Search

In this work we report a joint experimental and computational study on the 2,5-dimethylfuran oxidation reaction in the gas phase initiated by atomic oxygen O(3P). The experiments have been performed by using vacuum-ultraviolet synchrotron radiation at the Advanced Light Source (ALS) of the Lawrence Berkeley National Laboratory (LBNL), at a temperature of 550 K and a pressure of 8 Torr. The experimental data were supported by quantum-chemical calculations along with a kinetic model, also taking into account the possible involvement of different magnetic states, performed in the framework of the RRKM theory. Propyne, acetaldehyde, methylglyoxal, dimethylglyoxal, 3-penten-2-one, 2,5-dimethylfuran-3(2H)-one, and 1,2-diacetyl ethylene have been identified as the main primary products arising under the conditions of the experiment. Our computational model suggests that these species can be formed at the concentration and branching ratio experimentally observed only in the presence of a non-negligible fraction of non-thermalized intermediates.

An amphiphilic calix[6]arene, alone or complexed with an axle to form a pseudo-rotaxane, has been embedded into liposomes prepared from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and the permeability of the membrane-doped liposomes towards Cl− ions has been evaluated by using lucigenin as the fluorescent probe. The pseudo-rotaxane promotes transmembrane transport of Cl− ions more than calix[6]arene does. Surprisingly, the quenching of lucigenin was very fast for liposomes doped with the positively charged axle alone. Molecular dynamics (MD) simulations and quantum-chemical calculations were also carried out for providing a semi-quantitative support to the experimental results.

The investigation on tandem addition/cyclization reactions of β-(2-aminophenyl)-α,β-ynones with aryl isocyanates/benzoyl isothiocyanate is reported. Experimental results show the suitable conditions to selectively direct the reaction outcome towards the product of 6-exo-dig N-, O-, or S-annulation of the in situ generated alkynyl urea/thiourea intermediate. The reaction of a variety of β-(2-aminophenyl)-α,β-ynones with aryl isocyanates/benzoyl isothiocyanate led to the selective formation of quinazoline or benzoxazine/benzothiazine derivatives, respectively. Density functional theory calculations provide a plausible rationale for the reaction outcome.

Two oxovanadium(IV) complexes containing 4-acyl-5-pyrazolonate-κ2-O,O' bidentate ligands with different chain lengths in the acyl moiety, namely HQC6 (complex I) and HQC17 (complex II), have been synthetized and full characterized, to study their catalytic activity toward the mild and selective oxidation of olefins or model organosulphur substrates, promoted by H2O2 or tert-butyl hydroperoxide (TBHP). The influence due to the type of solvent, likewise ionic liquids (ILs) or conventional medium, was analysed. H2O2 has proven less efficient, in comparison to TBHP. Quantum-chemical calculations have shown that, the key catalytic species involved and, consequently, the actual mechanism might be slightly different according to the oxidant used, i.e. the peroxo VO(QMe)(O2) adduct in the case of H2O2 and the tert-butylperoxo VO(QMe)2(OOt-Bu) adduct in the case of TBHP. Preliminary calculations suggested that, in ionic liquids, the VO(QMe)2 complex might reveal relatively unstable, hence qualitatively explaining the moderate efficiency observed in these media.

A series of cis-dioxomolybdenum(VI) α-amino acid containing compounds I–V has been investigated as potential catalyst precursors for the mild and selective oxyfunctionalization of conjugated or unconjugated olefins like styrene, α-methylstyrene, cis-β-methylstyrene, cyclohexene and cyclooctene, using tert-butyl hydroperoxide (TBHP) as main oxidant. All the I–V complexes behaved as active heterogeneous and recyclable catalysts, showing good to quantitative conversion values of the substrate. In all cases, high selectivity toward the corresponding epoxide formation was detected. No substantial difference in terms of efficiency has been observed among the different catalysts I–V, thus confirming that the different nature of the amino acidic side-chain does not strictly affect the catalytic process. Insights into mechanistic details and reaction free energy profile of catalytic oxidations by means of quantum chemical calculations have been discussed.

The scientific relevance of quinolines is strictly linked to the fine-tuning of their features by functionalizing the heterocyclic core. Consequently, the compounds of this class are very versatile and can be used as possible drugs for a lot of medical applications. In this work, the inclusion of eight synthetic quinoline derivatives in liposomes formulated with different lipids was investigated in terms of the encapsulation efficiency and to highlight the effect on the liposome size distribution and thermotropic behavior. Excellent encapsulation was accomplished with all the quinoline/phospholipid combinations. Differences in the interactions at the molecular level, dependent on the quinoline molecular scaffolds and lipid structure, were observed, which could significantly bias the interaction with the drug and its release in pharmaceutical applications. Experiments in combination with computational studies demonstrated that the UV absorption of quinolines with expanded conjugation could be affected by the environment polarity. This was probably due to a solvent-dependent ability of these quinolines to stack into aggregates, which could also occur upon inclusion into the lipid bilayer.

