Theoretical Study of Hydration of Cyanamide and Carbodiimide

Energy Landscape and Structural and Spectroscopic Characterization of Diazirine and Its Cyclic Isomers

Identifying new nitrogenated hydrocarbon molecules in the interstellar medium (ISM) is challenging because of the lack of comprehensive spectroscopic data from experiments. In this computational work, we focus on investigating the structures, relative energies, spectroscopic constants, and energy landscape of the cyclic isomers of diazirine (c-CH2N2) using ab initio quantum chemical methods. Density functional theory (DFT) methods and coupled cluster theory with singles and doubles including perturbative triples [CCSD(T)] and CCSD(T) with the explicitly correlated F12b correction [CCSD(T)-F12b] were employed for this purpose along with large correlation consistent cc-pVTZ, cc-pVQZ, and cc-pV5Z basis sets. Harmonic vibrational frequencies, infrared vibrational intensities, rotational constants, and dipole moments are reported. Anharmonic vibrational fundamentals along with centrifugal distortion constants, and vibration-rotation interaction constants are also reported for all the cyclic isomers. The energies computed with the CCSD(T) and CCSD(T)-F12b methods were extrapolated to the one-particle complete basis set (CBS) limit following a three-point formula. At the CCSD(T)-F12b/CBS level of theory, the 3,3H-diazirine (c-CH2N2) is the lowest energy cyclic isomer followed by 1,3H-diazirine, (E)-1,2H-diazirine, and (Z)-1,2H-diazirine, which are 20.1, 47.8, and 51.3 kcal mol-1 above the 3,3H-diazirine, respectively. Accurate structures and spectroscopic constants that are reported here could be useful for future identification of these cyclic nitrogenated organic molecules in the interstellar medium or circumstellar disks.

Chemical fuels for molecular machinery

Chemical reaction networks that transform out-of-equilibrium 'fuel' to 'waste' are the engines that power the biomolecular machinery of the cell. Inspired by such systems, autonomous artificial molecular machinery is being developed that functions by catalysing the decomposition of chemical fuels, exploiting kinetic asymmetry to harness energy released from the fuel-to-waste reaction to drive non-equilibrium structures and dynamics. Different aspects of chemical fuels profoundly influence their ability to power molecular machines. Here we consider the structure and properties of the fuels that biology has evolved and compare their features with those of the rudimentary synthetic chemical fuels that have so far been used to drive autonomous non-equilibrium molecular-level dynamics. We identify desirable, but context-specific, traits for chemical fuels together with challenges and opportunities for the design and invention of new chemical fuels to power synthetic molecular machinery and other dissipative nanoscale processes.

A theoretical insight into the curing mechanism of phthalonitrile resins promoted by aromatic amines

High-temperature phthalonitrile resins have a wide range of applications, and understanding their curing mechanism is of great importance for academic research and engineering applications. However, the actual curing mechanism is still elusive. We presented a density functional theory study on the curing mechanism of phthalonitrile resins promoted by aromatic amines using phthalonitrile and aniline as the model compounds. We found that the rate-determining step is the initial nucleophilic addition of amines with nitrile groups on phthalonitrile to generate an amidine intermediate. The amines play a vital role in the H-transfer promoter throughout the curing reaction. The amidine and isoindoline are the critical intermediates, which can readily react with phthalonitrile through 6-membered transition states. The intramolecular cyclization of amidine intermediates is the vital step in forming isoindoline intermediates, which can be significantly promoted by amines. The proposed curing reaction pathways are kinetically more favorable than the previously reported ones, which can account for the formation of triazine, polyisoindoline, and phthalocyanine and provide a molecular-level understanding of the curing reaction.

