Ca2+ ions facilitate the organization of the Annexin A2/S100A10 heterotetramer.

Annexin A2 (A2) is a member of the Annexin family, which contains Ca2+ -regulated phospholipid-binding proteins. Annexins associate with S100 proteins to form heterotetramers. The A2/S100A10 heterotetramer (A2t) is the most extensively studied of these heterotetramers. It induces membrane microdomain formation, causes membrane budding, and facilitates proliferation of some cancers. In this work, the first molecular dynamics (MD) study on the complete A2t of 868 amino acids was performed. MD trajectories of more than 600 ns each were generated for complete A2t complexes with and without Ca2+ ions. The outward extension of membrane-binding residues A2-K279 and A2-K281 was shown to be inhibited in the absence of Ca2+ as they were captured by Ca2+ -binding residue D322. F-actin binding residue A2-D339 was observed to occupy either an exposed or buried state in the absence of Ca2+ , while it only occupied the buried state in the presence of Ca2+ . The observed motions of the A2t subunits are highly organized with a strongly correlated central region which is negatively correlated with the periphery of the complex. The central region contains the S100A10 (p11) dimer, A2-N, and A2-I, while the periphery contains A2-II, A2-III, and A2-IV. Novel interactions between A2 and p11 were identified. A2 residues outside of A2-N (K80, R77, E82, and R145) had strong interactions with p11. Residue R145 of A2 may have a significant effect on the dynamics of the system, with its interaction resulting in asymmetric motions of A2. The presented results provide novel insights to inform future experimental studies.

Theoretical Appraisal of Cyclopropenone: Aggregation and Complexes with Water.

Cyclopropenone (HCCOCH, "CPN") is an exotic quasi-aromatic cyclic carbene that abounds in the interstellar medium (ISM). Astronomical observations suggest that (i) stagnate CPN exhibits a tendency to polymerize and that (ii) interactions may occur between CPN and water that is also ubiquitous in the ISM. In this light, density functional theory investigations reveal cooperative hydrogen bonding, which leads to stable polymeric conformations of (CPN)n, tracked up to n = 14. Stable agglomerations with water, however, constitute at best only two CPN and two water molecules, signifying that while CPN exhibits remarkable cooperativity for "cohesive" clustering via hydrogen bonding, this tendency is markedly diminished for "hetero"-interactions. Multifaceted data are employed to probe cogent molecular descriptors, such as structure and energetics of various conformers, vibrational spectroscopic response, molecular electrostatic potential (MESP), effective atomic charges: all these, in unison, describe the evolution of the characteristics upon cluster formation. Salient stretching frequency shifts, as well as charge redistribution gleaned from MESP morphology, have a direct bearing on variegated hydrogen bonding patterns: linear, nonlinear, as well as bifurcated. In particular, characteristic C-H, C═O stretching, and O-H vibrations in the water complexes reveal a "softening" (downshift) of frequencies. While small conformers have markedly distinct MESP variations, the differences become less pronounced with incremental clustering, an effect substantiated by corresponding emergent atomic charges.

Theoretical Probe to the Mechanism of Pt-Catalyzed C-H Acylation Reaction: Possible Pathways for the Acylation Reaction of a Platinacycle.

Density functional theory (DFT) and nudged elastic band (NEB) theory have been used to study the possible pathways for the acylation of cycloplatinated complex A derived from 2-phenoxypyridine, which is conceived as the key step in the platinum-catalyzed acylation of 2-aryloxypyridines. Geometry optimization indicates that the previously proposed intermediate, an arenium ion species as a result of analogous aromatic substitution, is not an energy minimum, but rather cationic Pt-arene η2-complex E is obtained as a stable intermediate. NEB simulations suggest that the minimum energy pathway for the acylation reaction has energy barrier of 33.6 kcal/mol and consists of the following steps: (1) Nucleophilic substitution at acetyl chloride by the platinum of the reactant A forms five-coordinate Pt(IV) acylplatinum complex B with an energy barrier of 21.7 kcal/mol. (2) B undergoes 1,2-acyl migration from the platinum to the cyclometalated carbon through a three-membered platinacycle transition state to give Pt-arene η2-complex E with an energy barrier of 14.0 kcal/mol. (3) E undergoes ligand exchange with chloride to form neutral Pt-arene η2-complex F. (4) F undergoes ligand substitution with acetonitrile to give the product and the energy barrier is small (10.6 kcal/mol). The rate-determining step is the 1,2-acyl migration step. It is interesting to note that intermediate F was not included in the proposed mechanism but was identified by the NEB simulations. Five-coordinate Pt(IV) acylplatinum complex B undergoes barrierless ligand coordination with chloride to form neutral formal oxidative addition acylplatinum complex D; however, D is less stable than reactant A by 2.9 kcal/mol, which also implies that the isolation of an oxidative addition product Pt(IV) complex may be very challenging. The direct reductive elimination of D to form product P has a higher energy barrier (36.6 kcal/mol).