Liposomes loaded with drug&ndash, cyclodextrin complexes are widely used as drug delivery systems, especially for species with low aqueous solubility and stability. Investigation of the intimate interactions of macrocycles with liposomes are essential for formulation of efficient and stable drug-in-cyclodextrin-in-liposome carriers. In this work, we reported the preparation of unilamellar vesicles of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) embedded with native &beta, cyclodextrin and two synthetic derivatives: heptakis(2,3,6-tri-O-methyl)-&beta, cyclodextrin (TMCD) and heptakis(2,3-di-O-acetyl)-&beta, cyclodextrin (DACD). We then studied the effect of these macrocycles on the liposomal size, membrane viscosity, and liposomal stability at different temperatures and concentrations. We observed that TMCD and DACD affected vesicle size and the change of size was related to CD concentration. Irrespective of its nature, the macrocycle established interactions with the phospholipidic head groups, preventing cyclodextrins to diffuse into the lipid bilayer, as confirmed by molecular dynamics simulations. Such supramolecular structuring improves liposome stability making these colloid systems promising carriers for biologically active compounds.

Two calix[4]resorcinarenes, which differ in the length of the alkyl chain on the methylene bridge between the aromatic rings, have been embedded in unilamellar liposomes prepared from 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine in three host/guest ratios, following two different procedures. The effect of the insertion of the guests has been evaluated through the measurements of the viscosity and the kinetic stability of the liposomal systems by means of the fluorescent probes pyrene and 5(6)-carboxyfluorescein. The presence of the guests reduces the viscosity of the liposomes, suggesting a modification of the bilayer structure. However, this does not affect liposome stability. A calix[4]resorcinarene cavitand with a more rigid conformation compared to the parent resorcinarene, has been also synthetized and embedded in liposomes. The free energy of the insertion of the substrates in the lipid bilayer has been evaluated through Molecular Dynamics simulations.

The theoretical modeling of chemical reactions in condensed phase still represents an open field of investigation for theoretical–computational chemistry. In this context, we have proposed a methodology (the Perturbed Matrix Method [PMM]), based on the first principles of statistical mechanics and on the use of molecular simulations, which has demonstrated its ability in quantitatively predicting the kinetics and the thermodynamics of chemical reactions in complex atomistic environments. In this study, we demonstrate the features of PMM by modeling the resonant Electron Transfer bimolecular reaction between ferrocene and ferrocenium in solution. The obtained results, despite the adopted approximations and the intrinsic limitations of the approach, are in very good agreement with the experimental data and demonstrate the ability of the method for addressing complex reactions in solution and for evaluating the kinetics of slow events out of the potentialities of the state-of-the-art molecular simulations.

We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra. (C) 2017 Elsevier B.V. All rights reserved.

β-(2-Aminophenyl)-α,β-ynones afforded 3-unsubstituted 2-acylindoles in good yields in the presence of 20 mol % AgOTf under (microwave) MW heating. The use CuOTf as a catalyst resulted in a similar reaction outcome, generally with a lower efficiency. This transformation represents the first example of 5- endo-dig cyclization of 2-alkynylanilines bearing an acyl group linked to the triple bond. By contrast with the previously reported gold-catalyzed reaction of β-(2-aminophenyl)-α,β-ynones, which resulted in the formation of dibenzo[1,5]diazocines through a sequential process triggered by an intermolecular hydroamination, a selective intramolecular anti-Michael hydroamination was observed in the present study by silver/copper catalysis. Density functional theory calculations on the Ag-catalyzed reaction revealed that the catalyst induces an electrostatic arrangement in the TS coherent with the experimentally observed cyclization.

Anoplin, a cationic decapeptide amide GLLKRIKTLL-NH2 derived from venom sac of the solitary wasp Anoplius samariensis has been investigated through Molecular Dynamics. The wild-type (WT) and four isoforms were simulated both in water and in the membrane-mimicking solvent trifluoroethanol (TFE). In water all the investigated species, found to be in rapid equilibrium between different conformational states, can be considered as unfolded. On the other hand, in TFE all the systems enhance their rigidity and, in general, show α-helix as the main folded conformation. Interestingly, a semi-quantitative thermodynamic analysis has suggested that the folding driving force is not always the same being in some cases (e.g., the WT Anoplin) of entropic nature and in other cases of energetic nature.

A theoretical–computational study based on Molecular Dynamics simulations and Perturbed Matrix Method (MD–PMM) calculations was carried out for evaluating some properties of solvated Ferrocene including the UV–Vis spectrum and the redox potential. The results, in rather good agreement with the experimental values, display that Ferrocene low-lying excited states are scarcely affected by the change of solvent polarity. On the other hand, the Ferrocene/Ferricinum redox potential show a sharp, although not dramatic, dependency on the nature of the solvent essentially because of the sensitivity of the charged Ferricinium species to the solvent electric field fluctuation. The present study is the first one theoretically addressing, with the use of explicit solvent calculations, the Ferrocene UV spectrum and the Ferricinium/Ferrocene couple redox potential, a quantity proposed by the IUPAC Electrochemical Commission as reference electrode potential for non-aqueous solutions.