Theoretical Study of Possible Reaction Mechanisms for the Formation of Carbodiimide in the Interstellar Medium (ISM) and Polarizabilities of Carbodiimide

The Structure of carbodiimide has been studied by using quantum chemical methods. Carbodiimide (HNCNH) has been detected towards Sagittarius B2 (N) in interstellar medium (ISM). Two reaction mechanisms have been proposed to study the formation of interstellar Carbodiimide. The first reaction mechanism is based on molecule-radical and the second one is a radical-radical mechanism, through previously detected interstellar molecules or radicals. Quantum chemical calculations have been performed by using density functional theory (DFT) and Moller-Plesset second order perturbation (MP2) theory, in gas phase as well as in polarizable continuum model (PCM). The proposed reaction paths are exothermic and barrierless which indicates the possibility of carbodiimide formation in ISM. Several basis sets have been used to verify the validity and accuracy of the results. The isotropic and anisotropic polarizabilities of carbodiimide have been calculated from relevant tensor components for both reaction mechanisms with the help of data obtained by DFT/B3LYP and MP2 methods using aug-cc-pVTZ basis sets in gaseous phase as well as in PCM.

How Prebiotic Chemistry and Early Life Chose Phosphate

The very specific thermodynamic instability and kinetic stability of phosphate esters and anhydrides impart them invaluable properties in living organisms in which highly efficient enzyme catalysts compensate for their low intrinsic reactivity. Considering their role in protein biosynthesis, these properties raise a paradox about early stages: How could these species be selected in the absence of enzymes? This review is aimed at demonstrating that considering mixed anhydrides or other species more reactive than esters and anhydrides can help in solving the paradox. The consequences of this approach for chemical evolution and early stages of life are analysed.

Formation of Cyanamide-Glyoxal Oligomers in Aqueous Environments Relevant to Primeval and Astrochemical Scenarios: A Spectroscopic and Theoretical Study

The condensation of cyanamide and glyoxal, two well-known prebiotic monomers, in an aqueous phase has been investigated in great detail, demonstrating the formation of oligomeric species of varied structure, though consistent with generalizable patterns. This chemistry involving structurally simple substances also illustrates the possibility of building molecular complexity under prebiotically plausible conditions, not only on Earth, but also in extraterrestrial scenarios. We show that cyanamide-glyoxal reactions in water lead to mixtures comprising both acyclic and cyclic fragments, largely based on fused five- and six-membered rings, which can be predicted by computation. Remarkably, such a mixture could be identified using high-resolution electrospray ionization (ESI) mass spectrometry and spectroscopic methods. A few mechanistic pathways can be postulated, most involving the intermediacy of glyoxal cyanoimine and further chain growth, thus increasing the diversity of the observed products. This rationale is supported by theoretical analyses with clear-cut identification of all of the stationary points and transition-state structures. The properties and structural differences of oligomers obtained under thermodynamic conditions in water as opposed to those isolated by precipitation from organic media are also discussed.

Prebiotic-Like Condensations of Cyanamide and Glyoxal: Revisiting Intractable Biotars

We report a detailed investigation into the nature of products that are generated by the reactions of cyanamide and glyoxal, two small molecules of astrochemical and prebiotic significance, under different experimental conditions. The experimental data suggest that the formation of oligomeric structures is related in part to the formation of insoluble tholins in the presence of oxygen-containing molecules. Although oligomerization proceeds well in water, product isolation turned out to be impractical. Instead, solid precipitates were obtained easily in acetone. Crude mixtures have been thoroughly scrutinized by spectroscopic methods, in particular NMR and mass spectroscopy (ESI mode), which are all consistent with the generation of a few functional groups that are embedded into regular chains of five- and six-membered rings, thereby pointing to a supramolecular organization. Three different models of cross-condensation and chain growth are suggested. These synthetic explorations provide further insights into the formation of complex organic matter in interstellar scenarios and extraterrestrial bodies that might have played a pivotal role in chemical evolution.

