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At least 37 records · Page 2

Kinetic preference for the 3'-5'-linked dimer in the reaction of guanosine 5'-phosphorylmorpholinamide with deoxyguanosine 5'-phosphoryl-2-methylimidazolide as a function of poly(C) concentration

The formation of the internucleotide bond in diguanylate synthesis was studied in aqueous solution at pH 8 and 0.2 M Mg2+ in the presence and absence of polycytidylate, poly(C). The investigation was simplified by using guanosine 5'-phosphorylmorpholinamide, mor-pG, which can act only as a nucleophile, and deoxyguanosine 5'-phosphoryl-2-methylimidazolide, 2-MeImpdG, which can act only as an electrophile. The time-dependent product distribution was monitored by high-performance liquid chromatography (HPLC) and liquid chromatography mass spectrometry (LC/MS). In the absence of poly(C) the reaction between mor-pG and 2-MeImpdG yielded small amounts of the dimer mor-pGpdG with a regioselectivity of 2'-5':3'-5' = 3.5. In the presence of poly(C) dimer yields increased and a reversal in regioselectivity occurred; both effects were in proportion to the concentration of the polymer. The results can be quantitatively explained with the proposition that poly(C), acting as the template, catalyzes the reaction between template-bound monomers by about a factor of 4-5 over the reaction in solution and yields dimers with a regioselectivity of 2'-5':3'-5' approximately 0.33. These findings illustrate the intrinsic preference of guanosine monomers to correctly self-assemble on the appropriate template.

NASA Discipline Exobiology

New Insights into the Heterogeneity of the Tagish Lake Meteorite: Soluble Organic Compositions of Variously Altered Specimens

The Tagish Lake carbonaceous chondrite exhibits a unique compositional heterogeneity that may be attributed to varying degrees of aqueous alteration within the parent body asteroid. Previous analyses of soluble organic compounds from four Tagish Lake meteorite specimens (TL5b, TL11h, TL11i, TL11v) identified distinct distributions and isotopic compositions that appeared to be linked to their degree of parent body processing (Herd et al. 2011; Glavin et al. 2012; Hilts et al. 2014). In the present study, we build upon these initial observations and evaluate the molecular distribution of amino acids, aldehydes and ketones, monocarboxylic acids, and aliphatic and aromatic hydrocarbons, including compound‐specific δ13C compositions, for three additional Tagish Lake specimens: TL1, TL4, and TL10a. TL1 contains relatively high abundances of soluble organics and appears to be a moderately altered specimen, similar to the previously analyzed TL5b and TL11h lithologies. In contrast, specimens TL4 and TL10a both contain relatively low abundances of all of the soluble organic compound classes measured, similar to TL11i and TL11v. The organic‐depleted composition of TL4 appears to have resulted from a relatively low degree of parent body aqueous alteration. In the case of TL10a, some unusual properties (e.g., the lack of detection of intrinsic monocarboxylic acids and aliphatic and aromatic hydrocarbons) suggest that it has experienced extensive alteration and/or a distinct organic‐depleted alteration history. Collectively, these varying compositions provide valuable new insights into the relationships between asteroidal aqueous alteration and the synthesis and preservation of soluble organic compounds.

Tagish Lake

Extraterrestrial Amino Acids and Amines Identified in Asteroid Ryugu Samples Returned By the Hayabusa2 Mission

