Nanoporous, gas-selective membranes have shown encouraging results for the removal of CO2 from flue gas, yet the optimal design for such membranes is often unknown. Therefore, we used molecular dynamics simulations to elucidate the behavior of CO2 within aqueous and ionic liquid (IL) systems ([EMIM][TFSI] and [OMIM][TFSI]), both confined individually and as an interfacial aqueous/IL system. We found that within aqueous systems the mobility of CO2 is reduced due to interactions between the CO2 oxygens and hydroxyl groups on the pore surface. Within the IL systems, we found that confinement has a greater effect on the [EMIM][TFSI] system as opposed to the [OMIM][TFSI] system. Paradoxically, the larger and more asymmetrical [OMIM]+ molecule undergoes less efficient packing, resulting in fewer confinement effects. Free energy surfaces of the nanoconfined aqueous/IL interface demonstrate that CO2 will transfer spontaneously from the aqueous to the IL phase.
Continued dependence on crude oil and natural gas resources for fossil fuels has caused global atmospheric carbon dioxide (CO2) emissions to increase to record-setting proportions. There is an urgent need for efficient and inexpensive carbon sequestration systems to mitigate large-scale CO2 emissions from industrial flue gas. Carbonic anhydrase (CA) has shown high potential for enhanced CO2 capture applications compared to conventional absorption-based methods currently utilized in various industrial settings. This study aims to understand structural aspects that contribute to the stability of CA enzymes critical for their applications in industrial processes, which require the ability to withstand conditions different from their native environments. Here, we evaluated the thermostability and enzyme activity of mesophilic and thermophilic CA variants at different temperature conditions and in the presence of atmospheric gas pollutants like nitrogen oxides (NOx) and sulphur oxides (SOx). Based on our enzyme activity assays and molecular dynamics simulations, we see increased conformational stability and CA activity levels in thermostable CA variants incubated week-long at different temperature conditions. The thermostable CA variants also retained high levels of CA activity despite changes in solution pH due to increasing NOx and SOx concentrations. Furthermore, a loss of CA activity was observed only at high concentrations of NOx/SOx that possibly can be minimized with appropriate buffered solutions.
Pyrimidine has two in-plane CH(δ+)/N̈(δ–)/CH(δ+) binding sites that are complementary to the (δ–/2δ+/δ–) quadrupole moment of CO2. For this study, we recorded broadband microwave spectra over the 7.5–17.5 GHz range for pyrimidine-(CO2)n with n = 1 and 2 formed in a supersonic expansion. Based on fits of the rotational transitions, including nuclear hyperfine splitting due to the two 14N nuclei, we have assigned 313 hyperfine components across 105 rotational transitions for the n = 1 complex and 208 hyperfine components across 105 rotational transitions for the n = 2 complex. The pyrimidine-CO2 complex is planar, with CO2 occupying one of the quadrupolar binding sites, forming a structure in which the CO2 is stabilized in the plane by interactions with the C–H hydrogens adjacent to the nitrogen atom. This structure is closely analogous to that of the pyridine-CO2 complex studied previously by (Doran, J. L. J. Mol. Struct. 2012, 1019, 191–195). The fit to the n = 2 cluster gives rotational constants consistent with a planar cluster of C2v symmetry in which the second CO2 molecule binds in the second quadrupolar binding pocket on the opposite side of the ring. The calculated total binding energy in pyrimidine-CO2 is –13.7 kJ mol–1, including corrections for basis set superposition error and zero-point energy, at the CCSD(T)/ 6-311++G(3df,2p) level, while that in pyrimidine-(CO2)2 is almost exactly double that size, indicating little interaction between the two CO2 molecules in the two binding sites. The enthalpy, entropy, and free energy of binding are also calculated at 300 K within the harmonic oscillator/rigid-rotor model. This model is shown to lack quantitative accuracy when it is applied to the formation of weakly bound complexes.
A major hurdle in utilizing carbon dioxide (CO2) lies in separating it from industrial flue gas mixtures and finding suitable storage methods that enable its application in various industries. To address this issue, we utilized a combination of molecular dynamics simulations and experiments to investigate the behavior of CO2 in common room-temperature ionic liquids (RTIL) when in contact with aqueous interfaces. Our investigation of RTILs, [EMIM][TFSI] and [OMIM][TFSI], and their interaction with a pure water layer mimics the environment of a previously developed ultrathin enzymatic liquid membrane for CO2 separation. We analyzed diffusion constants and viscosity, which reveals that CO2 molecules exhibit faster mobility within the selected ILs compared to what would be predicted solely based on the viscosity of the liquids using the standard Einstein-Stokes relation. Moreover, we calculated the free energy of translocation for various species across the aqueous-IL interface, including CO2 and HCO3-. Free energy profiles demonstrate that CO2 exhibits a more favorable partitioning behavior in the RTILs compared to that in pure water, while a significant barrier hinders the movement of HCO3- from the aqueous layer. Experimental measurement of the CO2 transport in the RTILs corroborates the model. These findings strongly suggest that hydrophobic RTILs could serve as a promising option for selectively transporting CO2 from aqueous media and concentrating it as a preliminary step toward storage.
Conceptually, single-ion polymer electrolytes (SIPE) with the anion bound to the polymer could solve major issues in Li-ion batteries, but their conductivity is too low. Experimentally, weakly interacting anionic groups have the best conductivity. To provide a theoretical basis for this result, density functional theory calculations of the optimized geometries and energies are performed for charged ligands used in SIPE. Comparison is made to neutral ligands found in dual-ion conductors, which demonstrate higher conductivity. Further, the free energy differences between adding and subtracting a ligand are small enough for the neutral ligands to have the conductivity seen experimentally. However, charged ligands have large barriers, implying that lithium transport will coincide with the slow polymer diffusion, as observed in experiments. Overall, SIPE will require additional solvent to achieve a sufficiently high conductivity. Additionally, the binding of mono- and bidentate geometries varies, providing a simple and clear reason that polarizable force fields are required for detailed interactions.
The interactions of carboxylate anions with water and cations are important for a wide variety of systems, both biological and synthetic. Here, in order to gain insight on properties of the local complexes, we apply density functional theory, to treat the complex electrostatic interactions, and investigate mixtures with varied numbers of carboxylate anions (acetate) and waters binding to monovalent cations, Li+, Na+ and K+. The optimal structure with overall lowest free energy contains two acetates and two waters such that the cation is four-fold coordinated, similar to structures found earlier for pure water or pure carboxylate ligands. More generally, the complexes with two acetates have the lowest free energy. In transitioning from the overall optimal state, exchanging an acetate for water has a lower free energy barrier than exchanging water for an acetate. In most cases, the carboxylates are monodentate and in the first solvation shell. As water is added to the system, hydrogen bonding between waters and carboxylate O atoms further stabilizes monodentate structures. These structures, which have strong electrostatic interactions that involve hydrogen bonds of varying strength, are significantly polarized, with ChelpG partial charges that vary substantially as the bonding geometry varies. Overall, these results emphasize the increasing importance of water as a component of binding sites as the number of ligands increases, thus affecting the preferential solvation of specific metal ions and clarifying Hofmeister effects. Finally, structural analysis correlated with free energy analysis supports the idea that binding to more than the preferred number of carboxylates under architectural constraints are a key to ion transport.
UV photofragment spectroscopy and IR-UV double resonance methods are used to determine the structure and spectroscopic responses of a three-dimensional [2.2.2]-benzocryptand cage to the incorporation of a single K+ or Ba2+ imbedded inside it (labeled as K+-BzCrypt, Ba2+-BzCrypt). We studied the isolated ion-cryptand complex under cryo-cooled conditions, brought into the gas phase by nano-electrospray ionization. Incorporation of a phenyl ring in place of the central ethyl group in one of the three N-CH2-CH2-O-CH2-CH2-O-CH2-CH2-N chains provides a UV chromophore whose S0-S1 transition we probe. K+-BzCrypt and Ba2+-BzCrypt have their S0-S1 origin transitions at 35,925 and 36,446 cm-1, respectively, blue-shifted by 174 and 695 cm-1 from that of 1,2-dimethoxybenzene. These origins are used to excite a single conformation of each complex selectively and record their IR spectra using IR-UV dip spectroscopy. The alkyl CH stretch region (2800-3000 cm-1) is surprisingly sensitive to the presence and nature of the encapsulated ion. We carried out an exhaustive conformational search of cage conformations for K+-BzCrypt and Ba2+-BzCrypt, identifying two conformations (A and B) that lie below all others in energy. We extend our local mode anharmonic model of the CH stretch region to these strongly bound ion-cage complexes to predict conformation-specific alkyl CH stretch spectra, obtaining quantitative agreement with experiment for conformer A, the gas-phase global minimum. The large electrostatic effect of the charge on the O- and N-lone pairs affects the local mode frequencies of the CH2 groups adjacent to these atoms. The localized CH2 scissors modes are pushed up in frequency by the adjacent O/N-atoms so that their overtones have little effect on the alkyl CH stretch region. However, the localized CH2 wags are nearly degenerate and strongly coupled to one another, producing an array of delocalized wag normal modes, whose highest frequency members reach up above 1400 cm-1. As such, their overtones mix significantly with the CH stretch modes, most notably involving the CH2 symmetric stretch fundamentals of the central ethyl groups in the all-alkyl chains and the CH stretches adjacent to the N-atoms and antiperiplanar to the nitrogen lone pair.
