THEORETICAL AND COMPUTATIONAL CHEMISTRY

Abbreviations: EGFR-Epidermal growth factor receptor; WT-wild type; u.c. unit cell. Motivation: EGF receptor and its ligands are involved in over 70 % of all cancers. Mutations of the EGFR gene have been identified in specimens from patients with nonsmall lung cancer who have a response to quinazolin inhibitors such as CI1033, Gefitinib, and Erlotinib. Substitution mutations G719S and L858R were reported by Guillermo Paez et al. (2004). Both types of mutation increase the sensitivity of the tumor to quinazoline inhibitors of EGFR. This prompted us to take up this study on mutation of EGFR gene and its sensitivity to quinazolin inhibitors using cheminformatics. Methodology: The homology modeling was carried out with the Insight II Modeller module. The interaction energy of the quinazolin inhibitors with each individual amino acid in the active site of EGFR was calculated by the advanced program Affinity. Results and Validation: The crystal structure of Syk Tyrosine Kinase Domain was ...

The effect of Mg(2+) cations on the electronic spectra and dynamics and efficiency of hole transport has been determined by means of femtosecond time-resolved transient absorption spectroscopy for DNA hairpins possessing stilbene electron acceptor and donor chromophores. The results are compared with those obtained previously for the same hairpins in the presence of Na(+) cations and for one hairpin with no added salt. Quantum yields and rate constants for charge separation are smaller in the presence of Mg(2+) than Na(+), the largest differences being observed for the hairpins with the largest number of base pairs. Slower charge separation is attributed to minor groove binding by Mg(2+), which results in a stiffer duplex structure rather than a change in ground state geometry. Reduction in the Na(+) concentration has little effect on either the dynamics or efficiency of hole transport.

The work here focusing on the synthesize of a novel (E)-N'-(thiophen-2-ylmethylene)-isonicotinohydrazide as polydentate O-N-S-tridentate Schiff base ligand derived from isonicotinohydrazide and their complexation with CuCl 2 center. The structure of O-N-S-ligand was determined by XRD-crystal diffraction and characterized by IR, UVeVis., CHN-EA, EDX, 1 H and 13 C-NMR spectroscopy. The DFT/NMR, IR, UVeVis and optimized structure parameters of the free ligand were matched with their corresponding exp. spectral. The XRD-packing intermolecular has been correlated with the computed Hirshfeld surface analysis (HSA) and MEP-calculation. The Mulliken population and NPA charge analysis, HOMO/LUMO, DOS and global reactivity descriptor quantum parameters (GRD) of the (E)-N'-(thiophen-2-ylmethylene)isonicotinohydrazide ligand were also computed under B3LYP/6-311G(d) theory. The coordination of the ligand to Cu(II) centered were monitored by EDX, FT-IR and UVeVisible analysis. The thermal stability of free ligand and its Cu(II)-complex were evaluated by TG-analysis.

In this study, the functionalization of diamond-like carbon (DLC) with carboxyl (COOH), hydroxyl (OH) and amine (NH₂) groups was investigated to understand its impact on the structural, electronic and nonlinear optical (NLO) properties. Dispersion-corrected density functional theory (DFT-D) calculations using the B3LYP-D3(BJ) exchange-correlation functional were performed in all calculations. The results indicated that functionalization with these groups enhanced the reactivity of the DLC surface. Molecular reactivity descriptors revealed that COOH-DLC exhibited the highest softness (S = 0.25 eV), significant electrophilicity (ω = 2.55 eV) and a reduced energy gap (∆E g = 3.97 eV). Time-dependent DFT (TD-DFT) analysis showed that COOH-DLC achieved the maximum absorption wavelength among the systems investigated. Additionally, functionalization improved the NLO properties, including increased polarity, with COOH-DLC displaying the highest first hyperpolarizability value. Natural bond orbital (NBO) analysis indicated significant orbital delocalization between the functional groups and the pristine DLC surface. Quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analyses, based on the reduced density gradient (RDG), provided a detailed characterization of interactions, highlighting the presence of van der Waals forces.

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tetracarbonyl complexes of type W(CO) 4 L 2 (L: 4-chlorobenzylimidazoline; 4methylbenzylimidazoline; 3,5-dimethylbenzylimidazoline; 2,4,6-trimethylbenzylimidazoline; 2,3,5,6tetramethylbenzylimidazoline) were synthesized. Then newly synthesized novel compounds were characterized by IR, 1 H NMR, 13 C NMR and LC-MS. The characterizations of two of the complexes have also been confirmed with single crystal X-Ray diffraction and DFT optimization results of these complexes have been compared with single crystal results. We have investigated the solvent effect on the structure and metal-to-ligand charge transfer (MLCT) transitions with DFT/TDDFT calculations with ORCA package program with BP86 functional.

Fluids confined in nanopores exhibit significant deviations in their structure and dynamics from the bulk behavior. Although phase, structural, and diffusive behaviors of confined fluids have been investigated and reported extensively, confinement effects on the vibrational properties are less understood. We study the vibrational behavior of propane confined in 1.5 nm nanopores of MCM-41-S using inelastic neutron scattering (INS) and molecular dynamics (MD) simulations. Vibrational spectra have been obtained from INS data as functions of temperature and pressure. At ambient pressure, a strong quasielastic signal observed in the INS spectrum at 80 K suggests that confined propane remains liquid below the bulk phase melting point of 85 K. The quasielastic signal is heavily suppressed when either the pressure is increased to 1 kbar or the temperature is lowered to 30 K, indicating solidification of pore-confined propane. Confinement in MCM-41-S pores results in a glass-like state of pr...

