Thermal stability of amino acids

Thermal decomposition of L-α-amino acids RCH₂(NH₂)COOH where R = Me₂CH, Me₂CHCH₂, MeEtCH, and C₆H₅CH₂ was studied at temperatures below the melting points of their crystals. From the effective rate constants of the first order reactions energy parameters in the Arrhenius equation were calculated. Correlations between the reaction rate constants k _R and the inductive constants σ* of substituents R and also between the rate constants of the reactions and the dipole moments of amino acids was established. Value of ρ* parameter +8.8 in the Taft equation indicates the heterolytic mechanism of transformation of the amino acids. Chromato-mass spectrometric analysis of decomposition products shows that condensation, decarboxylation, and deamination of the amino acids take place.     

Carbon nitride formation in gas-phase reactions of CH4, NH3 and H2: an ab initio study

Ab initio QCISD(T)/6-311++(2d,2p) calculations have been carried out for an extensive study of gas-phase reactions among CH₄, NH₃ and their radicals. Our study shows that stable HCN molecules are readily formed by successive H abstraction reactions. Some of the reactions are strongly exothermic and have negligible energy barriers. In agreement with some recent experiments, our results indicate that H abstraction reactions, which make the chemical vapor deposition of diamond thin films successful, do not favor the formation of carbon nitride thin films.     

Adsorption Sequence of Multifunctional Groups: A Study on the Reaction Pathway and the Adsorption Structure of Homocysteine on the Ge(100) Surface

We investigated the adsorption mechanism of homocysteine (HS? CH₂? CH₂? CH(NH₂)? COOH) on the Ge(100) surface along with its electronic structures and adsorption geometries to determine the sequence of adsorption of this amino acid′s functional groups using core‐level photoemission spectroscopy (CLPES) in conjunction with density functional theory (DFT) calculations. We found that the “SH‐dissociated OH‐dissociated N‐dative‐bonded structure” and the “SH‐dissociated OH‐dissociation‐bonded structure” were preferred at a monolayer (ML) coverage of 0.30 (lower coverage) and 0.60 (higher coverage), respectively. The “SH‐dissociated OH‐dissociated N‐dative‐bonded structure” was the most stable structure. Moreover, we systematically confirmed the sequence of adsorption of the functional groups of the homocysteine molecule on the Ge(100) surface, which is thiol group (? SH), carboxyl group (? COOH), and amine group (? NH₂).     

Electron driven processes in ices: Surface functionalization and synthesis reactions

The ability to control and orientate chemical reactivity in the condensed phase is a major challenge of modern research. Upon interaction with condensed molecules electrons drive bond cleavage thus generating a population of very reactive species in the condensed medium. These reactive species may interact either within the volume leading to the synthesis of new molecules or with the substrate surface by forming strong chemical bonds. The former reaction is known as electron induced synthesis and the latter one as electron induced surface functionalization.High-energy electrons achieve only a low chemical specificity due to the large number of dissociating open channels. In contrast, electrons with energies below ionization threshold of the irradiated matter are capable of high selectivity because of the dissociative electron attachment mechanism.In this review recent studies of electron interaction with condensed molecules on hydrogenated diamond substrates will be described. In particular electron induced functionalization of diamond surfaces by CH₂CN groups, decarboxylation reactions in condensed films of pure organic acids RCOOH (R = H, CH₃, C₂H₅, CF₃), carbamic acid formation in CO₂:NH₃, HCOOH:NH₃ and CF₃COOH:NH₃ binary ice mixtures, and glycine formation in a CH₃COOD:NH₃ mixture are presented and discussed.     

Metal Complexes of Biologically Important Ligands,CLXXVII. Dichlorido Platinum(II) and Palladium(II) Complexes with Long Chain Amino Acids and Amino Acid Amides

The synthesis of Cl₂Pt[NH₂(CH₂)_nCOOH]₂ (n = 5, 10) and the reactions of their carboxylic groups with H₂N(CH₂)₁₇CH₃, d ‐glucosamine, and (R,R)‐1,2‐diaminocyclohexane to give complexes with amino acid amides as ligands, are reported. Cl₂Pd(histidine) is coupled with amino alcohols to give Cl₂Pd(histidineamide) complexes.     

Towards Accurate Predictions of Proton NMR Spectroscopic Parameters in Molecular Solids

The factors contributing to the accuracy of quantum-chemical calculations for the prediction of proton NMR chemical shifts in molecular solids are systematically investigated. Proton chemical shifts of six solid amino acids with hydrogen atoms in various bonding environments (CH, CH₂, CH₃, OH, SH and NH₃) were determined experimentally using ultra-fast magic-angle spinning and proton-detected 2D NMR experiments. The standard DFT method commonly used for the calculations of NMR parameters of solids is shown to provide chemical shifts that deviate from experiment by up to 1.5 ppm. The effects of the computational level (hybrid DFT functional, coupled-cluster calculation, inclusion of relativistic spin-orbit coupling) are thoroughly discussed. The effect of molecular dynamics and nuclear quantum effects are investigated using path-integral molecular dynamics (PIMD) simulations. It is demonstrated that the accuracy of the calculated proton chemical shifts is significantly better when these effects are included in the calculations.     

