Molecular constants and internuclear potential of ground-state molecular iodines
Internuclear potential of ground state molecular iodine computed from rotational constants and vibrational energies
Le Roy, R. J.↗
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Europan Molecular Indicators of Life Investigation (EMILI) for a Future Europa Lander Mission
The Europan Molecular Indicators of Life Investigation (EMILI) is an instrument concept being developed for the Europa Lander mission currently under study. EMILI will meet and exceed the scientific and technical/resource requirements of the organic composition analyzer identified as a core instrument on the Lander. EMILI tightly couples two complementary analytical techniques, based on 1) liquid extraction and processing with capillary electrophoresis and 2) thermal and chemical extraction with gas chromatography, to robustly detect, structurally characterize, and quantify the broadest range of organics and other Europan chemicals over widely-varying concentrations. Dual processing and analysis paths enable EMILI to perform a thorough characterization of potential molecular biosignatures and contextual compounds in collected surface samples. Here we present a summary of the requirements, design, and development status of EMILI with projected scientific opportunities on the Europa Lander as well as on other potential life detection missions seeking potential molecular biosignatures in situ.
Europa↗
On the ionization potential of molecular oxygen
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Samson, J. A. R.↗
Microgravity research in plant biological systems: Realizing the potential of molecular biology
The sole all-pervasive feature of the environment that has helped shape, through evolution, all life on Earth is gravity. The near weightlessness of the Space Station Freedom space environment allows gravitational effects to be essentially uncoupled, thus providing an unprecedented opportunity to manipulate, systematically dissect, study, and exploit the role of gravity in the growth and development of all life forms. New and exciting opportunities are now available to utilize molecular biological and biochemical approaches to study the effects of microgravity on living organisms. By careful experimentation, we can determine how gravity perception occurs, how the resulting signals are produced and transduced, and how or if tissue-specific differences in gene expression occur. Microgravity research can provide unique new approaches to further our basic understanding of development and metabolic processes of cells and organisms, and to further the application of this new knowledge for the betterment of humankind.
Lewis, Norman G.↗
An Ongoing Quantum Chemistry Study of Molecules with Potential for Molecular Quantum Communications Using Density Functional Theory (DFT) and Other Techniques
Molecular quantum communications (the term here being used to define the transfer of information using the movement of quantum states between molecules or between molecules and a sensing environment that can be queried) can be achieved with a wide range of phenomena. Although there are excellent materials databases such as the Open Quantum Materials Database (http://oqmd.org/analysis/gclp/) and the Materials Project (https://materialsproject.org/), there is no centralized database of materials correlated to their quantum communications possibilities.
Harry Shaw↗
Molecular constants and internuclear potential of ground-state molecular iodine
Vibrational energies, rotational constants and internuclear potential of ground state molecular iodine, using reanalyzed spectroscopic data
Leroy, R. J.↗
Calculations of molecular ionization energies using a self-consistent-charge Hartree-Fock-Slater method
A numerical-variational method for performing self-consistent molecular calculations in the Hartree-Fock-Slater (HFS) model is presented. Molecular wavefunctions are expanded in terms of basis sets constructed from numerical HFS solutions of selected one-center atomlike problems. Binding energies and wavefunctions for the molecules are generated using a discrete variational method for a given molecular potential. In the self-consistent-charge (SCC) approximation to the complete self-consistent-field (SCF) method, results of a Mulliken population analysis of the molecular eigenfunctions are used in each iteration to produce 'atomic' occupation numbers. The simplest SCC potential is then obtained from overlapping spherical atomlike charge distributions. Molecular ionization energies are calculated using the transition-state procedure; results are given for CO, H2O, H2S, AlCl, InCl, and the Ni5O surface complex. Agreement between experimental and theoretical ionization energies for the free-molecule valence levels is generally within 1 eV. The simple SCC procedure gives a reasonably good approximation to the molecular potential, as shown by comparison with experiment, and with complete SCF calculations for CO, H2O, and H2S.
Rosen, A.↗
Modeling of Branched (L, T and Y) Carbon Nanotubes
Models for connecting two or three carbon nanotubes (CNT) using topological defects (i.e., pentagons and heptagons) are presented for the characterization of experimentally observed L, T and Y CNT junctions. The effects of the separation and orientation of the topological defects on the structures and energetics of these junctions are investigated using the nonlocal density function theory (DFT) and semi-empirical molecular orbital (AM1) calculations, and the Brenner empirical potential molecular mechanics simulations. The potential applications of L, Y and T CNT junctions in nanoelectronic devices are also discussed.
Han, Jie↗
The repulsive 1 Sigma g/+/ He2 potential obtained from total cross sections
An improved apparatus for obtaining short-range molecular potentials is described. The setup is a refined version of that used by Jordan-Amdur and by Leonas. The ion source is provided with a mass analyzing magnet, the capacitance manometer in the scattering cell is calibrated with a McCleod gauge, and the detection unit substitutes a Channeltron multiplier for the thermopile. The measured ground-state He-He potential for radii between 0.49 and 1.56 A is approximately V(r) = 215 x exp(-3.95r) eV, which is 25% higher than the earlier experiments. The result is supported by molecular orbital and statistical model calculations.