Numerous experimental investigations indicated that expansive clays such as montmorillonite can intercalate CO2 preferentially into their interlayers and therefore potentially act as a material for CO2 separation, capture, and storage. However, an understanding of the energy-structure relationship during the intercalation of CO2 into clay interlayers remains elusive. Here, we use metadynamics molecular dynamics simulations to elucidate the energy landscape associated with CO2 intercalation. Our free energy calculations indicate that CO2 favorably partitions into nanoconfined water in clay interlayers from a gas phase, leading to an increase in the CO2/H2O ratio in clay interlayers as compared to that in bulk water. CO2 molecules prefer to be located at the centers of charge-neutral hydrophobic siloxane rings, whereas interlayer spaces close to structural charges tend to avoid CO2 intercalation. The structural charge distribution significantly affects the amount of CO2 intercalated in the interlayers. These results provide a mechanistic understanding of CO2 intercalation in clays for CO2 separation, capture, and storage.
Understanding the formation of H2CO3 in water from CO2 is important in environmental and industrial processes. Although numerous investigations have studied this reaction, the conversion of CO2 to H2CO3 in nanopores, and how it differs from that in bulk water, has not been understood. We use ReaxFF metadynamics molecular simulations to demonstrate striking differences in the free energy of CO2 conversion to H2CO3 in bulk and nanoconfined aqueous environments. We find that nanoconfinement not only reduces the energy barrier but also reverses the reaction from endothermic in bulk water to exothermic in nanoconfined water. Also, charged intermediates are observed more often under nanoconfinement than in bulk water. Stronger solvation and more favorable proton transfer with increasing nanoconfinement enhance the thermodynamics and kinetics of the reaction. Here our results provide a detailed mechanistic understanding of an important step in the carbonation process, which depends intricately on confinement, surface chemistry, and CO2 concentration.
Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. In this report we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La3+) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La3+–ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion–water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion–protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.
Almost all studies of specific ion binding by carboxylates (-COO−) have considered only a single cation, but clustering of ions and ligands is a common phenomenon. We apply density functional theory to investigate how variations in the number of acetate ligands in binding to two monovalent cations affects ion binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) ions relevant to experimental work on many topics, including ion channels, battery storage, water purification and solar cells. We find that the preferred optimal structure has 3 acetates except for Cs+, which has 2 acetates. The optimal coordination of the cation by the carboxylate O atoms is 4 for both Na+ and K+, and 3 for Li+ and Cs+. There is a 4-fold coordination minimum just a few kcal mol−1 higher than the optimal 3-fold structure for Li+. For two cations, multiple minima occur in the vicinity of the lowest free energy state. We find that, for Li, Na and K, the preferred optimal structure with two cations is favored over a mixture of single cation complexes, providing a basis for understanding ionic cluster formation that is relevant for engineering proteins and other materials for rapid, selective ion transport.
Gomez, Diego T.; Pratt, Lawrence R.; Asthagiri, Dilipkumar N.; Rempe, Susan
ConspectusThe interactions of hydrated ions with molecular and macromolecular solution and interface partners are strong on a chemical energy scale. Here, we recount the foremost ab initio theory for the evaluation of the hydration free energies of ions, namely, quasi-chemical theory (QCT). We focus on anions, particularly halides but also the hydroxide anion, because they have been outstanding challenges for all theories. For example, this work supports understanding the high selectivity for F-over Cl-in fluoride-selective ion channels despite the identical charge and the size similarity of these ions. QCT is built by the identification of inner-shell clusters, separate treatment of those clusters, and then the integration of those results into the broader-scale solution environment. Recent work has focused on a close comparison with mass-spectrometric measurements of ion-hydration equilibria. We delineate how ab initio molecular dynamics (AIMD) calculations on ion-hydration clusters, elementary statistical thermodynamics, and electronic structure calculations on cluster structures sampled from the AIMD calculations obtain just the free energies extracted from the cluster experiments. That theory-experiment comparison has not been attempted before the work discussed here, but the agreement is excellent with moderate computational effort. This agreement reinforces both theory and experiment and provides a numerically accurate inner-shell contribution to QCT. The inner-shell complexes involving heavier halides display strikingly asymmetric hydration clusters. Asymmetric hydration structures can be problematic for the evaluation of the QCT outer-shell contribution with the polarizable continuum model (PCM). Nevertheless, QCT provides a favorable setting for the exploitation of PCM when the inner-shell material shields the ion from the outer solution environment. For the more asymmetrically hydrated, and thus less effectively shielded, heavier halide ions clustered with waters, the PCM is less satisfactory. We therefore investigate an inverse procedure in which the inner-shell structures are sampled from readily available AIMD calculations on the bulk solutions. This inverse procedure is a remarkable improvement; our final results are in close agreement with a standard tabulation of hydration free energies, and the final composite results are independent of the coordination number on the chemical energy scale of relevance, as they should be. Finally, a comparison of anion hydration structure in clusters and bulk solutions from AIMD simulations emphasize some differences: the asymmetries of bulk solution inner-shell structures are moderated compared with clusters but are still present, and inner hydration shells fill to slightly higher average coordination numbers in bulk solution than in clusters.
Ion trap quantum computing utilizes electronic states of atomic ions such as Ca+ to encode information on to a qubit. To explore the fundamental properties of Ca+ inside molecular cavities, we describe here a computational study of Ca+ bound inside neutral [n]-cycloparaphenylenes (n = 5-12), often referred to as “nanohoops”. This ab initio study characterizes optimized structures, harmonic vibrational frequencies, potential energy surfaces, and ion molecular orbital distortion as functions of increasing nanohoop size. The results of this work provide a first step in guiding experimental studies of the spectroscopy of these ion-molecular cavity complexes.
Organophosphorus hydrolase (OPH) is a metalloenzyme that can hydrolyze organophosphorus agents resulting in products that are generally of reduced toxicity. The best OPH substrate found to date is diethyl p-nitrophenyl phosphate (paraoxon). Most structural and kinetic studies assume that the binding orientation of paraoxon is identical to that of diethyl 4-methylbenzylphosphonate, which is the only substrate analog co-crystallized with OPH. In the current work, we used a combined docking and molecular dynamics (MD) approach to predict the likely binding mode of paraoxon. Then, we used the predicted binding mode to run MD simulations on the wild type (WT) OPH complexed with paraoxon, and OPH mutants complexed with paraoxon. Additionally, we identified three hot-spot residues (D253, H254, and I255) involved in the stability of the OPH active site. We then experimentally assayed single and double mutants involving these residues for paraoxon binding affinity. The binding free energy calculations and the experimental kinetics of the reactions between each OPH mutant and paraoxon show that mutated forms D253E, D253E-H254R, and D253E-I255G exhibit enhanced substrate binding affinity over WT OPH. Interestingly, our experimental results show that the substrate binding affinity of the double mutant D253E-H254R increased by 19-fold compared to WT OPH.
The objective of this project was to eliminate and/or render bulk agent unusable by a threat entity via neutralization and/or polymerization of the bulk agent using minimal quantities of additives. We proposed the in situ neutralization and polymerization of bulk chemical agents (CAs) by performing reactions in the existing CA storage container via wet chemical approaches using minimal quantities of chemical based materials. This approach does not require sophisticated equipment, fuel to power generators, electricity to power equipment, or large quantities of decontaminating materials. By utilizing the CA storage container as the batch reactor, the amount of logistical resources can be significantly reduced. Fewer personnel are required since no sophisticated equipment needs to be set up, configured, or operated. Employing the CA storage container as the batch reactor enables the capability to add materials to multiple containers in a short period of time as opposed to processing one container at a time for typical batch reactor approaches. In scenarios where a quick response is required, the material can be added to all the CA containers and left to react on its own without intervention. Any attempt to filter the CA plus material solution will increase the rate of reaction due to increased agitation of the solution.