Computational studies on the reactions of 3‐butenyl and 3‐butenylperoxy radicals

The reactions of 3‐butenyl (^?CH₂CH₂CH?CH₂) radicals—unimolecular decomposition, isomerization, as well as reaction with O₂—and the subsequent unimolecular rearrangement reactions of the 3‐butenylperoxy radicals have been investigated and are compared to the analogous reactions of butyl (^?CH₂CH₂CH₂CH₃) and butylperoxy radicals using transition‐state theory based on the quantum chemical calculations at the CBS‐QB3 level. For alkyl‐analogue processes, the reactions of 3‐butenyl and 3‐butenylperoxy radicals can be well characterized by the decreased and increased bond dissociation energies at the allylic and vinylic sites, respectively. The intramolecular addition reactions of the radical center atoms to the double bonds were found to be important non‐alkyl‐analogue reactions of 3‐butenyl and 3‐butenylperoxy radicals. As a consequence, the thermal decomposition of 3‐butenyl radicals was found to be slower than that of butyl radicals by one order of magnitude at temperature near 1000 K. Intramolecular addition reactions are suggested to be the predominant unimolecular rearrangement processes of 3‐butenylperoxy radicals over the entire temperature range investigated (500–1200 K). The intramolecular addition reactions of the alkenyl peroxy radicals, which have not been included in combustion kinetic models, and their implications for the autoignition of alkenes are discussed. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 273–288, 2010     

On the use of localized orbitals and restricted alternant orbitals in chemical systems

An analysis of the transformation of localized orbitals into restricted alternant orbitals is proposed. This approach has the advantage of expressing the wave-function in an orbital product while some electron correlation is introduced permitting the study of dissociation reactions. All applications of the orbital technique may be made as easily as with RHF, but with the additional possibility of studying chemical radicals. Some illustrations of this fact are shown for the molecules HF, H₂O, NH₃, CH₄, C₂H₆ and for the dissociation reactions of CH₄ and C₂H₆ generating CH₃ radicals.     

15N NMR spectral parameters of compounds of the N-methylpyrazole series

The¹⁵N NMR chemical shifts and¹⁵N-¹H SSCCs are presented for substituted N-methylpyrazoles with substituents such as CH₃, NO₂, Br, Cl, NH₂, O=CNH₂, O=CPh, and COOH at the carbon atoms. The¹⁵N chemical shifts of the cyclic atoms of nitrogen and the nitro groups are discussed as well as the geminal and vicinal SSCCs of the ring nitrogen atoms with the hydrogen atoms of the CH and CH₃ fragments.N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 117334 Moscow. D. I. Mendeleev Chemico-Technological Institute, Moscow, Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 11, pp. 2554–2561, November, 1992.     

A theoretical kinetic study of the reactions of NH2 radicals with methanol and ethanol and their implications in kinetic modeling

Amino (NH₂) radicals play a central role in the pyrolysis and oxidation of ammonia. Several reports in the literature highlight the importance of the reactions of NH₂ radicals with fuel in NH₃-dual-fuel combustion. Therefore, we investigated the reactions of NH₂ radicals with methanol (CH₃OH) and ethanol (C₂H₅OH) theoretically. We explored the various reaction pathways by exploiting CCSD(T)/cc-pV(T, Q)Z//M06-2X/aug-cc-pVTZ level of theory. The reaction proceeds via complex formation at the entrance and exit channels in an overall exothermic process. We used canonical transition state theory to obtain the high-pressure limiting rate coefficients for various channels over the temperature range of 300–2000 K. We discerned the role of various channels in the potential energy surface (PES) of NH₂ + CH₃OH/C₂H₅OH reactions. For both reactions, the hydrogen abstraction pathway at the OH-site of alcohols plays a minor role in the entire T-range investigated. By including the title reactions into an extensive kinetic model, we demonstrated that the reaction of NH₂ radicals with alcohols plays a paramount role in accurately predicting the low-temperature oxidation kinetics of NH₃-alcohols dual fuel systems (e.g., shortening the ignition delay time). On the contrary, these reactions have negligible importance for high-temperature oxidation kinetics of NH₃-alcohol blends (e.g., not affecting the laminar flame speed). In addition, we calculated the rate coefficients for NH₂ + CH₄ = CH₃ + NH₃ reaction that are in excellent agreement with the experimental data.     

