A 2'-acylamido cap that increases the stability of oligonucleotide duplexes

[structure: see text]. Reported here is the synthesis of oligonucleotides containing a 2'-acylamido-2'-deoxyuridine residue at their 3'-terminus. Compared to control sequences bearing a thymidine residue, the quinolone-capped duplexes give higher UV melting points. In the case of (5'-ACGCGU-NA-2')2, where NA denotes a nalidixic acid residue, the melting point increase is up to 22 degrees C over that of (ACGCGT)2.     

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.     

DNA stability in the gas versus solution phases: A systematic study of thirty-one duplexes with varying length, sequence, and charge level

We report herein a systematic mass spectrometric study of a series of thirty-one non-self-complementary, matched, DNA duplexes ranging in size from 5- to 12-mers. The purpose of this work is threefold: (1) to establish the viability of using mass spectrometry as a tool for examining solution phase stabilities of DNA duplexes; (2) to systematically assess gas-phase stabilities of DNA duplexes; and (3) to compare gas and solution phase stabilities in an effort to understand how media affects DNA stability. These fundamental issues are of importance both on their own, and also for harnessing the potential of mass spectrometry for biological applications. We have found that ion abundances do not always track with solution phase stability; GC content must be taken into account. Two duplexes with the same Tm yet with differing GC content can yield different ion abundances. That is, if two duplexes have the exact same melting temperature, yet one has a higher GC content, the duplex with the higher GC content yields a higher ion abundance. It thus appears that not only is a GC base pair stronger than an AT base pair, but the relative strengths of each differ in the gas phase versus in solution, such that the electrospray process can differentiate between them. We also characterize the gas-phase stabilities of the duplexes, using collision-induced dissociation (CID) as a method to assess stability. We focus on two aspects of this CID experiment. One, we examine what factors appear to control whether the duplexes dissociate into single strands or covalently fragment; we are able to utilize a charge state normalization we coin "charge level" to compare our results with others' and establish generalities regarding dissociation versus fragmentation patterns. Two, we examine those duplexes that primarily dissociate and use CID to assess the gas-phase stabilities. We find that correlation of gas-phase to solution-phase stabilities is more likely to occur when duplexes of varying GC content are examined. Duplexes with the same GC content tend to have stabilities that do not parallel those in solution. We discuss these results in light of the different roles that hydrogen bonding and base stacking play in solution versus the gas phase. Ultimately, we apply what we learn to lend insight into the biological problem of how the carcinogenic, damaged nucleobase O6-methylguanine causes mutations.     

Comparative quantum-chemical investigation of the CH acidity of some N-methyl-amino derivatives in the gas phase and in solution

The equilibrium configuration of the molecules of three derivatives of N-methylnitrosoamine, N,N-dimethylnitramine, and 1-phenyl-1-triazene and their carbanions were calculated by various semiempircal SCF methods and also in the nonempirical 3–21G⁺ approximation. The optimized geometric parameters of the AM-1 method and the nonempirical 3–21G⁺ calculation agree with each other and with the experimental data better than the geometric parameters calculated by the MINDO/3 method. The most reliable results are obtained by the AM1 method as applied to the gasphase CH acidity of the N-methylamino derivatives. The scheme for the breakdown of the deprotonation energies of the investigated CH acids into components characterizing the individual atoms and bonds was used to analyze the mechanism of internal stabilization of the conjugated carbanions. Comparison of the kinetic CH acidities of the standard hydrocarbons in the basic solution with their deprotonation energies calculated by the AM1 method made it possible to obtain a correlation, the existence of which confirms that there is a single type of mechanism for the stabilization of the carbanions, excluding the solvation effect. The deviation of N-methylamino derivatives from the main line indicates that the solvent has a strong effect on their kinetic CH acidity.Scientific-Production Association, State Institute of Applied Chemistry, Leningrad. Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 27, No. 4, pp. 426–437, July–August, 1991. Original article submitted February 25, 1991.     

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.     

