Toward quantification of hypoxia using fluorinated EuII/III-containing ratiometric probes.

Hypoxia is a prognostic biomarker of rapidly growing cancers, where the extent of hypoxia is an indication of tumor progression and prognosis; therefore, hypoxia is also used for staging while performing chemo- and radiotherapeutics for cancer. Contrast-enhanced MRI using EuII-based contrast agents is a noninvasive method that can be used to map hypoxic tumors, but quantification of hypoxia using these agents is challenging due to the dependence of signal on the concentration of both oxygen and EuII. Here, we report a ratiometric method to eliminate concentration dependence of contrast enhancement of hypoxia using fluorinated EuII/III-containing probes. We studied three different EuII/III couples of complexes containing 4, 12, or 24 fluorine atoms to balance fluorine signal-to-noise ratio with aqueous solubility. The ratio between the longitudinal relaxation time (T1) and 19F signal of solutions containing different ratios of EuII- and EuIII-containing complexes was plotted against the percentage of EuII-containing complexes in solution. We denote the slope of the resulting curves as hypoxia indices because they can be used to quantify signal enhancement from Eu, that is related to oxygen concentration, without knowledge of the absolute concentration of Eu. This mapping of hypoxia was demonstrated in vivo in an orthotopic syngeneic tumor model. Our studies significantly contribute toward improving the ability to radiographically map and quantify hypoxia in real time, which is critical to the study of cancer and a wide range of diseases.

Quantum Chemistry in the Age of Quantum Computing.

Practical challenges in simulating quantum systems on classical computers have been widely recognized in the quantum physics and quantum chemistry communities over the past century. Although many approximation methods have been introduced, the complexity of quantum mechanics remains hard to appease. The advent of quantum computation brings new pathways to navigate this challenging and complex landscape. By manipulating quantum states of matter and taking advantage of their unique features such as superposition and entanglement, quantum computers promise to efficiently deliver accurate results for many important problems in quantum chemistry, such as the electronic structure of molecules. In the past two decades, significant advances have been made in developing algorithms and physical hardware for quantum computing, heralding a revolution in simulation of quantum systems. This Review provides an overview of the algorithms and results that are relevant for quantum chemistry. The intended audience is both quantum chemists who seek to learn more about quantum computing and quantum computing researchers who would like to explore applications in quantum chemistry.

The divide-and-conquer second-order proton propagator method based on nuclear orbital plus molecular orbital theory for the efficient computation of proton binding energies.

An efficient computational method to evaluate the binding energies of many protons in large systems was developed. Proton binding energy is calculated as a corrected nuclear orbital energy using the second-order proton propagator method, which is based on nuclear orbital plus molecular orbital theory. In the present scheme, the divide-and-conquer technique was applied to utilize local molecular orbitals. This use relies on the locality of electronic relaxation after deprotonation and the electron-nucleus correlation. Numerical assessment showed reduction in computational cost without the loss of accuracy. An initial application to model a protein resulted in reasonable binding energies that were in accordance with the electrostatic environment and solvent effects.

Prediction of proton affinities of organic molecules using the any-particle molecular-orbital second-order proton propagator approach.

We assess the performance of the recently developed any-particle molecular-orbital second-order proton propagator (APMO/PP2) scheme [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes and R. Flores-Moreno, J. Chem. Phys., 2013, 138, 194108] on the calculation of gas phase proton affinities (PAs) of a set of 150 organic molecules comprising several functional groups: amines, alcohols, aldehydes, amides, ketones, esters, ethers, carboxylic acids and carboxylate anions. APMO/PP2 PAs display an overall mean absolute error of 0.68 kcal mol-1 with respect to experimental data. These results suggest that the APMO/PP2 method is an alternative approach for the quantitative prediction of gas phase proton affinities. One novel feature of the method is that a PA can be obtained from a single calculation of the optimized protonated molecule.

In quest of strong Be-Ng bonds among the neutral Ng-Be complexes.

The global minimum geometries of BeCN2 and BeNBO are linear BeN-CN and BeN-BO, respectively. The Be center of BeCN2 binds He with the highest Be-He dissociation energy among the studied neutral He-Be complexes. In addition, BeCN2 can be further tuned as a better noble gas trapper by attaching it with any electron-withdrawing group. Taking BeO, BeS, BeNH, BeNBO, and BeCN2 systems, the study at the CCSD(T)/def2-TZVP level of theory also shows that both BeCN2 and BeNBO systems have higher noble gas binding ability than those related reported systems. ΔG values for the formation of NgBeCN2/NgBeNBO (Ng = Ar-Rn) are negative at room temperature (298 K), whereas the same becomes negative at low temperature for Ng = He and Ne. The polarization plus the charge transfer is the dominating term in the interaction energy.