Foreman, P. B.↗
Mechanoregulation of Proliferation, Differentiation, Senescence and Survival of Bone Marrow Primary Osteoprecursor Cells
Cell and animal studies conducted onboard the International Space Station and during the Shuttle program have provided extensive data illustrating bone degenerative responses to mechanical unloading in microgravity. Specifically CDKN1a/p21, an inhibitory modulator of cell cycle progression, is upregulated in osteoprecursor cells of the femur during 15-day spaceflight, suggesting that microgravity can block stem cell-based tissue regenerative process at the level of progenitor proliferation and differentiation. To study a potential role for CDKN1a/p21 in regulating osteogenic mechanosensitivity, we cultured primary bone marrow osteoprogenitor cells from CDKN1a/p21-null (p21-null) and wildtype mice with and without mechanical stimulation, and compared their morphological, proliferative, and in-vitro mineralization responses. Structural cell alterations due to mechanical stimulation were assessed by florescence labeling of f-actin cytoskeleton and focal adhesions. Mechanical stimulation of p21-null cells resulted in more pronounced cytoskeletal alignment with the axis of stretch than for wildtype cells. In addition, p21-null cells subjected to stretch loading also formed significantly more focal adhesions than wildtype cells. Combined these findings suggest that p21-null cells are structurally more responsive to stretch stimulation than the wildtype cells. Because osteoprogenitor cells are well known to respond to mechanical stimulation with increased proliferation, we also tested this response in p21-null cells. Results from those experiments show the proliferative capacity of mechanically stimulated p21-null cells far exceeded that of wildtype controls. Specifically, cell counts from 14, and 21 days post mechanical stimulation, show that p21- null cells to have a 4-fold increase in proliferation compared to wildtype. When the p21-null cell differentiation response to mechanical stimulation was evaluated, the p21-null cultuers elicited more extensive mineralization at earlier assessed timepoints than control cultures. Specifically, Von Kossa staining for mineralized matrix showed that the p21-null cells produced more than twice the mineralized surface area of wildtype cells, and at an earlier 7-day time point in culture. Taken together these results suggest that CDKN1a/p21 normally plays a role in negatively regulating osteoprogenitor proliferation and differentiation responses to mechanostimulation in bone. Findings of CDKN1a/p21's increased expression during spaceflight in microgravity also suggest not only a potential molecular mechanism for arresting regenerative bone growth in space, but potentially also a reduced impact for bone-formation-promoting exercise mechanostimulation. The findings described here constitute a novel role for p21 as a regulator of tissue regeneration in response to mechanical load stimulation, and also suggest a new promising molecular target to promote regenerative health in disuse conditions.
gravity↗
Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials
Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine learning interatomic potential (MLIP) models. To this end, we first curate a large-scale molecular relaxation dataset comprising 3.5 million molecules and 300 million snapshots. Then MLIP pre-trained models are trained with supervised learning to predict energy and forces given 3D molecular structures. Once trained, we show that the pre-trained models can be used in different ways to obtain geometries either explicitly or implicitly. First, it can be used to obtain approximate low-energy 3D geometries via geometry optimization. While these geometries do not consistently reach DFT-level chemical accuracy or convergence, they can still improve downstream performance compared to non-relaxed structures. To mitigate potential biases and enhance downstream predictions, we introduce geometry fine-tuning based on the relaxed 3D geometries. Second, the pre-trained models can be directly fine-tuned for property prediction when ground truth 3D geometries are available. Our results demonstrate that MLIP pre-trained models trained on relaxation data can learn transferable molecular representations to improve downstream molecular property prediction and can provide practically valuable but approximate molecular geometries that benefit property predictions. Our code is publicly available at: https://github.com/divelab/AIRS/.
Fu, Cong [Texas A & M Univ., College Station, TX (↗
Methods in PES-Learn: Direct-Fit Machine Learning of Born–Oppenheimer Potential Energy Surfaces
The release of PES-L EARN version 1.0 as an open-source software package for the automatic construction of machine learning models of semi-global molecular potential energy surfaces (PESs) is presented. Improvements to PES-L EARN ’s interoperability are stressed with new Python API that simplifies workflows for PES construction via interaction with QCSchema input and output infrastructure. In addition, a new machine learning method is introduced to PES-L EARN : kernel ridge regression (KRR). The capabilities of KRR are emphasized with examination of select semi-global PESs. All machine learning methods available in PES-L EARN are benchmarked with benzene and ethanol datasets from the rMD17 database to illustrate PES-L EARN ’s performance ability. Fitting performance and timings are assessed for both systems. Finally, the ability to predict gradients with neural network models is presented and benchmarked with ethanol and benzene. PES-L EARN is an active project and welcomes community suggestions and contributions.