2-Cyano-2-( p-tolyl)sparteine (VI) and its monoperchlorate (VI-H þ ) have been obtained and characterized by IR and NMR spectroscopy as well as by X-ray diffraction analysis. Conformational-configurational change of the C/D ring system, upon protonation, from trans boat/chair to cis chair/chair, observed in the investigated doubly substituted derivative, follows the same pattern as in sparteine. However, while in the crystal of sparteine monoperchlorate the acidic H-atom bonds to N-1, being part of trans-quinolizidine system, in all three crystallographic independent molecules of 2-cyano-2-( p-tolyl)sparteine it bonds to N-16 nitrogen atom which belongs to cis-quinolizidine system.

In its crystal structure, determined by X-ray diffraction, the methyl ester of (R,R)-tartaric acid monoamide crystallizes with two molecules per assymetric unit. Each molecule displays subtle conformational differences effected by 180 ° rotation by the methyl ester group about the C-C* bond, whereas the staggered conformation around the central C*-C* bond, with a trans arrangement of the ester and amide substituents, and the eclipsed orientation of the amide nitrogen atom with respect to the nearest hydroxyl group, remains the same in both molecules. MNDO and ab initio single-point energies for the two molecules indicate that the lower energy molecule is that with the a-hydroxyl group eclipsed by the carbonyl group rather than the methoxy oxygen atom. Conformers observed in the crystal structure differ from those obtained by full MNDO optimization in the planarity of a-hydroxyester and a-hydroxyamide residues. Ab initio calculations at the 6-31G* level on smaller systems, i.e. (2R,3R)-2,3-butanediol and (2R,3R)-2,3-dihydroxybutanedinitrile, suggest different conformational preferences for the two model compounds (gauche vs. trans with respect to the carbon chain), and point to the importance of the intramolecular hydrogen bond in stabilizing the gauche orientation of the vicinal OH groups. A similar hydrogen bond may be present in one of two crystallographically independent molecules of the methyl ester of (R,R)-tartaric acid monoamide, but only as a minor component in a complex system of intermolecular hydrogen bonds.

Stereoisomers of one of the most important organic compounds, tartaric acid, optically active and meso as well as the ester or amide derivatives, can show diverse structures related to the rotation around the three carbon–carbon bonds. This study determines the controlling factors for conformational changes of these molecules in vacuo, in solution, and in the crystalline state using DFT calculations, spectroscopic measurements, and X‐ray diffraction. All structural variations can be logically accounted for by the possibility of formation and breaking of hydrogen bonds between the hydroxy or amide donors and oxygen acceptors, among these the hydrogen bonds that close five‐membered rings being the most stable. These findings are useful in designing molecular and crystal structures of highly polar, polyfunctional, chiral compounds.

In view of their promising photosensitizing features, expanded porphyrins are gaining wide attention for their potential use in both photodynamic therapy (PDT) of cancer or as likely photoactivated agent for water disinfection. Herein, we report a joint experimental and theoretical investigation on the 20-(4'-carboxyphenyl)-2,13-dimethyl-3,12-diethyl-[22]pentaphyrin complex 4. The synthesis, NMR, UV-Vis and mass characterization of the new Author's Pre-Print Version 2 compound together with a detailed theoretical investigation of the photophysical properties are presented. In particular, type I-and type II-photoreactions have been explored by means of DFT and its TDDFT formulation characterizing the electronic absorption spectra, providing singlettriplet energy gap, vertical ionization potential and electron affinity. Results show that title compound is able to generate the cytotoxic singlet oxygen species supporting the application of the proposed molecule as a photoactivated agent for water disinfection.

Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data. A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase (PNP) complexed with a fluorescent ligandformycin A (FA). FRET occurs between an excited Tyr residue (D*) and FA (A). This study aims to interpret experimental data that, among others, suggests the absence of FRET for the PNPF159A mutant in complex with FA, based on novel theoretical methodology. MD simulations for the protein molecule containing D*, and complexed with A, are carried out. Interactions of D* with its molecular environment are accounted by including changes of the ESP Keywords Deprotonation . Emission spectroscopy . Excited state . Formycin A . FRET . PNP . QC-MD . SCF-CI . Simulations . Tyrosinate anion Abbreviations Ado Adenosine CI Configurational interaction DTT Dithiotreitol EDTA Ethylenediaminetetraacetic acid ESP charges Electrostatic potential charges ETDM Electronic transition dipole moments ETP Energy transfer probabilities Co-authors M. Sobieraj and M. Prokopowicz equally contributed to this work. They are first co-authors from the theoretical (M. Sobieraj, K. A.

Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data. A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase (PNP) complexed with a fluorescent ligandformycin A (FA). FRET occurs between an excited Tyr residue (D*) and FA (A). This study aims to interpret experimental data that, among others, suggests the absence of FRET for the PNPF159A mutant in complex with FA, based on novel theoretical methodology. MD simulations for the protein molecule containing D*, and complexed with A, are carried out. Interactions of D* with its molecular environment are accounted by including changes of the ESP Keywords Deprotonation . Emission spectroscopy . Excited state . Formycin A . FRET . PNP . QC-MD . SCF-CI . Simulations . Tyrosinate anion Abbreviations Ado Adenosine CI Configurational interaction DTT Dithiotreitol EDTA Ethylenediaminetetraacetic acid ESP charges Electrostatic potential charges ETDM Electronic transition dipole moments ETP Energy transfer probabilities Co-authors M. Sobieraj and M. Prokopowicz equally contributed to this work. They are first co-authors from the theoretical (M. Sobieraj, K. A.

