Design Principles of Lipid-like Ionic Liquids for Gene Delivery.

We developed lipid-like ionic liquids, containing 2-mercaptoimidazolium and 2-mercaptothiazolinium headgroups tethered to two long saturated alkyl chains, as carriers for in vitro delivery of plasmid HEK DNA into 293T cells. We employed a combination of modular design, synthesis, X-ray analysis, and computational modeling to rationalize the self-assembly and desired physicochemical and biological properties. The results suggest that thioamide-derived ionic liquids may serve as a modular platform for lipid-mediated gene delivery. This work represents a step toward understanding the structure-function relationships of these amphiphiles with long-range ordering and offering insight into design principles for synthetic vectors based on self-assembly behavior.

Roles of Water Molecules and Counterion on HS- Sensing Reaction Utilizing a Pyrylium Derivative: A Computational Study.

In this paper, we present a comprehensive computational study on the hydrogen sulfide ion (HS-) sensing mechanism in aqueous solution using pyrylium-thiopyrylium transformation. Explicit water molecules up to three water molecules are considered using supramolecular models. The effect of water bulk solvent is also taken into account according to the polarizable continuum model. Our results demonstrate that water molecules are directly involved in the sensing reactions by altering reaction mechanisms and dramatically lower the activation energies. The most favorable HS- sensing mechanism involves a 10-membered ring transition structure formed by three water molecules and one hydronium. The catalytic effects of water molecule(s) due to the alleviation of ring strain and the stabilization from deprotonated hydronium significantly lower the activation energy. The activation energies in aqueous solution decrease from 40.2 kcal/mol for the hydronium-only-catalyzed reaction to 15.7, 14.8, and 7.4 kcal/mol for one-water-, two-water-, and three-water-catalyzed mechanisms, respectively. In addition, the effect of the counterion tetrafluoroborate (BF4-) on the reaction mechanisms was also investigated. Our results demonstrate that the counterion BF4- most likely behaves as a spectator and has minor influence on the reaction mechanism.

Role of an isoform-specific residue at the calmodulin-heme (NO synthase) interface in the FMN - heme electron transfer.

The interface between calmodulin (CaM) and the NO synthase (NOS) heme domain is the least characterized interprotein interface that the NOS isoforms must traverse through during catalysis. Our previous molecular dynamics simulations predicted a salt bridge between K497 in human inducible NOS (iNOS) heme domain and D118(CaM). Herein, the FMN - heme interdomain electron transfer (IET) rate was found to be notably decreased by charge-reversal mutation, while the IET in the iNOS K497D mutant is significantly restored by the CaM D118K mutation. The results of wild-type protein with added synthetic peptides further demonstrate the critical nature of K497 relative to the rest of the peptide sequence in modulating the IET. These data provide definitive evidence supporting the regulatory role of the isoform-specific K497 residue.

Ionic liquids with thioether motifs as synthetic cationic lipids for gene delivery.

This study introduces a novel class of imidazolium- and ammonium-based ionic liquids possessing two C12 and C14 tails and thioether linkers designed for lipoplex-mediated DNA delivery. Imidazolium-based ionic liquids displayed efficient gene delivery properties with low toxicity. Thiol-yne click chemistry was employed for the facile and robust synthesis of these thioether-based cationic lipioids with enhanced lipophilicity and low fluidity.

Insight into structural rearrangements and interdomain interactions related to electron transfer between flavin mononucleotide and heme in nitric oxide synthase: A molecular dynamics study.

Calmodulin (CaM) binding to nitric oxide synthase (NOS) enables a conformational change, in which the FMN domain shuttles between the FAD and heme domains to deliver electrons to the active site heme center. A clear understanding of this large conformational change is critical, since this step is the rate-limiting in NOS catalysis. Herein molecular dynamics simulations were conducted on a model of an oxygenase/FMN (oxyFMN) construct of human inducible NOS (iNOS). This is to investigate the structural rearrangements and the domain interactions related to the FMN-heme interdomain electron transfer (IET). We carried out simulations on the iNOS oxyFMN·CaM complex models in [Fe(III)][FMNH(-)] and [Fe(II)][FMNH] oxidation states, the pre- and post-IET states. The comparison of the dynamics and conformations of the iNOS construct at the two oxidation states has allowed us to identify key factors related to facilitating the FMN-heme IET process. The computational results demonstrated, for the first time, that the conformational change is redox-dependent. Predictions of the key interacting sites in optimal interdomain FMN/heme docking are well supported by experimental data in the literature. An intra-subunit pivot region is predicted to modulate the FMN domain motion and correlate with existence of a bottleneck in the conformational sampling that leads to the electron transfer-competent state. Interactions of the residues identified in this work are proposed to ensure that the FMN domain moves with appropriate degrees of freedom and docks to proper positions at the heme domain, resulting in efficient IET and nitric oxide production.

