) 3 reaction. Significant difference with other halogen systems, especially for barrier heights, are seen for the iodine systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the $P$-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

How Precisely Can Individual Molecules Be Analyzed? A Case Study on Locally Quantifying Forces and Energies Using Scanning Probe Microscopy

Recent advances in scanning probe microscopy methodology have enabled the measurement of tip-sample interactions with picometer accuracy in all three spatial dimensions, thereby providing a detailed site-specific and distance-dependent picture of the related properties. This paper explores the degree of detail and accuracy that can be achieved in locally quantifying probe-molecule interaction forces and energies for adsorbed molecules. Toward this end, cobalt phthalocyanine (CoPc), a promising CO 2 reduction catalyst, was studied on Ag(111) as a model system using low-temperature, ultrahigh vacuum noncontact atomic force microscopy. Data were recorded as a function of distance from the surface, from which detailed three-dimensional maps of the molecule's interaction with the tip for normal and lateral forces as well as the tip-molecule interaction potential were constructed. The data were collected with a CO molecule at the tip apex, which enabled a detailed visualization of the atomic structure. Determination of the tip-substrate interaction as a function of distance allowed isolation of the molecule-tip interactions; when analyzing these in terms of a Lennard-Jones-type potential, the atomically resolved equilibrium interaction energies between the CO tethered to the tip and the CoPc molecule could be recovered. Interaction energies peaked at less than 160 meV, indicating a physisorption interaction. As expected, the interaction was weakest at the aromatic hydrogens around the periphery of the molecule and strongest surrounding the metal center. In conclusion, the interaction, however, did not peak directly above the Co atom but rather in pockets surrounding it.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Dynamic processes in transient phases during self-assembly of organic semiconductor thin films

Understanding and manipulating crystallization processes has been an important challenge for solution-processed organic thin films, both for fundamental studies and for fabricating thin films with near-intrinsic charge transport properties. We report an in situ X-ray scattering study of the crystallization of 2-decyl-7-phenyl-[1]benzothieno[3,2-b][1]benzothiophene (Ph-BTBT-C 10 ) during its deposition from solution. At temperatures modestly below the smectic-E/crystalline phase boundary, the crystallization goes through a transient liquid crystal state before reaching the final stable crystalline phase. Significant dynamics occur in the first few seconds of the transition, which are observed through fluctuations in the X-ray scattering intensity, and are correlated with the time interval that the transient thin film coexists with the evaporating solvent. The transition to the stable crystalline phase takes minutes or even hours under these conditions, which may be a result of the asymmetry of the molecule. Transient phases are of potential interest for applications, since they can act as a route to self-assembly of organic thin films. However, our observations show that the long-lived monolayer-stacked intermediate state does not act as a template for the bilayer-stacked crystalline phase. Rather, the grain structure is replaced through nucleation, where the nucleation free-energy barrier is related to a potential barrier that prevents molecules to flip their long axis by 180°.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Vibrational levels of a generalized Morse potential

A Generalized Morse Potential (GMP) is an extension of the Morse Potential (MP) with an additional exponential term and an additional parameter that compensate for MP’s erroneous behavior in the long range part of the interaction potential. Because of the additional term and parameter, the vibrational levels of the GMP cannot be solved analytically, unlike the case for the MP. We present several numerical approaches for solving the vibrational problem of the GMP based on Galerkin methods, namely, the Laguerre Polynomial Method (LPM), the Symmetrized LPM, and the Polynomial Expansion Method (PEM), and apply them to the vibrational levels of the homonuclear diatomic molecules B 2 , O 2 , and F 2 , for which high level theoretical near full configuration interaction (CI) electronic ground state potential energy surfaces and experimentally measured vibrational levels have been reported. Overall, the LPM produces vibrational states for the GMP that are converged to within spectroscopic accuracy of 0.01 cm –1 in between 1 and 2 orders of magnitude faster and with much fewer basis functions/grid points than the Colbert–Miller Discrete Variable Representation (CN-DVR) method for the three homonuclear diatomic molecules examined in this study.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Testing molecules that disperse biofilms and biofouling and improve water recycling energy efficiency