Calculation of positron binding energies using the generalized any particle propagator theory.

We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ~0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.

C5Li7(+) and O2Li5(+) as noble-gas-trapping agents.

The noble-gas-trapping ability of the star-shaped C(5)Li(7)(+) cluster and O(2)Li(5)(+) super-alkali cluster is studied by using ab initio and density functional theory (DFT) at the MP2 and M05-2X levels with 6-311+G(d,p) and 6-311+G(d) basis sets. These clusters are shown to be effective noble-gas-trapping agents. The stability of noble-gas-loaded clusters is analyzed in terms of dissociation energies, reaction enthalpies, and conceptual DFT-based reactivity descriptors. The presence of an external electric field improves the dissociation energy.

Clarification of recombinant proteins from high cell density mammalian cell culture systems using new improved depth filters.

Increasingly high cell density, high product titer cell cultures containing mammalian cells are being used for the production of recombinant proteins. These high productivity cultures are placing a larger burden on traditional downstream clarification and purification operations due to higher product and impurity levels. Controlled flocculation and precipitation of mammalian cell culture suspensions by acidification or using polymeric flocculants have been employed to enhance clarification throughput and downstream filtration operations. While flocculation is quite effective in agglomerating cell debris and process related impurities such as (host cell) proteins and DNA, the resulting suspension is generally not easily separable solely using conventional depth filtration techniques. As a result, centrifugation is often used for clarification of cells and cell debris before filtration, which can limit process configurations and flexibility due to the investment and fixed nature of a centrifuge. To address this challenge, novel depth filter designs were designed which results in improved primary and secondary direct depth filtration of flocculated high cell density mammalian cell cultures systems feeds, thereby providing single-use clarification solution. A framework is presented here for optimizing the particle size distribution of the mammalian cell culture systems with the pore size distribution of the gradient depth filter using various pre-treatment conditions resulting in increased depth filter media utilization and improved clarification capacity. Feed conditions were optimized either by acidification or by polymer flocculation which resulted in the increased average feed particle-size and improvements in throughput with improved depth filters for several mammalian systems.

A generalized any-particle propagator theory: prediction of proton affinities and acidity properties with the proton propagator.

We have recently extended the electron propagator theory to the treatment of any type of particle using an Any-Particle Molecular Orbital (APMO) wavefunction as reference state. This approach, called APMO/PT, has been implemented in the LOWDIN code to calculate correlated binding energies, for any type of particle in molecular systems. In this work, we present the application of the APMO/PT approach to study proton detachment processes. We employed this method to calculate proton binding energies and proton affinities for a set of inorganic and organic molecules. Our results reveal that the second-order proton propagator (APMO/PP2) quantitatively reproduces experimental trends with an average deviation of less than 0.41 eV. We also estimated proton affinities with an average deviation of 0.14 eV and the proton hydration free energy using APMO/PP2 with a resulting value of -270.2 kcal/mol, in agreement with other results reported in the literature. Results presented in this work suggest that the APMO/PP2 approach is a promising tool for studying proton acid/base properties.

Elucidating the mechanisms associated with the anaerobic biotransformation of the emerging contaminant nitroguanidine.

Nitroguanidine (NQ) is a constituent of gas generators for automobile airbags, smokeless pyrotechnics, insecticides, propellants, and new insensitive munitions formulations applied by the military. During its manufacture and use, NQ can easily spread in soils, ground, and surface waters due to its high aqueous solubility. Very little is known about the microbial biotransformation of NQ. This study aimed to elucidate important mechanisms operating during NQ anaerobic biotransformation. To achieve this goal, we developed an anaerobic enrichment culture able to reduce NQ to nitrosoguanidine (NsoQ), which was further abiotically transformed to cyanamide. Effective electron donors for NQ biotransformation were lactate and, to a lesser extent, pyruvate. The results demonstrate that the enrichment process selected a sulfate-reducing culture that utilized lactate as its electron donor and sulfate as its electron acceptor while competing with NQ as an electron sink. A unique property of the culture was its requirement for exogenous nitrogen (e.g., from yeast extract or NH4Cl) for NQ biotransformation since NQ itself did not serve as a nitrogen source. The main phylogenetic groups associated with the NQ-reducing culture were sulfate-reducing and fermentative bacteria, namely Cupidesulfovibrio oxamicus (63.1% relative abundance), Dendrosporobacter spp. (12.0%), and Raoultibacter massiliens (10.9%). The molecular ecology results corresponded to measurable physiological properties of the most abundant members. The results establish the conditions for NQ anaerobic biotransformation and the microbial community associated with the process, improving our present comprehension of NQ environmental fate and assisting the development of NQ remediation strategies.