Sur quelques réactions par décharge électrique dans les systèmes phosphine-eau,phosphine-eau-ammoniac et phosphine-eau-ammoniac-méthane

Electric discharge reactions in the systems PH₃ + H₂O, PH₃ + H₂O + NH₃ and PH₃ + H₂O + NH₃ + CH₄ have been studied. In the system PH₃ + H₂O, they produce polyphosphines (insoluble in water) and hypophosphorous, phosphorous and orthophosphoric acids. In the system PH₃ + H₂O + NH₃, besides the above products, hypophosphate, pyrophosphate, polyphosphates and possibly polyhyphosphates are also present. In the system PH₃ + H₂O + NH₃ + CH₄, besides all the above inorganic P compounds, organic phosphorus derivatives such as aminoalkyl phosphates and aminoalkanephosphonates are also formed, as well as other non-phosphorus containing organic products (amino acids, ethanolamine, etc.). The presence of phosphine (or its transformation products), seems to promote condensation reactions in this system since the ratio of amino acids found after hydrolysis (in 6N HCl) to amino acids found before hydrolysis is greater in this system. than in the system (CH₄+ H₂O+ NH₃)iiot containing phosphine.     

ELECTRONIC EFFECTS OF DONOR AND ACCEPTOR SUBSTITUENTS ON DIPYRIDO(3,2-a:2′,3′-c)PHENAZINE (dppz)

Abstract

The chelate ligands 11-R-dipyrido[3,2-a:2′,3′-c]phenazine, dppz-R (R = NH₂, CH₃, H, COOH, NO₂) and the Re(dppz-R)(CO)₃Cl (R = NH₂, COOH, NO₂) complexes were synthesized and characterized by conventional techniques. The influence of the donor and acceptor properties of the R substituents on the ligand properties were studied by spectroscopic techniques such as ¹H-NMR and UV-Vis. Theoretical calculations were also achieved, mainly to interpret and understand the experimental spectra.     

On the role of solvent in complexation equilibiria. II. The acid-base chemistry of some sulfhydryl and ammonium-containing amino acids in water—acetonitrile mixed solvents

The macroscopic and microscopic acid-base chemistry of a series of sulfhydryl and ammonium-containing amino acids HS–R–NH₃ [R=–CH₂CH(COOH)–, cysteine (CYS); R=–C(CH₃)₂CH(COOH)–, penicillamine (PEN); R=–CH(COOH)CH₂CH₂CONHCH(–CH₂)CONHCH₂COOH, glutathione (GSH)] was characterized in water and its binary mixtures with acetonitrile (16.3, 34.2, and 53.9 mass % acetonitrile). Macroscopic acid dissociation constants were obtained by potentiometric titration using the glass-calomel electrode pair. Microscopic acid dissociation constants were calculated from ultraviolet absorption measurements at ca. 232 nm where the deprotonated sulfhydryl group absorbs. The macroscopic constants decrease uniformly as the solvent becomes enriched in acetonitrile. The microscopic constants, which characterize the relative concentrations of the two monoprotonated tautomers of the molecules (I and II) reveal that as the solvent becomes enriched in acetonitrile, the fraction of molecules existing as highly charged tautomer I decreases for CYS (0.68–0.40), PEN (0.85–0.34), and GSH (0.61–0.30). These results are related to the decreasing concentration of water as the solvent becomes enriched in acetonitrile.     

Solid-state chlorodecarboxylation of mono- and dicarboxylic acids with the Pb(OAc)<Subscript>4</Subscript>-MCl system

Solid state reactions of acids RCOOH (R = n-C₇H₁₅, BuC(Et)H, n-C₉H₁₉, PhCH₂, PhCH₂CH₂, H₂C=CH(CH₂)₈, or MeOOC(CH₂)₃) with Pb(OAc)₄ combined with KCl, NaCl, CdCl₂, or NH₄Cl in the absence of a solvent and without mechanical activation afford chlorohydrocarbons RCl. The corresponding reactions of acids HOOC(CH₂)_nCOOH (n = 3–6) give dichloroalkanes Cl(CH₂)_nCl and γ-butyrolactone (n = 3).__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2105–2109, October, 2004.     