Multigenerational Theoretical Study of Isoprene Peroxy Radical 1-5-Hydrogen Shift Reactions that Regenerate HO x Radicals and Produce Highly Oxidized Molecules.

A computational protocol is employed to glean new insight into the kinetics of several 1,5-hydrogen atom (H) shift reactions subsequent to first- and second-generation OH/O2 additions to isoprene. The M06-2X density functional was initially used with the Nudged Elastic Band (NEB) method to determine the potential energy surface of OH/O2 addition reactions, the 1,5-H shift reactions, and the fragmentation exit channels. The Master Equation Solver for Multi-Energy Well Reactions (MESMER) was applied to determine the rate constants for OH addition and the 1,5-H shifts. M06-2X was capable of quantifying the rate constants of OH addition to the first and second double bonds of isoprene with deviations less than 17% from the experimentally determined values. However, M06-2X underestimated the 1,5-H shift rate constants of second-generation isoprene peroxy radicals. Consequently, MN15, ωB97X-D, and CBS-QB3 methods were employed to compute average barrier heights to first- and second-generation 1,5-H shifts. In the first generation, the rate constants of H abstraction by ß-(1,2) and (4,3) isoprene hydroxy-peroxy radicals from the neighboring hydroxyl group are 1.1 × 10-3 and 2.4 × 10-3 s-1, respectively. These values are determined primarily by the barrier of the H shift reaction and, to a smaller albeit nonnegligible extent, by the stability of the resulting alkoxy radical and the exit barrier leading to C-C bond dissociation. In contrast, the average second-generation rate constant of 1,5-H shifts from H-R-OH sites to the peroxy radical is 1.8 × 10-1 s-1, with tunneling playing the significant role of increasing this value relative to first-generation 1,5-H shifts. Under low NO x conditions, first-generation isoprene oxidation reactions may recycle HO x at levels ranging from 10 to 30% due in large part to 1,5-H shifts, with the recycling efficiency being sensitive to HO2 concentrations and temperature. HO x recycling is expected to increase to levels beyond 80% in second-generation reactions of oxidized isoprene species because of isoprene epoxydiol (IEPOX) formation and further 1,5-H shifts that are kinetically favorable.

Harmonizing accuracy and efficiency: A pragmatic approach to fragmentation of large molecules.

Fragmentation methods offer an attractive alternative for ab initio treatment of large molecules and molecular clusters. However, balancing the accuracy and efficiency of these methods is a tight-rope-act. With this in view, we present an algorithm for automatic molecular fragmentation within Molecular Tailoring Approach (MTA) achieving this delicate balance. The automated code is tested out on a variety of molecules and clusters at the Hartree-Fock (HF)- and Møller-Plesset second order perturbation theory as well as density functional theory employing augmented Dunning basis sets. The results show remarkable accuracy and efficiency vis-à-vis the respective full calculations. Thus the present work forms an important step toward the development of an MTA-based black box code for implementation of HF as well as correlated quantum chemical calculations on large molecular systems.

Glycoconjugated Site-Selective DNA-Methylating Agent Targeting Glucose Transporters on Glioma Cells.