Conjugated organic polymers based on substituted thiophene units are versatile building blocks of many photoactive materials, such as photochromic molecular switches or solar energy conversion devices. Unraveling the different processes underlying their photochemistry, such as the evolution on different electronic states and multidimensional structural relaxation, is a challenge critical to defining their function. Using femtosecond stimulated Raman scattering (FSRS) supported by quantum chemical calculations, we visualize the reaction pathway upon photoexcitation of the model compound 2-methyl-5-phenylthiophene. Specifically, we find that the initial wavepacket dynamics of the reaction coordinates occurs within the first ≈1.5 ps, followed by a ≈10 ps thermalization. Subsequent slow opening of the thiophene ring through a cleavage of the carbon-sulfur bond triggers an intersystem crossing to the triplet excited state. Our work demonstrates how a detailed mapping of the excited-state dynamics can be obtained, combining simultaneous structural sensitivity and ultrafast temporal resolution of FSRS with the chemical information provided by time-dependent density functional theory calculations.

A computational study based on standard Density Functional Theory and polarized continuum model has been carried out for investigating the essential mechanistic features occurring in the catalytic oxidation of two model substrates, namely ethylene and 1,3-butadiene, promoted by vanadyl acetylacetonate [VO(acac)2] in the presence of hydrogen peroxide. Results, showing in general a qualitative agreement with experimental data carried out on more complex systems, provide quite different scenarios depending on the conditions employed for the reaction. In particular, under thermodynamic control, no selectivity is observed between the two competitive routes, either epoxidation or double bond oxidative cleavage, in both the substrates. On the other hand, under kinetic control, in both systems the double bond oxidative cleavage is always the favored path, although in the case of 1,3-butadiene the difference with the epoxidation route is enhanced, this confirming that the selectivity is sensitive to the nature of the substituent in the vinyl position.

The hydroarylation of 3-arylprop-2-yn-1-amine derivatives with arylboronic acids has been studied in the presence of rhodium or palladium catalysts. By using a rhodium-based catalytic system, β,γ-diarylallylamines were isolated in good yields. By contrast, the formation of the regiosomeric γ,γ-diarylallylamines was achieved by means of a palladium catalyst in the presence of acetic acid. The complementary regioselectivity displayed by these two processes is a consequence of different catalytic cycles, involving respectively carborhodation or hydropalladation of the coordinated alkyne as key steps. Calculated charge distributions in the π-complexes are in accord with the results obtained.

Objectives: The aim of this article is biochemical and kinetic characterization of CTX-M-43, a natural Asp-240!Gly mutant of CTX-M-44 (ex Toho-1), from a clinical isolate of Acinetobacter baumannii isolated in a Bolivian hospital. Methods: Steady-state kinetic parameters (Km and kcat) were determined for a large pattern of substrates. Analysis of inactivators and transient inactivators was performed to determine the efficiency of acylation (k12/K) and the deacylation constant (k13). Molecular modelling of Michaelis complex of ceftazidime, cefotaxime and ceftibuten, obtained from molecular mechanics calculations, was carried out. Results: CTX-M-43 showed a general increase in affinity towards all cephalosporins tested, with respect to CTX-M-44. Carbapenems acted as inactivators with a good acylation efficiency for meropenem and ertapenem and significant deacylation constant for imipenem. MICs of imipenem obtained at a higher bacterial inoculum of recombinant Escherichia coli were increased. Conclusions: Kinetic data and molecular modelling of Michaelis complex confirmed that Asp-240!Gly allows a better accommodation of the bulky C7b aminothiazol-oxyimino substituent, resulting in a general increase in the enzyme affinity towards oxyimino cephalosporins. The ascertained potentialities of CTX-M-type enzymes, supported by the kinetic data and the behaviour of the recombinant E. coli at different bacterial inocula towards carbapenems, make a possible evolution of those enzymes towards a carbapenemase activity plausible.

The Pd-catalyzed hydroarylation of β-(2-aminoaryl)-α,β-ynones with organoboron derivatives, leading to 2,4-diarylquinolines in good to excellent yields through sequential cycloamination, has been investigated. The reaction is catalyzed by both Pd(II) and Pd(0) precatalysts, and can be carried out even under neutral conditions. The regiochemical outcome is inverted with respect to the Pd-catalyzed hydroarylation of β-(2-aminoaryl)-α,β-ynones with aryl iodides. This aspect has been rationalized using quantum-chemical calculations, which show significant differences between the energy barriers of the regioisomeric transition states for the migratory insertion (hydropalladation) step, and are consistent with the charge density of the π complex that undergoes such insertion.