Tyrosine nitration is a widespread post-translational modification capable of affecting both the function and structure of the host protein molecule. Enzyme thymidylate synthase (TS), a homodimer, is a molecular target for anticancer therapy. Recently purified TS preparations, isolated from mammalian tissues, were found to be nitrated, suggesting this modification to appear endogenously in normal and tumor tissues. Moreover, human TS (hTS) nitration in vitro led to a by twofold lowered catalytic activity following nitration in average of 1 tyrosine residue per monomer (Da ˛browska-Mas ´et al. in Org Biomol Chem 10:323-331, 2012), with the modification identified by mass spectrometry at seven different sites (Y33, Y65, Y135, Y213, Y230, Y258 and Y301). In the present paper, combined computational approach, including molecular and essential dynamics and free energy computations, was used to predict the influence on the activity of hTS of nitration of each of the seven tyrosine residues. The simulations were based on the crystal structure of hTS ternary complex with dUMP and Tomudex (PDB code: 1I00), with the Tomudex molecule replaced by the molecule of TS cofactor analogue, tetrahydrofolate. The present results indicate that while with nitration of five out of seven residues (Y33, Y135, Y230, Y258 and Y301), single residue modification appears to have a strong reducing effect on the activity, with the remaining two, Y65 and Y213, no or a weaker influence is apparent. Taken together, these results demonstrate that tyrosine nitrations in the hTS enzyme show clear tendency to influence the structure and dynamics and, in turn, catalytic properties of the host enzyme. These effects are overall distance-dependent.

Tyrosine nitration is a widespread post-translational modification capable of affecting both the function and structure of the host protein molecule. Enzyme thymidylate synthase (TS), a homodimer, is a molecular target for anticancer therapy. Recently purified TS preparations, isolated from mammalian tissues, were found to be nitrated, suggesting this modification to appear endogenously in normal and tumor tissues. Moreover, human TS (hTS) nitration in vitro led to a by twofold lowered catalytic activity following nitration in average of 1 tyrosine residue per monomer (Da ˛browska-Mas ´et al. in Org Biomol Chem 10:323-331, 2012), with the modification identified by mass spectrometry at seven different sites (Y33, Y65, Y135, Y213, Y230, Y258 and Y301). In the present paper, combined computational approach, including molecular and essential dynamics and free energy computations, was used to predict the influence on the activity of hTS of nitration of each of the seven tyrosine residues. The simulations were based on the crystal structure of hTS ternary complex with dUMP and Tomudex (PDB code: 1I00), with the Tomudex molecule replaced by the molecule of TS cofactor analogue, tetrahydrofolate. The present results indicate that while with nitration of five out of seven residues (Y33, Y135, Y230, Y258 and Y301), single residue modification appears to have a strong reducing effect on the activity, with the remaining two, Y65 and Y213, no or a weaker influence is apparent. Taken together, these results demonstrate that tyrosine nitrations in the hTS enzyme show clear tendency to influence the structure and dynamics and, in turn, catalytic properties of the host enzyme. These effects are overall distance-dependent.

We applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach to evaluate relative stability of the extended (flat) and C-shaped (bent) solution conformational forms of the 5,10methylene-5,6,7,8-tetrahydrofolate (mTHF) molecule in aqueous solution. Calculations indicated that both forms have similar free energies in aqueous solution but detailed energy components are different. The bent solution form has lower intramolecular electrostatic and van der Waals interaction energies. The flat form has more favorable solvation free energy and lower contribution from the bond, angle and torsion angle molecular mechanical internal energies. We exploit these results and combine them with known crystallographic data to provide a model for the progressive binding of the mTHF molecule, a natural cofactor of thymidylate synthase (TS), to the complex forming in the TS-catalyzed reaction. We propose that at the time of initial weak binding in the open enzyme the cofactor molecule remains in a close balance between the flat and bent solution conformations, with neither form clearly favored. Later, thymidylate synthase undergoes conformational change leading to the closure of the active site and the mTHF molecule is withdrawn from the solvent. That effect shifts the thermodynamic equilibrium of the mTHF molecule toward the bent solution form. At the same time, burying the cofactor molecule in the closed active site produces numerous contacts between mTHF and protein that render change in the shape of the mTHF molecule. As a result, the bent solution conformer is converted to more strained L-shaped bent enzyme conformer of the mTHF molecule. The strain in the bent enzyme conformation allows for the tight binding of the cofactor molecule to the productive ternary complex that forms in the closed active site, and facilitates the protonation of the imidazolidine N10 atom, which promotes further reaction.

We applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach to evaluate relative stability of the extended (flat) and C-shaped (bent) solution conformational forms of the 5,10methylene-5,6,7,8-tetrahydrofolate (mTHF) molecule in aqueous solution. Calculations indicated that both forms have similar free energies in aqueous solution but detailed energy components are different. The bent solution form has lower intramolecular electrostatic and van der Waals interaction energies. The flat form has more favorable solvation free energy and lower contribution from the bond, angle and torsion angle molecular mechanical internal energies. We exploit these results and combine them with known crystallographic data to provide a model for the progressive binding of the mTHF molecule, a natural cofactor of thymidylate synthase (TS), to the complex forming in the TS-catalyzed reaction. We propose that at the time of initial weak binding in the open enzyme the cofactor molecule remains in a close balance between the flat and bent solution conformations, with neither form clearly favored. Later, thymidylate synthase undergoes conformational change leading to the closure of the active site and the mTHF molecule is withdrawn from the solvent. That effect shifts the thermodynamic equilibrium of the mTHF molecule toward the bent solution form. At the same time, burying the cofactor molecule in the closed active site produces numerous contacts between mTHF and protein that render change in the shape of the mTHF molecule. As a result, the bent solution conformer is converted to more strained L-shaped bent enzyme conformer of the mTHF molecule. The strain in the bent enzyme conformation allows for the tight binding of the cofactor molecule to the productive ternary complex that forms in the closed active site, and facilitates the protonation of the imidazolidine N10 atom, which promotes further reaction.

Free energy perturbation calculations have been applied to evaluate the relative free energies of binding of 2deoxyuridine-5 -monophosphate (dUMP) and its 2-and/or 4-thio and/or 5-fluoro analogues to the wild-type E. coli thymidylate synthase (ecTS). The results accurately reproduce experimentally measured differences in the free energy of binding of dUMP versus 5-fluoro-dUMP to thymidylate synthase. They indicate that preferred binding of dUMP compared to 5-fluoro-dUMP in the binary complex is equally related to (i) more favorable electrostatic interactions of the dUMP molecule in the enzyme active site, and (ii) its less favorable solvation in the aqueous solution. The relative free energies of binding in the binary complex show moderate and qualitatively indistinguishable discrimination among the studied fluorinated and non-fluorinated 2-and/or 4-thio analogues of dUMP. The binding free energies of monothio analogues of dUMP and 5-fluoro-dUMP correspond quite well with experimentally measured activities of these nucleotides in the thymidylate synthase reaction. On the other hand, the binding free energies of both dithio analogues, 2,4-dithio-dUMP and 2,4-dithio-FdUMP, show lack of such correlation. The latter suggests that very low activities of the dithio analogues of dUMP and 5-fluoro-dUMP may relate more to the covalent reaction of these nucleotides within the ternary complex with TS and 5,10-methylenetetrahydrofolate, than to their pre-covalent binding. We speculate that a lack of substrate activity of 2,4-dithio-dUMP is related to the high aromaticity of its pyrimidine ring that prevents the Michael addition of the active site cysteine thiol to the pyrimidine C6 atom. A stronger affinity of the fluorinated analogues of dUMP to thymidylate synthase, compared to the non-fluorinated congeners, results from the fluorine substituent producing a local strain in the C6 region in the pyrimidine ring, thus sensitizing C6 to the Michael addition of the cysteine thiol.

Free energy perturbation calculations have been applied to evaluate the relative free energies of binding of 2deoxyuridine-5 -monophosphate (dUMP) and its 2-and/or 4-thio and/or 5-fluoro analogues to the wild-type E. coli thymidylate synthase (ecTS). The results accurately reproduce experimentally measured differences in the free energy of binding of dUMP versus 5-fluoro-dUMP to thymidylate synthase. They indicate that preferred binding of dUMP compared to 5-fluoro-dUMP in the binary complex is equally related to (i) more favorable electrostatic interactions of the dUMP molecule in the enzyme active site, and (ii) its less favorable solvation in the aqueous solution. The relative free energies of binding in the binary complex show moderate and qualitatively indistinguishable discrimination among the studied fluorinated and non-fluorinated 2-and/or 4-thio analogues of dUMP. The binding free energies of monothio analogues of dUMP and 5-fluoro-dUMP correspond quite well with experimentally measured activities of these nucleotides in the thymidylate synthase reaction. On the other hand, the binding free energies of both dithio analogues, 2,4-dithio-dUMP and 2,4-dithio-FdUMP, show lack of such correlation. The latter suggests that very low activities of the dithio analogues of dUMP and 5-fluoro-dUMP may relate more to the covalent reaction of these nucleotides within the ternary complex with TS and 5,10-methylenetetrahydrofolate, than to their pre-covalent binding. We speculate that a lack of substrate activity of 2,4-dithio-dUMP is related to the high aromaticity of its pyrimidine ring that prevents the Michael addition of the active site cysteine thiol to the pyrimidine C6 atom. A stronger affinity of the fluorinated analogues of dUMP to thymidylate synthase, compared to the non-fluorinated congeners, results from the fluorine substituent producing a local strain in the C6 region in the pyrimidine ring, thus sensitizing C6 to the Michael addition of the cysteine thiol.

Nanotechnology deals with the construction of new materials, devices, and different technological systems with a wide range of potential applications at the atomic and molecular level. Nanomaterials have attracted great attention for numerous applications in chemical, biological, and industrial world because of their fascinating physicochemical properties. Nanomaterials and nanodevices are being produced intentionally, unintentionally, and manufactured or engineered by different methods and released into the environment without any safety test. Nantoxicity has become the subject of concern in nanoscience and nanotechnology because of the increasing toxic effects of nanomaterials on the living organisms. Nanomaterials can move freely as compared to the large-sized particles; therefore, they can be more toxic than bulky materials. This review article delineates the toxic effects of different types of nanomaterials on the living organisms through different sources, like water, air, con...