Biodegradation of the emerging contaminant 3-nitro-1,2,4-triazol-5-one and its product 3-amino-1,2,4-triazol-5-one in perlite/soil columns.

3-Nitro-1,2,4-triazol-5-one (NTO) is an ingredient of new safer-to-handle military insensitive munitions formulations. NTO can be microbially reduced to 3-amino-1,2,4-triazol-5-one (ATO) under anaerobic conditions if an electron donor is available. Conversely, ATO can undergo aerobic biodegradation. Previously, our research group developed an anaerobic enrichment culture that reduces NTO to ATO. A second culture could aerobically mineralize ATO. This study aimed to combine anaerobic/aerobic conditions within a down-flow perlite/soil column for simultaneous NTO reduction and ATO oxidation. Acetate biostimulation was investigated to promote oxygen depletion and create anaerobic micro-niches for NTO reduction, whereas perlite increased soil porosity and oxygen convection, allowing ATO oxidation. Two columns packed with a perlite/soil mixture (70:30, wet wt.%) or 100% perlite were operated aerobically and inoculated with the NTO- and ATO-degrading cultures. Initially, the influent consisted of ∼280 µM ATO, and after 30 days, the feeding was switched to ∼260 µM NTO and ∼250 µM acetate. By progressively increasing acetate from 250 to 4000 µM, the NTO removal gradually improved in both columns. The perlite/soil column reached a 100% NTO removal after 4000 µM acetate was supplemented. Additionally, there was no ATO accumulation, and inorganic nitrogen was produced, indicating ATO mineralization. Although NH4+ was produced following ATO oxidation, most nitrogen was recovered as NO3- likely via nitrification reactions. Microbial community analysis revealed that phylotypes hosted in the enrichment cultures specialized in NTO reduction (e.g., Geobacter) and ATO oxidation (e.g., Hydrogenophaga, Ramlibacter, Terrimonas, and Pseudomonas) were established in the columns. Besides, the predominant genera (Azohydromonas, Zoogloea, and Azospirillum) are linked to nitrogen cycling by performing nitrogen fixation, NO3- reduction, and nitroaromatics degradation. This study applied a bulking agent (perlite) and acetate biostimulation to achieve simultaneous NTO reduction and ATO oxidation in a single column. Such a strategy can assist with real-world applications of NTO and ATO biodegradation mechanisms.

Outersphere Approach to Increasing the Persistance of Oxygen-Sensitive Europium(II)-Containing Contrast Agents for Magnetic Resonance Imaging with Perfluorocarbon Nanoemulsions toward Imaging of Hypoxia.

Radiographic mapping of hypoxia is needed to study a wide range of diseases. Complexes of Eu(II) are a promising class of molecules to fit this need, but they are generally limited by their rapid oxidation rates in vivo. Here, a perfluorocarbon-nanoemulsion perfused with N2 , forms an interface with aqueous layers to hinder oxidation of a new perfluorocarbon-soluble complex of Eu(II). Conversion of the perfluorocarbon solution of Eu(II) into nanoemulsions results in observable differences between reduced and oxidized forms by magnetic resonance imaging both in vitro and in vivo. Oxidation in vivo occurrs over a period of ≈30 min compared to <5 min for a comparable Eu(II)-containing complex without nanoparticle interfaces. These results represent a critical step toward delivery of Eu(II)-containing complexes in vivo for the study of hypoxia.

A generalized any particle propagator theory: assessment of nuclear quantum effects on electron propagator calculations.

In this work we propose an extended propagator theory for electrons and other types of quantum particles. This new approach has been implemented in the LOWDIN package and applied to sample calculations of atomic and small molecular systems to determine its accuracy and performance. As a first application of the method we have studied the nuclear quantum effects on electron ionization energies. We have observed that ionization energies of atoms are similar to those obtained with the electron propagator approach. However, for molecular systems containing hydrogen atoms there are improvements in the quality of the results with the inclusion of nuclear quantum effects. An energy term analysis has allowed us to conclude that nuclear quantum effects are important for zero order energies whereas propagator results correct the electron and electron-nuclear correlation terms. Results presented for a series of n-alkanes have revealed the potential of this method for the accurate calculation of ionization energies of a wide variety of molecular systems containing hydrogen nuclei. The proposed methodology will also be applicable to exotic molecular systems containing positrons or muons.

Reductive transformation of the insensitive munitions compound nitroguanidine by different iron-based reactive minerals.