Recently, lithium nitride (Li3N) has been proposed as a chemical warfare agent (CWA) neutralization reagent for its ability to produce nucleophilic ammonia molecules and hydroxide ions in aqueous solution. Quantum chemical calculations can provide insight into the Li3N neutralization process that has been studied experimentally. Here, we calculate reaction-free energies associated with the Li3N-based neutralization of the CWA VX using quantum chemical density functional theory and ab initio methods. We find that alkaline hydrolysis is more favorable to either ammonolysis or neutral hydrolysis for initial P-S and P-O bond cleavages. Reaction-free energies of subsequent reactions are calculated to determine the full reaction pathway. Notably, products predicted from favorable reactions have been identified in previous experiments.
The addition of a common amino acid, phenylalanine, to a Layer-by-Layer (LbL) deposited polyelectrolyte (PE) film on a nanoporous membrane can increase its ionic selectivity over a PE film without the added amino acid. The addition of phenylalanine is inspired by detailed knowledge of the structure of the channelrhodopsins family of protein ion channels, where phenylalanine plays an instrumental role in facilitating sodium ion transport. The normally deposited and crosslinked PE films increase the cationic selectivity of a support membrane in a controllable manner where higher selectivity is achieved with thicker PE coatings, which in turn also increases the ionic resistance of the membrane. The increased ionic selectivity is desired while the increased resistance is not. We show that through incorporation of phenylalanine during the LbL deposition process, in solutions of NaCl with concentrations ranging from 0.1 to 100 mM, the ionic selectivity can be increased independently of the membrane resistance. Specifically, the addition is shown to increase the cationic transference of the PE films from 81.4% to 86.4%, an increase on par with PE films that are nearly triple the thickness while exhibiting much lower resistance compared to the thicker coatings, where the phenylalanine incorporated PE films display an area specific resistance of 1.81 Ω cm2in 100 mM NaCl while much thicker PE membranes show a higher resistance of 2.75 Ω cm2in the same 100 mM NaCl solution.
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated byab initiocalculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations.
Rempe, Susan; Gomez, Diego T.; Pratt, Lawrence R.; Rogers, David M.
With a longer-term goal of addressing the comparative behavior of the aqueous halides F-, Cl-, Br-, and I-on the basis of quasi-chemical theory (QCT), here we study structures and free energies of hydration clusters for those anions. We confirm that energetically optimal (H2O)nX clusters, with X = Cl-, Br-, and I-, exhibit surface hydration structures. Computed free energies, based on optimized surface hydration structures utilizing a harmonic approximation, typically (but not always) disagree with experimental free energies. To remedy the harmonic approximation, we utilize single-point electronic structure calculations on cluster geometries sampled from an AIMD (ab initio molecular dynamics) simulation stream. This rough-landscape procedure is broadly satisfactory and suggests unfavorable ligand crowding as the physical effect addressed. Nevertheless, this procedure can break down when n≳4, with the characteristic discrepancy resulting from a relaxed definition of clustering in the identification of (H2O)nX clusters, including ramified structures natural in physical cluster theories. With ramified structures, the central equation for the present rough-landscape approach can acquire some inconsistency. Extension of these physical cluster theories in the direction of QCT should remedy that issue, and should be the next step in this research direction.
Ashbaugh, Henry S.; Asthagiri, Dilipkumar; Beck, Thomas L.; Rempe, Susan
Lawrence Pratt’s career following completion of his Ph.D. at the University of Illinois Urbana Champaign has taken him from Harvard University, to the University of California, Berkeley, and Los Alamos National Laboratory. Most recently, he joined the faculty of the Department of Chemical and Biomolecular Engineering at Tulane University in 2008. Over his career Lawrence has been a leader in theoretical physical chemistry, making influential contributions to a number of areas including the theory of the hydrophobic effect, the development of transition path sampling, contributions to orbital free density functional theory, and the theory of liquids and solutions.
Rempe, Susan; Vangordon, Monika R.; Prignano, Lindsey A.; Dempski, Robert E.; Rick, Steven W.
Channelrhodopsins (ChR) are light-sensitive cation channels used in optogenetics, a technique that applies light to control cells (e.g., neurons) that have been modified genetically to express those channels. Although mutations are known to affect pore kinetics, little is known about how mutations induce changes at the molecular scale. To address this issue, we first measured channel opening and closing rates of a ChR chimera (C1C2) and selected variants (N297D, N297V, and V125L). Then, we used atomistic simulations to correlate those rates with changes in pore structure, hydration, and chemical interactions among key gating residues of C1C2 in both closed and open states. Overall, the experimental results show that C1C2 and its mutants do not behave like ChR2 or its analogous variants, except V125L, making C1C2 a unique channel. Our atomistic simulations confirmed that opening of the channel and initial hydration of the gating regions between helices I, II, III, and VII of the channel occurs with 1) the presence of 13-cis retinal; 2) deprotonation of a glutamic acid gating residue, E129; and 3) subsequent weakening of the central gate hydrogen bond between the same glutamic acid E129 and asparagine N297 in the central region of the pore. Also, an aspartate (D292) is the unambiguous primary proton acceptor for the retinal Schiff base in the hydrated channel.
Electrodialysis (ED) desalination performance of different conventional and laboratoryscale ion exchange membranes (IEMs) has been evaluated by many researchers, but most of these studies used their own sets of experimental parameters such as feed solution compositions and concentrations, superficial velocities of the process streams (diluate, concentrate, and electrode rinse), applied electrical voltages, and types of IEMs. Thus, direct comparison of ED desalination performance of different IEMs is virtually impossible. While the use of different conventional IEMs in ED has been reported, the use of bioinspired ion exchange membrane has not been reported yet. The goal of this study was to evaluate the ED desalination performance differences between novel laboratory-scale bioinspired IEM and conventional IEMs by determining (i) limiting current density, (ii) current density, (iii) current efficiency, (iv) salinity reduction in diluate stream, (v) normalized specific energy consumption, and (vi) water flux by osmosis as a function of (a) initial concentration of NaCl feed solution (diluate and concentrate streams), (b) superficial velocity of feed solution, and (c) applied stack voltage per cell-pair of membranes. A laboratory-scale single stage batchrecycle electrodialysis experimental apparatus was assembled with five cell-pairs of IEMs with an active cross-sectional area of 7.84 cm2. In this study, seven combinations of IEMs (commercial and laboratory-made) were compared: (i) Neosepta AMX/CMX, (ii) PCA PCSA/PCSK, (iii) Fujifilm Type 1 AEM/CEM, (iv) SUEZ AR204SZRA/CR67HMR, (v) Ralex AMH-PES/CMH-PES, (vi) Neosepta AMX/Bare Polycarbonate membrane (Polycarb), and (vii) Neosepta AMX/Sandia novel bioinspired cation exchange membrane (SandiaCEM). ED desalination performance with the Sandia novel bioinspired cation exchange membrane (SandiaCEM) was found to be competitive with commercial Neosepta CMX cation exchange membrane.
Rempe, Susan; Cetuk, Hannah; Anishkin, Andriy; Scott, Alison J.; Ernst, Robert K.
The outer membrane (OM) of Gram-negative (G-) bacteria presents a barrier for many classes of antibacterial agents. Lipopolysaccharide (LPS), present in the outer leaflet of the OM, is stabilized by divalent cations and is considered to be the major impediment for antibacterial agent permeation. However, the actual affinities of major antibiotic classes toward LPS have not yet been determined. In the present work, we use Langmuir monolayers formed from E. coli Re and Rd types of LPS to record pressure-area isotherms in the presence of antimicrobial agents. Our observations suggest three general types of interactions. First, some antimicrobials demonstrated no measurable interactions with LPS. This lack of interaction in the case of cefsulodin, a third-generation cephalosporin antibiotic, correlates with its low efficacy against G-bacteria. Ampicillin and ciprofloxacin also show no interactions with LPS, but in contrast to cefsulodin, both exhibit good efficacy against G-bacteria, indicating permeation through common porins. Second, we observe substantial intercalation of the more hydrophobic antibiotics, novobiocin, rifampicin, azithromycin, and telithromycin, into relaxed LPS monolayers. These largely repartition back to the subphase with monolayer compression. We find that the hydrophobic area, charge, and dipole all show correlations with both the mole fraction of antibiotic retained in the monolayer at the monolayer-bilayer equivalence pressure and the efficacies of these antibiotics against G-bacteria. Third, amine-rich gentamicin and the cationic antimicrobial peptides polymyxin B and colistin show no hydrophobic insertion but are instead strongly driven into the polar LPS layer by electrostatic interactions in a pressure-independent manner. Their intercalation stably increases the area per molecule (by up to 20%), which indicates massive formation of defects in the LPS layer. These defects support a self-promoted permeation mechanism of these antibiotics through the OM, which explains the high efficacy and specificity of these antimicrobials against G-bacteria.
Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.
The interplay of a rapidly changing climate and infectious disease occurrence is emerging as a critical topic, requiring investigation of possible direct, as well as indirect, connections between disease processes and climate-related variation and phenomena. First, we introduce and overview three infectious disease exemplars (dengue, influenza, valley fever) representing different transmission classes (insect-vectored, human-to-human, environmentally-transmitted) to illuminate the complex and significant interplay between climate disease processes, as well as to motivate discussion of how Sandia can transform the field, and change our understanding of climate-driven infectious disease spread. We also review state-of-the-art epidemiological and climate modeling approaches, together with data analytics and machine learning methods, potentially relevant to climate and infectious disease studies. We synthesize the modeling and disease exemplars information, suggesting initial avenues for research and development (R&D) in this area, and propose potential sponsors for this work. Whether directly or indirectly, it is certain that a rapidly changing climate will alter global disease burden. The trajectory of climate change is an important control on this burden, from local, to regional and global scales. The efforts proposed herein respond to the National Research Councils call for the creation of a multidisciplinary institute that would address critical aspects of these interlocking, cascading crises.
Rempe, Susan; Lubkowski, Jacek; Vanegas, Juan; Chan, Wai K.; Lorenzi, Philip L.; Weinstein, John N.; Sukharev, Sergei; Fushman, David; Anishkin, Andriy; Wlodawer, Alexander
Two bacterial type II l-asparaginases, from Escherichia coli and Dickeya chrysanthemi, have played a critical role for more than 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and the apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by E. coli type II l-asparaginase (EcAII). Our model was developed on the basis of new structural and biochemical experiments combined with previously published data. The proposed mechanism is supported by quantum chemistry calculations based on density functional theory. We provide strong evidence that EcAII catalyzes the reaction according to the double-displacement (ping-pong) mechanism, with formation of a covalent intermediate. Several steps of catalysis by EcAII are unique when compared to reactions catalyzed by other known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile, threonine, without direct assistance of a general base, although a distant general base is identified. Furthermore, tetrahedral intermediates formed during the catalytic process are stabilized by a never previously described motif. Although the scheme of the catalytic mechanism was developed only on the basis of data obtained from EcAII and its variants, this novel mechanism of enzymatic hydrolysis could potentially apply to most (and possibly all) l-asparaginases.
Rempe, Susan; Chaudhari, Mangesh I.; Vanegas, Juan M.; Pratt, L.R.; Muralidharan, Ajay
Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if these protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an important reference condition for the ion permeation process. Assessment of this hydration mimicry concept depends on understanding the hydration structure and free energies of metal ions in water in order to provide a comparison for the membrane channel environment. To refine these considerations, we review local hydration structures of ions in bulk water and the molecular quasi-chemical theory that provides hydration free energies. In doing so, we note some current views of ion binding to membrane channels and suggest new physical chemical calculations and experiments that might further clarify the hydration mimicry concept.
Rempe, Susan; Maldonado, Alex M.; Basdogan, Yasemin; Berryman, Joshua T.; Keith, John A.
Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for specific reactions and applications. Apart from fully explicit solvation treatments that can be difficult to parameterize or computationally expensive, there is currently no well-established first-principles regimen for reliably modeling atomic-scale chemistry in mixed solvent environments. We offer our perspective on how this process could be achieved in the near future as mixed solvent systems become more explored using theoretical and computational chemistry. We first outline what makes mixed solvent systems far more complex compared to single-component solvents. An overview of current and promising techniques for modeling mixed solvent environments is provided. We focus on so-called hybrid solvation treatments such as the conductor-like screening model for real solvents and the reference interaction site model, which are far less computationally demanding than explicit simulations. We also propose that cluster-continuum approaches rooted in physically rigorous quasi-chemical theory provide a robust, yet practical, route for studying chemical processes in mixed solvents.
Rempe, Susan; Basdogan, Yasemin; Groenenboom, Mitchell C.; Henderson, Ethan; De, Sandip; Keith, John A.
Molecular-level understanding and characterization of solvation environments are often needed across chemistry, biology, and engineering. Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics-based cluster-continuum approach for calculating single-ion solvation free energies. This approach uses a global optimization procedure to identify low-energy molecular clusters with different numbers of explicit solvent molecules and then employs the smooth overlap for atomic positions learning kernel to quantify the similarity between different low-energy solute environments. From these data, we use sketch maps, a nonlinear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. After testing this approach on different ions having charges 2+, 1+, 1-, and 2-, we find that the solvation environment around each ion can be seen to usually become more similar in hand with its calculated single-ion solvation free energy. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies within 5% of experimental measurements for most cases, and it should be transferable for the study of other systems where dynamics simulations are not easily carried out.
Anion hydration is complicated by H-bond between neighboring water molecules in addition to H-bond donation to the anion. This situation leads to competing structures and anharmonic vibrations for simple clusters like (H2O)nCl-. This study applies quasi-chemical theory to study anion hydration and exploits dynamics calculations on isolated clusters to account for anharmonicity. Comparing singly hydrated halide clusters, classic H-bond donation to the anion occurs for F-, while Cl- clusters exhibit flexible dipole-dominated interactions. The predicted Cl- – F- hydration free energy difference agrees with experiment, a significant theoretical step for addressing issues like Hofmeister ranking and selectivity in ion channels.
EmrE is a small, homodimeric membrane transporter that exploits the established pH gradient across the E. coli inner membrane to export polyaromatic cations that might otherwise inhibit cellular growth. While herculean efforts through experimental studies have established many fundamental facts about the specificity and rate of substrate transport in EmrE, the low resolution of the available structures have hampered efforts to tie those findings to the EmrE coupling mechanism between proton and small molecule substrates. Here we present a full three-dimensional structure of EmrE optimized against available cyro-EM data to delineate the critical interactions by which EmrE regulates its conformation. We use the generated structural model to conduct equilibrium and nonequilibrium molecular dynamics simulations to probe EmrE dynamics under different substrate loading states, representing different states in the transport cycle. The model is stable under extended simulation, and reveals that water dynamics within the EmrE lumen change substantially with the loading state. The water dynamics cause hydrogen bonding networks to shift radically when the protonation states change for a pair of solvent-exposed glutamate residues (E14) within the lumen of the transporter, which are proposed to act as proton binding sites during the transport cycle. One specific hydrogen bond from a tyrosine (Y60) of one monomer to a glutamate (E14) on the opposite monomer is especially critical, as it locks the protein conformation when the glutamate is deprotonated. Furthermore, the hydrogen bond provided by Y60 lowers the pKa of the interacting glutamate relative to its partner on the opposite monomer such that it will protonate second, establishing the need for both glutamates to be protonated for the hydrogen bond to break and a substrate-free transition to take place.
Li+ transport within a solid electrolyte interphase (SEI) in lithium ion batteries has challenged molecular dynamics (MD) studies due to limited compositional control of that layer. In recent years, experiments and ab initio simulations have identified dilithium ethylene dicarbonate (Li2EDC) as the dominant component of SEI layers. Here, we adopt a parameterized, non-polarizable MD force field for Li2EDC to study transport characteristics of Li+ in this model SEI layer at moderate temperatures over long times. The observed correlations are consistent with recent MD results using a polarizable force field, suggesting that this non-polarizable model is effective for our purposes of investigating Li+ dynamics. Mean-squared displacements distinguish three distinct Li+ transport regimes in EDC-ballistic, trapping, and diffusive. Compared to liquid ethylene carbonate (EC), the nanosecond trapping times in EDC are significantly longer and naturally decrease at higher temperatures. New materials developed for fast-charging Li-ion batteries should have a smaller trapping region. The analyses implemented in this paper can be used for testing transport of Li+ ion in novel battery materials. Non-Gaussian features of van Hove self-correlation functions for Li+ in EDC, along with the mean-squared displacements, are consistent in describing EDC as a glassy material compared with liquid EC. Vibrational modes of Li+ ion, identified by MD, characterize the trapping and are further validated by electronic structure calculations. Some of this work appeared in an extended abstract and has been reproduced with permission from ECS Transactions, 77, 1155-1162 (2017). Copyright 2017, Electrochemical Society, INC.
