Theoretical studies of the structure and stability of protonated olefins in the gas phase and in solution

The calculation of carbenium and carbonium type cations resulting from the protonation of olefins with growing length and increasing chain branching was carried out by quantum chemical methods which were tested elsewhere.One result is the distinction of olefins with an equal number of alkyl substituents on both sides of the double bond and other ones with different number. In the latter case generally no bridged structures could be defined.The influence of nucleophilic solvents on the stability of the cationic structures is simulated on the basis of Klopman's solvaton model. These calculations show that solvents may change the gas phase data in a remarkable way.     

Theoretical studies on the hydrolysis of phosphate diesters in the gas phase,solution, and RNase A

Density functional theory, polarizable continuum models and semiempirical hybrid quantum mechanical/molecular mechanical (QM/MM) calculations were applied to the hydrolysis of phosphate diesters in the gas phase, in solution, and in the enzyme RNase A. Neutralization of the negative charge of the pentacovalent phosphorane intermediates provides a substantial stabilization of the transition‐state structures in the gas phase. Inclusion of solvent effects on the phosphate/phosphorane species was critical to reproducing the trends in reactivity observed experimentally. Finally, the catalytic mechanism for the hydrolysis of uridine 2′,3′‐cyclic phosphate by RNase A was studied by QM/MM calculations. Our results suggest that the rate‐limiting transition state of the reaction corresponds to the approach of a water molecule to the phosphate and its activation by His119. Thus, His119 acts as a generalized base for the reaction. The water attack leads to a pentacovalent phosphorane transition state of formal charge ?2; this excess of negative charge in the transition state is stabilized by a number of positively charged residues including His12 and Lys41. In the second stage of the reaction, the phosphorane is converted into products. This part of the reaction proceeds without a detectable barrier, and it is facilitated by a proton transfer from Lys41 to the departing O_2′. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Comparative stability determination of oligonucleotide duplexes in gas and solution phase

The relative stability of RNA duplexes were determined in both solution and gas phase. Solution stability as determined by a spectrophotometric method indicated that the Watson-Crick duplexes were more stable than duplexes containing one GA mismatch or two tandem GA mismatches. Gas phase stability was determined using ESI-MS through variation of the collision energy in an ion trap. Stability curves similar to the melting curves obtained in solution were observed. The relative stability in gas phase differed, however, from that in solution. The duplexes with two tandem GA mismatches were found to be more stable than the Watson-Crick and single GA mismatch duplexes. The different trends observed in solution versus gas phase can be attributed to the primary means of interaction. In solution, stacking is expected to be the dominant interaction mode. In the gas phase, hydrogen bonding is expected to be the dominant interaction mode. Duplexes with tandem GA mismatches have the potential to undergo additional hydrogen bonding relative to the other duplexes which could account for their increased stability in the gas phase.     

Mechanisms of nucleophilic reactions of carbonyl compounds in the gas phase and in a solution

The effect of substituents on nucleophilic addition at the C=O bond, which occurs by the mechanism of intramolecular proton transfer, has been studied by the quantum-chemical MNDO/H method. The effect of nucleophiles and substituents at the carbonyl C atom in the gas phase is opposite to that in solution. Strengthening of the bond between the nucleophile and the carbonyl compound as the result of the transfer of electron density to the carbonyl C atom results in the stabilization of the tetrahedral bipolar adduct. In the formation of an adduct with a strong nucleophile the geometry of the transition state (TS) is closer to that of the reaction product, whereas in the case of a weak nucleophile it is similar to that of the initial reagents. Attack by a weak nucleophile and electron-donating groups at the carbonyl C atom favor the situation in which the reaction system achieves a TS earlier and proton transfer occurs with a low activation barrier.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 227–230, February, 1994.     

Theoretical study of the kojic acid structure in gas phase and aqueous solution

Density functional calculations at the B3LYP/6‐311++G** level have been performed to determine the ground‐state conformational preference for kojic acid, a widely used skin‐whitening, antibrowning, and antibacterial agent. It is found that the gas phase consists almost entirely of the 5‐hydroxy‐2‐(hydroxymethyl)‐4H‐pyran‐4‐one tautomer, although several rotamers of this are prevalent. In aqueous solution, however, other tautomers are also present. The validity of the calculations is confirmed by the observed FTIR, NMR, and UV–vis spectra, which show good correspondence with the theoretical spectra. The electronic interactions are interpreted in terms of charge and bond order analysis as well as the composition of the HOMO and LUMO. The calculations show that kojic acid has partial aromatic character and is a good nucleophile. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A direct comparison of protein structure in the gas and solution phase: the Trp-cage

Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location, there is significant difference in the structures, with a substantial increase in hydrogen bonds and exposure of hydrophobic parts in the gas phase. The structure of the salt bridge in the gas phase is also much more stable than in the (experimental) solution structure.     