Nitroguanidine (NQ) is an emerging contaminant being used by the military as a constituent of new insensitive munitions. NQ is also used in rocket propellants, smokeless pyrotechnics, and vehicle restraint systems. Its uncontrolled transformation in the environment can generate toxic and potentially mutagenic products, posing hazards that need to be remediated. NQ transformation has only been investigated to a limited extent. Thus, it is crucial to expand the narrow spectrum of NQ remediation strategies and understand its transformation pathways and end products. Iron-based reactive minerals should be investigated for NQ treatment because they are successfully used in existing technologies, such as permeable reactive barriers, for treating a wide range of organic pollutants. This study tested the ability of micron-sized zero-valent iron (m-ZVI), mackinawite, and commercial FeS, to transform NQ under anoxic conditions. NQ transformation followed pseudo-first-order kinetics. The reaction rate constants decreased as follows: commercial FeS > mackinawite > m-ZVI. For the assessed minerals, the NQ transformation started with the reduction of the nitro group forming nitrosoguanidine (NsoQ). Then, aminoguanidine (AQ) was accumulated during the reaction of NQ with m-ZVI, accounting for 86% of the nitrogen mass recovery. When NQ was reacted with commercial FeS, 45% and 20% of nitrogen were recovered as AQ and guanidine, respectively, after 24 h. Nonetheless, NsoQ persisted, contributing to the N-balance. When mackinawite was present, NsoQ disappeared, but AQ was not detected, and guanidine accounted for 11% of the nitrogen recovery. AQ was ultimately transformed into cyanamide, whose dimerization triggered the formation of cyanoguanidine. Alternatively, NsoQ was transformed into guanidine, which reacted with cyanamide to form biguanide. This is the first report systematically investigating the NQ transformation by different iron-based reactive minerals. The evidence indicates that these minerals are attractive alternatives for developing NQ remediation strategies.

A Potential Role for Substance P in West Nile Virus Neuropathogenesis.

Of individuals who develop West Nile neuroinvasive disease (WNND), ~10% will die and >40% will develop long-term complications. Current treatment recommendations solely focus on supportive care; therefore, we urgently need to identify novel and effective therapeutic options. We observed a correlation between substance P (SP), a key player in neuroinflammation, and its receptor Neurokinin-1 (NK1R). Our study in a wild-type BL6 mouse model found that SP is upregulated in the brain during infection, which correlated with neuroinvasion and damage to the blood−brain barrier. Blocking the SP/NK1R interaction beginning at disease onset modestly improved survival and prolonged time to death in a small pilot study. Although SP is significantly increased in the brain of untreated WNND mice when compared to mock-infected animals, levels of WNV are unchanged, indicating that SP likely does not play a role in viral replication but may mediate the immune response to infection. Additional studies are necessary to define if SP plays a mechanistic role or if it represents other mechanistic pathways.

A Mouse Holder for Awake Functional Imaging in Unanesthetized Mice: Applications in 31P Spectroscopy, Manganese-Enhanced Magnetic Resonance Imaging Studies, and Resting-State Functional Magnetic Resonance Imaging.

Anesthesia is often used in preclinical imaging studies that incorporate mouse or rat models. However, multiple reports indicate that anesthesia has significant physiological impacts. Thus, there has been great interest in performing imaging studies in awake, unanesthetized animals to obtain accurate results without the confounding physiological effects of anesthesia. Here, we describe a newly designed mouse holder that is interfaceable with existing MRI systems and enables awake in vivo mouse imaging. This holder significantly reduces head movement of the awake animal compared to previously designed holders and allows for the acquisition of improved anatomical images. In addition to applications in anatomical T2-weighted magnetic resonance imaging (MRI), we also describe applications in acquiring 31P spectra, manganese-enhanced magnetic resonance imaging (MEMRI) transport rates and resting-state functional magnetic resonance imaging (rs-fMRI) in awake animals and describe a successful conditioning paradigm for awake imaging. These data demonstrate significant differences in 31P spectra, MEMRI transport rates, and rs-fMRI connectivity between anesthetized and awake animals, emphasizing the importance of performing functional studies in unanesthetized animals. Furthermore, these studies demonstrate that the mouse holder presented here is easy to construct and use, compatible with standard Bruker systems for mouse imaging, and provides rigorous results in awake mice.

Modeling industrial centrifugation of mammalian cell culture using a capillary based scale-down system.

