Density functional theory study of 1:1 glycine–water complexes in the gas phase and in solution

We present a systematic study of 1:1 glycine-water complexes involving all possible glycine conformers. The complex geometries are fully optimized for the first time both in the gas phase and in solution using three DFT methods (B3LYP, PBE1PBE, X3LYP) and the MP2 method. We calculate the G3 energies and use them as the reference data to gauge hydrogen bond strength in the gas phase. The solvent effects are treated via the integral equation formalism-polarizable continuum model (IEF-PCM). Altogether, we loca...     

Calculated vertical ionization energies of the common α-amino acids in the gas phase and in solution

The vertical ionization energies of the low-lying conformers of the α-amino acids found in proteins have been calculated. Geometry optimizations were first performed at the B3LYP/6-311G(d,p) level of theory, and then reoptimized at the MP2/6-311G(d,p) level of theory. Vertical ionization energies were then computed by three methods, electron propagator in the partial third-order (P3) approximation, Outer-Valence-Green's Functions, and by evaluating the difference in the total energy between the cation radical and the neutral amino acid in the geometry of the neutral species. When available, the results are compared to the experimental vertical ionization energies. The vertical ionization energies calculated using the MP2/P3 method gave the best overall agreement with the experimental results. Next, the ionization energies in solution are calculated for the zwitterionic forms of the α-amino acids by using IEFPCM methods. To obtain the vertical ionization energy in solution, it is necessary to use the nonequilibrium polarizable continuum model (NEPCM), the results of which are reported here for the α-amino acids.     

Direct and indirect photoinduced gas–liquid phase transitions

The condensation of supersaturated vapors of various substances in air under UV irradiation in a cloud chamber has been studied. The irradiation and subsequent photodissociation greatly facilitate the condensation of vapors in comparison with unirradiated mixtures, wherein both a vapor that directly absorbs radiation (direct photoinduced phase transition) and, for example, water vapor in the presence of photodissociating impurities (indirect photoinduced transition) can be condensed.     

Ab initio study of tautomerism and hydrogen bonding of β-carbonylamine in the gas phase and in water solution

All the possible conformations of the three tautomeric isomers of simple β-carbonylamine were fully optimized at ab initio MP2/6-31G** and B3LYP/6-31G** levels in order to determine the conformational equilibrium and the energies of the O—H···N and O···H—N hydrogen bridges. For the most interesting conformations, further calculations in water solution were also carried out. It was found that carbonylamine is the most stable tautomer, followed by enolimine and carbonylimine. This order of stability does not change in solution. O—H···N is the strongest hydrogen bridge, but in solution its energy as well as that of the O···H—N one are dramatically lowered. The deprotonation energy was also calculated and discussed. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 5 June 2000     

Cation–ether complexes in the gas phase: thermodynamic insight into molecular recognition

Trends in the bond dissociation energies for the binding of the alkali metal cations, Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺, to a series of ethers, 1–4 dimethyl ethers, 1 and 2 dimethoxy ethanes, and the crown ethers, 12c4, 15c5, and 18c6, are discussed. The bond energies have been determined in previous studies by analysis of the thresholds for collision-induced dissociation of the cation–ether complexes by xenon as measured in a guided ion beam tandem mass spectrometer. Details of the analysis of the data are reviewed and the accuracy of the results ascertained by comparison with theoretical results taken from the literature. Combined, the experimental and theoretical results provide an extensive thermochemical database for evaluation of the metal-crown complexes, a simple example of molecular recognition. These results indicate the importance of optimizing the metal–oxygen bond distances and the orientation of the local dipole on the oxygen towards the metal. Further, it is shown that excited state conformers of these complexes are probably observed in several systems as a result of interesting metal-dependent dynamics in the formation of the complexes.     

