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Dynamics Calculations (dynamics + calculation)
Kinds of Dynamics Calculations Selected AbstractsComment on "Disproving a Silicon Analog of an Alkyne with the Aid of Topological Analyses of the Electronic Structure and Ab Initio Molecular Dynamics Calculations"CHEMPHYSCHEM, Issue 4 2006Gernot Frenking Prof. Dr. Bond order of a silicon-silicon bond (1): The statement that the recently synthesized compound RSiSiR (1) (RSi[C(SiMe3)3]2CHMe2) has rather a double than a triple bond is challenged. Arguments are given which support the interpretation of the bonding situation in terms of two donor,acceptor bonds which are enhanced by one , bond (see picture). [source] Disproving a Silicon Analog of an Alkyne with the Aid of Topological Analyses of the Electronic Structure and Ab Initio Molecular Dynamics CalculationsCHEMPHYSCHEM, Issue 9 2005Carlo A. Pignedoli Dr. Abstract A silicon compound has recently been synthesized that was claimed to exhibit the first realization of a silicon,silicon triple bond. We debate this classification on the basis of a thorough investigation of the nature of the chemical bond, using the rigorous topological analysis of the electron density as developed in Bader's atoms-in-molecules theory, that of the electron localization function and the related orbital-independent definitions of the bond order. Our results refer both to the ground-state geometry and to nonequilibrium configurations, which are accessed by the system in a room-temperature ab initio molecular dynamics simulation. We also use the reciprocal compliance force constant as an independent chemical descriptor. All the above procedures are in agreement and do not support the classification of the silicon,silicon central bond as triple. The characterization which consistently emerges from the present study is one in which two electron pairs participate in the bonding and the other pair belongs mainly to nonbonding regions. [source] Theoretical study and rate constant calculation for reaction of CF3CH2OH with OHJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2007Ying Wang Abstract The reaction mechanism of CF3CH2OH with OH is investigated theoretically and the rate constants are calculated by direct dynamics method. The potential energy surface (PES) information, which is necessary for dynamics calculation, is obtained at the B3LYP/6-311G (d, p) level. The single-point energy calculations are performed at the MC-QCISD level using the B3LYP geometries. Complexes, with the energies being less than corresponding reactants and products, are found at the entrance and exit channels for methylene-H-abstraction channel, while for the hydroxyl-H-abstraction channel only entrance complex is located. By means of isodesmic reactions, the enthalpies of the formation for the species CF3CH2OH, CF3CHOH, and CF3CH2O are estimated at the MC-QCISD//B3LYP/6-311G (d, p) level of theory. The rate constants for two kinds of H-abstraction channels are evaluated by canonical variational transition state theory with the small-curvature tunneling correction (CVT/SCT) over a wide range of temperature 200,2000 K. The calculated results are in good agreement with the experimental values in the temperature region 250,430 K. The present results indicate that the two channels are competitive. Below 289 K, hydroxyl-H-abstraction channel has more contribution to the total rate constants than methylene-H-abstraction channel, while above 289 K, methylene-H-abstraction channel becomes more important and then becomes the major reaction channel. © 2007 Wiley Periodicals, Inc. J Comput Chem 28: 802,810, 2007 [source] Rider's net moment estimation using control force of motion system for bicycle simulatorJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 11 2004Jae-Cheol Shin One of the challenging problems with bicycle simulators is to deal with the virtual bicycle dynamics that is coupled with rider's motion. For the virtual bicycle dynamics calculation and the real time simulation, it is necessary to identify the control inputs from the rider as well as the virtual environments. The steering, pedaling, and braking torques can be easily measured by using torque sensors and the virtual environments can be generated and provided by a visual system. However, direct measurement of the rider's net moment that significantly affects the bicycle motion is not practical. In this work, it is shown that six control forces of the Stewart platform-based motion system can be used for effective estimation of the rider's net moment, incorporated with the sliding mode controller with perturbation estimation. © 2004 Wiley Periodicals, Inc. [source] Realistic simulations of combined DNA electrophoretic flow and EOF in nano-fluidic devicesELECTROPHORESIS, Issue 24 2008Duc Duong-Hong Abstract We present a three-dimensional dissipative particle dynamics model of DNA electrophoretic flow that captures both DNA stochastic motion and hydrodynamics without requiring expensive molecular dynamics calculations. This model enables us to efficiently and simultaneously simulate DNA electrophoretic flow and local EOF (generated by counterions near the DNA