Time-dependent density functional theory (TD-DFT) calculations were performed to obtain vertical excitation energies from the ground state to different low-lying singlet excited states of the protonated alpha-84 phycocyanobilin chromophore (alpha-84 PCBH(+)). It clearly emerges that three gradient-corrected approximation functionals (B3LYP, PBE0, and PBEPBE) show a similar description, confirming the proposed valence assignment of the strongest UV-vis absorption band at 618 nm. Moreover, our results show that there are not appreciable differences, in terms of excitation wavelength of the main peak, between the alpha-84 PCBH(+) chromophore and a model system in which the two propionic chains have not been taken into account. Finally, with the precise aim of investigating the effects of alpha-84 PCBH(+) conformational fluctuations on its electronic properties, vertical excitation energies obtained for the potential energy local minimum structure were also refined using a recently proposed TD-DFT/principal component analysis/Car-Parrinello molecular dynamics computational approach. Interestingly, and in line with previous results on another photosensitive complex, this study essentially suggests that interaction with the surrounding environment (protein matrix plus solvent molecules) coupled with the large amplitude fluctuation of the whole C-Phycocyanin (C-PC) pigment protein can affect the electronic properties of the alpha-84 PCB chromophore and therefore its biological activity.

Due to its high quantum yield and long fluorescence lifetime, pyrene molecule is a widely used fluorescence probe. From a theoretical–computational viewpoint, the modeling of its emission properties in different environments still represents a challenge, mainly because the coupling with the environment severely affects its emission behavior. We employed our computational–theoretical approach to quantitatively model the pyrene emission, which combines quantum chemical calculations with all-atom molecular dynamics simulations. Our calculated fluorescence properties, well matching the experimental data, highlight that even slight geometrical fluctuations of pyrene at room temperature can provide relevant effects on its radiative lifetime.

In this Letter, we use the recently introduced perturbed matrix method (PMM) to study in detail the electronic properties of formaldehyde in water, as obtained by applying this method to Molecular Dynamics simulation data. Results show that PMM provides an accurate description at relatively low computational costs.

Human neutrophil collagenase (HNC, MMP-8) is one of the target enzymes for drug treatment of pathologic extracellular matrix degradation. Peptidomimetic inhibitors bind in the S'-side of the enzyme active site occupying the S-1(') primary specificity pocket by their large hydrophobic side-chains. The crystal structure of the complex between the catalytic domain of MMP-8 and Pro-Leu-l-Trp(P)(OH)(2) (PLTP) showed that this phosphonate inhibitor binds in the S side of the active site. This finding was unexpected since it represents the first example of accommodation of the bulky Trp indolyl chain in the S-1 rather than in the S-1(') subsite. Dynamical and structural factors favouring this uncommon mode of binding were therefore investigated. MD simulations performed on the uncomplexed enzyme show that its structure in aqueous solution is only slightly different from the crystal structure found in the complex with PLTP. ED analysis of the MD simulations, performed on PLTP alternatively interacting with the S- or S'-side of the active site, shows that the enzyme fluctuation increases in both cases. The main contribution to the overall enzyme fluctuation is given by the loop 164-173. The fluctuation of this loop is spread over more degrees of freedom when PLTP interacts with the S-side. This dynamical factor can enhance the preference of PLTP for the S subsites of MMP-8. MD simulations also show that ligation of PLTP in the S subsites is further favoured by better zinc chelation, a cation-pi interaction at the S-3 subsite and unstrained binding conformations. The role of the S-3, S-3(') and S-1(') subsites in determining the inhibitor binding is discussed.

The thermal reaction between S+(4S) and acetylene has been studied in the framework of the statistical theories in order to extract informations concerning its actual efficiency at different temperatures and bath gas densities. The results of the present work are in reasonable agreement with the available experimental data concerning both the efficiency and the generated products. The spin-forbidden paths have been also re-addressed and their actual role within the overall process, discussed.

The positive ion chemistry of peroxynitric acid ( 1 ) was investigated in the gas phase by mass-analyzed ion kinetic, collisionally activated dissociation, and Fourier transform-ion cyclotron resonance mass spectrometric techniques and theoretical methods up to the B3LYP/6-311++g(3 df ,2 pd ) and G2, i.e. QCISD(T)/6-311+g(3 df ,2 pd ), levels. The ion–neutral complex HOOH–NO 2 + ( 1a ) is the only detectable protomer in CI experiments involving the protonation of 1 by H 3 O + , and can also be obtained from the reaction of NO 2 + with H 2 O 2 . 1a behaves as a protonating and nitrating agent toward gaseous nucleophiles. The experimental proton affinity of 1 is estimated to be 176 ± 3 kcal mol −1 , in excellent agreement with the 175 ± 2 kcal mol −1 G2 PA. The theoretical results show that 1a is more stable than the HOONO 2 H + ( 1b ) and the H 2 OONO 2 + ( 1c ) protomers by 13 and 16 kcal mol −1 , respectively, at the B3LYP level of theory, and account for the exclusive formation of 1a in the CI experiments. The experimental and B3LYP theoretical binding energy of NO 2 + to H 2 O 2 amounts to 18 ± 2 kcal mol −1 .