DNA-alkylating drugs continue to remain an important weapon in the arsenal against cancers. However, they typically suffer from several shortcomings because of the indiscriminate DNA damage that they cause and their inability to specifically target cancer cells. We have developed a strategy for overcoming the deficiencies in current DNA-alkylating chemotherapy drugs by designing a site-specific DNA-methylating agent that can target cancer cells because of its selective uptake via glucose transporters, which are overexpressed in most cancers. The design features of the molecule, its synthesis, its reactivity with DNA, and its toxicity in human glioblastoma cells are reported here. In this molecule, a glucosamine unit, which can facilitate uptake via glucose transporters, is conjugated to one end of a bispyrrole triamide unit, which is known to bind to the minor groove of DNA at A/T-rich regions. A methyl sulfonate moiety is tethered to the other end of the bispyrrole unit to serve as a DNA-methylating agent. This molecule produces exclusively N3-methyladenine adducts upon reaction with DNA and is an order of magnitude more toxic to treatment resistant human glioblastoma cells than streptozotocin is, a Food and Drug Administration-approved, glycoconjugated DNA-methylating drug. Cellular uptake studies using a fluorescent analogue of our molecule provide evidence of uptake via glucose transporters and localization within the nucleus of cells. These results demonstrate the feasibility of our strategy for developing more potent anticancer chemotherapeutics, while minimizing common side effects resulting from off-target damage.

Noncovalent interactions underlying binary mixtures of amino acid based ionic liquids: insights from theory.

Mixtures of ionic liquids formed by blending a common 1-methyl-3-butylimidazolium [Bmim] cation with the dicarboxylic amino acid anions viz., aspartic acid [Asp], asparagine [Asn], glutamic acid [Glu], and glutamine [Gln], have been investigated by employing dispersion corrected density functional theory. Binary mixtures of [Bmim]2[Asp][Asn] and [Bmim]2[Glu][Gln] ionic liquids emerge with distinct structural patterns. Competition between the constituting anions towards cationic binding sites in acidic and basic (polar) amino acid binary mixtures engenders diverse noncovalent interactions, viz., C-HO hydrogen bonding, π-π stacking, and lpπ and CHπ interactions, which impart local liquid structure to these systems governing the structural and physicochemical properties of such double salt ionic liquids (DSILs). The DSIL conformers reveal distinct structural features arising from the middle, normal and front arrangements of anions combined with parallel, antiparallel, rotated or displaced orientations of the cations. The inclusion of dispersion corrections through the D3 method affects their binding energies significantly bringing forth alteration in their energy rank order. Molecular insights accompanying the ion aggregates provide directives for the use of DSILs with improved performance in tribological applications.

Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene.

The chemical reaction mechanism of NO addition to two ß and δ isoprene hydroxy-peroxy radical isomers is examined in detail using density functional theory, coupled cluster methods, and the energy resolved master equation formalism to provide estimates of rate constants and organic nitrate yields. At the M06-2x/aug-cc-pVTZ level, the potential energy surfaces of NO reacting with ß-(1,2)-HO-IsopOO• and δ-Z-(1,4)-HO-IsopOO• possess barrierless reactions that produce alkoxy radicals/NO2 and organic nitrates. The nudged elastic band method was used to discover a loosely bound van der Waals (vdW) complex between NO2 and the alkoxy radical that is present in both exit reaction channels. Semiempirical master equation calculations show that the ß organic nitrate yield is 8.5 ± 3.7%. Additionally, a relatively low barrier to C-C bond scission was discovered in the ß-vdW complex that leads to direct HONO formation in the gas phase with a yield of 3.1 ± 1.3%. The δ isomer produces a looser vdW complex with a smaller dissociation barrier and a larger isomerization barrier, giving a 2.4 ± 0.8% organic nitrate yield that is relatively pressure and temperature insensitive. By considering all of these pathways, the first-generation NOx recycling efficiency from isoprene organic nitrates is estimated to be 21% and is expected to increase with decreasing NOx concentration.

Probing Molecular Interactions in Functionalized Asymmetric Quaternary Ammonium-Based Dicationic Ionic Liquids.