The problem of the existence of a prostaglandin (PG) receptor is still controversial, but it seems to be clear that the main action of the PGs concerns the interface of the cellular membrane (which has a predominantly lipid character) and the extracellular liquid (which mainly consists of water). Also especially in the case of the exogenous PGs, the transport of these substances in the organism in influenced by the hydrophilic‐hydrophobic properties of the reactive molecules. These properties can be estimated by MO studies using a solvation model and a semiempirical method of calculation. This paper is concerned with the molecules of PGA1 and PGE1. MO studies were performed for these molecules with the CNDO/SW method in order to calculate ionization potentials, dipole moments, and molecular polarizabilities. With these computed molecular properties, the electrostatic and van der Waals interactions with water and octanol molecules are evaluated and compared within the framework of th...

The aim of this study was to test sonochemical method to modify surface of catalysts to obtain highly dispersed and active materials for methane combustion. The catalysts were characterised by various physicochemical characterisation methods including: DLS, BET nitrogen adsorption, SEM, EDX and ED-XRF. The results of classical surface analyses and catalytic tests were correlated with the operando DRIFT/MS spectroscopy results. The sonochemical preparation method has proven an efficient way to obtain the active catalysts for methane catalytic combustion. The chromium oxide catalyst has revealed great activity compared to the commercially used palladium catalysts. The DRIFT/MS operando analyses have proven that the formate intermediates at the catalyst surface are stable during methane catalytic combustion.

2-(2′-Hydroxyphenyl)benzoxazole (HBO) has three isomers: a ketone (Kt), an enol (1) which is intramolecularly hydrogen bonded, and a second enol (2) which is not. Enol 1 does not emit but transforms in the excited state to the ketone Kt which can emit fluorescence or return by various paths to the ground state of enol 1. Enol 2 fluoresces but at atmospheric pressure is present, in general, in very low concentration except in hydrogen-bonding media. The fluorescence of HBO was measured as a function of pressure to 60 kbar in five media: poly(methyl methacrylate) (PMMA), poly(ethyl methacrylate) (PEMA), poly(butyl methacrylate) (PBMA), poly(2-hydroxyethyl methacrylate), (PHEMA), and poly(vinyl chloride) (PVCl). In all cases enol 2 is stabilized relative to enol 1 by pressure. With reasonable assumptions it was possible to extract ∆V h, the difference in partial molar volume of enol 1 -enol 2, as a function of pressure. For the methacrylates ∆V h decreases strongly with increasing pressure. The indications are that enol 2, which hydrogen bonds to the methacrylate, has initially a smaller ∆V h but also the configuration has a smaller compressibility. In PVCl ∆V h is relatively small but independent of pressure.

To elucidate the reactive behavior of RDX crystals at pressures and temperatures relevant to shock wave initiation, Raman spectroscopy and optical imaging were used to determine the pressuretemperature (P-T) stability and the decomposition of γ-RDX, the high pressure phase of RDX. Experiments were performed on single crystals in a diamond anvil cell at pressures from 6 to 12 GPa and at temperatures up to 600 K. Evidence for the direct decomposition of γ-RDX above 6 GPa, without the involvement of other phases, is provided. The upper limit of the P-T locus for the γ-RDX thermal decomposition was determined. A refined P-T phase diagram of RDX is presented that includes the current findings for γ-RDX. The static compression results are used to gain key insight into the shock initiation of RDX, including a determination of the RDX phase at decomposition and understanding the role of pressure and temperature in accelerating shock induced decomposition. This study has established the important role that γ-RDX plays in decomposition of RDX under static and shock compression conditions; thus theoretical modeling of RDX decomposition at high pressures and temperatures needs to incorporate the γ-phase response.

Raman spectroscopy was used to determine the vibrational structure and the stability of the high-pressure-hightemperature (HP-HT) polymorph of RDX after it had been quenched to room temperature. Although this polymorph has limited chemical stability under high pressure and temperature, we show that it is chemically and structurally stable from 0.6 GPa to at least 20 GPa at room temperature. Below 0.6 GPa, it readily converts to the R-polymorph. Pressure dependence of the vibrational structure of the HP-HT polymorph was measured and compared with the vibrational structures of other known RDX polymorphs: R, β, and γ. In contrast with previous suggestions, our data indicate that the HP-HT polymorph can have a different structure than the β-polymorph. This finding supports the recent suggestion that the HP-HT polymorph should be given a separate designation, ε-RDX. Furthermore, symmetry correlation analyses of Raman spectra indicate that the HP-HT polymorph (ε-RDX) may assume the space group isomorphous with the C 2V [C 1 (4)] point group and with molecules adopting the pseudo-AAA conformation.

We report a strong emission change induced by continuous light irradiation in two ketones, benzophenone and 4,4′-dichlorobenzophenone, and an aldehyde, 4-(dimethylamino)benzaldehyde, in their crystalline state as well as dissolved in solid polymers. With prolonged laser irradiation, a time evolution of the emission intensity shows complex features, but two clear competing trends can be distinguished: an increase and/or decrease of the emission intensity. It is shown that these trends may be a result of creation of either an emissive or a nonemissive species. The relative importance of these two pathways is significantly dependent on the type of medium and external pressure. The most characteristic feature of these dependencies is the fact that in crystalline environments, in contrast to polymers, the emission intensity at all pressures only decreases. A kinetic model is developed that assumes the lowest triplet state as the origin of the high photoreactivity of these molecules, causing their emission intensity change. This model embraces the observations either in crystalline or polymeric environments and is solved for two limiting cases: a predominance of the hydrogen abstraction reaction from the polymer or a predominance of the ionization due to biphotonic excitation of the triplet state. These processes are assumed responsible, respectively, for the creation of emissive and nonemissive photoproducts. By comparison of the model with experimental results some of the parameters involved in these processes are extracted and their pressure dependence can be predicted.