Water-catalyzed isomerization of the glycine radical cation. From hydrogen-atom transfer to proton-transport catalysis

The isomerization reactions of the glycine radical cation, from [NH₂CH₂COOH]⁺, I, to [NH₃CHCOOH]⁺, II, or [NH₂CHC(OH)₂]⁺, III, in the presence of a water molecule have been studied theoretically. The water molecule reduces dramatically the energy barriers of the III and IIII tautomerizations owing to a change in the nature of the process. However, the role of the water molecule depends on the kind of isomerization, the catalytic effect being more important for the IIII reaction. As a consequence, the preferred mechanism for the interconversion of glycine radical cation I to the stablest isomer, III, is the direct one-step mechanism instead of the two step (III and IIIII) process found for isolated [NH₂CH₂COOH]⁺. When using ammonia as a solvent molecule, a spontaneous proton-transfer process from [NH₂CH₂COOH]⁺ to NH₃ is observed and so no tautomerization reactions take place. This behavior is the same as that observed in aqueous solution, as has been confirmed by continuum model calculations.Contribution to the Jacopo Tomasi Honorary Issue     

Estimation of the excitation and ionization energies of NH4, H3O and H2F radicals using core analogies applied to K-shell electron energy loss spectra

Energy levels and ionization potentials for the NH₄, H₃O and H₂F radicals are predicted using core analogies applied to the K-shell electron energy loss spectra of CH₄, NH₃ and H₂O, respectively. In the case of the ammonium radical (NH₄) excellent agreement is obtained with the results from theoretical calculations.     

Hydrogen-Bonding Interaction in a Complex of Amino Acid with <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethylformamide Studied by DFT Calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine and leucine) and N,N-dimethylformamide (DMF) in gas phase have been carried out using density functional theory (DFT) and ab initio calculations at the B3LYP/6-311++G** and MP2/6-311++G** theory levels. The structures, binding energy, stretching frequency and bond characteristics of the mentioned complexes were calculated. The NH₂ and COOH groups of amino acids form different types of hydrogen bonds with the DMF molecule, as well as alkyl side chains. High binding energy suggests multiple hydrogen bonds present in one complex. The nearly linear OH???O and NH???O contacts are stronger than a conventional hydrogen bond interaction with their H???O separation between 1.74 and 2.14 Å. The weaker CH???O H-bond is also discussed as being a crucial interaction in biological systems involving amino acids. The formation of this interaction results in a blue shift in the CH stretching frequency.     

A Multicoincidence Study of Fragmentation Dynamics in Collision of γ‐Aminobutyric Acid with Low‐Energy Ions

Fragmentation of the γ‐aminobutyric acid molecule (GABA, NH₂(CH₂)₃COOH) following collisions with slow O⁶⁺ ions (v≈0.3 a.u.) was studied in the gas phase by a combined experimental and theoretical approach. In the experiments, a multicoincidence detection method was used to deduce the charge state of the GABA molecule before fragmentation. This is essential to unambiguously unravel the different fragmentation pathways. It was found that the molecular cations resulting from the collisions hardly survive the interaction and that the main dissociation channels correspond to formation of NH₂CH₂⁺, HCNH⁺, CH₂CH₂⁺, and COOH⁺ fragments. State‐of‐the‐art quantum chemistry calculations allow different fragmentation mechanisms to be proposed from analysis of the relevant minima and transition states on the computed potential‐energy surface. For example, the weak contribution at [M?18]⁺, where M is the mass of the parent ion, can be interpreted as resulting from H₂O loss that follows molecular folding of the long carbon chain of the amino acid.     

Quantum Chemical Studies on Solvents for Post‐Combustion Carbon Dioxide Capture: Calculation of pKa and Carbamate Stability of Disubstituted Piperazines

Piperazine is a widely studied solvent for post‐combustion carbon dioxide capture. To investigate the possibilities of further improving this process, the electronic and steric effects of ?CH₃, ?CH₂F, ?CH₂OH, ?CH₂NH₂, ?COCH₃, and ?CN groups of 2,5‐disubstituted piperazines on the pK_a and carbamate stability towards hydrolysis are investigated by quantum chemical methods. For the calculations, B3LYP, M11L, and spin‐component‐scaled MP2 (SCS‐MP2) methods are used and coupled with the SMD solvation model. The experimental pK_a values of piperazine, 2‐methylpiperazine, and 2,5‐dimethylpiperazine agree well with the calculated values. The present study indicates that substitution of ?CH₃, ?CH₂NH₂, and ?CH₂OH groups on the 2‐ and 5‐positions of piperazine has a positive impact on the CO₂ absorption capacity by reducing the carbamate stability towards hydrolysis. Furthermore, their higher boiling points, relative to piperazine itself, will lead to a reduction of volatility‐related losses.     

A quantum chemistry study of ruthenabenzene complexes

The electronic structure and properties of the ruthenabenzenes and substituted ruthenabenzenes have been explored using the hybrid density functional B3LYP theory. Systematic studies on the substituent effect in para-substituted ruthenabenzenes complexes have been studied. The following substituents were taken into consideration: H, NO₂, CN, CHO, COOH, F, CH₃, OH, and NH₂. Basic measures of aromatic character were derived from the structure and nucleus-independent chemical shift (NICS). The NICS calculations indicate a correlation between NICS(1.5) and the hardness in all species. The atoms in molecule analysis indicates a correlation between r(Ru-C) bonds and the electron density of bond critical point in all species.