Conformational memory in photodissociation of formic acid

The trans and cis forms of formic acid (HCOOH) in solid argon favor essentially different photodissociation (193 nm) products, H2O + CO and H2 + CO2, respectively. The branching ratio of these channels differs between the two conformers by a factor of >10. The observed selective photodissociation features conformational memory when the transition state of a molecule is reached before torsional randomization. These data demonstrate that the photodissociation products can be efficiently steered with selective narrow-band infrared radiation promoting rotational isomerism, which makes a strong case of optically controlled chemical reactions     

A matrix infrared study of association of formamide

The association of formamide has been studied in argon. In the spectral region from 800 to 200 cm⁻¹ several characteristic bands due to association were found and assigned to the out-of-plane bending modes of the NH group. The widths of these low-frequency bands are of the same order of magnitude as those of the fundamental bands of the monomer. By comparing the spectra of self-associated species with spectra of heteroassociated species between formamide and N,N-dimethyl formamide, it was possible to assign association bands to the open dimers as well as to the cyclic dimers. A band appearing upon warming at about 230 cm⁻¹ has been assigned to a H-bond stretching mode. The results indicate that dimers trapped from the gas phase are predominantly open, and that both open and cyclic structures are formed upon diffusion-controlled association in the matrix.     

Formation of HXeO in a xenon matrix: indirect evidence of production, trapping, and mobility of XeO (1(1)Sigma+) in solid Xe

IR spectroscopy, laser induced fluorescence (LIF), and thermoluminescence (TL) measurements have been combined to monitor trapping, thermal mobility, and reactions of oxygen atoms in solid xenon. HXeO and O(3) have been used as IR active species that probe the reactions of oxygen atoms. N(2)O and H(2)O have been used as precursors for oxygen atoms by photolysis at 193 nm. Upon annealing of matrices after photolysis, ozone forms at two different temperatures: at 18-24 K from close O ...O(2) pairs and at approximately 27 K due to global mobility of oxygen atoms. HXeO forms at approximately 30 K reliably at higher temperature than ozone. Both LIF and TL show activation of oxygen atoms around 30 K. Irradiation at 240 nm after the photolysis at 193 nm depletes the oxygen atom emission at 750 nm and reduces the amount of HXeO generated in subsequent annealing. Part of the 750 nm emission can be regenerated by 266 nm and this process increases the yield of HXeO in annealing as well. Thus, we connect oxygen atoms emitting at 750 nm with annealing-induced formation of HXeO radicals. Ab initio calculations at the CCSD(T)/cc-pV5Z level show that XeO (1(1)Sigma(+)) is much more deeply bound [D(e) = 1.62 eV for XeO --> Xe+O((1)D)] than previous calculations have predicted. Taking into account the interactions with the medium in an approximate way, it is estimated that XeO (1(1)Sigma(+)) has a similar energy in solid xenon as compared with interstitially trapped O((3)P) suggesting that both possibly coexist in a low temperature solid. Taking into account the computational results and the behavior of HXeO and O(3) in annealing and irradiations, it is suggested that HXeO may be formed from singlet oxygen atoms which are trapped in a solid as XeO (1(1)Sigma(+)).     

Insertion of noble gas atoms into cyanoacetylene: an ab initio and matrix isolation study

A computational and experimental matrix isolation study of insertion of noble gas atoms into cyanoacetylene (HCCCN) is presented. Twelve novel noble gas insertion compounds are found to be kinetically stable at the MP2 level of theory, including four molecules with argon. The first group of the computationally studied molecules belongs to noble gas hydrides (HNgCCCN and HNgCCNC), and we found their stability for Ng = Ar, Kr, and Xe. The HNgCCCN compounds with Kr and Xe have similar stability to that of previously reported HKrCN and HXeCN. The HArCCCN molecule seems to have a weaker H-Ar bond than in the previously identified HArF molecule. The HNgCCNC molecules are less stable than the HNgCCCN isomers for all noble gas atoms. The second group of the computational insertion compounds, HCCNgCN and HCCNgNC, are of a different type, and they also are kinetically stable for Ng = Ar, Kr, and Xe. Our photolysis and annealing experiments with low-temperature cyanoacetylene/Ng (Ng = Ar, Kr, and Xe) matrixes evidence the formation of two noble gas hydrides for Ng = Kr and Xe, with the strongest IR absorption bands at 1492.1 and 1624.5 cm(-1), and two additional absorption modes for each species are found. The computational spectra of HKrCCCN and HXeCCCN fit most closely the experimental data, which is the basis for our assignment. The obtained species absorb at quite similar frequencies as the known HKrCN and HXeCN molecules, which is in agreement with the theoretical predictions. No strong candidates for an Ar compound are observed in the IR absorption spectra. As an important side product of this work, the data obtained in long-term decay of KrHKr+ cations suggest a tentative assignment for the CCCN radical.     