The Pt+-mediated coupling of methane and ammonia has been studied both experimentally and computationally. This system serves as a model for the Degussa process for the industrial production of the valuable feedstock hydrogen cyanide. Mass spectrometric studies demonstrate that C−N bond formation is catalyzed efficiently by Pt+. Details of the experimentally observed reaction channels have been explored computationally using the B3LYP hybrid DFT/HF functional. In the first reaction step, Pt+ dehydrogenates CH4 to yield PtCH2+; in contrast, dehydrogenation of ammonia by Pt+ is endothermic and does not occur experimentally. Starting from PtCH2+ and NH3, C−N bond formation, which constitutes the crucial step in making HCN from CH4 and NH3, is achieved via two independent pathways. The major pathway is found to be exothermic by 23 kcal mol-1 and yields neutral PtH and CH2NH2+. The second pathway involves a dehydrogenation to yield the aminocarbene complex PtC(H)NH2+ (ΔrH = −36 kcal mol-1); dehydrogenation of ...

A non-adiabatic version of RRKM theory is applied to predicting the microcanonical rates for different mechanisms of spin-forbidden dissociation of methoxy cation and its isotopically substituted derivatives, to formyl cation and dihydrogen. The predictions are in agreement with experimental results on this system, and in particular with the occurrence of a “direct’' mechanism for dissociation, rather than of an indirect one via hydroxymethyl cation. Abinitio computations were used throughout to provide the parameters needed to apply the non-adiabatic RRKM theory, and the success of this strategy is shown to be promising for other applications in polyatomic systems. Finally, the kinetic energy release distribution for loss of hydrogen from methoxy and hydroxymethyl cations are computed using abinitio “direct dynamics’' classical trajectories at the HF/6-31G** level, their similarity is also in agreement with experiment.

The singlet and triplet potential energy surfaces of a series of p-X-substituted aryl cations (X = H, CN, CH3, F, OH, NH2) are investigated computationally at the B3LYP/6-31G(d) level of theory. The first four species are found to be ground state singlets, the last has a triplet ground state, and the spin states of the OH derivative are almost isoenergetic. The minimum energy crossing points (MECPs) between the two surfaces are found to lie very little above the higher of the two minima in all cases, and the spin-orbit coupling is significant at those points. Therefore, it is expected that aryl cations will rapidly convert to their most stable spin state, and that in cases of near degeneracy such as for p-HO-C6H4+, the states may interconvert rapidly enough to both be accessible in thermal reactions.

Ab initio calculations have been performed on the structure and stability of (MeONO)H + and the proton affinity (PA) of RONO (R = H, Me). At the MP4/6-311G ∗∗ // MP2(FULL)/6-31G ∗ level of theory, the ion-dipole adduct MeOHNO + 1 is by far the most stable promoter. At the G2 level, the dissociation enthalpy into MeOH and NO + is computed as 25.3 kcal mol −1 and the PAs of MeONO and HONO amount to 187 and 188 kcal mol −1 , respectively. This finding marks a departure from the expected order and parallels the anomalous trend recently ascertained in the PAs of the strictly related RONO 2 (R = H, Me).

Firefly luciferin and its oxidated form, oxyluciferin, are two heterocyclic compounds involved in the enzymatic reaction, catalyzed by redox proteins called luciferases, which provides the bioluminescence in a wide group of arthropods. Whereas the electronic absorption spectra of d -luciferin in water at different pHs are known since 1960s, only recently reliable experimental electronic spectra of oxyluciferin have become available. In addition oxyluciferin is involved in a triple chemical equilibria (deprotonation of the two hydroxyl groups and keto-enol tautomerism of the 4-hydroxythiazole ring), that obligates to select during an experiment a predominant species, tuning pH or solvent polarity besides introducing chemical modifications. In this study we report the absorption spectra of luciferin and oxyluciferin in each principal chemical form, calculated by means of perturbed matrix method (PMM), which allowed us to successfully introduce the effect of the solvent on the spectroscopic absorption properties, and compare the result with available experimental data.

Large-scale periodic quantum mechanical calculations (509 atoms, 7852 atomic orbitals) based on the hybrid B3LYP functional focused on the peptide folding induced by the adsorption on the (001) and (010) hydroxyapatite (HA) surfaces give interesting insights on the role of specific interactions between surface sites and the peptide, which stabilize the helix conformation over the "native" random coil ones for in silico designed model peptides. The two peptides were derived from the 12-Gly oligomer, with one (P1, C-tGGKGGGGGGEGGN-t) and two (P2, C-tGGKGGKEGGEGGN-t) glutamic acid (E) and lysine (K) residue mutations. The most stable gas-phase "native" conformation for both peptides resulted in a random coil (RC) structure, with the helix (H) conformation being ≈100 kJ mol(-1) higher in free energy. The two peptide conformations interact with the HA (001) and (010) surfaces by C═O groups via Ca(2+) ions, by hydrogen bond between NH(2) groups and the basic PO(4)(3-) groups and by a relevant fraction due to dispersion forces. Peptide adsorption was studied on the dry (001) surface, the wet one envisaging 2 H(2)O per surface Ca(2+) and, on the latter, also considering the adsorption of microsolvated peptides with 4 H(2)O molecules located at sites responsible of the interaction with the surface. The P1 mutant does prefer to be adsorbed as a random coil by ≈160 kJ/mol, whereas the reverse is computed for P2, preferring the helix conformation by ≈50 kJ/mol. Adsorption as helix of both P1 and P2 mutants brings about proton transfer toward the HA surfaces with a large charge transfer component to the interaction energy.