Electronic structure, binding energies, and spectral characteristics of functionalized asymmetric dicationic ionic liquids (DILs) composed of quaternary ammonium cations substituted with the ethoxyethyl and allyl/3-phenylpropyl/methoxyethoxyethyl/pentyl functionalities on two different nitrogen centers of the dication and the bis(trifluoromethanesulfonyl)imide (Tf2N-) anion were derived employing the dispersion-corrected density functional theory. DILs based on methoxyethoxyethyl-substituted cation reveal stronger binding toward the Tf2N- anion. The measured glass transition temperatures are found to be strongly dependent on the cation-anion binding facilitated through noncovalent interactions with dominant contributions from the electrostatics and hydrogen bonding. The manifestations of these interactions to vibrational spectra, in particular, to SO2 and CF3 stretchings in the complexes are presented. It has been demonstrated that the frequency down (red)-shift of the SO2 stretching in these DILs with varying substituent follows the order: methoxyethoxyethyl (35 cm-1) > allyl (23 cm-1) > pentyl (20 cm-1) > 3-phenylpropyl (5 cm-1), which is consistent with the strength of cation-anion binding. The CF3 stretching of the anion exhibits the frequency shift in the opposite direction with its hierarchy being reversed to that of SO2 stretchings; the largest upshift (blue shift) of 60 cm-1 was predicted for the DILs composed of 3-phenlpropyl substituted dications. The direction of such frequency shift has been rationalized through the difference molecular electron density maps in conjunction with the electron density at the bond critical point in the quantum theory of atoms in molecules. The underlying cation-anion binding has been analyzed through charge distribution analysis characterized in terms of molecular electrostatic potential topography. Furthermore, the observed decomposition temperatures of DILs are shown to correlate well with the maximum surface electrostatic potential parameters in quantum theory of atoms in molecules.

Encaged molecules in external electric fields: A molecular "tug-of-war".

Response of polar molecules CH3OH and H2O2 and a non-polar molecule, CO2, as "guests" encapsulated in the dodecahedral water cage (H2O)20 "host," to an external, perturbative electric field is investigated theoretically. We employ the hybrid density-functionals M06-2X and ωB97X-D incorporating the effects of damped dispersion, in conjunction with the maug-cc-pVTZ basis set, amenable for a hydrogen bonding description. While the host cluster (cage) tends to confine the embedded guest molecule through cooperative hydrogen bonding, the applied electric field tends to rupture the cluster-composite by stretching it; these two competitive effects leading to a molecular "tug-of-war." The composite remains stable up to a maximal sustainable threshold electric field, beyond which, concomitant with the vanishing of the HOMO-LUMO gap, the field wins over and the cluster breaks down. The electric-field effects are gauged in terms of the changes in the molecular geometry of the confined species, interaction energy, molecular electrostatic potential surfaces, and frequency shifts of characteristic normal vibrations in the IR regime. Interestingly, beyond the characteristic threshold electric field, the labile, distorted host cluster fragmentizes, and the guest molecule still tethered to a remnant fragment, an effect attributed to the underlying hydrogen-bonded networks.

Epoxide as a precursor to secondary organic aerosol formation from isoprene photooxidation in the presence of nitrogen oxides.

Isoprene is a substantial contributor to the global secondary organic aerosol (SOA) burden, with implications for public health and the climate system. The mechanism by which isoprene-derived SOA is formed and the influence of environmental conditions, however, remain unclear. We present evidence from controlled smog chamber experiments and field measurements that in the presence of high levels of nitrogen oxides (NO(x) = NO + NO2) typical of urban atmospheres, 2-methyloxirane-2-carboxylic acid (methacrylic acid epoxide, MAE) is a precursor to known isoprene-derived SOA tracers, and ultimately to SOA. We propose that MAE arises from decomposition of the OH adduct of methacryloylperoxynitrate (MPAN). This hypothesis is supported by the similarity of SOA constituents derived from MAE to those from photooxidation of isoprene, methacrolein, and MPAN under high-NOx conditions. Strong support is further derived from computational chemistry calculations and Community Multiscale Air Quality model simulations, yielding predictions consistent with field observations. Field measurements taken in Chapel Hill, North Carolina, considered along with the modeling results indicate the atmospheric significance and relevance of MAE chemistry across the United States, especially in urban areas heavily impacted by isoprene emissions. Identification of MAE implies a major role of atmospheric epoxides in forming SOA from isoprene photooxidation. Updating current atmospheric modeling frameworks with MAE chemistry could improve the way that SOA has been attributed to isoprene based on ambient tracer measurements, and lead to SOA parameterizations that better capture the dependency of yield on NO(x).

The N-terminal of annexin A1 as a secondary membrane binding site: a molecular dynamics study.