Formation and structural characterization of novel polynuclear palladium selenolato complexes [Pd3Se(SePh)3(PPh3)3]Cl and [Pd6Cl2Se4(SePh)2(PPh3)6]

In addition to well-known dinuclear phenylselenolato palladium complexes, the reaction of [PdCl₂(PPh₃)₂] and NaSePh affords small amounts of novel trinuclear and hexanuclear complexes [Pd₃Se(SePh)₃(PPh₃)₃]Cl (1) and [Pd₆Cl₂Se₄(SePh)₂(PPh₃)₆] (2). Complex 1 is triclinic, P1?, a=13.6310(2), b=16.2596(2), c=16.9899(3) Å, α=83.1738(5), β=78.9882(5), γ=78.7635(5)°. Complex 2 is monoclinic, C2/c, a=25.7165(9), b=17.6426(8), c=27.9151(14) Å, β=110.513(2)°. There are no structural forerunners for 1, but the hexanuclear complex 2 is isostructural with [Pd₆Cl₂Te₄(TeR)₂(PPh₃)₆] (R=Ph, C₄H₃S) that have been observed as one of the products in the oxidative addition of R₂Te₂ to [Pd(PPh₃)₄]. Mononuclear palladium complexes may play a significant role as building blocks in the formation of the polynuclear complexes.     

Ab initio and density functional theory reinvestigation of gas-phase sulfuric acid monohydrate and ammonium hydrogen sulfate

We have calculated the thermochemical parameters for the reactions H(2)SO(4) + H(2)O <--> H(2)SO(4).H(2)O and H(2)SO(4) + NH(3) <--> H(2)SO(4).NH(3) using the B3LYP and PW91 functionals, MP2 perturbation theory and four different basis sets. Different methods and basis sets yield very different results with respect to, for example, the reaction free energies. A large part, but not all, of these differences are caused by basis set superposition error (BSSE), which is on the order of 1-3 kcal mol(-1) for most method/basis set combinations used in previous studies. Complete basis set extrapolation (CBS) calculations using the cc-pV(X+d)Z and aug-cc-pV(X+d)Z basis sets (with X = D, T, Q) at the B3LYP level indicate that if BSSE errors of less than 0.2 kcal mol(-1) are desired in uncorrected calculations, basis sets of at least aug-cc-pV(T+d)Z quality should be used. The use of additional augmented basis functions is also shown to be important, as the BSSE error is significant for the nonaugmented basis sets even at the quadruple-zeta level. The effect of anharmonic corrections to the zero-point energies and thermal contributions to the free energy are shown to be around 0.4 kcal mol(-1) for the H(2)SO(4).H(2)O cluster at 298 K. Single-point CCSD(T) calculations for the H(2)SO(4).H(2)O cluster also indicate that B3LYP and MP2 calculations reproduce the CCSD(T) energies well, whereas the PW91 results are significantly overbinding. However, basis-set limit extrapolations at the CCSD(T) level indicate that the B3LYP binding energies are too low by ca. 1-2 kcal/mol. This probably explains the difference of about 2 kcal mol(-1) for the free energy of the H(2)SO(4) + H(2)O <--> H(2)SO(4).H(2)O reaction between the counterpoise-corrected B3LYP calculations with large basis sets and the diffusion-based experimental values of S. M. Ball, D. R. Hanson, F. L Eisele and P. H. McMurry (J. Phys. Chem. A. 2000, 104, 1715). Topological analysis of the electronic charge density based on the quantum theory of atoms in molecules (QTAIM) shows that different method/basis set combinations lead to qualitatively different bonding patterns for the H(2)SO(4).NH(3) cluster. Using QTAIM analysis, we have also defined a proton transfer degree parameter which may be useful in further studies.     