Computational study on a HS- sensing reaction utilizing a pyrylium derivative.

In this paper, we present a comprehensive computational study on the hydrogen sulfide sensing mechanism in aqueous solution using a pyrylium derivative. The possible sensing mechanisms were investigated under the neutral condition and acidic condition in the gas phase and in aqueous solution. The pyrylium-thiopyrylium transformation under the neutral condition is thermodynamically unfavorable, while it is greatly facilitated in the acidic condition catalyzed by a hydronium cation. In addition, the UV-vis absorption maxima of pyryliums and thiopyryliums were investigated at the TDDFT/B3LYP/6-31G+(d,p) level. The red shift of absorption maximum from unsubstituted pyrylium and thiopyrylium to dimethylamino-substituted pyrylium and thiopyrylium as well as the red shift seen in the pyrylium-thiopyrylium transformation is interpreted in terms of the molecular orbital theory.

Determination of derivatized urea in exhaled breath condensate by LC-MS.

Elevation in one or more compounds in exhaled breath condensate (EBC) has been reported to be related to one or another lung disease. The increased concentration might be caused by increased chemicals in the airway surface liquid. However, it might also be due to an increased delivery of liquid samples into the airstream. Being evenly distributed throughout the body, urea is a likely candidate for a marker of such dilution. A liquid chromatography-tandem mass spectrometry method was developed for determination of EBC urea. Urea in EBC samples was converted to 2-hydroxypyrimidine (2-HPM) through a one step reaction, along with (15)N(2)-urea added as an internal standard. The product ion m/z 97/42 was selected for quantification with m/z 99/43 from (15)N(2)-2-HPM as a standard. Concentrations of urea in EBC from five lung cancer patients were found to be 35.1, 2.2, 103.5, 19.3, and 3.6 microM, respectively. The highest values were in patients dying of respiratory distress, whose lungs were filled with fluid. Lower values were seen in patients whose conditions were improving. Lately, one of the low EBC urea values was observed in a patient whose airway status did not contribute to his poor clinical condition.

Comprehensive investigation of the energetics of pyrimidine nucleoside formation in a model prebiotic reaction.

The problem of beta-nucleoside formation under prebiotic conditions represents one of the most significant challenges to the "RNA world" hypothesis. The possibility exists that alternative bases may have come before the contemporary bases (i.e., A, G, C, and U), including bases that more readily form nucleosides. We previously reported the first successful synthesis of a pyrimidine nucleoside from a free base and a nonactivated sugar in a plausible prebiotic reaction. Here we present a detailed computational study on the reaction at the density functional theory (DFT) level. The catalytic role of a Mg(2+) ion on the reaction mechanism is also investigated. Our calculations demonstrate that a Mg(2+) ion, serving as a Lewis acid, can afford the necessary stabilization to the base and leaving water molecule during glycoside bond formation. The solvent effect is considered by the Onsager solvation model and also by an extended model with the addition of explicit water molecules within the SCRF solvation model. In addition, predictions regarding the formation of nucleosides from other pyrimidine bases are also addressed, providing valuable insights into what chemical features of the bases facilitate glycoside formation in drying-heating reactions.

Neutral hydrolyses of carbon disulfide: An ab initio study of water catalysis.

The water-catalyzed hydrolysis reaction of carbon disulfide (CS(2)) has been investigated at the levels of HF and MP2 with the basis set of 6-311++G(d,p) using the combined supramolecular/continuum models, in which up to six water molecules are involved in the hydrolysis and the effect of water bulk solvent is taken into account according to the polarizable continuum model (PCM). The activation Gibbs free energies in water solution, DeltaG(sol) (not equal) (298 K), for the rate-determining steps of one up to six water hydrolyses are 247.9, 184.2, 152.3, 141.8, 134.4, and 118.9 kJ/mol, respectively. The most favorable hydrolysis path of CS(2) involves a sort of eight-membered ring transition structure formed by six water molecules, among which three water molecules are not involved in the proton transfer, two near to the nonreactive sulfur atom, and one below the parent carbon disulfide. This suggests that the hydrolysis of CS(2) can be mediated with the water molecule(s) and be significantly facilitated by the cooperative effects of the water molecule(s) in the nonreactive region. The catalytic effects of water molecule(s) due to the alleviation of ring strain in the proton transfer process may result from the synergistic effects of rehybridization and charge reorganization from the prereaction complex to the rate-determining transition state structure induced by water molecule(s). PCM solvation models could significantly lower the rate-determining activation Gibbs free energies by 20-38 kJ/mol when two up to six explicit water molecules involved in the neutral hydrolysis of CS(2).

