Vibrational spectroscopy of protonated imidazole and its complexes with water molecules: ab initio anharmonic calculations and experiments

The results of anharmonic frequency calculations on neutral imidazole (C3N2H4, Im), protonated imidazole (ImH+), and its complexes with water (ImH+)(H2O)n, are presented and compared to gas phase infrared photodissociation spectroscopy (IRPD) data. Anharmonic frequencies are obtained via ab initio vibrational self-consistent field (VSCF) calculations taking into account pairwise interactions between the normal modes. The key results are: (1) Prediction of anharmonic vibrational frequencies on an MP2 ab initio potential energy surface show excellent agreement with experiment and outstanding improvement over the harmonic frequencies. For example, the ab initio calculated anharmonic frequency for (ImH+)(H2O)N2 exhibits an overall average percentage error of 0.6% from experiment. (2) Anharmonic vibrational frequencies calculated on a semiempirical potential energy surface fitted to ab initio harmonic data represents spectroscopy well, particularly for water complexes. As an example, anharmonic frequencies for (ImH+)H2O and (ImH+)(H2O)2 show an overall average deviation of 1.02% and 1.05% from experiment, respectively. This agreement between theory and experiment also supports the validity and use of the pairwise approximation used in the calculations. (3) Anharmonic coupling due to hydration effects is found to significantly reduce the vibrational frequencies for the NH stretch modes. The frequency of the NH stretch is observed to increase with the removal of a water molecule or replacement of water with N2. This result also indicates the ability of the VSCF method to predict accurate frequencies in a matrix environment. The calculation provides insights into the nature of anharmonic effects in the potential surface. Analysis of percentage anharmoncity in neutral Im and ImH+ shows a higher percentage anharmonicity in the NH and CH stretch modes of neutral Im. Also, we observe that anharmonicity in the NH stretch modes of ImH+ have some contribution from coupling effects, while that of neutral Im has no contribution whatsoever from mode-mode coupling. It is concluded that the incorporation of anharmonic effects in the calculation brings theory and experiment into much closer agreement for these systems.     

Anharmonic vibrational calculations modeling the raman spectra of intermediates in the photoactive yellow protein (PYP) photocycle

The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C8-C9 stretching mode nu29 (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C9-O2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.     

Dynamic Coupling at the Ångström Scale

While momentum transfer from active particles to their immediate surroundings has been studied for both synthetic and biological micron‐scale systems, a similar phenomenon was presumed unlikely to exist at smaller length scales due to the dominance of viscosity in the ultralow Reynolds number regime. Using diffusion NMR spectroscopy, we studied the motion of two passive tracers—tetramethylsilane and benzene—dissolved in an organic solution of active Grubbs catalyst. Significant enhancements in diffusion were observed for both the tracers and the catalyst as a function of reaction rate. A similar behavior was also observed for the enzyme urease in aqueous solution. Surprisingly, momentum transfer at the molecular scale closely resembles that reported for microscale systems and appears to be independent of swimming mechanism. Our work provides new insight into the role of active particles on advection and mixing at the Ångström scale.     

Flexible Hierarchical TiO2/Fe2O3 Composite Membrane with High Separation Efficiency for Surfactant‐Stabilized Oil‐Water Emulsions

Globally, efficient oil‐water separation for surfactant‐stabilized oil‐water emulsions has been in urgent demand. The current options available for separation are neither sustainable nor resistant to fouling. Herein, we introduce a hierarchically nanostructured TiO₂/Fe₂O₃ composite membrane, which is capable of separating surfactant‐stabilized oil‐water emulsions with high separation efficiency. The high oil rejection rate is contributed by the acquisition of an interconnected delicate network and underwater superoleophobic interface. Meanwhile, its self‐cleaning function promote the facile recovery of the contaminated membrane. Furthermore, the mechanical flexible characteristic of the TiO₂/Fe₂O₃ composite membrane widens its applicability in industrial employment. Thanks to these properties, this novel membrane can be considered as a practical option for treating surfactant‐stabilized oil‐water emulsions.     

On triazoles XIX: The reaction of 5-amino-1,2,4-triazoles with functionalized acetoacetic esters

Summary Different functionalized alkyl 3-oxo-butyrates (2) were reacted with 5-amino-3-Q-1H-1,2,4-triazoles (1) to yield3 and4 type 1,2,4-triazolo[1,5-a]pyrimidinones. In case of2 (R ¹=methyl,R ²=1-ethoxycarbonylethyl,R ³=ethyl) beside the corresponding derivative4 the unexpected 5,6-dihydro-6,8-dimethyl-7-ethoxycarbonyl-3-methylthio-1,2,4-triazolo[4,3-a]-1,3-diazepin-5(9H)-one (7) was isolated, representing a novel ring system.

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Über Triazole, 19. Mitt.: Die Reaktion von 5-Amino-1,2,4-triazolen mit funktionalisierten Acetoessigestern

Zusammenfassung Verschiedene funktionalisierte 3-Oxo-buttersäurealkylester (2) wurden mit 5-Amino-3-Q-1H-1,2,4-triazolen (1) umgesetzt, wobei 1,2,4-Triazolo[1,5-a]pyrimidinone der Typen3 und4 erhalten wurden. Im Fall von2 (R ¹=Methyl,R ²=1-Ethoxycarbonylethyl,R ³=Ethyl) wurde neben dem erwarteten Derivat4 das unerwartete 5,6-Dihydro-6,8-dimethyl-7-ethoxycarbonyl-3-me-thylthio-1,2,4-triazolo[4,3-a]-1,3-diazepin-5(9H)-on (7) isoliert, welches ein neues Ringsystem darstellt.

     

Syntheses and conformational analyses of some 3-amino-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine derivatives: X-ray crystal structure of 35–3-[[(1,1-dimethylethoxy)carbonyl]amino]-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine

The constrained dipeptide mimic 1 was synthesized from 2 in three steps with 65% overall yield. Analyses of the ¹H nmr data of a number of 3-amino-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine derivatives led to the conclusion that these compounds adopt a similar conformation and that this ring system is rigid. X-ray crystallography was used to define the structure of 3 , and computer-aided energy minimization of 6 gave a preferred conformation similar to that observed in the crystal of 3 .     

Effect of water on the low temperature conductivity of polymer electrolytes

The proton conductivity of radiation-grafted ethylenetetrafluoroethylene-grafted-poly(styrene sulfonic) acid (ETFE-g-PSSA) and Nafion 117 membranes between 25 and -37 degrees C is reported. The freezing of water in the membranes, which strongly depends on the internal acid concentration, results in a 4-fold decrease in proton conductivity. The activation energies before and after the freezing of the membranes are approximately 0.15 and 0.4 eV, consistent with proton transport through liquid water and strongly bound water, respectively. Differential scanning calorimetry data show that up to 14 H(2)O molecules per H(+)/SO(3)(-) group remain unfrozen at subzero temperatures and are believed to be responsible for the low temperature conductivity that is observed. These results indicate that proton conductivity in membranes may be achieved via strongly bound and highly polarized water.     

Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.     

Vibrational spectroscopy of the G...C base pair: experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.