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions     

Comparison between solution-phase stability and gas-phase kinetic stability of oligodeoxynucleotide duplexes

The relative kinetic stabilities of different 16-mer oligonucleotide duplexes were investigated by source collision-induced dissociation (CID) in a heated capillary electrospray ion source. They were compared with the relative stabilities in solution obtained by thermal denaturation monitored by UV spectrophotometry. The results clearly show that both hydrogen bonding and base stacking interactions that are present in solution are maintained in the gas phase. This suggests that the electrospray process preserves the double-helix structure of DNA. A step by step opening of the double helix structure is proposed for the gas-phase dissociation, competing with the covalent bond cleavage of bases. We also draw attention to the fact that by source CID, it is the kinetic stability of the complexes that is probed. In particular, this implies that only complexes of the same size can be compared.     

Semiclassical simulations of azomethane photochemistry in the gas phase and in solution

We present semiclassical simulations of the dynamical events which follow the n --> pi excitation of an azomethane molecule: decay to the ground state, isomerization, and dissociation. Ab initio potential energy surfaces and couplings, slightly modified according to available experimental data, are employed in conjunction with a trajectory-surface-hopping method. For an isolated molecule, we show that dissociation takes place in the ground state, because the radiationless decay is very fast. The dissociation is mainly sequential: the methyldiazenyl radical first produced fragmentates very rapidly to N(2) + CH(3)*. The results of previous experiments by Lee's and Zewail's groups, from which partially conflicting conclusions had been drawn, are reproduced and interpreted. Molecular dynamics, coupled to the surface-hopping algorithm, allows us to simulate the photochemistry in acqueous solution. Here the fragmentation is suppressed because of vibrational energy loss to the solvent: only the isomerization takes place.     

Fluorescence probe of Trp-cage protein conformation in solution and in gas phase

Measurements of protein unfolding in the absence of solvent, when combined with unfolding studies in solution, offer a unique opportunity to measure the effects of solvent on protein structure and dynamics. The experiments presented here rely on the fluorescence of an attached dye to probe the local conformational dynamics through interactions with a Trp residue and fields originating on charge sites. We present fluorescence measurements of thermal fluctuations accompanying conformational change of a miniprotein, Trp-cage, in solution and in gas phase. Molecular dynamics (MD) simulations are performed as a function of temperature, charge state, and charge location to elucidate the dye-protein conformational dynamics leading to the changes in measured fluorescence. The results indicate that the stability of the unsolvated protein is dominated by hydrogen bonds. Substituting asparagine for aspartic acid at position 9 results in a dramatic alteration of the solution unfolding curve, indicating that the salt bridge involving Lys8, Asp9, and Arg16 (+ - +) is essential for Trp-cage stability in solution. In contrast, this substitution results in minor changes in the unfolding curve of the unsolvated protein, showing that hydrogen bonds are the major contributor to the stability of Trp-cage in gas phase. Consistent with this hypothesis, the decrease in the number of hydrogen bonds with increasing temperature indicated by MD simulations agrees reasonably well with the experimentally derived enthalpies of conformational change. The simulation results display relatively compact conformations compared with NMR structures that are generally consistent with experimental results. The measured unfolding curves of unsolvated Trp-cage ions are invariant with the acetonitrile content of the solution from which they are formed, possibly as a result of conformational relaxation during or after desolvation. This work demonstrates the power of combined solution and gas-phase studies and of single-point mutations to identify specific noncovalent interactions which contribute to protein-fold stability. The combination of experiment and simulation is particularly useful because these approaches yield complementary information which can be used to deduce the details of structural changes of proteins in the gas phase.     

On-line solution stability determination of pharmaceuticals by capillary electrophoresis

Summary Good agreement between the impurity levels in a batch of a related impurity of ranitidine were obtained by CE and HPLC. A solution of the impurity was positioned on the CE autosampler and analysed sequentially. The extent of degradation was monitored by loss of main peak and the formation of two principal degradation products. It was found that after 9.25 hours only 2% area/area of the original impurity remained. Buffering of the sample solution to pH 7 was shown to minimise this degradation.Unattended in-situ stability testing of an solution of the impurity in water was performed by CE.     