The hot water and acid extracts of two different Ryugu samples collected by the Hayabusa2 mission were analyzed for the presence of aliphatic amines and amino acids. The abundances and relative distributions of both classes of molecules were determined, as well as the enantiomeric compositions of the chiral amino acids. The Ryugu samples studied here were recovered from sample chambers A and C, which were composed of surface material, and a combination of surface and possible subsurface material, respectively. A total of thirteen amino acids were detected and quantitated in these samples, with an additional five amino acids that were tentatively identified but not quantitated. The abundances of four aliphatic amines identified in the Ryugu samples were also determined in the current work. Amino acids were observed in the acid hydrolyzed and unhydrolyzed hot water extracts of asteroid Ryugu regolith using liquid chromatography with UV fluorescence detection and high-resolution mass spectrometry. Conversely, aliphatic amines were only analyzed in the unhydrolyzed hot water Ryugu extracts. Two- to six-carbon (C 2 -C 6 ) amino acids with individual abundances ranging from 0.02 to 15.8 nmol g −1 , and one- to three-carbon (C 1 -C 3 ) aliphatic amines with individual abundances from 0.05 to 34.14 nmol g −1 , were found in the hot water extracts. Several non-protein amino acids that are rare in biology, including β-amino-n-butyric acid (β-ABA) and β-aminoisobuytric acid (β-AIB), were racemic or very nearly racemic, thus indicating their likely abiotic origins. Trace amounts of select protein amino acids that were enriched in the ւ-enantiomer may indicate low levels of terrestrial amino acid contamination in the samples. However, the presence of elevated abundances of free and racemic alanine, a common protein amino acid in terrestrial biology, and elevated abundances of the predominately free and racemic non-protein amino acids, β-ABA and β-AIB, indicate that many of the amino acids detected in the Ryugu water extracts were indigenous to the samples. Although the Ryugu samples have been found to be chemically similar to CI type carbonaceous chondrites, the measured concentrations and relative distributions of amino acids and aliphatic amines in Ryugu samples were notably different from those previously observed for the CI1.1 carbonaceous chondrite, Orgueil. This discrepancy could be the result of differences in the original chemical compositions of the parent bodies and/or alteration conditions, such as space weathering. In addition to α-amino acids that could have been formed by Strecker cyanohydrin synthesis during a low temperature aqueous alteration phase, β-, γ-, and δ-amino acids, including C 3 – C 5 straight-chain n-ω-amino acids that are not formed by Strecker synthesis, were also observed in the Ryugu extracts. The suite of amino acids measured in the Ryugu samples indicates that multiple amino acid formation mechanisms were active on the Ryugu parent body. The analytical techniques used here are well-suited to search for similar analytes in asteroid Bennu material collected by the NASA OSIRIS-REx mission scheduled for Earth return in September 2023.

Hayabusa2

The Spatial Distribution of Organic Matter and Mineralogical Relationships in Carbonaceous Chondrites

Organic matter present within primitive carbonaceous meteorites represents the complex conglomeration of species formed in a variety of physically and temporally distinct environments including circumstellar space, the interstellar medium, the Solar Nebula & Jovian sub-nebulae and asteroids. In each case, multiple chemical pathways would have been available for the synthesis of organic molecules. Consequently these meteorites constitute a unique record of organic chemical evolution in the Universe and one of the biggest challenges in organic cosmochemistry has been in deciphering this record. While bulk chemical analysis has provided a detailed description of the range and diversity of organic species present in carbonaceous chondrites, there is virtually no hard experimental data as to how these species are spatially distributed and their relationship to the host mineral matrix, (with one exception). The distribution of organic phases is nevertheless critical to understanding parent body processes. The CM and CI chondrites all display evidence of low temperature (< 350K) interaction with aqueous fluids, which based on O isotope data, flowed along thermal gradients within the respective parent bodies. This pervasive aqueous alteration may have led to aqueous geochromatographic separation of organics and synthesis of new organics coupled to aqueous mineral alteration. To address such issues we have applied the technique of microprobe two-step laser desorption / photoionization mass spectrometry (L2MS) to map in situ the spatial distribution of a broad range of organic species at the micron scale in the freshly exposed matrices of the Bells, Tagish Lake and Murchison (CM2) carbonaceous chondrites.

Clemett, S. J.