Annexin A1 has been shown to cause membrane aggregation and fusion, yet the mechanism of these activities is not clearly understood. In this work, molecular dynamics simulations were performed on monomeric annexin A1 positioned between two negatively charged monolayers using AMBER's all atom force field to gain insight into the mechanism of fusion. Each phospolipid monolayer was made up of 180 DOPC molecules and 45 DOPG molecules to achieve a 4:1 ratio. The space between the two monolayers was explicitly solvated using TIP3P waters in a rectilinear box. The constructed setup contained up to 0.14 million atoms. Application of periodic boundary conditions to the simulation setup gave the desired effect of two continuous membrane bilayers. Nonbonded interactions were calculated between the N-terminal residues and the bottom layer of phospholipids, which displayed a strong attraction of K26 and K29 to the lipid head-groups. The side-chains of these two residues were observed to orient themselves in close proximity (∼3.5 Å) with the polar head-groups of the phospholipids.

Photochemistry of 6-amino-2-azido, 2-amino-6-azido and 2,6-diazido analogues of purine ribonucleosides in aqueous solutions.

The photochemistry of 6-amino-2-azidopurine, 2-amino-6-azidopurine and 2,6-diazidopurine ribonucleosides has been investigated in aqueous solutions under aerobic and anaerobic conditions. Near UV irradiation of 6-amino-2-azido-9-(2',3',5'-tri-O-acetyl-ß-D-ribofuranosyl)purine and 2-amino-6-azido-9-(2',3',5'-tri-O-acetyl-ß-D-ribofuranosyl)purine in the presence of oxygen leads to efficient formation of 6-amino-2-nitro-9-(2',3',5'-tri-O-acetyl-ß-D-ribofuranosyl)purine and 2-amino-6-nitro-9-(2',3',5'-tri-O-acetyl-ß-D-ribofuranosyl)purine. Under anaerobic conditions, both azidopurine ribonucleosides preferentially undergo photoreduction to 2,6-diamino-9-(2',3',5'-tri-O-acetyl-ß-D-ribofuranosyl)purine. The structures of the photoproducts formed were confirmed by UV, NMR and HR ESI-TOF MS spectral data. The photoproducts observed in this study for the aminoazidopurines are distinctly different from those observed previously for 6-azidopurine. When no amino group is present, the photochemistry of 6-azidopurine leads to the formation of a 1,3,5-triazepinone nucleoside. The energetics of the 6-nitreno moiety along both oxidation and ring expansion pathways was calculated using the nudged elastic band (NEB) method based on density functional theory (DFT) using DMol3. The role of the 2-amino group in regulating the competition between these pathways was elucidated in order to explain how the striking difference in reactivity under irradiation arises from the greater spin density on the 6-nitreno-9-methyl-9H-purin-2-amine, which essentially eliminates the barrier to oxidation observed in 6-nitreno-9-methyl-9H-purine. Finally, the importance of tetrazolyl intermediates for the photochemical activation of azide bond cleavage to release N2 and form the 6-nitreno group was also corroborated using the DFT methods.

The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids.

Anionic and zwitterionic micelles are often used as simple models for the lipids found in bacterial and mammalian cell membranes to investigate antimicrobial peptide-lipid interactions. In our laboratory we have employed a variety of 1D, 2D, and diffusion ordered (DOSY) NMR experiments to investigate the interactions of antimicrobial peptides containing unnatural amino acids with SDS and DPC micelles. Complete assignment of the proton spectra of these peptides is prohibited by the incorporation of a high percentage of unnatural amino acids which don't contain amide protons into the backbone. However preliminary assignment of the TOCSY spectra of compound 23 in the presence of both micelles indicated multiple conformers are present as a result of binding to these micelles. Chemical Shift Indexing agreed with previously collected CD spectra that indicated on binding to SDS micelles compound 23 adopts a mixture of α-helical structures and on binding to DPC micelles this peptide adopts a mixture of helical and ß-turn/sheet like structures. DOSY NMR experiments also indicated that the total positive charge and the relative placement of that charge at the N-terminus or C-terminus are important in determining the mole fraction of the peptide that will bind to the different micelles. DOSY and (1) H-NMR experiments indicated that the length of Spacer #1 plays a major role in defining the binding conformation of these analogs with SDS micelles. Results obtained from molecular simulations studies of the binding of compounds 23 and 36 with SDS micelles were consistent with the observed NMR results.

Synthesis, structure, photophysics, and a DFT study of phosphorescent C*N∧N- and C∧N∧N-coordinated platinum complexes.