The structure and dynamics of DNA in the gas phase

The impact of the transfer from water to the vacuum in the duplex DNA has been explored by using long molecular dynamic simulations. In opposition to chemical intuition, it is found that vaporization of DNA, even at high temperatures, does not lead to a total disruption of the double helix. Rather, the DNA duplex preserves gross structural, energetic, and dynamic features of the conformation of the double helix in aqueous solution. Thus, the two strands remain bound, the global structure has a slight helicity, and the total number of DNA-DNA interactions is not dramatically different from that found in solution. The results provide detailed structural and dynamic information useful to complement current mass spectroscopy studies of DNA structures.     

天花粉蛋白溶液构象与稳定性及生物活性的关系

用圆二色性研究了天花粉蛋白在不同PH,不同温度和不同的时间条件下的溶液构象变化.阐明了天花粉蛋白溶液的外部环境,并研究了天花粉蛋白的溶液构象与抗生育活性的关系,结果表明随着溶液中a-helix含量的增加,抗生育活性也相应增加,当a-helix含量减少到15%以下,其抗生育活性也就丧失.     

The structure,stability, and reactivity of oxalato-monoperoxovanadium(V) in solution

In order to understand the solution chemistry of an oxalato-monoperoxovanadium(V) complex (K₃[VO(O₂)(C₂O₄)₂] · ½H₂O, mpVox), the solid and solution-state NMR characteristics, transformation behavior, and exchange phenomena in the solution are described in this article. NMR experimental and theoretical results indicated that the vanadium of mpVox in solid and solution state are seven coordinate. However, some geometric parameters tend to change upon dissolution. The dynamic transformation of mpVox in solution was investigated using NMR, IR, and UV-Vis. The reduction product is oxalato-bisoxovanadate. Concentration, pH, and temperature affect this transformation. ⁵¹V NMR investigation on the system of mpVox with picolinc acid showed that two oxalates are substituted to produce [VO(O₂)(ox)(pic)]^2? and [VO(O₂)(pic)₂]^?.     

Quantum chemical calculations for the determination of the molecular structure of conjugated compounds: Part XIII. On the conformational structure of rans-benzylideneaniline in the gas phase and in solution

Contrary to the results of other semi-empirical all-valence electron methods, the main features concerning the conformation of trans-benzylideneaniline are correctly accounted for using the NDDO method. Based on a modified continuum model the influence of solvents on the molecular structure was estimated.     

离子色谱法测定海产品中磷酸盐、焦磷酸盐、偏磷酸盐和总磷

建立了离子色谱法测定海产品中磷酸盐、焦磷酸盐、偏磷酸盐和总磷的分析方法。样品经100 mmol/L NaOH溶液浸提,固相萃取柱去除有机物、阳离子、中和OH~后用于海产品中磷酸盐、焦磷酸盐和偏磷酸盐的测定;样品经干灰化法消化,固相萃取柱净化后用于总磷测定。考察了提取溶液的pH、有机物和共存离子对测定结果的影响。该方法的线性范围为0.3～60 mg/L,检出限为2.1～2.3 mg/kg,相对标准偏差为1.6%～2.6%。海鱼和虾仁样品中目标物的加标回收率为81.8%～100.0%。该方法选择性好,灵敏度高,用于实际样品测定结果令人满意。     

Dependence of cyano bonded phase hydrolytic stability on ligand structure and solution pH