Abundant Extraterrestrial Amino Acids in the Primitive CM Carbonaceous Chondrite Asuka 12236

The Asuka (A)-12236 meteorite has recently been classified as a CM carbonaceous chondrite of petrologic type 3.0/2.9 and is among the most primitive CM meteorites studied to date. Here, we report the concentrations, relative distributions, and enantiomeric ratios of amino acids in water extracts of the A-12236 meteorite and another primitive CM chondrite Elephant Moraine(EET) 96029 (CM2.7) determined by ultra-high-performance liquid chromatography time-of-flight mass spectrometry. EET 96029 was highly depleted in amino acids and dominated by glycine, while a wide diversity of two- to six-carbon aliphatic primary amino acids were identified in A-12236, which had a total amino acid abundance of 360 ± 18 nmol g-1, with most amino acids present without hydrolysis (free). The amino acid concentrations of A-12236 were double those previously measured in the CM2.7 Paris meteorite, consistent with A-12236 being a highly primitive and unheated CM chondrite. The high relative abundance of α-amino acids in A-12236 are consistent with formation by a Strecker-cyanohydrin dominated synthesis during a limited early aqueous alteration phase on the CM meteorite parent body. The presence of predominantly free glycine, a near racemic mixture of alanine (D/L ~0.93 to 0.96), and elevated abundances of several terrestrially rare non-protein amino acids including α-amino isobutyric acid (α-AIB) and racemic isovaline, indicate that these amino acids in A-12236 are extraterrestrial in origin. Given a lack of evidence for biological amino acid contamination in A-12236, it is possible that some of the L-enantiomeric excesses (Lee ~34 to 64%) of the protein amino acids aspartic and glutamic acids and serine are indigenous to the meteorite; however, isotopic measurements are needed for confirmation. In contrast to more aqueously altered CMs of petrologic types ≤ 2.5, no L-isovaline excesses were detected in A-12236. This observation strengthens the hypothesis that extensive parent body aqueous activity is required to produce or amplify the large L-isovaline excesses that cannot be explained solely by exposure to circularly polarized radiation or other chiral symmetry breaking mechanisms prior to incorporation into the asteroid parent body.

Daniel P Glavin

Template-directed synthesis and selective adsorption of oligoadenylates in hydroxyapatite

Polyuridylic acid is adsorbed completely from aqueous solution by hydroxyapatite under conditions that permit template-directed synthesis of oligoadenylates in free solution. The yield of oligoadenylates is enhanced to almost the same extent by poly(U) in the presence or the absence of hydroxyapatite. Under very similar conditions small quantities of hydroxyapatite adsorb higher-molecular-weight oligoadenylates selectively from a mixture of oligomers. On the basis of these results a mechanism for prebiotic oligonucleotide formation is proposed in which selective adsorption on hydroxyapatite or some other immobilized anion-exchanging material plays a major role. Monomers are released from the surface for reactivation, while oligomers are retained in a protected environment by adsorption to the apatite surface.

Gibbs, D.

Relative reactivity of ribosyl 2'-OH vs. 3'-OH in concentrated aqueous solutions of phosphoimidazolide activated nucleotides

Phosphoimidazolide activated ribomononucleotides (*pN, see structure) are useful substrates for the non-enzymatic synthesis of oligonucleotides. In the presence of metal ions, aqueous solutions of *pN yield primarily the two internucleotide-linked (pN2' pN and pN3' pN) and the pyrophosphate-linked (N5' ppN) dimers. Small amounts of cyclic dimers and higher oligomers are also produced. In this study the relative reactivity of 2'-OH vs. 3'-OH was determined from the ratio of the yields of pN2' pN vs. pN3' pN. Experiments were performed at 23 degrees C in the range 7.2 < or = pH < or = 8.4 with substrates that differ in nucleobase (guanosine (G), cytidine (C), uridine (U), and adenosine (A)) and leaving group (imidazole (Im), 2-methylimidazole (2-MeIm) and 2,4-dimethylimidazole (2,4-diMeIm)). Two metal ions (Mg2+ or Mn2+) were employed as catalysts. The conditions used here, i.e. a substrate concentration in the range 0.1 M to 1.0 M and metal ion concentration in the range 0.05 M to 0.2 M, favor base-stacking interactions. The ratio pN2' pN: pN3' pN = 2'-5': 3'-5' was found independent of nucleobase and typically varied between 2 to 3 indicating that the 2'-OH is about 2 to 3 times more reactive than the 3'-OH. *pN with Im, compared to 2-MeIm and 2,4-diMeIm leaving group, produce lower yields of internucleotide linked dimers, and a higher pN2' pN: pN3' pN ratio. Trends in the data, observed with all three leaving groups, suggest an increase in pN2' pN: pN3' pN ratio with decreasing substrate concentration (up to 5.47 with 0.051 M ImpG). The observations are in accord with earlier studies reporting a relative reactivity 2'-5': 3'-5' = 6 to 9 obtained with Im as the leaving group, in dilute nucleotide solutions and under conditions that disfavor stacking. It is speculated that the concentration induced change in the relative reactivity is the result of self-association via base-stacking that enhances selectively the proximity of the 3'-OH of one molecule to the reactive P-N bond of an other molecule. The implication of these conclusions for oligomerization/ligation reactions is discussed.