backbone), in mesoscale (,,m) fluidic devices. Our model is used to study the electrophoretic separation of long DNA chains under entropic trapping conditions [Han and Craighead, Science 2000, 288, 1026,1029]. Our simulation results are in good agreement with experimental data for realistic geometries (tapered walls) and reveal that wall tapering in entropic traps has a profound impact in the DNA trapping behavior, an effect which was largely ignored in previous modeling. [source] The solution structure of gomesin, an antimicrobial cysteine-rich peptide from the spiderFEBS JOURNAL, Issue 4 2002Nicolas Mandard Gomesin is the first peptide isolated from spider exhibiting antimicrobial activities. This highly cationic peptide is composed of 18 amino-acid residues including four cysteines forming two disulfide linkages. The solution structure of gomesin has been determined using proton two-dimensional NMR (2D-NMR) and restrained molecular dynamics calculations. The global fold of gomesin consists in a well-resolved two-stranded antiparallel ,,sheet connected by a noncanonical ,,turn. A comparison between the structures of gomesin and protegrin-1 from porcine and androctonin from scorpion outlines several common features in the distribution of hydrophobic and hydrophilic residues. The N- and C-termini, the ,,turn and one face of the ,,sheet are hydrophilic, but the hydrophobicity of the other face depends on the peptide. The similarities suggest that the molecules interact with membranes in an analogous manner. The importance of the intramolecular disulfide bridges in the biological activity of gomesin is being investigated. [source] Direct ab initio dynamics calculations of the rate constants for the reaction of CHF2CF2OCH3 with ClINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 4 2007Lei Yang A dual-level direct dynamics method is employed to reveal the dynamical properties of the reaction of CHF2CF2OCH3 (HFE-254pc) with Cl atoms. The optimized geometries and frequencies of the stationary points and the minimum energy path (MEP) are calculated at the B3LYP/6-311G(d,p) level by using GAUSSIAN 98 program package, and energetic information is further refined by the G3(MP2) method. Two H-abstraction channels have been identified. For the reactant CHF2CF2OCH3 and the two products, CHF2CF2OCH2 and CF2CF2OCH3, the standard enthalpies of formation are evaluated with the values of ,256.71 ± 0.88, ,207.79 ± 0.12, and ,233.43 ± 0.88 kcal/mol, respectively, via group-balanced isodesmic reactions. The rate constants of the two reaction channels are evaluated by means of canonical variational transition-state theory (CVT) including the small-curvature tunneling (SCT) correction over a wide range of temperature from 200 to 2000 K. The calculated rate constants agree well with the experimental data, and the Arrhenius expressions for the title reaction are fitted and can be expressed as k1 = 9.22 × 10,19 T2.06 exp(219/T), k2 = 4.45 × 10,14T0.90 exp(,2220/T), and k = 4.71 × 10,22 T3.20) exp(543/T) cm3 molecule,1 s,1. Our results indicate that H-abstraction from CH3 group is the main reaction pathway in the lower temperature range, while H-abstraction from CHF2 group becomes more competitive in the higher temperature range. © 2007 Wiley Periodicals, Inc. 39: 221,230, 2007 [source] Crossed-Beam and Quantum Dynamics Studies of the Reaction Cl + CHD3ISRAEL JOURNAL OF CHEMISTRY, Issue 1 2007Gunnar Nyman The ground-state reaction of Cl + CHD3 was studied with joint experimental and theoretical efforts. Experiments were performed under crossed-beam conditions using a time-sliced velocity imaging detection method. By taking the images over the energy range of chemical significance,from threshold to about 9 kcal/mol,the reactive excitation functions as well as the dependence of product angular distributions and of the energy disposal on initial collision energies were obtained for both isotopic product channels. Theoretically, reduced dimensionality quantum dynamics calculations were performed for the HCl + CD3 channel, and the results are in excellent agreement with experimental findings. Comparisons with previously reported results on Cl + CH4/CD4, both experimental and theoretical, were also made to gain deeper insights into the dynamics of this benchmark atom + polyatomic reaction. [source] Energetic materials: variable-temperature crystal structure of ,-NTOJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003Nadezhda B. Bolotina The crystal structure of the metastable , form of 5-nitro-2,4-dihydro-3H -1,2,4-triazol-3-one (,-NTO, monoclinic, P21/c) has been investigated at five temperatures in the range 100,298,K using single-crystal X-ray diffraction techniques. The second-rank thermal expansion tensor has been determined to describe thermal behavior of the crystal. The most significant thermal expansion is in a plane, which is almost perpendicular to the planes of all the NTO molecules. Perpendicular to the plane of maximal thermal expansion, a modest thermal contraction takes place. Both thermal expansion and contraction of the crystal lattice indicate anharmonicity of the atomic thermal motion. The experimental thermal variation of the unit-cell