Molecular recognition at methyl methacrylate/n-butyl acrylate (MMA/nBA) monomer unit boundaries of phospholipids at p-MMA/nBA copolymer surfaces.

Lipid structural features and their interactions with proteins provide a useful vehicle for further advances in membrane proteins research. To mimic one of potential lipid-protein interactions we synthesized poly(methyl methacrylate/ n-butyl acrylate) (p-MMA/nBA) colloidal particles that were stabilized by phospholipid (PLs). Upon the particle coalescence, PL stratification resulted in the formation of surface localized ionic clusters (SLICs). These entities are capable of recognizing MMA/nBA monomer interfaces along the p-MMA/nBA copolymer backbone and form crystalline SLICs at the monomer interface. By utilizing attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and selected area electron diffraction (SAD) combined with ab initio calculations, studies were conducted that identified the origin of SLICs as well as their structural features formed on the surface of p-MMA/nBA copolymer films stabilized by 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) PL. Specific entities responsible for SLIC formation are selective noncovalent bonds of anionic phosphate and cationic quaternary ammonium segments of DLPC that interact with two neighboring carbonyl groups of nBA and MMA monomers of the p-MMA/nBA polymer backbone. To the best of our knowledge this is the first example of molecular recognition facilitated by coalescence of copolymer colloidal particles and the ability of PLs to form SLICs at the boundaries of the neighboring MMA and nBA monomer units of the p-MMA/nBA chain. The dominating noncovalent bonds responsible for the molecular recognition is a combination of H-bonding and electrostatic interactions.

Light-induced cytotoxicity of 16 polycyclic aromatic hydrocarbons on the US EPA priority pollutant list in human skin HaCaT keratinocytes: relationship between phototoxicity and excited state properties.

The photocytotoxicity of 16 polycyclic aromatic hydrocarbons (PAHs) on the priority pollutant list of the United States Environmental Protection Agency (US EPA) were tested in human skin HaCaT keratinocytes. A selected PAH was mixed with HaCaT cells and irradiated with a solar simulator lamp for a dose equivalent to 5 min of outdoor sunlight and the cell viability was determined immediately and also after 24 h of incubation. For the cells without incubation after the treatments, it is found that all PAHs with three rings or less, except anthracene, are not photocytotoxic, while the four or five-ring PAHs (except chrysene), benz[a]anthracene, dibenzo[a,h]anthracene, benzo[ghi]perylene, benzo[a]pyrene, indeno[1,2,3-cd]pyrene, benzo[b]fluorenthene, fluorenthene, and pyrene, are photocytotoxic to the human skin HaCaT keratinocytes. If the cells were incubated for 24 h after the treatments, the photocytotoxic effect of the PAHs was greatly amplified in comparison to the nonincubated cells. For the 24 h incubated cells, all PAHs except naphthalene exhibit photocytotoxicity to some extent. Exposure to 5 microM of the 4- and 5-ring PAHs (except chrysene) and 3-ring anthracene more than 80% of the cells lose viability. The photocytotoxicity of the PAHs correlates well with several of their excited state properties: light absorption, excited singlet-state energy, excited triplet-state energy, and HOMO-LUMO energy gap. All the photocytotoxic PAHs absorb light at >300 nm, in the solar UVB and UVA region. There is a threshold for each of the three excited state descriptors of a photocytotoxic PAH: singlet energy <355 kJ/mol (corresponding to 337 nm light), triplet energy <230 kJ/mol (corresponding to 520 nm light), HOMO-LUMO gap <3.6 eV (corresponding to 344 nm light) obtained at the Density Functional Theory B3LYP/6-31G(d) level.

Capillary electrophoresis for diastereomers of (R,S)-tetrahydroisoquinoline-3-carboxylic acid derivatized with (R)-4-nitro-7-(3-aminopyrrolidin-1-yl)-2,1,3-benzoxadiazole: effect of molecular geometries.