As part of our program to develop more stable cyano (CN) high-performance liquid chromatography (HPLC) column packings, we have evaluated hydrolytic stability as a function of ligand connectivity, chain length, and side group steric protection and the pH of the mobile phase. Three accelerated tests were used to evaluate stability: (1) A non-HPLC screening test measuring carbon loss in refluxing MeOH-100 mM KH2PO4 pH 4.5 (1:1, v/v) solution; (2) a continuous flow HPLC test measuring capacity factor maintenance in 1% trifluoroacetic acid in water (pH 1.02) at 80 degrees C; and (3) a continuous flow HPLC test measuring column efficiency maintenance in 50 mM triethylamine in water (pH 10.00) at 50 degrees C. The stability of the CN phases was found to be dependent on both ligand chemical structure and the pH of the test conditions. The starting screen test of intermediate pH was least able to differentiate the CN phases based on structure, because two different degradation mechanisms appear to offset each other (acid induced siloxane bond cleavage vs. base induced silica dissolution). A trifunctional and a sterically protected CN phase were notably stable under the acidic test conditions, but had poor stability under basic conditions. Conversely, chain extension afforded poor stability under acidic conditions, but did afford improved stability at higher pH. In total, the data indicate that good CN column stability can be achieved by using a trifunctional or a sterically protected phase in acidic mobile phases. However, as mobile phases of intermediate or higher pH are employed, shorter column lifetimes can be expected due to an accelerated dissolution of the underlying silica substrate. Materials were also compared chromatographically using a mixture of non-polar, polar, and basic analytes under reversed-phase conditions.     

The stability of gold iodides in the gas phase and the solid state

The stability of gold iodides in the oxidation state +I and +III is investigated at the ab initio and density functional level using relativistic and nonrelativistic energy-adjusted pseudopotentials for gold and iodine. The calculations reveal that relativistic effects stabilize the higher oxidation state of gold as expected, that is Au2I6 is thermodynamically stable at the relativistic level, whilst at the nonrelativistic level the complex of two iodine molecules weakly bound to both gold atoms in Au2I2 is energetically preferred. The rather low stability of AuI3 with respect to dissociation into AuI and I2 will make it difficult to isolate this species in the solid state as (possibly) Au2I6 or detect it by matrix-isolation techniques. The monomer AuI3 is Jahn-Teller distorted from the ideal trigonal planar (D3h) form, but adopts a Y-shaped structure (in contrast to AuF3 and AuCl3), and in the nonrelativistic case can be described as I2 weakly bound to AuI. Relativistic effects turn AuI3 from a static Jahn-Teller system to a dynamic one. For the yet undetected gas-phase species AuI accurate coupled-cluster calculations for the potential energy curve are used to predict vibrational-rotational constants. Solid-state density functional calculations are performed for AuI and Au2I6 in order to predict cohesive energies.     

Thermal decomposition of 1,3,3-trinitroazetidine in the gas phase, solution, and melt

1,3,3-Trinitroazetidine (TNAZ) was synthesized using the alternative approach based on the transformation of 3-oximino-1-(p-toluenesulfonyl)azetidine in the reaction with nitric acid through intermediate pseudonitrol. The thermal decomposition of TNAZ in the gas phase, melt and m-dinitrobenzene solution in a wide concentration range (5–80%) was studied by manometry, volumetry, thermogravimetry, IR spectroscopy, and mass spectrometry. In the gas phase in the temperature range from 170 to 220°C the thermal decomposition proceeds according to the first-order kinetic law with the activation energy 40.5 kcal mol^?1 and pre-exponential factor 10^15.0 s^?1. The major gaseous reaction products are N₂, NO, NO₂, CO₂, H₂O, and nitroacetaldehyde, and trace amounts of CO and HCN are formed. The rate-determining step of the process is the homolytic cleavage of the N-NO₂ bond in the TNAZ molecule. In melt at 170–210 °C the thermal decomposition proceeds with the pronounced self-acceleration and the maximum reaction rates are observed at conversions 53.9–67.4%. The solid decomposition products accelerate the reaction. It is most likely that the autocatalysis of TNAZ decomposition in the liquid phase is due to the autocatalytic decomposition of 1-nitroso-3,3-dinitroazetidine, which is formed by the thermal decomposition of TNAZ. In m-dinitrobenzene TNAZ also decomposes with self-acceleration. The higher the concentration in the solution, the more pronounced the self-acceleration. Additives of picric acid moderately accelerate the thermal decomposition of TNAZ, whereas hexamethylenetetraamine additives exert a strong acceleration.     