parameters is in qualitative agreement with that previously obtained from molecular dynamics calculations. Rigid-body analysis of the molecular thermal motion was performed using the libration and translation second-rank tensors. Although the translation part of the thermal motion is not strongly anisotropic, the largest displacements of the NTO molecules are oriented in the plane of maximal thermal expansion of the crystal and have significant anharmonic components. The libration motion is more anisotropic, and the largest libration as well as the largest translation principal axes are directed along the C5,N5 bond in each NTO molecule. [source] A simple approach for improving the hybrid MMVB force field: Application to the photoisomerization of s - cis butadieneJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2003Marco Garavelli Abstract MMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Qij and Kij, whose expressions are partitioned here into a primary contribution and second-order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second-order correction terms for the particular molecule(s) being studied. This "local" reparametrization is based on values of Kij extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s - cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1357,1363, 2003 [source] Structure,function relationship studies of PTH(1,11) analogues containing sterically hindered dipeptide mimeticsJOURNAL OF PEPTIDE SCIENCE, Issue 8 2007Nereo Fiori Abstract The N -terminal 1,34 fragment of parathyroid hormone (PTH) is fully active in vitro and in vivo and reproduces all biological responses characteristic of the native intact PTH. In order to develop safer and non-parenteral PTH-like bone anabolic agents, we have studied the effect of introducing conformationally constrained dipeptide mimetics into the N -terminal portion of PTH in an effort to generate miniaturized PTH-mimetics. To this end, we have synthesized and conformationally and biologically characterized PTH(1,11) analogues containing 3R -carboxy-6S -amino-7,5-bicyclic thiazolidinlactam (7,5-bTL), a rigidified dipeptide mimetic unit. The wild type sequence of PTH(1,11) is H-Ser-Val-Ser-Glu-Ile-Gln-Leu-Met-His-Asn-Leu-NH2. The following pseudo-undecapeptides were prepared: [Ala1, 7,5-bTL3, 4, Nle8, Arg11]hPTH(1,11)NH2 (I); [Ala1, 7,5-bTL6, 7, Nle8, Arg11]hPTH(1,11)NH2 (II); [Ala1, Nle8, 7,5-bTL9, 10, Arg11]hPTH(1,11)NH2 (III). In aqueous solution containing 20% TFE, only analogue I exhibited the typical CD pattern of the ,-helical conformation. NMR experiments and molecular dynamics calculations located the ,-helical stretch in the sequence Ile5 -His9. The dipeptide mimetic unit 7,5-bTL induces a type III ,-turn, occupying the positions i , 1 and i of the turn. Analogue II exhibited an equilibrium between a type I ,-turn and an ,-helix, and analogue III did not show any ordered structure. Biological tests revealed poor activity for all analogues (EC50 > 0.1 mM). Apparently, the relative side-chain orientation of Val2, Ile5 and Met8 can be critical for effective analogue-receptor interaction. Considering helicity as an essential property to obtain active PTH agonists, one must decorate the correctly positioned dipeptide mimetic azabicycloalkane scaffold with substitutions corresponding to the displaced amino acids. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Conformational study on glycosylated asparagine-oligopeptides by NMR spectroscopy and molecular dynamics calculationsJOURNAL OF PEPTIDE SCIENCE, Issue 8 2005Stefania Mazzini Abstract The conformational properties of the homo oligomers of increasing chain length Boc-(Asn)n -NHMe (n = 2, 4, 5), (GlcNAc-,-Asn)n -NHMe (n = 2, 4, 5, 8) and Boc-[GlcNAc(Ac)3 -,-Asn]n -NHMe (n = 2, 4, 5) were studied by using NOE experiments and molecular dynamic calculations (MD). Sequential NOEs and medium range NOEs, including (i,i+2) interactions, were detected by ROESY experiments and quantified. The calculated inter-proton distances are longer than those characteristic of ,-turn secondary structures. Owing to the large conformational motions expected for linear peptides, MD simulations were performed without NMR constraints, with explicit water and by applying different treatments of the electrostatic interactions. In agreement with the NOE results, the simulations showed, for all peptides, the presence of both folded and unfolded structures. The existence of significant populations of ,-turn structures can be excluded for all the examined compounds, but two families of structures were more often recognized. The first one with sinusoidal or S-shaped forms, and another family of large turns together with some more extended conformations. Only the glycosylated pentapeptide shows in vacuo a large amount of structures with helical shaped form. The results achieved in water and in DMSO are compared and discussed, together with the effect of the glycosylation. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] The role of segment 32,47 of cholecystokinin receptor type A in CCK8 binding: synthesis, nuclear magnetic resonance, circular dichroism and fluorescence studiesJOURNAL OF PEPTIDE SCIENCE, Issue 3 2003Stefania De Luca Abstract The segment 32,47 of the N -terminal extracellular domain of the type A cholecystokinin receptor, CCKA -R(32,47), was synthesized and structurally characterized in a membrane mimicking environment by CD, NMR and molecular dynamics calculations. The region of CCKA -R(32,47) encompassing residues 39,46 adopted a well-defined secondary structure in the presence of DPC micelles, whereas the conformation of the N -terminal region (segment 32,37) could not be uniquely defined by the NOE derived distance constraints because of local flexibility. The conformation of the binding domain of CCKA -R(32,47) was different from that found for the intact N -terminal receptor tail, CCKA -R(1,47). To assess whether CCKA -R(32,47) was still able to bind the nonsulfated cholecystokinin C -terminal octapeptide, CCK8, a series of titrations was carried out in SDS and DPC micelles, and the binding interaction was followed by fluorescence spectroscopy. These titrations gave no evidence for complex formation, whereas a high binding affinity was found between CCKA -R(1,47) and CCK8. The different affinities for the ligand shown by CCKA -R(32,47) and CCKA -R(1,47) were paralleled by different interaction modes between the receptor segments and the micelles. The interaction of CCKA -R(32,47) with DPC micelles was much weaker than that of CCKA -R(1,47), because the former receptor segment lacks proper stabilizing contacts with the micelle surface. In the case of SDS micelles CCKA -R(32,47) was found to form non-micellar adducts with the detergent that prevented the onset of a functionally significant interaction between the receptor segment and the micelle. It is concluded that tertiary structure interactions brought about by the 1,31 segment play a key role in the stabilization of the membrane bound, biologically active conformation of the N -terminal extracellular tail of the CCKA receptor. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Lattice dynamics of Ca4GdO(BO3)3JOURNAL OF RAMAN SPECTROSCOPY, Issue 4 2004M. Ma, czka Abstract Polarized Raman and IR spectra were obtained for Ca4GdO(BO3)3 crystal at ambient temperature. The assignment of the observed bands to the respective internal and external phonons is proposed on the basis of lattice dynamics calculations. This study also shows that significant LO,TO splitting exists for some internal modes. Copyright © 2004 John Wiley & Sons, Ltd. [source] Hopping transport in 1D chains (DNA vs.PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 1 2004Abstract We discuss charge transport in one-dimensional organic solids (DNA and discotic liquid-crystalline glass (DLC)), focusing on the effects of static and dynamic disorder. In the presence of static disorder it can be shown that the temperature dependence of the low-field mobility is , , exp [,(T0/T)2], with characteristic temperature T0 depending on the scale of the energy distribution of localized states responsible for transport. In the case of both static and dynamic disorder the situation is different. We obtain a temperature independent mobility in our molecular dynamics calculations in the case of large static and dynamic disorder compared to the energy overlap integral between the neighbouring sites. The theoretical results are in good agreement with experimental data. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Insights into the anthrax lethal factor,substrate interaction and selectivity using docking and molecular dynamics simulationsPROTEIN SCIENCE, Issue 8 2009Georgios A. Dalkas Abstract The anthrax toxin of the bacterium Bacillus anthracis consists of three distinct proteins, one of which is the anthrax lethal factor (LF). LF is a gluzincin Zn-dependent, highly specific metalloprotease with a molecular mass of ,90 kDa that cleaves most isoforms of the family of mitogen-activated protein kinase kinases (MEKs/MKKs) close to their amino termini, resulting in the inhibition of one or more signaling pathways. Previous studies on the crystal structures of uncomplexed LF and LF complexed with the substrate MEK2 or a MKK-based synthetic peptide provided structure-activity correlations and the basis for the rational design of efficient inhibitors. However, in the crystallographic structures, the substrate peptide was not properly oriented in the active site because of the absence of the catalytic zinc atom. In the current study, docking and molecular dynamics calculations were employed to examine the LF-MEK/MKK interaction along the catalytic channel up to a distance of 20 Å from the zinc atom. This residue-specific view of the enzyme-substrate interaction provides valuable information about: (i) the substrate selectivity of LF and its inactivation of MEKs/MKKs (an issue highly important not only to anthrax infection but also to the pathogenesis of cancer), and (ii) the discovery of new, previously unexploited, hot-spots of the LF catalytic channel that are important in the enzyme/substrate binding and interaction. [source] Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulersPROTEIN SCIENCE, Issue 7 2001Nora S. Green Abstract Homobifunctional chemical cross-linking reagents are important tools for functional and