Diastereomers derived from (R,S)-tetrahydroisoquinoline-3-carboxylic acid (Tic), a potential neurotoxin with a chiral fluorescence tagging reagent, (R)-4-nitro-7-(3-aminopyrrolidin-1-yl)-2,1,3-benzoxadiazole (NBD-APy), are well resolved by capillary electrophoresis (CE). For a better understanding of the separation mechanism, a semiempirical computational method (i.e., AM1 method) is used to study the molecular geometry, relative energy, and size of the derivatives. The molecular sizes are estimated to be 216.3 and 240.6 cm3/mol for (R)-NBD-APy-(R)-Tic and (R)-NBD-APy-(S)-Tic, respectively. The CE elution order of the diastereomeric derivatives confirms the AM1 computational results: (R)-NBD-APy-(R)-Tic elutes before (R)-NBD-APy-(S)-Tic. The effects of running buffer pH and the addition of a chiral selector, beta-cyclodextrin (beta-CD), on the separation are studied. In the presence of beta-CD, the migration behavior of the diastereomers is changed because of the formation of CD inclusion complexes. Study of the space-filling models for optimized conformations of the diastereomeric derivatives and beta-CD suggests that the geometries of the diastereomers decides that the diastereomers are incorporated into the CD cavity to form CD inclusion complexes with different volumes. Experimental results from CE separations conclude the same.

Chiral CE separation of dopamine-derived neurotoxins.

An enantiomeric separation of dopamine-derived neurotoxins by capillary electrophoresis has been developed. Tetrahydroisoquinoline (TIQ), dopamine (DA), (R/S)-1-benzyl-TIQ (BTIQ), (R/S)-6,7-dihydroxy-1-methyl-TIQ (salsolinol, Sal), and (R/S)-6,7-dihydroxy-1, 2-dimethyl-TIQ (N-methyl-salsolinol, NMSal) were studied as model compounds. The CE running buffer (50 mM phosphate buffer at pH 3.0) contained 1.5 M urea and 12 mM beta-CD as a chiral selector. During separation, the (R)-enantiomers formed more stable inclusion complexes with beta-CD, and thus had a longer migration time than their optical antipodes. It was noticed that the recovery rates of these TIQ derivatives were very poor (< 15%) during protein precipitation, a procedure widely used for cleaning up biological samples. The recovery was significantly improved by pre-mixing the sample with a surfactant (e.g., sodium hexanesulfonate or Triton X-100) to reduce the co-precipitation. The present method in combination with electrospray ionization tandem mass spectrometry (ESI-MS/MS) was applied to study samples obtained from in vitro incubation of two catecholamines, dopamine and epinine, with aldehydes forming neurotoxins including (S)- and (R)-NMSal enantiomers. The later is known to induce Parkinsonism in rats.

Microsolvation of N2H): the nature of interactions in N2H+-(H2)n (n = 1-14) complexes.

Experimental studies of the consecutive growth of N2H + (H2)n clusters led to the discovery of an unusual bonding pattern for species with n = 2-4. Theoretical studies revealed that the ligands are located within five well-separated solvation shells that are visible in structures, values of successive enthalpies and entropies of clustering reactions, vibrational motions, the distribution of atomic charges, and interaction energy decomposition components. The pattern of consecutive enthalpy changes for the second shell (n = 2-5) is complicated. This pattern shows anomalous behavior, although its interpretation is not univocal. A large part of consecutive enthalpies for the clustering reactions is a contribution due to the rotational and vibrational properties of clusters which are difficult for adequate modeling in large systems. The structures of clusters are rationalized based on interaction energy contributions of a different nature. Geometries of complexes are determined by prevailing covalent forces.

Computational studies of tungsten-catalyzed endo-selective cycloisomerization of 4-pentyn-1-ol.

Endo- and exo-cycloisomerizations of 4-pentyn-1-ol have been studied computationally with density functional theory, in conjunction with double-zeta and triple-zeta basis sets, both in the absence and in the presence of tungsten carbonyl catalyst. In the absence of the catalyst, both endo- and exo-cycloisomerizations have been calculated to have a very high activation barrier of approximately 50-55 kcal/mol and cannot take place. With tungsten pentacarbonyl catalyst, endo-cycloisomerization becomes a complex multiple-step reaction and proceeds with a rate-determining barrier of 26 kcal/mol at the C(alpha) --> C(beta) hydride migration step to form a vinylidene intermediate. The primary role of the tungsten catalyst is to stabilize the vinylidene intermediate, thus lowering the rate-determining barrier. The second important role of the tungsten catalyst in endo-cycloisomerization is to assist the OH hydride migration to C(alpha) by making it a multistep process with small activation barriers. The exo-cycloisomerization with the catalyst still has a high rate-determining barrier of 47 kcal/mol. These findings clearly explain the experimentally observed endo-selectivity in the cycloisomerization of 4-pentyn-1-ol derivatives and support the experimentally proposed mechanism.