UV photolysis of α-cyclohexanedione in the gas phase

Ultraviolet absorption spectrum of α-cyclohexanedione (α-CHD) vapor in the wavelength range of 220-320 nm has been recorded in a 1 m long path gas cell at room temperature. With the aid of theoretical calculation, the band has been assigned to the S(2) ← S(0) transition of largely ππ* type. The absorption cross section at the band maximum (～258 nm) is nearly 3 orders of magnitude larger compared to that for the S(2) ← S(0) transition of a linear α-diketo prototype, 2,3-pentanedione. The photolysis was performed by exciting the sample vapor near this band maximum, using the 253.7 nm line of a mercury vapor lamp, and the products were analyzed by mass spectrometry as well as by infrared spectroscopy. The identified products are cyclopentanone, carbon monoxide, ketene, ethylene, and 4-pentenal. Geometry optimization at the CIS/6-311++G** level predicts that the carbonyl group is pyramidally distorted in the excited S(1) and S(2) states, but the α-CHD ring does not show dissociative character. Potential energy curves with respect to a ring rupture coordinate (C-C bond between two carbonyl groups) for S(0), S(1), S(2), T(1), T(2), and T(3) states have been generated by partially optimizing the ground state geometry at DFT/B3LYP/6-311++G** level and calculating the vertical transition energies to the excited states by TDDFT method. Our analysis reveals that the reactions can take place at higher vibrational levels of S(0) as well as T(1) states.     

Experimental validation of the α-effect in the gas phase

The α-effect-enhanced nucleophilicity of an anion with a lone pair of electrons adjacent to the attacking atom-has been well documented in solution; however, there is continuing disagreement about whether this effect is a purely solvent-induced phenomenon or an intrinsic property of the α-nucleophiles. To resolve these discrepancies, we explore the α-effect in the bimolecular nucleophilic substitution reaction in the gas phase. Our results show enhanced nucleophilicity for HOO(-) relative to "normal" alkoxides in three separate reaction series (methyl fluoride, anisole, and 4-fluoroanisole), validating an intrinsic origin of the α-effect. Caution must be employed when making comparisons of the α-effect between the condensed and gas phases due to significant shifts in anion basicity between these media. Variations in electron affinities and homolytic bond strengths between the normal and α-anions indicate that HOO(-) has distinctive thermochemical properties.     

μSr studies of free radicals in the gas phase

Muonium (Mu=₊+e^-) is the bound state of a positive muon and an electron. Since the positive muon has a mass about 1/9 of the proton, Mu can be regarded as an ultra light isotope of hydrogen with unusually large mass ratios (MuHDT=1/9123). The muon spin rotation technique (SR) relies on the facts that (1) the muon produced in pion decay, ^{+ +} + , is 100% spin polarized and (2) the positron from muon decay is emitted preferentially along the instantaneous muon spin direction at the time of the muon decay.In transverse field SR (TF-SR), the precession of the muon spin in muonium substituted radicals is directly observed by detecting decay positrons time differentially. From observed radical frequencies, the hyperfine coupling constants (A ) of C₂H₄Mu, C₂D₄Mu,¹³C₂H₄Mu, C₂F₄Mu, and C₂H₃FMu are determined. In the longitudinal field avoided level crossing (LF-ALC) technique, one observes the resonant loss of the muon spin polarization caused by the crossing of hyperfine levels at particular magnetic fields. The LF-ALC method together with the information onA obtained from TF-SR allows one to determine the magnitude and sign of the nuclear hyperfine constants at - and -positions. Results are compared with hydrogen substituted ethyl-radicals and isotope effects are discussed.     

Thermal properties of chlorosulfonated polyethylene via gas–solid phase method

The thermal properties of chlorosulfonated polyethylene (CSM), which was prepared via gas–solid phase method, were studied in this article. The thermal curves were completely tested by differential thermal analysis, thermogravimetry, and differential thermogravimetry. The results showed that CSM 3550 and CSM 3570 prepared by gas–solid phase method had more excellent thermal properties (high initial/final temperature of degradation) than those via solution method, due to the uniform chlorine distribution of them in macromolecular chain. The differential scanning calorimetry curves showed that the transitions of CSM 3550 and CSM 3570 from glassy to the elastic state were also higher than those via solution method. Particularly, CSM 3570 was amorphous and no clear melting peak was observed during the melting process.     