We report strongly pressure-dependent up-conversion fluorescence from an organic crystal, 4-(p-nitrophenyl)-3,4-dihydropyrazo[c]-benzo[b]morpholine (NDPB). The fluorescence has a similar pressure dependence following both one-and two-photon excitation. In both cases, we observe a significant shift of the emission spectrum to lower energies and decrease of emission intensity in a relatively narrow pressure range (0-20 kbar). Time-resolved measurements of fluorescence decay yield two lifetimes corresponding to the local and charge-transfer state, which decrease with pressure. Similar pressure dependence of the emission energies and lifetimes in one-and two-photon-induced fluorescence indicate that in both cases the same excited states participate in the fluorescence. The same decrease of fluorescence intensity in both cases indicates that the one-and two-photon absorption spectra have similar pressure dependence.

Zunahme der Fluoreszenzintensitàt. Ursache dafür ¡st die Erhöhung der Barriere für die intramolekulare Verdrillung. Oberhalb von 20 kbar (für PY) und im gesamten Druckbereich für para-N,N-dimethylaminobenzylidenmalonodinitril (DMABMN) und für Julolidinemalonodinitril (JDMN) nimmt die Fluoreszenzintensitàt mit steigendem Druck ab, was durch strahlungslose Prozesse der ursprünglich angeregten Zustânde erklârt werden kann. Insbesondere wird gezeigt, daB das Energielückengesetz (energy gap law) anwendbar ist, um das Verhalten der Fluoreszenzenergie und Fluoreszenz- intensitàt ais Funktion des Druckes zu beschreiben.

The probe absorption-dispersion spectra of a driven three-level atom in a double-band photonic crystal have been investigated. We use the model which assumes the upper levels of the atomic transitions coupled via a classical driving field. One of the transitions interacts with the free vacuum modes, and the other transition couples to the modes of the modified reservoir (photonic band gap). The effect of the classical driving field on the absorption-dispersion spectra of an atom is investigated in detail. Most interestingly, it is shown that the atom becomes transparent to a probe laser field coupled to the free space transition, and slow group velocities are obtained near the transparency window.

The effect of a modified reservoir on the nature of the quantum interference in the spontaneous emission of a driven double V-type four-level atom has been investigated. In the model used, the double V-type transitions of a driven atom interact respectively with a free vacuum reservoir and a modified reservoir, leading to the two possible types of quantum interference. The results show that the construction or the destruction of interference in the free vacuum reservoir depends on the type of the modified reservoir and the absence or the presence of interference in the modified reservoir. More interesting, it is shown that based on the presence or the absence of interference in the modified reservoir, interference in the free vacuum reservoir can be constructive or destructive if the modified reservoir is of the type of the free vacuum reservoir. On the other hand, the interference in the free vacuum reservoir is constructive, regardless of the presence or the absence of interference in the modified reservoir, if the modified reservoir is of the type of the photonic band gap. This case, therefore, can be used to control effectively the spontaneous emission and absorption spectra.

This article aims to design and construct a plasma generation device using the surface dielectric barrier discharge method (SDBD) on a laboratory scale to produce a stable and uniform atmospheric pressure plasma layer. For this purpose, a copper electrode with a thickness of 100 microns with a comb-like structure was designed and constructed for this system, and a mica sheet with a thickness of 0.5 mm and dimensions of 10 × 10 cm was built to make the dielectric. According to the experimental data and analytical calculations of the constructed SDBD system in working conditions of 3 kV voltage and 12.5 kHz frequency, the consumption power of this system is calculated at 50 watts. Due to the production of stable and uniform plasma created on the dielectric surface and the measured power consumption, this system will be able to be used in various sciences and industries, including surface processing industries.

Co2+/ZSM5 catalysts (Co/Al = 1, overstoichiometric ratio) have been prepared by solid-state reaction at 500 °C in argon from H-ZSM5 and four Co(II) precursors: formate, nitrate, chloride and acetate. Co3O4 particles supported by the zeolite grains are the only cobalt-containing phases detected when formate is used. When cobalt nitrate is the precursor, Co3O4 particles appear to be independent from the grains. A fraction of cobalt has nevertheless migrated into the zeolite; this is linked with [Co(H2O)6](NO3)2 low melting point and wetting of the zeolite grains by the molten salt at the beginning of the thermal treatment. Catalysts prepared from cobalt chloride contain both nanometric Co3O4 particles on the support grains and cobalt ions inside the zeolitic channels. Ion exchange is possible, at least partly, due to the fact that unlike nitrate and formate, cobalt chloride has not decomposed before reaching the temperature at which the exchange process is activated. This process is c...

In this work, we performed a theoretical density functional theory (DFT) and semi-empirical (PM3) analysis to calculate thermodynamic properties of biokerosene from coconut and palm kernel oils, Jet Propulsion Fuel 8 (JP-8), and mixtures of these fuels. All simulations were performed in thermal equilibrium and for a temperature range of 0.5-1500 K, considering the canonical ensemble model. We predicted the thermal properties energy, enthalpy, enthalpy change, Gibbs free energy, entropy, and specific heat at constant pressure with respect to temperature. In addition, we compared the performances of the DFT functional hybrid B3LYP and the basis set 6-311++G(d,p) and PM3 methods, in order to determine their accuracy for thermodynamic predictions relating to the fuels. Calculations for combustion enthalpy were carried out using the following methods: B3LYP/6-311++G(d,p), B3LYP/6-31+G(d), CBS-QB3, G3, G4, and G3/G4. The results showed good agreement with measured values, indicating that DFT may be a good method to calculate and predict thermodynamic properties of the combustion reactions of kerosene and biokerosene.