In collaboration with Aequor, Inc, ABPDU researchers have evaluated a number of antibiofouling compounds for biofilm reduction potential in biomanufacturing applications. In addition to verifying their efficacy as dispersants, studies with bacteria, fungi, and algae indicate compatibility with canonical industrial host organisms. In addition, these molecules were found to significantly enhance growth rates of heterotrophic algae, indicating potential applications in algal cultivations.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Data for Optimizing Chemical-Free Pretreatment for Maximizing Oil/Lipid Recovery from Transgenic Bioenergy Crops and its Rapid Analysis Using Time Domain-NMR

Transgenic bioenergy crops have shown the potential to produce vegetative oil by accumulating energy-rich triacylglyceride molecules that can be converted into biofuels (biodiesel and biojet). These transgenic crops cater to improved biofuel yield by providing lipids along with cellulosic sugars. Efficient bioprocessing technologies are needed to utilize these transgenic plants to their maximum potential. To this end, this study investigates a low- and high-severity chemical-free hydrothermal pretreatment of transgenic oilcane 1566 bagasse with in situ lipids to maximize the recovery of lipids for biodiesel and fermentable sugars for ethanol with minimal inhibitor generation. Hydrothermal pretreatment at 170°C recovered ∼25% of total lipids in the pretreatment liquor, leaving the remainder in bagasse residue for hexane recovery post fermentation. The recovery of lipids in pretreatment liquor remained constant beyond 170°C. Along with lipids, ∼35% w/w and ∼50% w/w fermentable sugars were recovered post saccharification from bagasse pretreated at 170°C and 210°C for 20 min, respectively. Hydrothermal pretreatment at 170°C for 20 min provided the optimum conditions for maximum recovery of lipids and cellulosic sugars that resulted in enhanced biofuel yield per unit biomass. High severity pretreatment increased the generation of inhibitors beyond the tolerance of fermentation microorganisms. In addition, the application of time-domain proton NMR spectroscopy was extended to bioprocessing. NMR technology facilitated the analysis of total lipids, the composition of fatty acids, and the characterization of free and bound lipids in untreated and pretreated oilcane 1566 bagasse subsequent to each step of biomass to biofuel conversion.

Conversion↗
DOE OSTI2021

SpectrumSDT: A program for parallel calculation of coupled rotational-vibrational energies and lifetimes of bound states and scattering resonances in triatomic systems

In this work, we present SpectrumSDT – a program for calculations of energies and lifetimes of bound rotational-vibrational states below and scattering resonances above the dissociation threshold on a global potential energy surface of a triatomic system, which may include stable molecules, weekly-bound van-der-Waals complexes, and unbound atom + diatom scattering systems. Large-amplitude vibrational motion is treated explicitly using hyper-spherical coordinates. Three options for the rotational-vibrational interaction are supported: uncoupled (symmetric top rotor), partially coupled (to include interaction between several nearest states only) and full-coupled (vibrating asymmetric-top rotor). In addition to energies and lifetimes, SpectrumSDT is able to integrate ro-vibrational wave functions over the user-defined regions of potential energy surface, which helps to classify these states. In this release of the code, SpectrumSDT is limited to ABA-type molecules with wave functions that do not extend into the regions near Eckart singularities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Single- and multi-photon-induced ultraviolet excitation and photodissociation of CH 3 I probed by coincident ion momentum imaging

The UV-induced photodissociation dynamics of iodomethane (CH 3 I) in its A-band are investigated by time-resolved coincident ion momentum imaging using strong-field ionization as a probe. The delay-dependent kinetic energy distribution of the photofragments resulting from double ionization of the molecule maps the cleavage of the carbon–iodine bond and shows how the existence of a potential well in the di-cationic potential energy surfaces shapes the observed distribution at small pump–probe delays. Furthermore, the competition between single- and multi-photon excitation and ionization of the molecule is studied as a function of the intensity of the UV-pump laser pulse. Two-photon excitation to Rydberg states is identified by tracking the transformation of the delay-dependent singly-charged iodomethane yield from a pure Gaussian distribution at low intensity to a Gaussian with an exponentially decaying tail at higher intensities. In conclusion, dissociative ionization induced by absorption of three UV photons is resolved as an additional delay-dependent feature in the kinetic energy of the fragment ions detected in coincidence.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Simultaneous mitigation of density and energy errors in approximate DFT for transition metal chemistry (Final Technical Report)