The limited flux and selectivities of current carbon dioxide membranes and the high costs associated with conventional absorption-based CO2 sequestration call for alternative CO2 separation approaches. Here we describe an enzymatically active, ultra-thin, biomimetic membrane enabling CO2 capture and separation under ambient pressure and temperature conditions. The membrane comprises a ~18-nm-thick close-packed array of 8 nm diameter hydrophilic pores that stabilize water by capillary condensation and precisely accommodate the metalloenzyme carbonic anhydrase (CA). CA catalyzes the rapid interconversion of CO2 and water into carbonic acid. By minimizing diffusional constraints, stabilizing and concentrating CA within the nanopore array to a concentration 10× greater than achievable in solution, our enzymatic liquid membrane separates CO2 at room temperature and atmospheric pressure at a rate of 2600 GPU with CO2/N2 and CO2/H2 selectivities as high as 788 and 1500, respectively, the highest combined flux and selectivity yet reported for ambient condition operation.
Anthrax toxin consists of a cation channel and two protein factors. Translocation of the anthrax protein factors from endosomal to the cytosolic compartment is a complex process which utilizes the cation channel. An atomically detailed understanding of the function of the anthrax translocation machinery is incomplete. We report atomically detailed simulations of the lethal factor and channel mutants. Kinetic and thermodynamic properties of early events in the translocation process are computed within the Milestoning theory and algorithm. Several mutants of the channel illustrate that long-range electrostatic interactions provide the dominant driving force for translocation. No external energy input is required because the lower pH in the endosome relative to the cytosol drives the initial translocation process forward. Channel mutants with variable sizes cause smaller effects on translocation events relative to charge manipulations. Comparison with available experimental data is provided.
EmrE is a small, homodimeric membrane transporter that exploits the established electrochemical proton gradient across the Escherichia coli inner membrane to export toxic polyaromatic cations, prototypical of the wider small-multidrug resistance transporter family. While prior studies have established many fundamental aspects of the specificity and rate of substrate transport in EmrE, low resolution of available structures has hampered identification of the transport coupling mechanism. Here we present a complete, refined atomic structure of EmrE optimized against available cryo-electron microscopy (cryo-EM) data to delineate the critical interactions by which EmrE regulates its conformation during the transport process. With the model, we conduct molecular dynamics simulations of the transporter in explicit membranes to probe EmrE dynamics under different substrate loading and conformational states, representing different intermediates in the transport cycle. The refined model is stable under extended simulation. The water dynamics in simulation indicate that the hydrogen-bonding networks around a pair of solvent-exposed glutamate residues (E14) depend on the loading state of EmrE. One specific hydrogen bond from a tyrosine (Y60) on one monomer to a glutamate (E14) on the opposite monomer is especially critical, as it locks the protein conformation when the glutamate is deprotonated. The hydrogen bond provided by Y60 lowers the pKa of one glutamate relative to the other, suggesting both glutamates should be protonated for the hydrogen bond to break and a substrate-free transition to take place. These findings establish the molecular mechanism for the coupling between proton transfer reactions and protein conformation in this proton-coupled secondary transporter.
Electrochemical double-layer capacitances of charged carbon nanotube (CNT) forests with tetraethyl ammonium tetrafluoro borate electrolyte in propylene carbonate are studied on the basis of molecular dynamics simulation. Direct molecular simulation of the filling of pore spaces of the forest is feasible even with realistic, small CNT spacings. The numerical solution of the Poisson equation based on the extracted average charge densities then yields a regular experimental dependence on the width of the pore spaces, in contrast to the anomalous pattern observed in experiments on other carbon materials and also in simulations on planar slot-like pores. The capacitances obtained have realistic magnitudes but are insensitive to electric potential differences between the electrodes in this model. This agrees with previous calculations on CNT forest supercapacitors, but not with experiments which have suggested electrochemical doping for these systems. Those phenomena remain for further theory/modeling work.
The role that van der Waals (vdW) attractive forces play in the hydration and association of atomic hydrophobic solutes such as argon (Ar) in water is reanalyzed using the local molecular field (LMF) theory of those interactions. In this problem, solute vdW attractive forces can reduce or mask hydrophobic interactions as measured by contact peak heights of the ArAr correlation function compared to reference results for purely repulsive core solutes. Nevertheless, both systems exhibit a characteristic hydrophobic inverse temperature behavior in which hydrophobic association becomes stronger with increasing temperature through a moderate temperature range. The new theoretical approximation obtained here is remarkably simple and faithful to the statistical mechanical LMF assessment of the necessary force balance. Our results extend and significantly revise approximations made in a recent application of the LMF approach to this problem and, unexpectedly, support a theory of nearly 40 years ago.
Laying a basis for molecularly specific theory for the mobilities of ions in solutions of practical interest, we report a broad survey of velocity autocorrelation functions (VACFs) of Li+ and PF6- ions in water, ethylene carbonate, propylene carbonate, and acetonitrile solutions. We extract the memory function, γ(t), which characterizes the random forces governing the mobilities of ions. We provide comparisons controlling for the effects of electrolyte concentration and ion-pairing, van der Waals attractive interactions, and solvent molecular characteristics. For the heavier ion (PF6-), velocity relaxations are all similar: negative tail relaxations for the VACF and a clear second relaxation for γt, observed previously also for other molecular ions and with n-pentanol as the solvent. For the light Li+ ion, short time-scale oscillatory behavior masks simple, longer time-scale relaxation of γt. But the corresponding analysis of the solventberg Li+H2O4 does conform to the standard picture set by all the PF6- results.
Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li+ deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li+ ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li+ thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li+ transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.
Here, we study quasi-chemical theory (QCT) for the free energies of divalent alkaline earth ions (Ba 2+, Sr 2+, Ca 2+, Mg 2+) in water, emphasizing that: (a) interactions between metal ions and proximal water molecules are as strong as traditional chemical effects; (b) QCT builds directly from accessible electronic structure calculations but rests on fully elaborated molecular statistical thermodynamics; (c) QCT offers choices of convenience in identifying coordination numbers for analysis. We investigate utilisation of direct QCT with inner-shell conditioning (Formula presented.), alternative to the traditional nλ=0 conditioning motivated by a generalised van der Waals view. The alternative (Formula presented.) works well: deleterious non-Gaussian effects of van der Waals repulsive interactions are not serious, and the alternative conditioning improves the convenience of QCT calculations. Comparison between ab initio and force field molecular dynamics (AIMD and FFMD) with standard models suggests that FFMD likely exaggerates the anharmonicity in the thermal motion of inner-shell ion-water clusters. Together with the general encouraging support for the harmonic approximations implied by the (Formula presented.) conditioning, that observation helps explain the remarkable success of the cluster-based QCT solution free energies, which do not require assessment of all inner-shell occupancies by simulation.
This work demonstrates that the ionic selectivity and ionic conductivity of nanoporous membranes can be controlled independently via layer-by-layer (LbL) deposition of polyelectrolytes and subsequent selective cross-linking of these polymer layers. LbL deposition offers a scalable, inexpensive method to tune the ion transport properties of nanoporous membranes by sequentially dip coating layers of cationic polyethyleneimine and anionic poly(acrylic acid) onto polycarbonate membranes. The cationic and anionic polymers are self-assembled through electrostatic and hydrogen bonding interactions and are chemically crosslinked to both change the charge distribution and improve the intermolecular integrity of the deposited films. Both the thickness of the deposited coating and the use of chemical cross-linking agents influence charge transport properties significantly. Increased polyelectrolyte thickness increases the selectivity for cationic transport through the membranes while adding polyelectrolyte films decreases the ionic conductivity compared to an uncoated membrane. Once the nanopores are filled, no additional decrease in conductivity is observed with increasing film thickness and, upon cross-linking, a portion of the lost conductivity is recovered. The cross-linking agent also influences the ionic selectivity of the resulting polyelectrolyte membranes. Increased selectivity for cationic transport occurs when using glutaraldehyde as the cross-linking agent, as expected due to the selective cross-linking of primary amines that decreases the net positive charge. Together, these results inform deposition of chemically robust, highly conductive, ion-selective membranes onto inexpensive porous supports for applications ranging from energy storage to water purification.