Prebiotic Lipidic Amphiphiles and Condensing Agents on the Early Earth

It is still uncertain how the first minimal cellular systems evolved to the complexity required for life to begin, but it is obvious that the role of amphiphilic compounds in the origin of life is one of huge relevance. Over the last four decades a number of studies have demonstrated how amphiphilic molecules can be synthesized under plausibly prebiotic conditions. The majority of these experiments also gave evidence for the ability of so formed amphiphiles to assemble in closed membranes of vesicles that, in principle, could have compartmented first biological processes on early Earth, including the emergence of self-replicating systems. For a competitive selection of the best performing molecular replicators to become operative, some kind of bounded units capable of harboring them are indispensable. Without the competition between dynamic populations of different compartments, life itself could not be distinguished from an otherwise disparate array or network of molecular interactions. In this review, we describe experiments that demonstrate how different prebiotically-available building blocks can become precursors of phospholipids that form vesicles. We discuss the experimental conditions that resemble plausibly those of the early Earth (or elsewhere) and consider the analytical methods that were used to characterize synthetic products. Two brief sections focus on phosphorylating agents, catalysts and coupling agents with particular attention given to their geochemical context. In Section 5, we describe how condensing agents such as cyanamide and urea can promote the abiotic synthesis of phospholipids. We conclude the review by reflecting on future studies of phospholipid compartments, particularly, on evolvable chemical systems that include giant vesicles composed of different lipidic amphiphiles.

Low energy electron attachment to cyanamide (NH2CN)

Cyanamide (NH2CN) is a molecule relevant for interstellar chemistry and the chemical evolution of life. In the present investigation, dissociative electron attachment to NH2CN has been studied in a crossed electron-molecular beams experiment in the electron energy range from about 0 eV to 14 eV. The following anionic species were detected: NHCN(-), NCN(-), CN(-), NH2(-), NH(-), and CH2(-). The anion formation proceeds within two broad electron energy regions, one between about 0.5 and 4.5 eV and a second between 4.5 and 12 eV. A discussion of possible reaction channels for all measured negative ions is provided. The experimental results are compared with calculations of the thermochemical thresholds of the anions observed. For the dehydrogenated parent anion, we explain the deviation between the experimental appearance energy of the anion with the calculated corresponding reaction threshold by electron attachment to the isomeric form of NH2CN--carbodiimide.

5(4H)-oxazolones as intermediates in the carbodiimide- and cyanamide-promoted peptide activations in aqueous solution

The early days: although considered a species to be avoided in peptide chemistry, the intermediacy of 5(4H)-oxazolones is demonstrated to be essential for the formation of peptides through cyanamide and carbodiimide activation in aqueous solution.

Pathways for the formation and evolution of peptides in prebiotic environments

α-Amino acids are easily accessible through abiotic processes and were likely present before the emergence of life. However, the role they could have played in the process remains uncertain. Chemical pathways that could have brought about features of self-organization in a peptide world are considered in this review and discussed in relation with their possible contribution to the origin of life. An overall scheme is proposed with an emphasis on possibilities that may have led to dynamically stable far from equilibrium states. This analysis defines new lines of investigation towards a better understanding of the contribution of the systems chemistry of amino acids and peptides to the emergence of life.

DFT and MP2 investigations of L-proline and its hydrated complexes

A theoretical study of L-proline-nH(2)O (n = 1-3) has been performed using the hybrid DFT-B3LYP and MP2 methods together with the 6-311++G(d,p) basis set. The results show that the P2 conformer is energetically favorable when forming a hydrated structure, and the hydration of the carboxyl group leads to the greatest stability. For hydrated complexes, the adiabatic and vertical singlet-triplet excitation energies tend to decrease with the addition of water molecules. The hydration energy indicates that in the hydrated complexes the order of stability is: binding site 2 > binding site 1 > binding site 3, and binding site 12 > binding site 23 > binding site 13. As water molecules are added, the stabilities of these hydrated structures gradually increase. In addition, an infrared frequency analysis indicated that there are some differences in the low-frequency range, which are mainly dominated by the O-H stretching or bending vibrations of different water molecules. All of these results should aid our understanding of molecular behavior and provide reference data for further studies of biological systems.

Ammonia elimination from protonated nucleobases and related synthetic substrates

The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH(3) elimination does present a major path for the fragmentations of the ions [1h + H](+), [2h + H](+), and [3h + H](+). The ion [2h + H - NH(3)](+) also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH(2) replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15-55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate's best protonation site, and possible mechanisms for NH(3) elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.