NASA Discipline Exobiology

Template-independent enzymatic synthesis of RNA oligonucleotides

Abstract RNA oligonucleotides have emerged as a powerful therapeutic modality to treat disease, yet current manufacturing methods may not be able to deliver on anticipated future demand. Here, we report the development and optimization of an aqueous-based, template-independent enzymatic RNA oligonucleotide synthesis platform as an alternative to traditional chemical methods. The enzymatic synthesis of RNA oligonucleotides is made possible by controlled incorporation of reversible terminator nucleotides with a common 3′-O-allyl ether blocking group using new CID1 poly(U) polymerase mutant variants. We achieved an average coupling efficiency of 95% and demonstrated ten full cycles of liquid phase synthesis to produce natural and therapeutically relevant modified sequences. We then qualitatively assessed the platform on a solid phase, performing enzymatic synthesis of severalN + 5 oligonucleotides on a controlled-pore glass support. Adoption of an aqueous-based process will offer key advantages including the reduction of solvent use and sustainable therapeutic oligonucleotide manufacturing.

Biotechnology & Applied Microbiology

Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Mononucleotides

Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2- methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2(+) in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MelmpU and 2-MelmpC produce about 65% of oligomers including 4% of the 3',5'-Iinked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of intemucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MelmpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

Kanavarioti, Anastassia

Aqueous Phase Non Enzymatic Chemistry of Cyanide, Formaldehyde and RNH2

It is postulated that amino acids were produced on the early earth from dilute aqueous solution of cyanide, carbonyls and ammonia (the Strecker synthesis RNH2 + R"R""C=O + KCN yields H-N(R)-C(R")(R"")-CO2H. We have studied the products obtained from dilute aqueous solutions of cyanide, formaldehyde (R"=R""=H), ammonia (R=H) and amino acids. Solutions in the pH range from 8 to 10. at room temperature and at reactant concentrations from 0.001 M to 0.3 M have been studied. With R= H product yields were low (less than 3%). Only with R"=R""=H and R represented by the following: CH2CO2H (glycine); CH(CH3)CO2H (alanine); CH(CH2CH3)CO2H (a-amino n=butyric acids); C(CH3)2(CO2H) (a-aminoisobutyric acid); CH(CH(CH3)2)CO2H (valine); and CH(CH2CO2H)CO2H (aspartic acid), were product yields high (greater than 10%). The yields of glycine were larger with R not equal to H. The prebiotic implications of these findings will be discussed.

Lerner, Narcinda R.