Rempe, Susan; Wen, Po C.; Vanegas, Juan M.; Tajkhorshid, Emad
Teixobactin (Txb) is a recently discovered antibiotic against Gram-positive bacteria that induces no detectable resistance. The bactericidal mechanism is believed to be the inhibition of cell wall biosynthesis by Txb binding to lipid II and lipid III. Txb binding specificity likely arises from targeting of the shared lipid component, the pyrophosphate moiety. Despite synthesis and functional assessment of numerous chemical analogs of Txb, and consequent identification of the Txb pharmacophore, the detailed structural information of Txb-substrate binding is still lacking. Here, we use molecular modeling and microsecond-scale molecular dynamics simulations to capture the formation of Txb-lipid II complexes at a membrane surface. Two dominant binding conformations were observed, both showing characteristic lipid II phosphate binding by the Txb backbone amides near the C-terminal cyclodepsipeptide (d-Thr8-Ile11) ring. Additionally, binding by Txb also involved the side chain hydroxyl group of Ser7, as well as a secondary phosphate binding provided by the side chain of l-allo-enduracididine. Interestingly, those conformations differ by swapping two groups of hydrogen bond donors that coordinate the two phosphate moieties of lipid II, resulting in opposite orientations of lipid II binding. In addition, residues d-allo-Ile5 and Ile6 serve as the membrane anchors in both Txb conformations, regardless of the detailed phosphate binding interactions near the cyclodepsipeptide ring. The role of hydrophobic residues in Txb activity is primarily for its membrane insertion, and subsidiarily to provide non-polar interactions with the lipid II tail. Based on the Txb-lipid II interactions captured in their complexes, as well as their partitioning depths into the membrane, we propose that the bactericidal mechanism of Txb is to arrest cell wall synthesis by selectively inhibiting the transglycosylation of peptidoglycan, while possibly leaving the transpeptidation step unaffected. The observed "pyrophosphate caging" mechanism of lipid II inhibition appears to be similar to some lantibiotics, but different from that of vancomycin or bacitracin.
We use ab initio molecular dynamics (AIMD) calculations and quasi-chemical theory (QCT) to study the inner-shell structure of F-(aq) and to evaluate that single-ion free energy under standard conditions. Following the "no split occupancies" rule, QCT calculations yield a free energy value of -101 kcal/mol under these conditions, in encouraging agreement with tabulated values (-111 kcal/mol). The AIMD calculations served only to guide the definition of an effective inner-shell constraint. QCT naturally includes quantum mechanical effects that can be concerning in more primitive calculations, including electronic polarizability and induction, electron density transfer, electron correlation, molecular/atomic cooperative interactions generally, molecular flexibility, and zero-point motion. No direct assessment of the contribution of dispersion contributions to the internal energies has been attempted here, however. We anticipate that other aqueous halide ions might be treated successfully with QCT, provided that the structure of the underlying statistical mechanical theory is absorbed, i.e., that the "no split occupancies" rule is recognized.
Enzymes that degrade specific small molecules could save lives by neutralizing threats from chemical agents in the blood or environment, or by starving pathogenic cells, but promiscuous interactions with other molecules typically limit their effectiveness by blocking the enzyme active site. An obvious solution would be to re-engineer the enzyme to enhance catalytic fidelity, but lack of understanding about how enzymes discriminate between molecules remains a formidable challenge to this approach. Our recent work in collaboration with the University of Texas (UT) suggested a new approach and a model system for understanding enzyme specificity. Asparaginase enzymes catalyze degradation of asparagine, which forms the basis of a medical treatment. Competition by the abundant and chemically similar molecule, glutamine, interferes with asparagine decomposition, thus hindering enzyme efficacy. Asparaginase is advantageous as a model degradation enzyme because variants that demonstrate different binding affinities and catalytic rates can be compared. Here, we leveraged Sandia and the University of Maryland's strengths in molecular simulation, and UT experimental expertise in asparaginase modification and functional assays, to understand asparaginase specificity. Our results advanced a new hypothesis about asparaginase catalytic mechanism that explains for the first time why proximity between the substrate's alpha-carboxyl and carboxamide is absolutely required for catalysis. Based on those insights, we developed the first mutant (Q59L) asparaginase from E. coli that lacks activity toward glutamine. We used that mutant to show that glutaminase activity is required to kill cancer cells that have asparagine synthetase enzymes (ASNS), but not ASNS-negative cancer cells.
We recently developed an enzymatically active, ultra-thin, nano-stabilized liquid membrane for CO2 separation from a mixture of gases, which was recognized by an international R&D 100 Award in 2015. The separation membrane is an approximately 18-nm thick water layer stabilized by capillary condensation within a hydrophilic mesoporous silica film and embedded with the metallo-enzyme carbonic anhydrase. The enzyme speeds CO2 uptake and release from the membrane by catalyzing the rapid inter-conversion of carbon dioxide and water to bicarbonate and a proton. The membrane separates CO2 from 1:1 gas mixtures at a rate of 2600 GPU with CO2/N2 and CO2/H2 selectivities exceeding 788 and 1500, the highest combined flux and selectivity yet reported. That membrane performance exceeds, for the first time, the U.S. Department of Energy standards for CO2 capture technology. CO2 flux depends sensitively on nanopore surface chemistry in the active region. To understand that dependence, we applied molecular simulations to interrogate enzyme behavior in the presence of varied surface chemistries. The results indicate that a polar surface chemistry within the membrane nanopores prevents aggregation of enzymes that would otherwise occur in both bulk liquid solution and non-polar nanopores. Additionally, the enzyme active site maintains a stable structure, even when the overall protein structure deforms within the nanopores. In summary, confinement in the ultra-thin layer of water within mesoporous silica nanopores facilitates a 15x higher enzyme concentration than in bulk conditions, without affecting the structure of the enzyme active site, when the nanopore surfaces are covered with polar functional groups. Thus, confinement of the carbonic enzymes in the membrane water-filled nanopores facilitates higher rates of CO2 uptake and release than achievable in bulk solutions.
Specific ion binding by carboxylates (-COO-) is a broadly important topic because -COO- is one of the most common functional groups coordinated to metal ions in metalloproteins and synthetic polymers. We apply quantum chemical methods and the quasi-chemical free-energy theory to investigate how variations in the number of -COO- ligands in a binding site determine ion-binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) and divalent (Zn2+, Ca2+) ions relevant to experimental work on ion channels and ionomers. Of two competing hypotheses, our results support the ligand field strength hypothesis and follow the reverse Hofmeister series for ion solvation and ion transfer from aqueous solution to binding sites with the preferred number of ligands. New insight arises from the finding that ion-binding sequences can be manipulated and even reversed just by constraining the number of carboxylate ligands in the binding sites. Our results help clarify the discrepancy in ion association between molecular ligands in aqueous solutions and ionomers, and their chemical analogues in ion-channel binding sites.
Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li+ to PC from water, based on electronic structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li+/PF6- transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.
Water is the backbone of our economy - safe and adequate supplies of water are vital for agriculture, industry, recreation, and human consumption. While our supply of water today is largely safe and adequate, we as a nation face increasing water supply challenges in the form of extended droughts, demand growth due to population increase, more stringent health-based regulation, and competing demands from a variety of users. To meet these challenges in the coming decades, water treatment technologies, including desalination, will contribute substantially to ensuring a safe, sustainable, affordable, and adequate water supply for the United States. This overview documents Sandia National Laboratories' (SNL, or Sandia) Water Treatment Program which focused on the development and demonstration of advanced water purification technologies as part of the larger Sandia Water Initiative. Projects under the Water Treatment Program include: (1) the development of desalination research roadmaps (2) our efforts to accelerate the commercialization of new desalination and water treatment technologies (known as the 'Jump-Start Program),' (3) long range (high risk, early stage) desalination research (known as the 'Long Range Research Program'), (4) treatment research projects under the Joint Water Reuse & Desalination Task Force, (5) the Arsenic Water Technology Partnership Program, (6) water treatment projects funded under the New Mexico Small Business Administration, (7) water treatment projects for the National Energy Technology Laboratory (NETL) and the National Renewable Energy Laboratory (NREL), (8) Sandia- developed contaminant-selective treatment technologies, and finally (9) current Laboratory Directed Research and Development (LDRD) funded desalination projects.
We describe a new method to measure the activation energy for unbinding (enthalpy ΔH*u and free energy ΔG*u) of a strongly-bound membrane-associated protein from a lipid membrane. It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method is used to determine ΔH*u and ΔG*u for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH 5.5. ΔH*u is determined from the Arrhenius equation whereas ΔG*u is determined by fitting the data to a model based on mean first passage time for escape from a potential well. The binding free energy ΔGb of sE was also measured at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipid bilayer. The unbinding free energy (20 ± 3 kcal/mol, 20% PG) was found to be roughly three times the binding energy per monomer, (7.8 ± 0.3 kcal/mol for 30% PG, or est. 7.0 kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH 5.5, but assembles into trimers after associating with membranes. This new method to determine unbinding energies should be useful to understand better the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.