Photochemical dehydration of acetamide in a cryogenic matrix

Vacuum ultraviolet (VUV) irradiation of acetamide has been monitored by Fourier transform infrared spectroscopy in argon matrix at 10 K. Several primary photoproducts, including HNCO ratio CH(4) and CO ratio CH(3)NH(2) molecular complexes, and acetimidic acid, which is reported for the first time, were characterized. The acetimidic acid identification was based on comparison between the experimental and theoretical (B3LYP) infrared spectra. Acetimidic acid is found in argon matrix in the (s-Z)-(E) and (s-Z)-(Z) configurations. It is also an intermediate in the VUV decomposition process, its dehydration leads to the formation of CH(3)CN ratio H(2)O molecular complex. The assignment of the complex was achieved by co-depositing the pairs of respective species and by ab initio calculation.

Mechanism of Formation of Organic Carbonates from Aliphatic Alcohols and Carbon Dioxide under Mild Conditions Promoted by Carbodiimides. DFT Calculation and Experimental Study

Dicyclohexylcarbodiimide (CyN=C=NCy, DCC) promotes the facile formation of organic carbonates from aliphatic alcohols and carbon dioxide at temperatures as low as 310 K and moderate pressure of CO2 (from 0.1 MPa) with an acceptable rate. The conversion yield of DCC is quantitative, and the reaction has a very high selectivity toward carbonates at 330 K; increasing the temperature increases the conversion rate, but lowers the selectivity. A detailed study has allowed us to isolate or identify the intermediates formed in the reaction of an alcohol with DCC in the presence or absence of carbon dioxide. The first step is the addition of alcohol to the cumulene (a known reaction) with formation of an O-alkyl isourea [RHNC(OR')=NR] that may interact with a second alcohol molecule via H-bond (a reaction never described thus far). Such an adduct can be detected by NMR. In alcohol, in absence of CO2, it converts into a carbamate and a secondary amine, while in the presence of CO2, the dialkyl carbonate, (RO)2CO, is formed together with urea [CyHN-CO-NHCy]. The reaction has been tested with various aliphatic alcohols such as methanol, ethanol, and allyl alcohol. It results in being a convenient route to the synthesis of diallyl carbonate, in particular. O-Methyl-N,N'-dicyclohexyl isourea also reacts with phenol in the presence of CO2 to directly afford for the very first time a mixed aliphatic-aromatic carbonate, (MeO)(PhO)CO. A DFT study has allowed us to estimate the energy of each intermediate and the relevant kinetic barriers in the described reactions, providing reasonable mechanistic details. Calculated data match very well the experimental results. The driving force of the reaction is the conversion of carbodiimide into the relevant urea, which is some 35 kcal/mol downhill with respect to the parent compound. The best operative conditions have been defined for achieving a quantitative yield of carbonate from carbodiimide. The role of temperature, pressure, and catalysts (Lewis acids and bases) has been established. As the urea can be reconverted into DCC, the reaction described in this article may further be developed for application to the synthesis of organic carbonates under selective and mild conditions.

Vacuum Ultraviolet (VUV) Photodecomposition of Urea Isolated in Cryogenic Matrix: First Detection of Isourea

Vacuum ultraviolet (VUV) irradiation at wavelengths of lambda > 160 nm of urea-h4 (NH2CONH2) and urea-d4 (ND2COND2) has been monitored by Fourier transform infrared spectroscopy in argon and xenon matrixes. Several primary photoproducts, such as HNCO:NH3 (isocyanic acid:ammonia), CO:N2H4 (carbon monoxide:hydrazine) molecular complexes, and isourea (H2N(OH)C=NH), which is reported for the first time, were characterized. The assignment of complexes was achieved by co-depositing the pairs of respective species, whereas the isourea identification was based on the comparison between the experimental and theoretical (B3LYP) infrared spectra. Isourea is found in the argon matrix in its most stable (s-Z)-(E) configuration. It is an intermediate in the VUV decomposition process; its dehydration leads to the NH2CN:H2O complex. In the xenon matrix, the photochemistry of urea yields the HNCO:NH3 complex as a major product, whereas the CO:N2H4 complex is observed in trace amounts. The observed differences between the argon and xenon matrixes suggest the crossing between S1 and T1 potential surfaces of urea to be responsible for the formation of the HNCO:NH3 complex. A comparison is also performed with other carboxamides, such as formamide (HCONH2) or acetamide (CH3CONH2).