The structure of ionized 1,5 hexadiene in the gas phase

The structure of ionized 1,5-hexadiene, prepared by charge transfer between 1,5-hexadiene and CS2+*, is examined using energy-resolved collision-induced dissociation (CID). By comparing the product distributions and product appearance curves with those of authentic low-energy C6H10+* ions, it is determined that 1,5-hexadiene cation spontaneously rearranges to cyclohexene cation in the gas-phase. The proposed mechanism for formation of cyclohexene cation in the gas phase is analogous to that determined for this process under matrix isolation conditions, where it proceeds via a Cope rearrangement to the cyclohexane-1,4-diyl cation, followed by isomerization to cyclohexene cation. It is shown that electron ionization (EI) of 1,5-hexadiene gives a different molecular ion than is obtained upon chemical ionization (CI). The energy-resolved CID mass spectrum for the EI product is consistent with what would be obtained for a mixture of low energy ion isomers.     

Acidity and proton affinity of hypoxanthine in the gas phase versus in solution: intrinsic reactivity and biological implications

Hypoxanthine is a mutagenic purine base that most commonly arises from the oxidative deamination of adenine. Damaged bases such as hypoxanthine are associated with carcinogenesis and cell death. This inevitable damage is counteracted by glycosylase enzymes, which cleave damaged bases from DNA. Alkyladenine DNA glycosylase (AAG) is the enzyme responsible for excising hypoxanthine from DNA in humans. In an effort to understand the intrinsic properties of hypoxanthine, we examined the gas-phase acidity and proton affinity using quantum mechanical calculations and gas-phase mass spectrometric experimental methods. In this work, we establish that the most acidic site of hypoxanthine has a gas-phase acidity of 332 +/- 2 kcal mol-1, which is more acidic than hydrochloric acid. We also bracket a less acidic site of hypoxanthine at 368 +/- 3 kcal mol-1. We measure the proton affinity of the most basic site of hypoxanthine to be 222 +/- 3 kcal mol-1. DFT calculations of these values are consistent with the experimental data. We also use calculations to compare the acidic and basic properties of hypoxanthine with those of the normal bases adenine and guanine. We find that the N9-H of hypoxanthine is more acidic than that of adenine and guanine, pointing to a way that AAG could discriminate damaged bases from normal bases. We hypothesize that AAG may cleave certain damaged nucleobases as anions and that the active site may take advantage of a nonpolar environment to favor deprotonated hypoxanthine as a leaving group versus deprotonated adenine or guanine. We also show that an alternate mechanism involving preprotonation of hypoxanthine is energetically less attractive, because the proton affinity of hypoxanthine is less than that of adenine and guanine. Last, we compare the acidity in the gas phase versus that in solution and find that a nonpolar environment enhances the differences in acidity among hypoxanthine, adenine, and guanine.     

Ionization of imidazole in the gas phase, microhydrated environments, and in aqueous solution

Hydration of neutral and cationic imidazole is studied by means of ab initio and molecular dynamics calculations, and by photoelectron spectroscopy of the neutral species in a liquid microjet. The calculations show the importance of long range solvent polarization and of the difference between the structure of water molecules in the first shell around the neutral vs cationic species for determining vertical and adiabatic ionization potentials. The vertical ionization potential of neutral imidazole of 8.06 eV calculated using a nonequilibrium polarizable continuum model agrees well with the value of 8.26 eV obtained experimentally for an aqueous solution at pH 10.6.     

Choice of quantum chemical methods and the calculation of the structure,dipole moment,and polarizability of phosphoryl compounds in the gas phase

Journal of Structural Chemistry - Molecules of phosphoryl compounds (H3PO, HF2PO, F3PO, Cl3PO, CH3POF2, CH3POCl2, and (CH3)3PO) are calculated at the Hartree-Fock, density functional theory with...     

Theoretical study of the relative stability of rotational conformers of alpha and beta-D-glucopyranose in gas phase and aqueous solution

The alpha-beta anomer energy difference and the stability of 10 rotamers of counterclockwise D-glucopyranose were studied in vacuo and in aqueous solution at the B3LYP/6-31+G(d,p) level. To obtain the solute charge distribution and the solvent structure around it, we used the averaged solvent electrostatic potential from molecular dynamics method, ASEP/MD, which alternates molecular dynamics and quantum mechanics calculations in an iterative procedure. The main characteristics of the anomeric equilibrium, both in vacuo and in solution, are well reproduced. The relative stability of the different anomers is related to the availability of the free pairs of electrons in the anomeric oxygen to interact with the water molecules. The influence of solvation in the conformer equilibrium is also analyzed.