kernel ridge regression↗
Iron Impurity Impairs the CO 2 Capture Performance of MgO: Insights from Microscopy and Machine Learning Molecular Dynamics
Magnesium oxide (MgO) is a promising sorbent for direct air capture (DAC) of carbon dioxide. Iron (Fe) is a common impurity in naturally occurring MgO and minerals used to produce MgO, yet a molecular-scale understanding of Fe-doping effects on carbonation is lacking. Here, in this study, we observed reduced carbonation performance in Fe-doped MgO experimentally. The energetics of adsorbing a (bi)carbonate ion on pristine and Fe-doped MgO(001) surfaces were further investigated using ab initio and machine learning potential molecular dynamics coupled with metadynamics simulations. Both pristine and Fe-doped surfaces exhibited a basic (OH – ) hydration layer, where the (bi)carbonate ion adsorption is thermodynamically favorable. However, the dissolution of surface Fe had smaller energy barriers and was more favorable than Mg. Leached Fe likely neutralized the near-surface basicity, yielding reduced reactivity on Fe-doped MgO. Our observations offer critical insights for material selection and emphasize the importance of evaluating the geologic origin of earth materials used for DAC.
36 MATERIALS SCIENCE↗
NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials
Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.
59 BASIC BIOLOGICAL SCIENCES↗
Microscopic Origin of Twist-Dependent Electron Transfer Rate in Bilayer Graphene
Using molecular simulation and continuum dielectric theory, we consider how electrochemical kinetics are modulated by the twist angle in bilayer graphene electrodes. By establishing a connection between the twist angle and the screening length of charge carriers within the electrode, we investigate how tunable metallicity modifies the statistics of the electron transfer energy gap. Constant potential molecular simulations show that the activation free energy for electron transfer increases with screening length, leading to a non-monotonic dependence on the twist angle. Here, the twist angle alters the density of states, tuning the number of thermally accessible channels for electron transfer and the reorganization energy by affecting the stability of the vertically excited state through attenuated image charge interactions. Understanding these effects allows us to express the Marcus rate of interfacial electron transfer as a function of the twist angle in a manner consistent with experimental observations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Transition from Vehicular to Structural Ionic Transport in Electrified Alkali Aqueous Solutions
A molecular understanding of the solvation and dynamics of ions under static electric fields is crucial for modelling a wide range of natural and technological processes. Yet, traditional simulation methods suffer from a trade-off that has to be made between accuracy and statistical convergence. To bridge this gap, herein we extend our recently introduced Perturbed Neural Network Potential Molecular Dynamics (PNNP MD) approach to investigate the solvation structures and ionic transport mechanisms of electrified alkali cationic solutions. We obtain ionic conductivities for Li+, Na+ and Cs+ from the field dependence of the ionic current density in good agreement with experiment. Surprisingly, the migration mechanism is found to be strikingly different for the three ions despite their similar ionic conductivities. While Li+ conducts predominantly through vehicular migration of a stable 4-fold coordinated ion at all field strengths, Cs+ conducts strictly through a structural diffusion mechanism, where 9-12 transient first shell water coordination bonds are broken and renewed. Notably, aqueous Na+ emerges as a “Goldilocks” ion: its ion-water interactions are strong enough to maintain distinct 5-6 fold coordination shells at zero field (unlike Cs+) yet labile enough to be strongly perturbed by electric fields (unlike Li+). As a consequence, we observe an electric field-induced transition from vehicular to structural ionic transport for Na+ that is accompanied by a marked increase in the ionic current density. Our results imply that the conductance mechanism of ions with moderate ion-solvent interactions can be effectively tuned by external electric fields.
Joll, Kit↗
New screening methodology to select low outgassing materials for cold, spaceborne optical instruments
Standardized techniques for outgassing tests are developed and set forth for use in the screening of materials for aerospace instruments with cooled sensors, optics, and/or detectors. Materials for optical instruments are discussed in terms of molecular outgassing, and material-outgassing test results are presented which relate to several test conditions. The existing outgassing standard is found to be inadequate, and revised outgassing standards related to four application levels are given. The test protocols are designed for the development of materials for optical instruments that operate in environments with temperatures below 20 C. Consideration is also given to potential molecular contamination in the space environment and to outgas screening of instruments with a variety of sensor/optics/detector temperatures. The standards are designed for use with existing outgassing-test data as well as contamination analyses relating to the instrument being tested.
O'Donnell, T.↗
Semiclassical vibration-rotation transition probabilities for motion in molecular state averaged potentials.
Collision-induced vibration-rotation transition probabilities are calculated from a semiclassical three-dimensional model, in which the collision trajectory is determined by the classical motion in the interaction potential that is averaged over the molecular rotational state, and compared with those for which the motion is governed by a spherically averaged potential. For molecules that are in highly excited rotational states, thus dominating the vibrational relaxation rate at high temperature, it is found that the transition probability for rotational state averaging is smaller than that for spherical averaging. For typical collisions, the transition cross section is decreased by a factor of about 1.5 to 2.
Stallcop, J. R.↗