This review focuses on the striking recent progress in solving for hydrophobic interactions between small inert molecules. We discuss several new understandings. First, the inverse temperature phenomenology of hydrophobic interactions, i.e., strengthening of hydrophobic bonds with increasing temperature, is decisively exhibited by hydrophobic interactions between atomic-scale hard sphere solutes in water. Second, inclusion of attractive interactions associated with atomic-size hydrophobic reference cases leads to substantial, nontrivial corrections to reference results for purely repulsive solutes. Hydrophobic bonds are weakened by adding solute dispersion forces to treatment of reference cases. The classic statistical mechanical theory for those corrections is not accurate in this application, but molecular quasi-chemical theory shows promise. Finally, because of the masking roles of excluded volume and attractive interactions, comparisons that do not discriminate the different possibilities face an interpretive danger.
The role of solute attractive forces on hydrophobic interactions is studied by coordinated development of theory and simulation results for Ar atoms in water. We present a concise derivation of the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions, a derivation that clarifies the close relation of LMF theory to the EXP approximation applied to this problem long ago. The simulation results show that change from purely repulsive atomic solute interactions to include realistic attractive interactions diminishes the strength of hydrophobic bonds. For the Ar-Ar rdfs considered pointwise, the numerical results for the effects of solute attractive forces on hydrophobic interactions are opposite in sign and larger in magnitude than predicted by LMF theory. That comparison is discussed from the point of view of quasichemical theory, and it is suggested that the first reason for this difference is the incomplete evaluation within LMF theory of the hydration energy of the Ar pair. With a recent suggestion for the system-size extrapolation of the required correlation function integrals, the Ar-Ar rdfs permit evaluation of osmotic second virial coefficients B2. Those B2's also show that incorporation of attractive interactions leads to more positive (repulsive) values. With attractive interactions in play, B2 can change from positive to negative values with increasing temperatures. This is consistent with the puzzling suggestions of decades ago that B2 ≈ 0 for intermediate cases of temperature or solute size. In all cases here, B2 becomes more attractive with increasing temperature.
Here, we describe a new method to measure the activation energy required to remove a strongly-bound membrane-associated protein from a lipid membrane (anchoring energy). It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method was used to determine anchoring energy for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH 5.5. We also measured the binding energy of sE at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipid bilayer. The anchoring energy (37 +/- 1.7 kcal/mol, 20% PG) was found to be much larger than the binding energy (7.8 +/- 0.3 kcal/mol for 30% PG, or est. 7.0 kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH 5.5, but assembles into trimers after associating with membranes. But, trimerization alone is insufficient to account for the observed difference in energies, and we conclude that some energy dissipation occurs during the release process. This new method to determine anchoring energy should be useful to understand the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.
Ethylene carbonate (EC) and propylene carbonate (PC) are widely used solvents in lithium (Li)-ion batteries and supercapacitors. Ion dissolution and diffusion in those media are correlated with solvent dielectric responses. Here, we use all-atom molecular dynamics simulations of the pure solvents to calculate dielectric constants and relaxation times, and molecular mobilities. The computed results are compared with limited available experiments to assist more exhaustive studies of these important characteristics. As a result, the observed agreement is encouraging and provides guidance for further validation of force-field simulation models for EC and PC solvents.
This report describes advances in electrolytes for lithium primary battery systems. Electrolytes were synthesized that utilize organosilane materials that include anion binding agent functionality. Numerous materials were synthesized and tested in lithium carbon monofluoride battery systems for conductivity, impedance, and capacity. Resulting electrolytes were shown to be completely non-flammable and showed promise as co-solvents for electrolyte systems, due to low dielectric strength.
Molecular dynamics simulations of water with both multi-Kr and single Kr atomic solutes are carried out to implement quasi-chemical theory evaluation of the hydration free energy of Kr(aq). This approach obtains free energy differences reflecting Kr-Kr interactions at higher concentrations. Those differences are negative changes in hydration free energies with increasing concentrations at constant pressure. The changes are due to a slight reduction of packing contributions in the higher concentration case. The observed Kr-Kr distributions, analyzed with the extrapolation procedure of Krüger et al., yield a modestly attractive osmotic second virial coefficient, B2 ≈ -60 cm3/mol. The thermodynamic analysis interconnecting these two approaches shows that they are closely consistent with each other, providing support for both approaches. (Graph Presented).
Anion receptors that bind strongly to fluoride anions in organic solvents can help dissolve the lithium fluoride discharge products of primary carbon monofluoride (CFx) batteries, thereby preventing the clogging of cathode surfaces and improving ion conductivity. The receptors are also potentially beneficial to rechargeable lithium ion and lithium air batteries. We apply Density Functional Theory (DFT) to show that an oxalate-based pentafluorophenyl-boron anion receptor binds as strongly, or more strongly, to fluoride anions than many phenyl-boron anion receptors proposed in the literature. Experimental data shows marked improvement in electrolyte conductivity when this oxalate anion receptor is present. The receptor is sufficiently electrophilic that organic solvent molecules compete with F– for boron-site binding, and specific solvent effects must be considered when predicting its F– affinity. To further illustrate the last point, we also perform computational studies on a geometrically constrained boron ester that exhibits much stronger gas-phase affinity for both F– and organic solvent molecules. After accounting for specific solvent effects, however, its net F– affinity is about the same as the simple oxalate-based anion receptor. Lastly, we propose that LiF dissolution in cyclic carbonate organic solvents, in the absence of anion receptors, is due mostly to the formation of ionic aggregates, not isolated F– ions.
Vanegas, Juan M.; Anishkin, Andriy; Rogers, David M.; Lorenzi, Philip L.; Chan, Wai K.; Purwaha, Preeti; Weinstein, John; Sukharev, Sergei; Rempe, Susan
New results derived from the experimental method of neutron diffraction and isotopic substitution (NDIS) are presented for the hydration structure of the lithium cation (Li+) in aqueous solutions of lithium chloride in heavy water (D2O) at concentrations of 6, 3, and 1 m and at 1.5 m lithium sulfate. By introducing new and more-accurate data reduction procedures than in our earlier studies (I. Howell and G. W. Neilson, J. Phys: Condens. Matter, 1996, 8, 4455-4463), we find, in the first hydration shell of Li+, ∼4.3(2) water molecules at 6 m, 4.9(3) at 3 m, 4.8(3) at 1 m in the LiCl solutions, and 5.0(3) water molecules in the case of Li2SO4 solution. The general form of the first hydration shell is similar in all four solutions, with the correlations for Li-O and Li-D sited at 1.96 (0.02) Å and 2.58 (0.02) Å, respectively. The results resemble those presented in 1996, in terms of ion-water distances and local coordination, but the hydration number is significantly lower for the case at 1 m than the 6.5 (1.0) given at that time. Thus, experimental and theoretical results now agree that lithium is hydrated by a small number of water molecules (4-5) in the nearest coordination shell.
Anion receptors that bind strongly to fluoride anions in organic solvents can help dissolve the lithium fluoride discharge products of primary carbon monofluoride (CFx) batteries, thereby preventing the clogging of cathode surfaces and improving ion conductivity. The receptors are also potentially beneficial to rechargeable lithium ion and lithium air batteries.We apply Density Functional Theory (DFT) to show that an oxalate-based pentafluorophenyl-boron anion receptor binds as strongly, or more strongly, to fluoride anions than many phenyl-boron anion receptors proposed in the literature. Experimental data shows marked improvement in electrolyte conductivity when this oxalate anion receptor is present. The receptor is sufficiently electrophilic that organic solvent molecules compete with F- for boron-site binding, and specific solvent effects must be considered when predicting its F- affinity. To further illustrate the last point, we also perform computational studies on a geometrically constrained boron ester that exhibits much stronger gas-phase affinity for both F- and organic solvent molecules. After accounting for specific solvent effects, however, its net F- affinity is about the same as the simple oxalate-based anion receptor. Finally, we propose that LiF dissolution in cyclic carbonate organic solvents, in the absence of anion receptors, is due mostly to the formation of ionic aggregates, not isolated F- ions.
Rempe, Susan; Fu, Yaqin; Li, Binsong; Jiang, Ying B.; Dunphy, Darren R.; Tsai, Andy; Tam, Siu Y.; Fan, Hongyou; Zhang, Hongxia; Rogers, David; Atanassov, Plamen; Cecchi, Joseph L.; Brinker, C.J.
l-Alanine polypeptide thin films were synthesized via atomic layer deposition (ALD). Instead of using an amino acid monomer as the precursor, an l-alanine amino acid derivatized with a protecting group was used to prevent self-polymerization, increase the vapor pressure, and allow linear cycle-by-cycle growth emblematic of ALD. The successful deposition of a conformal polypeptide film has been confirmed by FTIR, TEM, and Mass Spectrometry, and the ALD process has been extended to polyvaline.