Steric retardation of SN2 reactions in the gas phase and solution

The gas-phase S(N)2 reactions of chloride with ethyl and neopentyl chlorides and their alpha-cyano derivatives have been explored with B3LYP, CBS-QB3, and PDDG/PM3 calculations. Calculations predict that the steric effect of the tert-butyl group raises the activation energy by about 6 kcal/mol relative to methyl in both cases. Solvent effects have been computed with QM/MM Monte Carlo simulations for DMSO, methanol, and water, as well as with a polarizable continuum model, CPCM. Solvents cause a large increase in the activation energies of these reactions but have a very small differential effect on the ethyl and neopentyl substrates and their cyano derivatives. The theoretical results contrast with previous conclusions that were based upon gas-phase rate measurements.     

Comparative methodology in the determination of alpha-oxocarboxylates in aqueous solution ion chromatography versus gas chromatography after oximation, extraction and esterification

A direct, simple and rapid high-performance liquid chromatographic method has been developed for the determination of ketoprofen with ibuprofen as internal standard. Samples were chromatographed on a 5 μm Kromasil 100 C₁₈ column. The mobile phase was a mixture of acetonitrile–0.01 M KH₂PO₄ adjusted to pH 1.5 with orthophosphoric acid 85% (60:40, v/v). Detection was at 260 nm and the run time was 10 min. The detector response was found to be linear in the concentration range 0.02 to 40 μg/ml. This HPLC assay has been applied to measure the “in vitro” percutaneous penetration of ketoprofen through rat skin.     

Aromatic oligomers that form hetero duplexes in aqueous solution

The electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) and electron-rich 1,5-dialkoxynaphthalene (Dan) have been shown to complex strongly with each other in water due to the hydrophobic effect as modulated through the electrostatic complementarity of the stacked dimer. Previously, oligomers of alternating Ndi and Dan units, termed aedamers, were the first foldamers to employ intramolecular aromatic stacking to effect the formation of secondary structure of nonnatural chains in aqueous solution. Described here is the use of this aromatic-aromatic (or pi-pi) interaction, this time in an intermolecular format, to demonstrate the self-assembly of stable hetero duplexes from a set of molecular strands (1a-4a) and (1b-4b) incorporating Ndi and Dan units, respectively. A 1-to-1 binding stoichiometry was determined from NMR and isothermal titration calorimetry (ITC) investigations, and these experiments indicated that association is enthalpically favored with the tetra-Ndi (4a) and tetra-Dan (4b) strands forming hetero duplexes (4a:4b) with a stability constant of 350 000 M-1 at T = 318 K. Polyacrylamide gel electrophoresis (PAGE) also illustrated the strong interaction between 4a and 4b and support a 1-to-1 binding mode even when one component is in slight excess. Overall, this system is the first to utilize complementary aromatic units to drive discrete self-assembly in aqueous solution. This new approach for designing assemblies is encouraging for future development of duplex systems with highly programmable modes of binding in solution or on surfaces.     

Vibrational relaxation of CH3I in the gas phase and in solution

Transient electronic absorption measurements reveal the vibrational relaxation dynamics of CH(3)I following excitation of the C-H stretch overtone in the gas phase and in liquid solutions. The isolated molecule relaxes through two stages of intramolecular vibrational relaxation (IVR), a fast component that occurs in a few picoseconds and a slow component that takes place in about 400 ps. In contrast, a single 5-7 ps component of IVR precedes intermolecular energy transfer (IET) to the solvent, which dissipates energy from the molecule in 50 ps, 44 ps, and 16 ps for 1 M solutions of CH(3)I in CCl(4), CDCl(3), and (CD(3))(2)CO, respectively. The vibrational state structure suggests a model for the relaxation dynamics in which a fast component of IVR populates the states that are most strongly coupled to the initially excited C-H stretch overtone, regardless of the environment, and the remaining, weakly coupled states result in a secondary relaxation only in the absence of IET.     

