Biomedical subjects

Mark R Nimlos

Publications and source records attributed to Mark R Nimlos.

7 recordsLinked to original sources

PubMed2006

Energetics of xylose decomposition as determined using quantum mechanics modeling.

The decomposition of xylose has been studied using quantum mechanical calculations supported by NMR data. Proposed mechanisms for the decomposition of xylose have been investigated by obtaining the structures and energies of transition states and products. The intent of this study was to understand the experimentally observed formation of furfural and formic acid that occurs during the decomposition of xylose in mildly hot acidic solutions. A mechanism of furfural formation involving the opening of the pyranose ring and subsequent dehydration of the aldose was compared to a direct intramolecular rearrangement of the protonated pyranose. Energies were determined using CBS-QB3, and it was shown that the barriers for dehydration of the aldose were high compared to intramolecular rearrangement. This result suggests that the latter mechanism is a more likely mechanism for furfural formation. The intramolecular rearrangement step results from protonation of xylose at the O2 hydroxyl group. In addition, it has been shown that formic acid formation is a likely result of the protonation of xylose at the O3 hydroxyl group. Finally, solvation of xylose decomposition was studied by calculating energy barriers for xylose in selected water clusters. The mechanisms proposed here were supported in part by 13C-labeling studies using NMR.

Formates↗

PubMed2006

Mechanisms of glycerol dehydration.

Dehydration of neutral and protonated glycerol was investigated using quantum mechanical calculations (CBS-QB3). Calculations on neutral glycerol show that there is a high barrier for simple 1,2-dehydration, E(a)=70.9 kcal mol(-1), which is lowered to 65.2 kcal mol(-1) for pericyclic 1,3-dehydration. In contrast, the barriers for dehydration of protonated glycerol are much lower. Dehydration mechanisms involving hydride transfer, pinacol rearrangement, or substitution reactions have barriers between 20 and 25 kcal mol(-1). Loss of water from glycerol via substitution results in either oxirane or oxetane intermediates, which can inter-convert over a low barrier. Subsequent decomposition of these intermediates proceeds via either a second dehydration step or loss of formaldehyde. The computed mechanisms for decomposition of protonated glycerol are supported by the gas-phase fragmentation of protonated glycerol observed using a triple--quadrupole mass spectrometer.

Desiccation↗

PubMed2006

Infrared absorption spectra of matrix-isolated cis, cis-HOONO and its ab initio CCSD(T) anharmonic vibrational bands.

The infrared absorption spectra of matrix-isolated cis, cis-peroxynitrous acid (HOONO and DOONO) in argon have been observed. Six of the nine fundamental vibrational modes for cis, cis-HOONO have been assigned definitively, and one tentatively. Coupled-cluster, ab initio anharmonic force field calculations were used to help guide some of the assignments. The experimental matrix frequencies (cm(-1)) for cis, cis-HOONO are (a' modes) nu1 = 3303+/-1, nu2 = 1600.6+/-0.6, nu3 = 1392+/-1, nu4 = 922.8+/-0.5, nu5 = 789.7+/-0.4, nu6 = 617+/-1; and (a" mode) nu8 = 462+/-1. The fundamentals for the deuterated isotopomer, cis, cis-DOONO, are (a' modes) nu1 = 2447.2+/-0.6, nu2 = 1595.7+/-0.7, nu3 = 1089.1+/-0.4, nu4 = 888.1+/-0.4, nu5 = 786.6+/-0.5, nu6 = 613.9+/-0.9; and (a" mode) nu8 = 456.5+/-0.5.

Journal Article↗

PubMed2005

Hydrogen atom mediated Stone-Wales rearrangement of pyracyclene: a model for annealing in fullerene formation.