Membranes for liquid and gas separations and ion transport are critical to water purification, osmotic energy generation, fuel cells, batteries, supercapacitors, and catalysis. Often these membranes lack pore uniformity and robustness under operating conditions, which can lead to a decrease in performance. The lack of uniformity means that many pores are non-functional. Traditional membranes overcome these limitations by using thick membrane materials that impede transport and selectivity, which results in decreased performance and increased operating costs. For example, limitations in membrane performance demand high applied pressures to deionize water using reverse osmosis. In contrast, cellular membranes combine high flux and selective transport using membrane-bound protein channels operating at small pressure differences. Pore size and chemistry in the cellular channels is defined uniformly and with sub-nanometer precision through protein folding. The thickness of these cellular membranes is limited to that of the cellular membrane bilayer, about 4 nm thick, which enhances transport. Pores in the cellular membranes are robust under operating conditions in the body. Recent efforts to mimic cellular water channels for efficient water deionization produced a significant advance in membrane function. The novel biomimetic design achieved a 10-fold increase in membrane permeability to water flow compared to commercial membranes and still maintained high salt rejection. Despite this success, there is a lack of understanding about why this membrane performs so well. To address this lack of knowledge, we used highperformance computing to interrogate the structural and chemical environments experienced by water and electrolytes in the newly created biomimetic membranes. We also compared the solvation environments between the biomimetic membrane and cellular water channels. These results will help inform future efforts to optimize and tune the performance of synthetic biomimetic membranes for applications in water purification, energy, and catalysis.
Sandia's scientific and engineering expertise in the fields of computational biology, high-performance prosthetic limbs, biodetection, and bioinformatics has been applied to specific problems at the forefront of cancer research. Molecular modeling was employed to design stable mutations of the enzyme L-asparaginase with improved selectivity for asparagine over other amino acids with the potential for improved cancer chemotherapy. New electrospun polymer composites with improved electrical conductivity and mechanical compliance have been demonstrated with the promise of direct interfacing between the peripheral nervous system and the control electronics of advanced prosthetics. The capture of rare circulating tumor cells has been demonstrated on a microfluidic chip produced with a versatile fabrication processes capable of integration with existing lab-on-a-chip and biosensor technology. And software tools have been developed to increase the calculation speed of clustered heat maps for the display of relationships in large arrays of protein data. All these projects were carried out in collaboration with researchers at the University of Texas M. D. Anderson Cancer Center in Houston, TX.
A molecular-scale interpretation of interfacial processes is often downplayed in the analysis of traditional water treatment methods. However, such an approach is critical for the development of enhanced performance in traditional desalination and water treatments. Water confined between surfaces, within channels, or in pores is ubiquitous in technology and nature. Its physical and chemical properties in such environments are unpredictably different from bulk water. As a result, advances in water desalination and purification methods may be accomplished through an improved analysis of water behavior in these challenging environments using state-of-the-art microscopy, spectroscopy, experimental, and computational methods.
Single-wall carbon nanotubes (SWNTs) have shown great promise in novel applications in molecular electronics, biohazard detection, and composite materials. Commercially synthesized nanotubes exhibit a wide dispersion of geometries and conductivities, and tend to aggregate. Hence the key to using these materials is the ability to solubilize and sort carbon nanotubes according to their geometric/electronic properties. One of the most effective dispersants is single-stranded DNA (ssDNA), but there are many outstanding questions regarding the interaction between nucleic acids and SWNTs. In this work we focus on the interactions of SWNTs with single monomers of nucleic acids, as a first step to answering these outstanding questions. We use atomistic molecular dynamics simulations to calculate the binding energy of six different nucleotide monophosphates (NMPs) to a (6,0) single-wall carbon nanotube in aqueous solution. We find that the binding energies are generally favorable, of the order of a few kcal/mol. The binding energies of the different NMPs were very similar in salt solution, whereas we found a range of binding energies for NMPs in pure water. The binding energies are sensitive to the details of the association of the sodium ions with the phosphate groups and also to the average conformations of the nucleotides. We use electronic structure (Density Functional Theory (DFT) and Moller-Plesset second order perturbation to uncorrelated Hartree Fock theory (MP2)) methods to complement the classical force field study. With judicious choices of DFT exchange correlation functionals, we find that DFT, MP2, and classical force field predictions are in qualitative and even quantitative agreement; all three methods should give reliable and valid predictions. However, in one important case, the interactions between ions and metallic carbon nanotubes--the SWNT polarization-induced affinity for ions, neglected in most classical force field studies, is found to be extremely large (on the order of electron volts) and may have important consequences for various SWNT applications. Finally, the adsorption of NMPs onto single-walled carbon nanotubes were studied experimentally. The nanotubes were sonicated in the presence of the nucleotides at various weight fractions and centrifuged before examining the ultraviolet absorbance of the resulting supernatant. A distinct Langmuir adsorption isotherm was obtained for each nucleotide. All of the nucleotides differ in their saturation value as well as their initial slope, which we attribute to differences both in nucleotide structure and in the binding ability of different types or clusters of tubes. Results from this simple system provide insights toward development of dispersion and separation methods for nanotubes: strongly binding nucleotides are likely to help disperse, whereas weaker ones may provide selectivity that may be beneficial to a separation process.
We report on our studies of the structural properties of a hydrogen molecule dissolved in liquid water. The radial distribution function, coordination number and coordination number distribution are calculated using different representations of the interatomic forces within molecular dynamics (MD), Monte Carlo (MC) and ab initio molecular dynamics (AIMD) simulation frameworks. Although structural details differ in the radial distribution functions generated from the different force fields, all approaches agree that the average and most probable number of water molecules occupying the inner hydration sphere around hydrogen is 16. Furthermore, all results exclude the possibility of clathrate-like organization of water molecules around the hydrophobic molecular hydrogen solute.
Carbon nanotubes (CNT) are unique nanoscale building blocks for a variety of materials and applications, from nanocomposites, sensors and molecular electronics to drug and vaccine delivery. An important step towards realizing these applications is the ability to controllably self-assemble the nanotubes into larger structures. Recently, amphiphilic peptide helices have been shown to bind to carbon nanotubes and thus solubilize them in water. Furthermore, the peptides then facilitate the assembly of the peptide-wrapped nanotubes into supramolecular, well-aligned fibers. We investigate the role that molecular modeling can play in elucidating the interactions between the peptides and the carbon nanotubes in aqueous solution. Using ab initio methods, we have studied the interactions between water and CNTs. Classical simulations can be used on larger length scales. However, it is difficult to sample in atomistic detail large biomolecules such as the amphiphilic peptide of interest here. Thus, we have explored both new sampling methods using configurational-bias Monte Carlo simulations, and also coarse-grained models for peptides described in the literature. An improved capability to model these inorganichiopolymer interfaces could be used to generate improved understanding of peptide-nanotube self-assembly, eventually leading to the engineering of new peptides for specific self-assembly goals.
We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ({approx}8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 {angstrom} longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.
We apply density functional theory (DFT) and the DFT+U technique to study the adsorption of transition metal porphine molecules on atomistically flat Au(111) surfaces. DFT calculations using the Perdew?Burke?Ernzerhof exchange correlation functional correctly predict the palladium porphine (PdP) low-spin ground state. PdP is found to adsorb preferentially on gold in a flat geometry, not in an edgewise geometry, in qualitative agreement with experiments on substituted porphyrins. It exhibits no covalent bonding to Au(111), and the binding energy is a small fraction of an electronvolt. The DFT+U technique, parametrized to B3LYP-predicted spin state ordering of the Mn d-electrons, is found to be crucial for reproducing the correct magnetic moment and geometry of the isolated manganese porphine (MnP) molecule. Adsorption of Mn(II)P on Au(111) substantially alters the Mn ion spin state. Its interaction with the gold substrate is stronger and more site-specific than that of PdP. The binding can be partially reversed by applying an electric potential, which leads to significant changes in the electronic and magnetic properties of adsorbed MnP and 0.1 {angstrom} changes in the Mn-nitrogen distances within the porphine macrocycle. We conjecture that this DFT+U approach may be a useful general method for modeling first-row transition metal ion complexes in a condensed-matter setting.
This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.
This report summarizes research on the aging of Class I components in environments representative of nuclear power plants. It discusses Class IE equipment used in nuclear power plants, typical environments encountered by Class IE components, and aging techniques used to qualify this equipment. General discussions of radiation chemistry of polymers and accelerated aging techniques are also included. Based on the inadequacies of present aging techniques for Class IE equipment, a proposal for an experimental program on electrical cables is presented. One of the main purposes of the proposed work is to obtain relevant data in two areas of particular concern--the effect of radiation dose rate on polymer degradation, and the importance of synergism for combined thermal and radiation environments. A new model that allows combined environment accelerated aging to be carried out is introduced, and it is shown how the experimental data to be generated can be used to test this model.