The reaction of N,N-diphenyl-2,2'-bipyridin-6-amine (L1) and N,N-diphenyl-6-(1H-pyrazol-1-yl)pyridin-2-amine (L2) with K2PtCl4 produced C*N(∧)N-coordinated cycloplatinated compounds with a five-six fused metallacycle 1a and 2a, respectively, which were then converted into their phenylacetylide derivatives 1b and 2b, respectively. Similar reactions starting from 2-phenyl-6-(1H-pyrazol-1-yl)pyridine (L3) produced C(∧)N(∧)N-coordinated platinum complexes 3a and 3b with a five-five-fused metallacycle. The structures of 1a, 1b, 2b, 3a, and 3b were determined by X-ray crystallography. The C*N(∧)N-coordinated platinum complexes are closer to a square geometry, whereas the C(∧)N(∧)N-coordinated complexes display a nearly perfect planar geometry. The π···π interactions were revealed in the crystal packing for 1a, 2b, and 3a with a π···π contact of 3.450, 3.422, and 3.414 Å, respectively. Two conformers were revealed in the crystal structure of 2b, one with the phenyl ring of the phenylacetylide being approximately parallel with the coordination plane and the other with the phenyl ring being approximately perpendicular to the coordination plane. Both 1a and 1b are weakly emissive in the red region. Complexes 2a and 3a are also weakly emissive, but their acetylide derivatives 2b and 3b emitted strongly green light at room temperature with quantum yields of 43 and 62%, respectively. DFT/TDDFT calculations were performed to elucidate the nature of their electronic transitions. The calculations suggested that lowest singlet and triplet excited states are characteristic of a mixed state involving one or more charge-transfer transitions such as ILCT, MLCT, and LLCT.

A computational study of acid catalyzed aerosol reactions of atmospherically relevant epoxides.

Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that drive epoxide reactions in the particle phase. Specifically, the importance of acid catalysis and solvent polarity are investigated using a variety of epoxides and nucleophiles. The condensed phase is modeled using molecular clusters immersed in a dielectric continuum and a majority of the calculations are performed with the M062x density functional and the 6-311++G** basis set. Calculations of acid catalyzed epoxide hydrolysis transition states for simple primary, secondary and tertiary epoxides are consistent with an A-2 mechanism where the nucleophile (water) interacts with an epoxide carbon in the transition state. By applying transition state theory to this mechanism, the overall rate constants of epoxide reactions such as hydrolysis, organosulfate formation, organonitrate formation and oligomerization are determined. The calculations indicate that the acid catalyzed hydrolysis rate constant of 2-methyl-2,3-epoxybutane-1,4-diol (ß-IEPOX--an isoprene epoxide produced under low NOx conditions) is approximately 30 times greater than 2-methyl-2,3-epoxypropanoic acid (MAE--methacrylic acid epoxide derived from isoprene and produced at high NOx concentrations). Furthermore, acid catalyzed organosulfate formation and epoxide oligomerization reactions are competitive and appear to be kinetically favorable over the hydrolysis of IEPOX.

Exploring electric field induced structural evolution of water clusters, (H2O)n [n = 9-20]: density functional approach.

Response of neutral water clusters (H(2)O)(n), n = 9-20, to external uniform dipolar static electric fields is studied for some lowest-energy conformers for each "n" within an energy band of about 9 kcal mol(-1) of their field-free counterparts. We perform density functional theory computations with B3LYP∕6-311++G(2d,2p) model chemistry. Increasing the electric field destabilizes and distorts a cluster by elongating, hence weakening its hydrogen bonds, culminating into a catastrophic structural breakdown beyond a specific threshold field-strength. The electric field induced conformational transitions to extended structures stretched along the field direction to lower-energy configurations that appear as local minima on their potential energy surface are presented. It is observed that a typical structural transition of this type is always accompanied by an abrupt increase in the electric dipole moment of the cluster over and above its smooth increment with increasing applied field; the increase being phenomenal during breakdown. Interestingly, the HOMO-LUMO energy gap for a given conformer is found to diminish with increasing field strength, abruptly approaching zero at structural breakdown. In essence, the structural evolution traced through hydrogen-bond networks of the clusters reveals multiple enhancements in size by "opening up" of three-dimensional morphologies to form net-like structures with less number of hydrogen bonds. These clusters exhibit greater structural complexity than that encountered in the relatively small clusters reported previously.

Interactions and conformational changes of annexin A2/p11 heterotetramer models on a membrane: a molecular dynamics study.