We have investigated the Stone-Wales (SW) rearrangement of pyracyclene (C(14)H(12)) using quantum mechanical molecular modeling. Of particular interest in this study is the effect of an added hydrogen atom on the barriers to SW rearrangement. Hydrogen atoms are found in high abundance during combustion, and their effect upon isomerization of aromatic compounds to more stable species may play an important role in the combustion synthesis of fullerenes. We have calculated the barriers for the SW rearrangement in pyracyclene using density functional theory B3LYP/6-31G(d) and B3LYP/6-311G(d,p). Two mechanisms have been investigated: (i) a mechanism with two identical transition states of C(1) symmetry and a cyclobutyl intermediate and (ii) a mechanism with one transition state containing an sp(3) carbon (J. Am. Chem. Soc. 2003, 125, 5572-5580; Nature 1993, 366, 665-667). We find that the barriers for these mechanisms are 120.0 kcal mol(-1) for the cyclobutyl mechanism and 130.1 kcal mol(-1) for the sp(3) mechanism. Adding a hydrogen atom to the internal bridge carbon atoms of pyracyclene reduces the barrier of the cyclobutyl mechanisms to 67.0 kcal mol(-1) and the sp(3) mechanism to 73.1 kcal mol(-1). The bonding of carbon atoms in pyracyclene is similar to those found in isomers of C(60), and the barriers are low enough so that these reactions can become significant during fullerene synthesis in flames. Adding hydrogen atoms to the external bridge atoms on pyracyclene produces a smaller reduction in the SW barrier and adding hydrogen atoms to nonbridge external carbon atoms results in no reduction of the barrier.

Journal Article↗

PubMed2005

Ab initio molecular dynamics simulations of beta-D-glucose and beta-D-xylose degradation mechanisms in acidic aqueous solution.

Ab initio molecular dynamics simulations were employed to investigate, with explicit solvent water molecules, beta-D-glucose and beta-D-xylose degradation mechanisms in acidic media. The rate-limiting step in sugar degradation was found to be protonation of the hydroxyl groups on the sugar ring. We found that the structure of water molecules plays a significant role in the acidic sugar degradation pathways. Firstly, a water molecule competes with the hydroxyl group on the sugar ring for protons. Secondly, water forms hydrogen bonds with the hydroxyl groups on the sugar rings, thus weakening the C-C and C-O bonds (each to a different degree). Note that the reaction pathways could be altered due to the change of relative stability of the C-C and C-O bonds. Thirdly, water molecules that are hydrogen-bonded to sugar hydroxyls could easily extract a proton from the reaction intermediate, terminating the reaction. Indeed, the sugar degradation pathway is complex due to multiple protonation probabilities and the surrounding water structure. Our experimental data support multiple sugar acidic degradation pathways.

Computer Simulation↗

PubMed2005

Propargyl radical: ab initio anharmonic modes and the polarized infrared absorption spectra of matrix-isolated HCCCH2.

The propargyl radical has twelve fundamental vibrational modes, gamma(vib)(HCCCH2) = 5a1 [symbol: see text] 3b1 [symbol: see text] 4b2, and nine have been detected in a cryogenic matrix. Ab initio coupled-cluster anharmonic force field calculations were used to help guide some of the assignments. The experimental HC=:C-:CH2 matrix frequencies (cm(-1)) and polarizations are a1 modes--3308.5 +/- 0.5, 3028.3 +/- 0.6, 1935.4 +/- 0.4, 1440.4 +/- 0.5, 1061.6 +/- 0.8; b1 modes--686.6 +/- 0.4, 483.6 +/- 0.5; b2 modes--1016.7 +/- 0.4, 620 +/- 2. We recommend a complete set of gas-phase vibrational frequencies for the propargyl radical, HC=:C-:CH2 2 X (2)B1. From an analysis of the vibrational spectra, the small electric dipole moment, mu(D)(HCCCH2) = 0.150 D, and the large resonance energy (HCCCH2), roughly 11 kcal mol(-1), we conclude that propargyl is a completely delocalized hydrocarbon radical and is best written as HC=:C-:CH2.

Journal Article↗

PubMed2005

Acidic sugar degradation pathways: an ab initio molecular dynamics study.

Ab initio molecular dynamics (MD) simulations were employed to elucidate xylose and glucose degradation pathways. In the case of xylose, a 2,5-anhydride intermediate was observed leading to the formation of furfural through elimination of water. This pathway agrees with one of the mechanisms proposed in the literature in that no open chain intermediates were found. In the case of glucose, a series of intermediates were observed before forming the 2,5-anhydride intermediate that eventually leads to hydroxymethylfurfural (HMF). One of these intermediates was a very short-lived open-chain form. Furthermore, two novel side-reaction pathways were identified, which lead to degradation products other than HMF.

Anhydrides↗