Hydration of the carbonyl group — Acetic acid catalysis in the co-operative mechanism

In a co-operative reaction, solvent molecules, specifically water molecules, participate actively in the mechanism to circumvent the formation of charged intermediates. This paper extends our earlier theoretical treatment of the neutral co-operative hydration of acetone to include general acid catalysis by acetic acid. As before, the predominant neutral channel employs three catalytic water molecules. The principal acetic acid catalyzed channels employ one catalytic water molecule and, in approximately equal proportions, one or both oxygens of the carboxyl group. The theoretical rate constant for general acid catalysis is calculated to be 0.49 M–1s–1at 298 K. This compares to an estimated experimental value of 0.30 M–1s–1for acetic acid catalyzed hydration of acetone at 298 K in water solvent, determined by using the18O-isotope shift in the13C NMR spectrum of 2-13C-labelled acetone as a kinetic probe. It is concluded that the notion of co-operativity can be extended to include general acid catalysis of the hydration of a carbonyl group in water solvent. This creates an obvious problem for the generally accepted view that multistep ionic mechanisms are operative in the low dielectric media that exist at the active sites of hydrolytic enzymes. The relevance of this finding to the mechanisms of action of β-lactam antibiotics has been noted.Key words: hydration, reaction mechanism, co-operativity, general acid catalysis, ab initio, SCRF,18O-isotope shift.

Carbodiimide Production from Cyanamide by UV Irradiation and Thermal Reaction on Amorphous Water Ice

Cyanamide (NH(2)CN), an interstellar molecule, is a relevant molecule in prebiotic chemistry, because it can be converted into urea in liquid water. Carbodiimide (HNCNH), the most stable cyanamide isomer, is able to assemble amino acids into peptides. In this work, using FTIR spectroscopy, we show that carbodiimide can be formed from cyanamide at low temperature (10 K), by a photochemical process in argon matrix, in water matrix, or in solid film. We also report experimental evidence about the carbodiimide formation when cyanamide is condensed at low temperature (50-140 K) on an amorphous water ice surface, or when it is trapped in the water ice. The water ice acts as a catalyst. This isomerization reaction occurs at low temperature (T < 100 K), which agrees with those expected in the interstellar clouds composed of dust grains in which water is the most predominant compound. Finally, the hydrolysis reaction of cyanamide or carbodiimide leading to urea or isourea formation is not observed under our experimental conditions.

Experimental study of water-ice catalyzed thermal isomerization of cyanamide into carbodiimide: implication for prebiotic chemistry

Cyanamide (NH2CN) is a molecule of interstellar interest which can be implied in prebiotic chemistry. We showed, by FTIR spectroscopy, that cyanamide can be isomerized in carbodiimide (HNCNH), another interstellar relevant molecule, by a reaction involving the amorphous water-ice surface as catalyst. This isomerization occurs at low temperature (T < 100 K) which agrees quite well with that expected in the interstellar clouds composed of dust grains in which water is the most predominant constituent.