Ca2+-dependent membrane-binding by the Annexin A2/p11 heterotetramer (A2t) plays an important role in various biological processes including fibrinogen activation and exocytosis in neuroendocrine cells. Two models where A2t associates with a single membrane surface were generated and used to perform molecular dynamics simulations. The first model mimics initial A2t-membrane binding through both Annexin A2 (A2) subunits of A2t (TS model) while the second model mimics A2t-binding through a single A2 subunit (OS model). Conformational changes were summarized using principal component analysis (PCA), simulation snapshots, and distance plots from the simulations. The full TS model, including the p11 dimer, fully associates with the membrane adopting a stable structure with little conformational variation as evidence by PCA. The unassociated subunits of the OS model moved toward the membrane. The molecular mechanics/Generalized-Born surface area (MMGBSA) method was applied to investigate the energetics of the models. The MMGBSA results demonstrated that R63 of p11 was the primary contributor to the p11-membrane interaction. The TS model results were both consistent with those found in the literature and provide novel insights about the specific residues driving the A2t-membrane interaction. Additionally, it represents the most complete model of A2t on the membrane surface available.Communicated by Ramaswamy H. Sarma.

Intramolecular hydrogen bond energy and cooperative interactions in α-, ß-, and γ-cyclodextrin conformers.

Accurate estimation of individual intramolecular hydrogen bond (H-bond) energies is an intricate task for multiply H-bonded systems. In such cases, the hydrogen bond strengths could be highly influenced by the cooperative interactions, for example, those between hydroxyl groups in sugars. In this work, we use the recently proposed molecular tailoring approach-based quantification (Deshmukh, Gadre, and Bartolotti, J Phys Chem A 2006, 110, 12519) to the extended systems of cyclodextrins (CDs). Further, the structure and stability of different conformers of α-, ß-, and γ-CDs are explained based on the energetics and cooperative contribution to the strength of these H-bonds. The estimated O-H···O H-bond energies in the various CD conformers are found to vary widely from 1.1 to 8.3 kcal mol(-1). The calculated energy contributions to cooperativity toward the H-bond strengths fall in the range of 0.25-2.75 kcal mol(-1).

Highly luminescent tridentate N

A series of cyclometalating ligands, N-phenyl-N-(3-(pyridin-2-yl)phenyl)pyridin-2-amine (L1), N-(3-(1H-pyrazol-1-yl)phenyl)-N-phenylpyridin-2-amine (L2), N-phenyl-N-(3-(quinolin-2-yl)phenyl)pyridin-2-amine (L3), N-phenyl-N-(3-(pyridin-2-yl)phenyl)quinolin-2-amine (L4), N-(3-(isoquinolin-1-yl)phenyl)-N-phenylpyridin-2-amine (L5), and N-phenyl-N-(3-(pyridin-2-yl)phenyl)isoquinolin-1-amine (L6), were synthesized, which reacted with K(2)PtCl(4) in glacial acetic acid to produce N^C*N-coordinated platinum(II) complexes featured in a fused five-six-membered metallacycle, 1-6, respectively. The structures of 1, 3, 4, and 6 were determined by single crystal X-ray crystallography. The square geometries of the complexes are improved when compared with those of the N^C^N-coordinated complexes as the bite angles for the platinum in N^C*N-coordinated complexes 1, 3, and 4 are increased. The Pt-C bonds (1.94-1.95 Å) are shorter than those of C^N^N-coordinated platinum complexes but longer than those found for N^C^N-coordinated platinum complexes. With the increase of the steric interaction, the distortion of the molecules from a planar coordination geometry becomes more and more severe from 1 to 3 to 4 and 6, and in 6, the N-phenyl ring has to stand up on the coordination sphere to minimize the steric interaction with the N-isoquinolyl ring. The photophysical properties of the complexes were studied, and their absorption and emission spectra were interpreted by relating to the structural features revealed by the X-ray crystal structures and the orbital characters predicted by DFT calculations. All complexes are emissive in fluid at room temperature, and the quantum yields (up to 0.65) are comparable to those of highly emissive N^C^N-coordinated platinum complexes. Self-quenching was not observed in the concentration range of 10(-6) to 10(-4) M. Large rigidochromic shifts for the emissions of 2, 4, and 6 upon cooling from room temperature to rigid glass (77 K) were observed. Two different triplet states that control the emissions were proposed to account for the photophysical properties of 6.