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

We are presenting a theoretical study of the hydrolysis of a β‐lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06‐2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule. Moreover, the flexibility of the substrate implies the existence of a huge number of possible conformers, some of them implying formation of intramolecular hydrogen bond interaction that can determine the energetics of the conformers defining the different states along the reaction profile. The results show PM3 provides results that are in qualitative agreement with DFT calculations. The free energy profiles show a step‐wise mechanism that is kinetically determined by the nucleophilic attack of a water molecule activated by the proton transfer to the carboxylate group of the substrate (the first step). However, since the main role of the β‐lactamase would be reducing the free energy barrier of the first step, and keeping in mind the barrier obtained from second intermediate to products, population of this second intermediate could be significant and consequently experimentally detected in β‐lactamases, as shown in the literature. © 2012 Wiley Periodicals, Inc.     

Ab initio studies of aspartic acid conformers in gas phase and in solution

Systematic and extensive conformational searches of aspartic acid in gas phase and in solution have been performed. For the gaseous aspartic acid, a total of 1296 trial canonical structures and 216 trial zwitterionic structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were optimized at the B3LYP/6-311G* level and then subjected to further optimization at the B3LYP/6-311++G** level. A total of 139 canonical conformers were found, but no stable zwitterionic structure was found. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, and vertical ionization energies of the canonical conformers were determined. Single-point energies were also calculated at the MP2/6-311++G** and CCSD/6-311++G** levels. The equilibrium distributions of the gaseous conformers at various temperatures were calculated. The proton affinity and gas phase basicity were calculated and the results are in excellent agreement with the experiments. The conformations in the solution were studied with different solvation models. The 216 trial zwitterionic structures were first optimized at the B3LYP/6-311G* level using the Onsager self-consistent reaction field model (SCRF) and then optimized at the B3LYP/6-311++G** level using the conductorlike polarized continuum model (CPCM) SCRF theory. A total of 22 zwitterions conformers were found. The gaseous canonical conformers were combined with the CPCM model and optimized at the B3LYP/6-311++G** level. The solvated zwitterionic and canonical structures were further examined by the discrete/SCRF model with one and two water molecules. The incremental solvation of the canonical and zwitterionic structures with up to six water molecules in gas phase was systematically examined. The studies show that combining aspartic acid with at least six water molecules in the gas phase or two water molecules and a SCRF solution model is required to provide qualitatively correct results in the solution.     

Comparative characteristics of a tryptophan molecule in the gas phase and water

The L and D isomers of the tryptophan (Trp) molecule and the (Trp)⁺ cation in the gas phase and water are calculated at the DFT level to reveal the effect of water considered in the dielectric continuum approximation on the electronic characteristics of the molecule. The distribution of effective atomic charges and bond lengths enables the prediction of the most probable parts of the chemical bond cleavage during the fragmentation of the molecule under the ionizing particle flux. These data are supplemented with a calculation of fragmentation energies. Zwitterionic structures characterized by the appearance of considerable dipole moments and a change in their orientation with respect to the ground state are distinguished among the possible isomeric forms in water.     

Ammonium determination in wine by gas phase molecular absorption spectrometry

A procedure for the determination of ammonium is described, based on its transformation into ammonia gas and subsequent measurement by UV-visible molecular absorption spectrometry at 194 nm. Two different procedures for generating the ammonia are proposed, using NaOH solution and solid NaOH, respectively. After generation conditions for both procedures had been optimized, better sensitivity was observed with solid NaOH. In these conditions, the method showed two ranges of linear response: from 1 to 100 g and from 100 to 400 g of ammonium. Finally, we determined ammonium in wine samples. Preliminary studies indicated that the only observable interfering species was ethanol, which could be eliminated by subjecting the sample to vacuum evaporation until nearly dry. This process also increased the sensitivity of the method by as much as ten times. The values obtained from three different wine samples yielded results within the range of the concentration obtained by other authors. The recovery of ammonium added to the wine samples was around 95%.     

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