To model the double layer near an electrode, theories and simulations must include the different dielectric coefficients of the electrode, the commonly-postulated 'inner' layer, and the electrolyte. Recently, Boda et al. [D. Boda, D. Henderson, K.-Y. Chan, D.T. Wasan. Phys. Rev. E, 69, 046702, ( )] developed a technique to include inhomogeneous dielectric coefficients in arbitrary geometries in a simulation. Here, Monte Carlo simulation results based on this method are reported for the density profiles of 1:1, 2:2 and 2:1 aqueous electrolytes. The simulations include two dielectric boundaries, one from an inner layer of low dielectric coefficient and one from an uncharged metal electrode. In addition, an extension of a Poisson-Boltzmann (PB) type theory due to Onsager and Samara [L. Onsager, N.N.T. Samara. J. chem. Phys., 2, 528, (1934)] is developed and compared with our simulation results. This approach works best for 1:1 salts at low concentrations.

We describe, test, and apply a new computational algorithm for generating protein loop conformations subject to distance and secondary structure constraints. The algorithm is based upon initial scaling and subsequent relaxation of covalent bond lengths. The scaling‐relaxation procedure needs no additional energy terms and can be readily incorporated into existing molecular modeling packages. The algorithm uses an all‐atom energy function from the outset in a straightforward way so that about 60% of the generated loop conformations are free of severe distortions of covalent bond lengths and angles. An extensive application to the major loop conformations of TFIIIA‐type zinc fingers (Zif268 and ADR1) is presented, as well as preliminary calculations on hypervariable loops of two immunoglobulins (MCPC603 and Bence‐Jones). © 1993 John Wiley & Sons, Inc.

We present a new algorithm for identifying molecules that display a pharmacophore, or in general a structural motif, by efficiently constructing and screening huge virtual combinatorial libraries of diverse compounds. The uniqueness of this algorithm is its ability to build and screen libraries of ca. 10 18 3D molecular conformations within a reasonable time scale, thereby increasing the chemical space that can be virtually screened by many orders of magnitude. The algorithm may be used to design new molecules that display a desired pharmacophore on predefined sets of chemical scaffolds. This is demonstrated herein by screening a library of backbone cyclic peptides to find candidate peptido-and proteinomimetics.

This paper is aimed to assess the mechanical properties of a hybrid graphene-carbon nanotube carrier embedded with doxorubicin (DOX). Utilizing molecular dynamics simulation, the results reveal that by increasing the temperature from 309 to 313 K, the elastic modulus of the GS/CNT/DOX carrier decreases from 0.8 to 0.74 TPa. Also, it is shown that the presence of chitosan molecules enhances the mechanical characteristics of the proposed nanocarrier. Taking the chirality of the graphene sheet into account, the results indicate that by increasing the size of the graphene sheet, the failure stress is slightly increased for the armchair type. However, this value decreases as the size of the zigzag sample increases. Additionally, the influence of aspect ratio on the elastic modulus, fracture stress, and fracture strain of these systems is systematically examined. It has been shown that the failure stress may change significantly with increasing this parameter, especially for carrier systems having zigzag carbon nanostructures. Moreover considering various voids content in the CNT structure, the weakening effect of defects is systematically explored. Also, the dependence of the mechanical features of the proposed hybrid carrier on the presence of DOX molecules is studied via MD simulations. Finally, we have investigated the role of CNT physical characteristics including its size and chirality on the results.

In this research, an environmentally friendly, effective method is documented for the synthesis of pyrido[2,3-d]pyrimidine and 1,2,4-triazolo[4,3-a]pyrimidine derivatives using an affordable and facile-prepared dicationic molten salt based on Tropine. The aforementioned pyrimidine derivatives have found remarkable pharmacological and therapeutic roles. under the influence of this catalyst formulated as [(Tropine) 2 C 3 H 5 OH].2Cl, the products are obtained during 50 to 120 and 15 to 70 min for both reactions respectively, along with high yields from 90 to 98% which was measured through chromatography method, under solvent-free conditions or in EtOH as a green solvent. Also, the catalyst can be easily recovered and reused at least for three times.

Fibrous nanocomposites based on natural polysaccharides originated from algas were produced. Nanocomposite fibres were obtained by a wet method. Two kinds of ceramic nanofillers were applied i.e., nanometric amorphous silica (nSiO 2 ) and natural hydroxyapatite (HAp). The presence of the nanofillers in a biopolymer matrix was determined using point X-ray microanalysis (SEM/EDS). FT-IR studies and Raman spectroscopy revealed that the presence of the nanofillers effected structure of the biopolymer chain, and structural changes depended on the introduced modifier type. Stronger effects were observed in case of material containing HAp as the nanofiller.

Aim of this work was a surface modification and characterisation of composite membrane materials destined for regeneration of damaged bone tissue. The materials consisted of stable, hydrophobic PTFE-PVDF-PP polymer and resorbable, hydrophilic biopolymer fibres made of sodium alginate (NaAlg). The fibres were washed-out with water to create open porosity in the membranes, and part of the dissolved sodium alginate deposited on the composite surface. Distribution of a biopolymer layer modifying the composite surface was investigated with FT-IR method. FT-IR reflection (ATR) and transmission techniques revealed that the surface modification had a domain-type character. The deposited sodium alginate modified physicochemical properties of the membrane i.e., lowered the wetting angle, and increased the surface free energy. Such surface characteristics may be advantageous for cells adhesion and proliferation process in in vitro and in vivo conditions.