Experimental Shock Decomposition of Siderite to Magnetite

The debate about fossil life on Mars includes the origin of magnetites of specific sizes and habits in the siderite-rich portions of the carbonate spheres in ALH 84001 [1,2]. Specifically [2] were able to demonstrate that inorganic synthesis of these compositionally zoned spheres from aqueous solutions of variable ion-concentrations is possible. They further demonstrated the formation of magnetite from siderite upon heating at 550 C under a Mars-like CO2-rich atmosphere according to 3FeCO3 = Fe3O4 + 2CO2 + CO [3] and they postulated that the carbonates in ALH 84001 were heated to these temperatures by some shock event. The average shock pressure for ALH 84001, substantially based on the refractive index of diaplectic feldspar glasses [3,4,5] is some 35-40 GPa and associated temperatures are some 300-400 C [4]. However, some of the feldspar is melted [5], requiring local deviations from this average as high as 45-50 GPa. Indeed, [5] observes the carbonates in ALH 84001 to be melted locally, requiring pressures in excess of 60 GPa and temperatures > 600 C. Combining these shock studies with the above inorganic synthesis of zoned carbonates it seems possible to produce the ALH 84001 magnetites by the shock-induced decomposition of siderite.

Bell, M. S.

Scalable and adaptable two-ligand co-solvent transfer methodology for gold bipyramids to organic solvents

Large and faceted nanoparticles, such as gold bipyramids, presently require synthesis using alkyl ammonium halide ligands in aqueous conditions to stabilize the structure, which impedes subsequent transfer and suspension of such nanoparticles in low polarity solvents despite success with few nanometer gold nanoparticles of shapes such as spheres. Phase transfer methodologies present a feasible avenue to maintain colloidal stability of suspensions and move high surface energy particles into organic solvent environments. Here, we present a method to yield stable suspensions of gold bipyramids in low-polarity solvents, including methanol, dimethylformamide, chloroform, and toluene, through the requisite combination of two capping agents and the presence of a co-solvent. By utilizing PEG-SH functionalization for stability, dodecanethiol (DDT) as the organic-soluble capping agent, and methanol to aid in the phase transfer, gold bipyramids with a wide-range of aspect ratios and sizes can be transferred between water and chloroform readily and maintain colloidal stability. Subsequent transfer to various organic and low-polarity solvents is then demonstrated for the first time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Evidence that the protocell was also a protoneuron

A blueprint for a protocell was presented in 1960 (Fox) as a consequence of the newly discovered self-ordering of amino acids and the self-organization of the resultant thermal proteins into cellular structures. The biofunctions of the laboratory protocells (proteinoid microspheres) have since been cataloged; they display roots of many phenomena of modern cells, e.g. synthesis of internucleotide and peptide bonds in aqueous media. These results are inconsistent with a popular assumption that DNA/RNA preceded protein in earliest molecular evolution. The necessity for synthetic research on molecules and cells to 'begin at the beginning' is being realized. Ivanov and Fortsch (1986) have described by analysis how the self-ordering mechanism of amino acids into informed thermal proteins was conserved in evolution from the earliest stage as modern (reverse) mechanisms assumed control. Tyagi and Ponnamperuma (1990) have negated assumptions corollary to DNA/RNA. Ponnamperuma has demonstrated the powerful effect of self-ordering of amino acids in polymerization of aminoacyl nucleotides and the irrelevance of mononucleotide residues. Excitable thermal proteins (Vaughan et al, 1987) are neurotrophic and antiaging when added to cultures of real neurons (Hefti et al, 1991) and are memory enhancers in mice (Fox and Flood, 1992). Proteinoid microspheres of dominant hydrophobic constitution form 'gap junctions', sprout axon-like outgrowths, and form dendritic networks spontaneously. In the latest studies, phenylalanine-rich equimolar proteinoid or the leucine analog (Ishima et al 1981), is found to produce electrical signals for several days when lecithin is included in the assembly with the thermal polymer.

Bi, YU

Oxidative acylation using thioacids

Several important prebiotic reactions, including the coupling of amino acids into polypeptides by the formation of amide linkages, involve acylation. Theae reactions present a challenge to the understanding of prebiotic synthesis. Condensation reactions relying on dehydrating agents are either inefficient in aqueous solution or require strongly acidic conditions and high temperatures. Activated amino acids such as thioester derivatives have therefore been suggested as likely substrates for prebiotic peptide synthesis. Here we propose a closely related route to amide bond formation involving oxidative acylation by thioacids. We find that phenylalanine, leucine and phenylphosphate are acylated efficiently in aqueous solution by thioacetic acid and an oxidizing agent. From a prebiotic point of view, oxidative acylation has the advantage of proceeding efficiently in solution and under mild conditions. We anticipate that oxidative acylation should prove to be a general method for activating carboxylic acids, including amino acids.