The structure, stability, interconversion, and unimolecular decomposition processes of gaseous protonated nitrosyl fluoride, ONF, have been investigated by mass-analyzed ion kinetic energy (MIKE) and collisionally activated dissociation (CAD) mass spectrometry, as well as ab initio GAUSSIAN-1 calculations. Positive evidence has been obtained for the existence of two distinct, not easily interconvertible isomers, HO-NF + , 1, and ON-FH + , 3. These two species are distinguishable by both CAD and MIKE spectrometry, whose results are consistent with the theoretical description of the system. The fluorine-protonated isomer 3 is the global minimum on the surface and is more stable than the oxygen-protonated isomer 1 by 70.1 kcal mol -1

The 1-hexadecyl-3-vinylimidazolium bromide (hvimBr), a water-soluble long-chain imidazolium ionic liquid (IL) with surfactant properties, showed the ability to produce stable homogeneous aqueous dispersions of pristine Single-Walled Carbon Nanotubes (SWNTs). The purpose of this study is the improvement of SWNT dispersing ability by assessing the effect of different groups in position 3 of the imidazole ring. In this regard structural analogues were synthesized and, after characterization, their capability to dissolve SWNTs in water was investigated. Molecular Dynamics (MD) simulations have been performed to provide a semi-quantitative indication of the affinity of each dispersing agent toward SWNT and to attempt an explanation of the experimental results.

A reduced form of a synthetic hydrogen-assembled molecular shuttle for nano-technological applications has been investigated by molecular dynamics simulations and density functional theory calculations. It is composed by a benzylic amide macrocycle mechanically locked onto a thread in acetonitrile solution. Classical sampling indicates, in agreement with experimental findings, that in equilibrium condition at 298 K the macrocycle and the naphthalimide radical anion moiety within the thread strongly interact forming four strong OCN-H-O=CNR hydrogen bonds. Simulations also revealed that the geometry of the supramolecular assembly reversibly oscillates between unfolded and folded conformations, with the latter characterized by an electrostatic hook involving the succinamide end group and the macrocycle itself. Finally, the simulated UV-Vis absorption spectra for free and complexed reduced naphthalimide quantitatively confirm that the transient spectroscopic change experimentally used as a probe for monitoring the translational motion of the macrocycle, from succinamide to naphthalimide stations, accompanying the selective electrochemical reduction.

The hydroarylation of 3-arylprop-2-yn-1-amine derivatives with arylboronic acids has been studied in the presence of rhodium or palladium catalysts. By using a rhodium-based catalytic system, β,γ-diarylallylamines were isolated in good yields. By contrast, the formation of the regiosomeric γ,γ-diarylallylamines was achieved by means of a palladium catalyst in the presence of acetic acid. The complementary regioselectivity displayed by these two processes is a consequence of different catalytic cycles, involving respectively carborhodation or hydropalladation of the coordinated alkyne as key steps. Calculated charge distributions in the π-complexes are in accord with the results obtained.

Molecular dynamics simulations for the compound I species in horseradish peroxidase were carried out over a nanoseconds time-scale. Results indicate that the supramolecular assembly composed of compound I in interaction with highly conserved distal residues (His42 and Arg38) exists in two well-defined conformations basically differing in the local position of the distal histidine (i.e., His42). Furthermore, we observe the presence of a biological channel in the distal side of the heme cavity, between Arg38 and Pro139 residues, that represents a direct link connecting the compound I (CpdI) species to bulk molecules. Our investigation supports the idea that when CpdI is formed, the biological machinery relaxes the local electrostatic forces, opening a structural channel through which an exchange of water molecules with the bulk solvent takes place without any significant kinetic barrier. Interestingly, we also show that the combined effect of enzyme and solvent, modulated by thermal fluctuations, affects the order and the energy difference between the lowest doublet and quartet magnetic states of the CpdI-His42-Arg38 complex. Consequently, when passing from the gas phase to the biological environment, the doublet spin state becomes slightly more stable than the higher spin multiplicity state. The distribution of the perturbed low-lying states energy variation, induced by surrounding fluctuations, yields results rather close to that obtained by other state of the art quantum-mechanics/molecular mechanics calculations, and still in line with previous polarizable continuum calculations.