Continuous-flow centrifugation is widely utilized as the primary clarification step in the recovery of biopharmaceuticals from cell culture. However, it is a challenging operation to develop and characterize due to the lack of easy to use, small-scale, systems that can be used to model industrial processes. As a result, pilot-scale continuous centrifugation is typically employed to model large-scale systems requiring a significant amount of resources. In an effort to reduce resource requirements and create a system which is easy to construct and utilize, a capillary shear device, capable of producing energy dissipation rates equivalent to those present in the feed zones of industrial disk stack centrifuges, was developed and evaluated. When coupled to a bench-top, batch centrifuge, the capillary device reduced centrate turbidity prediction error from 37% to 4% compared to using a bench-top centrifuge alone. Laboratory-scale parameters that are analogous to those routinely varied during industrial-scale continuous centrifugation were identified and evaluated for their utility in emulating disk stack centrifuge performance. The resulting relationships enable bench-scale process modeling of continuous disk stack centrifuges using an easily constructed, scalable, capillary shear device coupled to a typical bench-top centrifuge.

Effects of solution environment on mammalian cell fermentation broth properties: enhanced impurity removal and clarification performance.

The processing of recombinant proteins from high cell density, high product titer cell cultures containing mammalian cells is commonly performed using tangential flow microfiltration (MF). However, the increased cellular debris present in these complex feed streams can prematurely foul the membrane, adversely impacting MF capacity and throughput. In addition, high cell density cell culture streams introduce elevated levels of process-related impurities, which increase the burden on subsequent purification operations to remove these complex media components and impurities. To address this challenge, an evaluation of mammalian cell culture broth buffer properties was examined to determine if enhanced impurity removal and clarification performance could be achieved. A framework is presented here for establishing optimized mammalian cell culture buffer conditions, involving trade-offs between product recovery and purification and improved clarification at manufacturing-scale production. A reduction in cell culture broth pH to 4.7-5.0 induced flocculation and impurity precipitation which increased the average feed particle-size. These conditions led to enhanced impurity removal and improved MF throughput and filter capacity for several mammalian systems. Feed conditions were further optimized by controlling ionic composition along with pH to improve product recovery from high cell density/high product titer cell cultures.

Understanding microsolvation of Li+: structural and energetical analyses.

A stochastic exploration of the quantum conformational space for the (H(2)O)(n)Li(+), n = 3, 4, 5 complexes produced 32 molecular clusters at the B3LYP/6-311++G** and MP2/6-311++G** levels. The first solvation shell is predicted to comprise a maximum of 4 water molecules. Energy decomposition analyses were performed to determine the relationship between the geometrical features of the complexes and the types of interactions responsible for their stabilization. Our findings reveal that electrostatic interactions are major players determining the structures and relative stabilities of the clusters. The formal charge on the Li atom leads to two distinct types of hydrogen bonds, scattered in a wide range of distances (1.61-2.32 Å), in many cases affording H-bonds that are considerably larger and considerably shorter than those in pure water clusters (typically ∼1.97 Å).

Early detection of myocardial changes with and without dexrazoxane using serial magnetic resonance imaging in a pre-clinical mouse model.

BACKGROUND: Cancer therapy-related cardiac dysfunction may occur in pediatric cancer survivors. Identification of early markers of myocardial damage secondary to anthracycline exposure is crucial to develop strategies that may ameliorate this complication. OBJECTIVES: The purpose of this study was to identify early myocardial changes induced by doxorubicin with and without cardioprotection using dexrazoxane detected by serial cardiac magnetic resonance imaging (CMR) in a pre-clinical mouse model. METHODS: Serial CMR examinations were performed in 90 mice distributed in 3 groups: 45 received doxorubicin (DOX group), 30 mice received doxorubicin with dexrazoxane (DOX/DEX group) and 15 mice received saline injections (control group). We obtained the following CMR parameters in all mice: T2, extracellular volume quantification (ECV), myocardial deformation, and functional quantification. RESULTS: Myocardial edema assessed by T2 time was the earliest parameter demonstrating evidence of myocardial injury, most notable in the DOX group at week 4 and 8 compared with DOX/DEX group. Similarly, global longitudinal strain was abnormal in both the DOX and DOX/DEX groups. However, this change persisted only in the DOX group. The ECV was significantly elevated in the DOX group at the final CMR, while only minimally elevated in the DOX/DEX group. The right and left ejection fraction was decreased, along with the mass to volume ratio in the DOX group. The T2 time, ECV, and deformation correlated with ejection fraction and left ventricular volume. CONCLUSIONS: T2 time and deformation by CMR identifies early myocardial injury from anthracyclines. Dexrazoxne did not prevent the initial edema, but the inflammatory changes were not sustained. CMR may be useful for early detection of cardiac dysfunction. Serial CMR demonstrates dexrazoxane minimizes cardiac dysfunction and aids recovery in a mouse model.