Heterogeneous multicomponent nucleation theorems for the analysis of nanoclusters

In this paper we present a new form of the nucleation theorems applicable to heterogeneous nucleation. These heterogeneous nucleation theorems allow, for the first time, direct determination of properties of nanoclusters formed on pre-existing particles from measured heterogeneous nucleation probabilities. The theorems can be used to analyze the size (first theorem) and the energetics (second theorem) of heterogeneous clusters independent of any specific nucleation model. We apply the first theorem to the study of small water and n-propanol clusters formed at the surface of 8 nm silver particles. According to the experiments the size of the two-component critical clusters is found to be below 90 molecules, and only less than 20 molecules for pure water, less than 300 molecules for pure n-propanol. These values are drastically smaller than the ones predicted by the classical nucleation theory, which clearly indicates that the nucleating clusters are too small to be quantitatively described using a macroscopic theory.     

Homogeneous single-label tyrosine kinase activity assay for high throughput screening

Protein post-translational modifications (PTMs) are regulatory mechanisms carried out by different enzymes in a cell. Kinase catalyzed phosphorylation is one of the most important PTM affecting the protein activity and function. We have developed a single-label quenching resonance energy transfer (QRET) assay to monitor tyrosine phosphorylation in a homogeneous high throughput compatible format. Epidermal growth factor receptor (EGFR) induced phosphorylation was monitored using Eu³⁺-chelate labeled peptide and label-free phosphotyrosine specific antibody in presence of a soluble quencher molecule. In the QRET kinase assay, antibody binding to phosphorylated Eu³⁺-peptide protects the Eu³⁺-chelate from luminescence quenching, monitoring high time-resolved luminescence (TRL) signals. In the presence of specific kinase inhibitor, antibody recognition and Eu³⁺-chelate protection is prevented, allowing an efficient luminescence quenching. The assay functionality was demonstrated with a panel of EGFR inhibitors (AG-1478, compound 56, erlotinib, PD174265, and staurosporine). The monitored IC₅₀ values ranged from 0.08 to 155.3 nM and were comparable to those found in the literature. EGFR activity and inhibition assays were performed using low nanomolar enzyme and antibody concentration in a 384-well plate format, demonstrating its compatibility for high throughput screening (HTS).     

A homogeneous quenching resonance energy transfer assay for the kinetic analysis of the GTPase nucleotide exchange reaction

A quenching resonance energy transfer (QRET) assay for small GTPase nucleotide exchange kinetic monitoring is demonstrated using nanomolar protein concentrations. Small GTPases are central signaling proteins in all eukaryotic cells acting as a “molecular switches” that are active in the GTP-state and inactive in the GDP-state. GTP-loading is highly regulated by guanine nucleotide exchange factors (GEFs). In several diseases, most prominently cancer, this process in misregulated. The kinetics of the nucleotide exchange reaction reports on the enzymatic activity of the GEF reaction system and is, therefore, of special interest. We determined the nucleotide exchange kinetics using europium-labeled GTP (Eu-GTP) in the QRET assay for small GTPases. After GEF catalyzed GTP-loading of a GTPase, a high time-resolved luminescence signal was found to be associated with GTPase bound Eu-GTP, whereas the non-bound Eu-GTP fraction was quenched by soluble quencher. The association kinetics of the Eu-GTP was measured after GEF addition, whereas the dissociation kinetics could be determined after addition of unlabeled GTP. The resulting association and dissociation rates were in agreement with previously published values for H-Ras^Wt, H-Ras^Q61G, and K-Ras^Wt, respectively. The broader applicability of the QRET assay for small GTPases was demonstrated by determining the kinetics of the Ect2 catalyzed RhoA^Wt GTP-loading. The QRET assay allows the use of nanomolar protein concentrations, as more than 3-fold signal-to-background ratio was achieved with 50 nM GTPase and GEF proteins. Thus, small GTPase exchange kinetics can be efficiently determined in a HTS compatible 384-well plate format.