The charge transfer thermodynamics of a simple model of DNA, a single stranded 10-mer poly-adenine oligonucleotide, in water is investigated by means of a computational/theoretical procedure, in which all the relevant environmental effects are considered. Our data indicate that water and counterions ultimately dominate the DNA reduction and oxidation free energies, which are also strongly influenced by the base position along the strand. In fact, we estimated that reduction free energies are large and negative, particularly for the bases close to the 5' and 3' positions, whereas the electron detachment is thermodynamically unfavoured all along the strand, but with a higher free energy cost in the central region of the molecule. Further investigation on double charging, i.e. one nucleobase is oxidized and one is reduced within the strand, predicts that charge-separated states are possible and thermodynamically largely stable when the ionic forms are separated by several nucleobases.

The effect of the luminescent heteroaromatic electron acceptor N,N'-dimethyl-2,7-diazapyrenium dichloride (DM-DAP(2+)) on the stability of 1-palmitoyl-2-oleoylphosphatydilcholine (POPC) liposomes is determined on the basis of the rate of release of different fluorescent probes entrapped within the liposome. The experiments show that DM-DAP(2+) exerts a substantial destabilizing action on the liposomal bilayer, particularly at low concentrations. Molecular dynamics simulations suggest that the activity of DM-DAP(2+) is related to its tendency to surround itself with water molecules, conceivably favoring the formation of transient pores across the bilayer.

The free-energy profile and the classical kinetics of the heme carbomonoxide binding-unbinding reaction have been derived by means of a theoretical method for the separated chains of human (HbA) and Trematomus newnesi major component (HbTn) hemoglobin. The results reveal that the alpha- and beta-chains of HbA have similar values of kinetic constants for the dissociation of the Fe-CO state, in agreement with experimental data. Comparisons of the present findings with the data obtained for the alpha- and beta-chains of HbTn and with theoretical and experimental results previously collected on myoglobin provide a detailed picture of this important biochemical reaction in globins. The sequence and structural differences among the globins are not reflected in meaningful variations in the rate of CO dissociation. These data support the conclusion that the differences observed for the reaction with CO of globins, if any, involve the rate of ligand migration to the solvent, rather than the Fe-CO complex formation/rupture. Furthermore, our results agree with the recent discovery that globin family proteins exhibit common dynamics, thus confirming the observation that the dynamic properties of proteins are strongly related to their overall architecture.

Molecular dynamics simulations on hydrogen peroxide complex with wild-type (WT) and Arg38Leu mutated (R38L) Horseradish Peroxidase (HRP) were carried out over nanoseconds timescale in water solution at 300 K. Comparison of the results provides interesting insights about the role of highly conserved Arg38 and His42 residues in the chemical features of HRP, underlying its biological activity which initiates with Compound0 (Cpd0). In the WT-HRP enzyme current molecular dynamics simulations show, for the first time, that Arg38 residue: i) prevents the entrance of water inside the reaction cavity, hence providing a hydrophobic reactive scenario, ii) it maintains the distance between His42 and heme–H 2 O 2 complex suitable for the occurrence of proton transfer reaction leading, thereafter, to heme–H 2 O 2 disruption according to Poulos-Kraut mechanism. On the other hand, R38L mutant can be considered as a “wet enzyme” where the presence of water solvent molecules in the heme reaction pocket, unfavoring the initial heme–H 2 O 2 complex formation, decreases the catalytic efficiency in agreement with experimental kinetics measurements. Furthermore, we note that Arg38Leu mutation pushes the His42 residue far from the heme–H 2 O 2 complex, making unlikely a direct proton transfer and suggesting that, in the mutant, a solvent water molecule could be involved in the first step of the Poulos-Kraut mechanism.

Here we report that at room temperature in acetonitrile after the reduction of the naphthalimide-site, a synthetic molecular thread undergoes a complete conformational change which makes possible an efficient conversion of chemical energy into mechanical work; such results point out the ability of the thread to act as a molecular device under electrochemical control.

In a previous paper we introduced a new Hamiltonian model for polarizable water, based on the atomic charge density expansion, whose reliability should in principle be independent of the system conditions. In this work we refine and apply this model to describe the structural and energetical features of clusters of increasing dimension and to evaluate the second virial coefficient. Results show that, despite its simplicity, such Hamiltonian provides an efficient and rather accurate description of the systems studied.

Contradictory data in the huge literature on microwaves bio-effects may result from a poor understanding of the mechanisms of interaction between microwaves and biological systems. Molecular simulations of biochemical processes seem to be a promising tool to comprehend microwave induced bio-effects. Molecular simulations of classical and quantum events involved in relevant biochemical processes enable to follow the dynamic evolution of a biochemical reaction in the presence of microwave fields. In this paper, the action of a microwave signal (1 GHz) on the covalent binding process of a ligand (carbon monoxide) to a protein (myoglobin) has been studied. Our results indicate that microwave fields, with intensities much below the atomic/molecular electric interactions, cannot affect such biochemical process.