Melt–gas phase equilibria and state diagrams of the selenium–tellurium system

The partial pressures of saturated vapor of the components in the Se–Te system are determined and presented in the form of temperature–concentration dependences from which the boundaries of the melt–gas phase transition are calculated at atmospheric pressure and vacuums of 2000 and 100 Pa. The existence of azeotropic mixtures is revealed. It is found that the points of inseparably boiling melts correspond to 7.5 at % of Se and 995°C at 101325 Pa, 10.9 at % at 673°C and 19.5 at % at 522°C in vacuums of 2000 and 100 Pa, respectively. A complete state diagram is constructed, including the fields of gas-liquid equilibria at atmospheric and low pressures, the boundaries of which allow us to assess the behavior of selenium and tellurium upon distillation fractionation.     

Analysis of capsaicin and dihydrocapsaicin in peppers and pepper sauces by solid phase microextraction–gas chromatography–mass spectrometry

A simple method for the analysis of capsaicin and dihydrocapsaicin in peppers and pepper sauces by solid phase microextraction–gas chromatography–mass spectrometry has been developed. A novel device was designed for direct extraction solid phase microextraction in order to avoid damage to the fiber. The analysis was performed without derivatization for the gas chromatography–mass spectrometry analysis. Selection fiber, extraction temperature, extraction time and pH, were optimized. The method was linear in the range 0.109–1.323 μg/mL for capsaicin and 0.107–1.713 μg/mL for dihydrocapsaicin with correlation coefficient up to r = 0.9970 for both capsaicinoids. The precision of the method was less than 10%. The method was applied to the analysis of 11 varieties of peppers and four pepper sauces. A broad range of capsaicin (55.0–25 459 μg/g) and dihydrocapsaicin (93–1 130 μg/g) was found in the pepper and pepper sauces samples (4.3–717.3 and 1.0–134.8 μg/g), respectively.     

Sequential methyl-fluorine exchange reactions of siloxide ions in the gas phase

Exchange Me for a fluorine: Trimethylsiloxide ions in the presence of NF(3) in the gas?phase undergo an unusual and sequential metathesis-type reaction wherein methyl groups are exchanged for fluorine. Theoretical calculations suggest that the reaction proceeds by a three-step internal-nucleophilic-displacement mechanism which features a pentacoordinated siliconate species as a transition state rather than as an intermediate.     

The photophysics of flavins: What makes the difference between gas phase and aqueous solution?

The ground and low-lying excited electronic states of isoalloxazine, 10-methylisoallox-azine and lumiflavin, three flavin-related compounds, were investigated by means of quantum chemical methods. Minimum structures were determined employing (time-dependent) Kohn–Sham density functional theory. Spectral properties were computed utilizing a combined density functional and multi-reference configuration interaction (DFT/MRCI) method. Solvent effects were mimicked by a conductor like screening model and micro-hydration with four explicit water molecules. At selected points along a linearly interpolated path connecting the Franck–Condon region and the S₁minimum, spin–orbit interaction was computed employing a nonempirical mean-field Hamiltonian. For isoalloxazine, intersystem crossing (ISC) rate constants were computed, taking both direct and vibronic spin–orbit coupling into account.On the basis of these calculations we suggest the following photo relaxation model. In the vacuum, efficient ISC takes place between the primarily excited state (S₁) and the lowest state (T₂). The energetic proximity of the state (S₂) enhances the nonradiative relaxation of S₁ by internal conversion (IC). In aqueous solution these ISC and IC channels are energetically not accessible due to the blue shift of the states. The high triplet quantum yield observed in experiment [J.T.M. Kennis, S. Crosson, M. Gauden, I.H.M. van Stokkum, K. Moffat, R. van Grondelle, Biochemistry 42 (2003) 3385–3392] is explained by the intersection between the state (S₁) potential energy hypersurface (PEH) and the second (T₂) PEH along the relaxation pathway and the strong enhancement of their spin–orbit coupling by vibronic interactions. The calculated ISC rate for this channel is in good agreement with experimental results. According to our model, lack of an efficient IC channel leads to an increased fluorescence quantum yield in aqueous solution.     