Non-NASA Center

Prebiotic syntheses of purines and pyrimidines

The results of experimental and theoretical investigations of the prebiotic synthesis of purines and pyramidines are surveyed. Topics examined include the synthesis of purines from HCN via 4,5-disubstituted imidazole derivatives in aqueous solutions or liquid NH3, simultaneous formation of amino acids and purines by electron irradiation of CH4-NH3-H2O mixtures, synthesis of pyrimadines from cynoacetylene, energetics, formation of bases under anhydrous or concentrated conditions, formation of bases under dilute conditions, Fischer-Tropsch-type reactions, and the role of activated intermediates. It is pointed out that the precursor compounds have been detected in the interstellar medium, on Titan, and in other solar-system bodies, and that solar-nebula HCN concentrations of the order of 1-10 mM have been estimated on the basis of meteorite measurements.

Basile, B.

The contribution of cometary volatiles to the primitive earth

It has been estimated that during its early history the earth captured a mass of cometary material of the order of 10 to the 23rd grams. Since carbon is supposed to be at least three times more abundant in comets than in carbonaceous chondrites (3.5 percent C in C 1 chondrites), it can be deduced that about 1 x 10 to the 22nd grams of carbon (as carbon compounds), were added by comets to the surface of the prebiotic earth. This carbon value is of the same order of magnitude as the value of the organic carbon buried in the earth's sedimentary shell, but approximately one order of magnitude lower than the earth's surface total carbon (7 x 10 to the 22nd gm). The capture of comets by the earth would also have contributed to generating the appropriate aqueous and reducing environmental conditions necessary for organic synthesis.

Oro, J.

In-Situ Ligand-Induced Chirality Transfer in Emissive CdSe Nanoplatelets

Terminating semiconductor nanocrystals with chiral organic ligands can induce chiroptical properties that combine the chiral character of the ligands with the strong and tunable optical properties of the nanocrystal. However, the synthesis of such chiral-modified nanocrystals is currently limited by solvent incompatibility between polar chiral ligands and nonpolar traditional ligands, as well as by ligand dissolution behavior that ultimately compromises nanocrystal quality and the degree to which chiroptical properties can be manipulated. In this work, we demonstrate a single-step synthesis of chiral cadmium selenide (CdSe) nanoplatelets (NPLs) that eliminates the need for postsynthetic ligand exchange in aqueous solvents, resulting in highly emissive chiral CdSe NPLs. By directly incorporating chiral aminodecanoic acid ligands during synthesis, we achieve in situ ligand binding and chirality transfer to CdSe NPLs. This approach produces CdSe NPLs with high photoluminescence quantum efficiencies of 50% and circular dichroism dissymmetry factors (gCD) on the order of 10 –4 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Post synthetic amine functionalization of MOF-808 for CO 2 sorption via ligand exchange and Michael addition

Post synthetic modification of metal organic frameworks presents a viable route for amine functionalization which can significantly enhance CO 2 sorption capacity. We present a facile means of amine incorporation using limited synthetic steps and low-cost reagents that results in a high density of primary alkyl amines distributed through a zirconium-based metal organic framework (MOF). Both the MOF synthesis and the post synthetic modification take place under aqueous conditions and result in strongly bound molecular amines available for sorbate interaction throughout the MOF pores. Furthermore, this amine incorporation protocol results in a significantly increased CO 2 capacity compared with the unmodified MOF-808. Specifically, CO 2 isotherms collected at 298 K for the unmodified MOF-808 show uptakes of 0.06, 0.2, and 1.2 mmol/g at 4, 15, and 100 kPa, respectively, which can be compared with 0.3, 0.7, and 2.5 mmol/g for the glycine grafted MOF-808 and 0.5, 0.9, and 2.3 mmol/g for ethylenediamine grafted MOF-808.

Amine sorbent