There were three major goals and objectives of this project: 1) Develop tools to understand density-driven errors in transition metal complexes, 2) Evaluate and minimize energy delocalization error and static correlation error through judicious functional choice, and 3) applying this workflow to machine-learning accelerated screening of redox couples. Over the reporting period, we developed a framework for eliminating flat plane errors. We introduced fully non-empirical coefficients. We demonstrated the approach on both molecules and solids. We investigated and eliminated density driven errors and demonstrated their impact on potential energy surfaces. We trained machine learning models both in a method-dependent fashion and to predict errors in method accuracy. We built large data sets of small molecule energetics and multi-reference character.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Discovery of Energy Storage Molecular Materials Using Quantum Chemistry-Guided Multiobjective Bayesian Optimization

Redox flow batteries (RFBs) are a promising technology for stationary energy storage applications due to their flexible design, scalability, and low cost. In RFBs, energy is carried in flowable redoxactive materials (redoxmers) which are stored externally and pumped to the cell during operation. Further improvements in the energy density of RFBs necessitates redoxmer designs with wider redox potential windows and higher solubility. Additionally, designing redoxmers with a fluorescence-enabled self-reporting functionality allows monitoring of the state of health of RFBs. To accelerate the discovery of redoxmers with desired properties, state-of-the- art machine learning ( ML) methods, such as multiobjective Bayesian optimization (MBO), are useful. Here, we first employed density functional theory calculations to generate a database of reduction potentials, solvation free energies, and absorption wavelengths for 1400 redoxmer molecules based on a 2,1,3-benzothiadiazole (BzNSN) core structure. From the computed properties, we identified 22 Pareto-optimal molecules that represent best trade-off among all of the desired properties. We further utilized these data to develop and benchmark an MBO approach to identify candidates quickly and efficiently with multiple targeted properties. With MBO, optimal candidates from the 1400-molecule data set can be identified at least 15 times more efficiently compared to the brute force or random selection approach. Importantly, we utilized this approach for discovering promising redoxmers from an unseen database of 1 million BzNSN-based molecules, where we discovered 16 new Pareto-optimal molecules with significant improvements in properties over the initial 1400 molecules. Furthermore, we anticipate that this active learning technique is general and can be utilized for the discovery of any class of functional materials that satisfies multiple desired property criteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

In Vitro Encapsulation of Functionally Active Abiotic Photosensitizers Inside a Bacterial Microcompartment Shell

Bacterial microcompartments (BMCs) are self-assembling, selectively permeable protein shells that encapsulate enzymes to enhance catalytic efficiency of segments of metabolic pathways through means of confinement. The modular nature of BMC shells' structure and assembly enables programming of shell permeability and underscores their promise in biotechnology engineering efforts for applications in industry, medicine, and clean energy. Realizing this potential requires methods for encapsulation of abiotic molecules, which have been developed here for the first time. We report in vitro cargo loading of BMC shells with ruthenium photosensitizers (RuPS) by two approaches-one involving site-specific covalent labeling and the other driven by diffusion, requiring no specific interactions between cargo molecules and shell proteins. The highly stable shells retain encapsulated cargo over 1 week without egress and preserve RuPS photophysical activity. Finally, this study is an important foundation for further work that will converge biological BMC architecture with synthetic chemistry to facilitate biohybrid photocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Atomic autoionization in the photo-dissociation of super-excited deuterated water molecules fragmenting into D + + O + + D

We present the relaxation dynamics of deuterated water molecules via autoionization, initiated by the absorption of a 61 eV photon, producing the very rare D + + O + + D breakup channel. We employ the COLd target recoil ion momentum spectroscopy method to measure the 3D momenta of the ionic fragments and emitted electrons from the dissociating molecule in coincidence. We interpret the results using the potential energy surfaces extracted from multi-reference configuration interaction calculations. The measured particle energy distributions can be related to a super-excited monocationic state located above the double ionization threshold of D 2 O. The autoionized electron energy shows a sharp distribution centered around 0.5 eV, which is a signature of the atomic oxygen autoionization occurring in the direct and sequential dissociation processes of D 2 O + * at a large internuclear distance. In this way, an O + radical fragment and a low-energy electron are created, both of which can trigger secondary reactions in their environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