5-Cyanoamino-4-imidazolecarboxamide and nitrosative guanine deamination: experimental evidence for pyrimidine ring-opening during deamination

5-Cyanoamino-4-imidazolecarboxamide 4a (R = CH2-O-CH2-CH2-OH) has been synthesized, purified, and fully characterized by MS, MS/MS, HRMS, IR spectroscopy, and by 1H and 13C NMR spectroscopy. It is shown that cyclization of 4a yields the guanine 6a and the isoguanine 12a. Our findings provide experimental evidence in support of our hypothesis that the formation of oxanine and xanthine in nitrosative guanine deamination may proceed via pyrimidine ring-opened intermediates. The observed formation of 6a from the amide 4a (XH2 = NH2) shows that, in analogy, oxanine can be formed from 3 (XH = OH). The formation of 12a from 4a reveals for the first time the possibility that oxanine might be formed by a second pathway that involves electrocyclic reaction of 3. Finally, the new chemistry suggests the possibility for a new dG-to-dG cross-link.

The Hydrolysis of Urea and the Proficiency of Urease

We present the results of a computational study of the solution phase decomposition of urea, which provides insight into probable reaction pathways for the urease-catalyzed reaction. Calculations, which were used to derive thermodynamic parameters that were further used for a kinetic analysis, have been done at the solvent-corrected MP2/6-311++G** level. Both elimination and hydrolytic pathways have been considered. Elimination is favored for the solution phase reaction, which proceeds by H-bond coordination of a water molecule to the amine nitrogen atoms. The coordination of one water molecule greatly facilitates the reaction by allowing it to proceed through a cyclic six-member transition state. Aspects of the water-urea H-bond interactions have also provided insights into critical aspects of the hydrogen bond pattern in the urease active site. On the basis of a kinetic analysis, we have estimated the proficiency of urease and have predicted that it is the most proficient enzyme identified to date.

5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazole and Nitrosative Guanine Deamination. A Theoretical Study of Geometries, Electronic Structures, and N-Protonation

The 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole 1 (R = H), its N1-derivatives 2 (R = Me) and 3 (R = MOM) and their cyano-N (4, 6, 8) and imino-N protonated (5, 7, 9) derivatives were studied with RHF, B3LYP, and MP2 theory. Solvation effects were estimated with the isodensity polarized continuum model (IPCM) at the MP2 level using the dielectric constant of water. Carbodiimide 10, cyanamide 12, N-cyanomethyleneimine 13, and its protonated derivatives 14 and 15 were considered for comparison as well. Adequate theoretical treatment requires the inclusion of dispersion because of the presence of intramolecular van der Waals, charge-dipole, and dipole-dipole (including H-bonding) interactions. All conformers were considered for the MOM-substituted systems, and direct consequences on the preferred site of protonation were found. The vicinal push (oxomethylene)-pull (cyanoimino) pattern of the 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazoles results in the electronic structure of aromatic imidazoles with 4-acylium and 5-cyanoamido groups. The gas-phase proton affinities of 1-3 are over 30 kcal/mol higher than that for N-cyanomethyleneimine 13, and this result provides compelling evidence in support of the zwitterionic character of 1-3. Protonation enhances the push-pull interaction; the OC charge is increased from about one-half in 1-3 to about two-thirds in the protonated systems. In the gas phase, cyano-N protonation is generally preferred but imino-N protonation can compete if the R-group contains a suitable heteroatom (hydrogen-bond acceptor, Lewis base). In polar solution, however, imino-N protonation is generally preferred. Solvation has a marked consequence on the propensity for protonation. Whereas protonation is fast and exergonic in the gas phase, it is endergonic in the polar condensed phase. It is an immediate consequence of this result that the direct observation of the cations 8 and 9 should be possible in the gas phase only.

Tailor-made strong exchange magnetic coupling through very long bridging ligands: theoretical predictions

Computational methods based on density functional theory have been applied to a prospective study of dinuclear transition metal complexes that may show strong exchange coupling interactions through very long bridging ligands. The results indicate that M(III) complexes (being M= Cr, Mn or Fe) with dicyanamidobenzene-type ligands are specially promising for this purpose, since strong ferromagnetic or antiferromagnetic coupling is predicted between paramagnetic metal cations at distances as long as 25 A. The existence of ferromagnetic or antiferromagnetic coupling in the complexes with the different isomers of dicyanamidobenzene can be rationalized in terms of molecular orbitals.