In the first part of this report experimental results are discussed which focus onto the importance of hydrogen atoms in the interaction of imidazolium-based ionic liquids. These include examples for the cation-anion interaction in neat ionic liquids as well as the interactions between ionic liquids and their molecular environment, water in particular. Most of the studies emphasize the importance of the C(2)-H group of the imidazolium ring for the intra-and intermolecular interactions; commonly, the interactions of the type C-H . . . X (X =: O, halide) are attributed to ''hydrogen bonding". In the second part it is analyzed whether these interactions and their consequences fulfill the criteria set by standard definitions of hydrogen bonding. Two cation-anion co-conformations at the C(2)-H group are found. One co-conformer (in-plane) often resembles a hydrogen bond while the other one (on-top) points to a non-hydrogen bonding behavior. Furthermore, the degree of hydrogen bonding for the in-plane structure is very dependent on the anion. Spatial distribution functions show that, in general, both co-conformations are occupied. However, the question of how long a particular co-conformer is populated in the liquid state has yet to be answered. Therefore, it is concluded that the term ''hydrogen bond" should, at present, be treated with care to characterize the cation-anion contacts, because of the above-mentioned difficulties. Once more it must be stressed that oversimplifications and generalizations, even for this subclass of ionic liquids have to be avoided, because these liquids are more complicated than it appears from first sight.

Summary Air-stable Co, Fe, and Fe/Co nanoparticles are accessible by thermolysis of the metal carbonyl precursors in the presence of aluminium alkyls and subsequent “smooth oxidation”. The structure of the particles was investigated by transmission electron microscopy (TEM, HRTEM), X-ray absorption spectroscopy (XAS), X-ray and ultraviolet photoelectron spectroscopy (XPS, UPS), metastable impact electron spectroscopy (MIES), and small-angle neutron scattering (SANS). The peptization of the nanoparticles with suitable surfactants (oleic and lauric acid, sodium dioctylsulfosuccinate (AOT), LP-4 (a fatty acid condensation polymer), and KorantinSH (N-oleyl sarcosine)) yields magnetic fluids dispersed in carrier liquids such as toluene, kerosene, vacuum and mineral oils which are remarkably stable in air under ambient conditions. The resulting magnetic fluids show good magnetic properties. Several methods for the preparation of water-based MF are presented, e.g., formation of surfactant ...

We present a Quantum Monte Carlo study of the dissociation energy and the dispersion curve of the water dimer, a prototype of hydrogen bonded system. Our calculations are based on a wave function which is a modern and fully correlated implementation of the Pauling's valence bond idea: the Jastrow Antisymmetrised Geminal Power (JAGP) [Casula et al J.Chem.Phys. 119,6500-6511 (2003)]. With this variational wave function we obtain a binding energy of -4.5(0.1) kcal/mol, that is only slightly increased to -4.9(0.1) kcal/mol by using the Lattice Regularized Diffusion Monte Carlo (LRDMC). This projection technique allows to improve substantially the correlation energy of a given variational guess and indeed, when applied to the JAGP, yields a binding energy in fair agreement with the value of -5.0 kcal/mol reported by experiments and other theoretical works. The minimum position, the curvature and the asymptotic behavior of the dispersion curve are well reproduced both at the variational and LRDMC level. Moreover, thanks to the simplicity and the accuracy of our variational approach, we are able to dissect the various contributions to the binding energy of the water dimer in a systematic and controlled way. This is achieved by appropriately switching off determinantal and Jastrow variational terms in the JAGP. Within this scheme, we estimate that the van der Waals contribution to the electron correlation is substantial and amounts to 1.5(0.2) kcal/mol, this value being comparable with the intermolecular covalent energy, that we find to be 1.1(0.2) kcal/mol. The present Quantum Monte Carlo approach based on the JAGP wavefunction reveals as a promising tool for the interpretation and the quantitative description of weakly interacting systems, where both dispersive and covalent energy contributions play an important role.

We present an extensive investigation of the vertical excitations of the anionic and neutral forms of wild-type green fluorescent protein using time-dependent density functional theory (TDDFT), multiconfigurational perturbation theory (CASPT2), and quantum Monte Carlo (QMC) methods within a quantum mechanics/molecular mechanics (QM/MM) scheme. The protein models are constructed via room-temperature QM/MM molecular dynamics simulations based on DFT and are representative of an average configuration of the chromophoreÀprotein complex. We thoroughly verify the reliability of our structures through simulations with an extended QM region, different nonpolarizable force fields, as well as partial reoptimization with the CASPT2 approach. When computing the excitations, we find that wave function as well as density functional theory methods with long-range corrected functionals agree in the gas phase with the extrapolation of solution experiments but fail in reproducing the bathochromic shift in the protein, which should be particularly significant in the neutral case. In particular, while all methods correctly predict a shift in the absorption between the anionic and neutral forms of the protein, the location of the theoretical absorption maxima is significantly blue-shifted and too close to the gas-phase values. These results point to either an intrinsic limitation of nonpolarizable force-field embedding in the computation of the excitations or to the need to explore alternative protonation states of amino acids in the close vicinity of the chomophore.