Hydrogen bonding and reactivity of water to azines in their S1 (n,π*) electronic excited states in the gas phase and in solution

A unified picture is presented of water interacting with pyridine, pyridazine, pyrimidine, and pyrazine on the S(1) manifold in both gas-phase dimers and in aqueous solution. As (n,π*) excitation to the S(1) state removes electrons from the ground-state hydrogen bond, this analysis provides fundamental understanding of excited-state hydrogen bonding. Traditional interpretations view the excitation as simply breaking hydrogen bonds to form dissociated molecular products, but reactive processes such as photohydrolysis and excited-state proton coupled electron transfer (PCET) are also possible. Here we review studies performed using equations-of-motion coupled-cluster theory (EOM-CCSD), multireference perturbation theory (CASPT2), time-dependent density-functional theory (TD-DFT), and excited-state Monte Carlo liquid simulations, adding new results from symmetry-adapted-cluster configuration interaction (SAC-CI) and TD-DFT calculations. Invariably, gas-phase molecular dimers are identified as stable local minima on the S(1) surface with energies less than those for dissociated molecular products. Lower-energy biradical PCET minima are also identified that could lead to ground-state recombination and hence molecular dissociation, dissociation into radicals or ions, or hydration reactions leading to ring cleavage. For pyridine.water, the calculated barriers to PCET are low, suggesting that this mechanism is responsible for fluorescence quenching of pyridine.water at low energies rather than accepted higher-energy Dewar-benzene based "channel three" process. Owing to (n,π*) excitation localization, much higher reaction barriers are predicted for the diazines, facilitating fluorescence in aqueous solution and predicting that the as yet unobserved fluorescence from pyridazine.water and pyrimidine.water should be observable. Liquid simulations based on the assumption that the solvent equilibrates on the fluorescence timescale quantitatively reproduce the observed spectral properties, with the degree of (n,π*) delocalization providing a critical controlling factor.     

Rapid automatic nucleic acid purification system based on gas–liquid immiscible phase

The continuous expansion of nucleic acid detection applications has resulted in constant developments in rapid, low-consumption, and highly automated nucleic acid extraction methods. Nucleic acid extraction using magnetic beads across an immiscible phase interface offers significant simplification and parallelization potential. The gas–liquid immiscible phase valve eliminates the requirement for complicated cassettes and is suitable for automation applications. By analyzing the process of magnetic beads crossing the gas-liquid interface, we utilized a low magnetic field strength to drive large magnetic bead packages to cross the gas-liquid interface, providing a solution of high magnetic bead recovery rate for solid-phase extraction with a low-surfactant system based on gas-liquid immiscible phase valve. The recovery rate of magnetic beads was further improved to 90%–95% and the carryover of the reagents was below 1%. Consequently, a chip and an automatic system were developed to verify the applicability of this method for nucleic acid extraction. The Hepatitis B virus serum standard was used for the extraction test. The extraction of four samples was performed within 7 minutes, with nucleic acid recovery maintained above 80% and good purity. Thus, through analysis and experiments, a fast, highly automated, and low-consumption nucleic acid recovery method was proposed in this study.     

Multiply-charged negative clusters of adenosine-5′-monophosphate in the gas phase

Multiply-charged noncovalent cluster anions of adenosine-5'-monophosphate (AMP) were formed by electrospray ionization (ESI). Ions in higher charge states were observed when the ions were accumulated in an ion trap with helium buffer gas before detection. We determined the smallest size (n(a)) or appearance size as a function of charge state (q), i.e., n(a) = 4 for q = 2, n(a) = 8 for q = 3, and n(a) = 13 for q = 4. The relation between n(a) and q can be described by a charged droplet model. When the size is larger than n(a) for a given q, the fragmentation pathway of an anion cluster is dominated by loss of neutral fragments. In contrast, when the size approaches the appearance size, only charged fragments are formed.