A feed-forward artificial neural network (ANN) learned by error back-propagation is used to generate a retention predictive model for phenoxy acid herbicides in isocratic reversed-phase high-performance liquid chromatography. The investigated solutes (18 compounds), apart from the most common herbicides of this class, include some derivatives of benzoic acid and phenylacetic acid structurally related to phenoxy acids, as a whole covering a pK(a) range between 2.3 and 4.3. A mixed model in terms of both solute descriptors and eluent attributes is built with the aim of predicting retention in water-acetonitrile mobile phases within a large range of composition (acetonitrile from 30% to 70%, v/v) and acidity (pH of water before mixing with acetonitrile ranging between 2 and 5). The set of input variables consists of solute pK(a) and quantum chemical molecular descriptors of both the neutral and dissociated form, %v/v of acetonitrile in the mobile phase and pH of aqueous phase before mixing with acetonitrile. After elimination of redundant variables, a nine-dimensional model is identified and its prediction ability is evaluated by external validation based on three solutes not involved in model generation and by cross-validation. A multilinear counterpart in terms of the same descriptors is seen to provide a noticeably poorer retention prediction.

In this article we use the perturbed matrix method and an extended molecular dynamics sampling of the carbon monoxide (CO) in the myoglobin distal pocket to characterize the CO vibrational spectrum and hence to relate its spectroscopic features with the atomic-molecular behavior. Results show the accuracy of the method employed and confirm the assignment of the spectroscopic B1 and B2 states proposed by Lim et al.

Molecular Dynamics simulations in aqueous solution were performed for the matrix metalloproteinase-8 (MMP-8) free catalytic domain and for its complexes with the (R)- and (S)-[1-(4‘-methoxybiphenyl-4-sulfonylamino)-2-methylpropyl] phosphonate. The 144−155 loop of the enzyme undergoes a drastic decrease of mobility once complexed with both enantiomers. The two enantiomers induce a different decrease of conformational entropy upon complexation. The higher affinity of the R-enantiomer can be related to the lower loss of conformational entropy accompanying its binding. The differences in the dynamical behavior of the protein induced by the two enantiomers are discussed at molecular level and the mode of binding of the simulated complexes is compared with that previously determined by X-ray crystallography.

The free energy profile and the (classical) kinetics of chemical reactions in (soft) condensed phase may be well modelled theoretically by means of molecular dynamics simulations, the perturbed matrix method (PMM) and statistical mechanics, as we provided in previous articles. In this paper, we describe the theoretical framework, discussing thoroughly its crucial points, and apply the model to an important biochemical reaction: the Haem carbon monoxide binding–unbinding reaction in Myoglobin, specifically investigating the reaction step involving the carbon–iron chemical bond formation (disruption) which is of particular biochemical interest.

In this paper, a quantitative structure-retention relationships (QSRR) method is employed to predict the retention behaviour of pesticides in reversed-phase high-performance liquid chromatography (HPLC). A six-parameter nonlinear model is developed by means of a feed-forward artificial neural network (ANN) with back-propagation learning rule. Accurate description of the retention factors of 26 compounds including commonly used insecticides, herbicides and fungicides and some metabolites is successfully achieved. In addition to the acetonitrile content, included to describe composition of the water-acetonitrile mobile phase, the octanol-water partition coefficient (from literature) and four quantum chemical descriptors are considered to account for the effect of solute structure on the retention. These are: the total dipole moment, the mean polarizability, the anisotropy of polarizability and a descriptor of hydrogen bonding ability based on the atomic charges on hydrogen bond donor and acceptor chemical functionalities. The proposed nonlinear QSRR model exhibits a high degree of correlation between observed and computed retention factors and a good predictive performance in wide range of mobile phase composition (40-65%, v/v acetonitrile) that supports its application for the prediction of the chromatographic behaviour of unknown pesticides. A multilinear regression model based on the same six descriptors shows a significantly worse predictive capability.

Molecular dynamics simulations carried out on short linear peptides incorporating β-Ala residues, namely Boc–β–Ala–Phe–OMe (1) and Boc–Met–β–Ala–Phe–OMe (2), reveal a markedly different conformational-dynamical behaviour. The tripeptide (2), showing free energy minima deeper than the dipeptide is predicted to be characterized by long-lived conformers. The present theoretical results may help in rationalizing experimental (IR, NMR) results on (1) and (2) and definitely show the importance of a dynamical approach for a correct interpretation and prediction of the conformational behaviour in solution even for relatively small molecules.

[reaction: see text] The gold-catalyzed reaction of 2-alkynyl-phenylamines with alpha,beta-enones represents a new general one-pot entry into C-3-alkyl-indoles by sequential reactions. Gold-catalyzed sequential cyclization/alkylation, N-alkylation/cyclization, or N-alkylation/cyclization/alkylation reactions leading to different indoles can be directed by changing the 2-alkynyl-phenylamine 1/alpha,beta-enone 3 ratio and the reaction temperature. Unusual gold-catalyzed rearrangement reaction of indoles are observed at 140 degrees C. New gold-catalyzed formation of propargyl-alkyl ether under mild conditions and the hydration reaction of N-acetyl-2-ethynyl-phenylamine are reported.