structural characterization of proteins. Accurate measures of the lengths of these molecules currently are not available, despite their widespread use. Stochastic dynamics calculations now provide quantitative measures of the lengths, and length dispersions, of 32 widely used molecular rulers. Significant differences from published data have been found. [source] Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulationsPROTEIN SCIENCE, Issue 1 2000David A. Horita Abstract Molecular dynamics calculations provide a method by which the dynamic properties of molecules can be explored over timescales and at a level of detail that cannot be obtained experimentally from NMR or X-ray analyses. Recent work (Philippopoulos M, Mandel AM, Palmer AG III, Lim C, 1997, Proteins 28:481,493) has indicated that the accuracy of these simulations is high, as measured by the correspondence of parameters extracted from these calculations to those determined through experimental means. Here, we investigate the dynamic behavior of the Src homology 3 (SH3) domain of hematopoietic cell kinase (Hck) via 15N backbone relaxation NMR studies and a set of four independent 4 ns solvated molecular dynamics calculations. We also find that molecular dynamics simulations accurately reproduce fast motion dynamics as estimated from generalized order parameter (S2) analysis for regions of the protein that have experimentally well-defined coordinates (i.e., stable secondary structural elements). However, for regions where the coordinates are not well defined, as indicated by high local root-mean-square deviations among NMR-determined structural family members or high B -factors/low electron density in X-ray crystallography determined structures, the parameters calculated from a short to moderate length (less than 5,10 ns) molecular dynamics trajectory are dependent on the particular coordinates chosen as a starting point for the simulation. [source] Proton-transfer dynamics in the (HCO3,)2 dimer of KHCO3 from Car,Parrinello and path-integrals molecular dynamics calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010Przemyslaw D. Dopieralski The proton motion in the (HCO)2 dimer of KHCO3 at 298,K has been studied with Car,Parrinello molecular dynamics (CPMD) and path-integrals molecular dynamics (PIMD) simulations. According to earlier neutron diffraction studies at 298,K hydrogen is disordered and occupies two positions with an occupancy ratio of 0.804/0.196. A simulation with only one unit cell is not sufficient to reproduce the disorder of the protons found in the experiments. The CPMD results with four cells, 0.783/0.217, are in close agreement with experiment. The motion of the two protons along the O...O bridge is highly correlated inside one dimer, but strongly uncoupled between different dimers. The present results support a mechanism for the disorder which involves proton transfer from donor to acceptor and not orientational disordering of the entire dimer. The question of simultaneous or successive proton transfer in the two hydrogen bonds in the dimer remains unanswered. During the simulation situations with almost simultaneous proton transfer with a time gap of around 1,fs were observed, as well as successive processes where first one proton is transferred and then the second one with a time gap of around 20,fs. The calculated vibrational spectrum is in good agreement with the experimental IR spectrum, but a slightly different assignment of the bands is indicated by the present simulations. [source] Enantiorecognition on solid chiral selectors using microbatch technology: an example of limitation in case of strong association in the racemateBIOMEDICAL CHROMATOGRAPHY, Issue 6 2005Christian Roussel Abstract When they were independently tested, the enantiomers of N,N,-bis(salicylidene)- trans -1,2-cyclohexanediamine showed a large difference in adsorption on new chiral selectors using microbatch technology. Surprisingly, when these enantiomers were applied on the same supports as a racemic mixture, no discrimination was observed even though suitable adsorption existed. When a mixture enriched in one enantiomer (scalemic mixture) was applied, the resulting supernatant contained the racemic form and the enantiomer in excess was adsorbed on the support together with a part of racemate. This behavior, which militates in favor of a strong heterochiral dimer formation in the racemate, was revealed using microbatch technology but remained hidden on classical column chromatography on chiral support. Molecular dynamics calculations corroborate this hypothesis, showing a favorite binding mode of the heterochiral dimer, which is stabilized by various inter- and intramolecular interactions. Our findings may be considered as a new limitation of microbatch technology, but they may have some inference in case of chiral amplification using the N,N,-bis(salicylidene)- trans -1,2-cyclohexanediamine enantiomers as chiral ligands. Copyright © 2005 John Wiley & Sons, Ltd. [source] Molecular dynamics calculations on amylose fragments.BIOPOLYMERS, Issue 2 2002Abstract Molecular dynamics simulations (NPT ensembles, 1 atm) using the all atom force field AMB99C (F. A. Momany and J. L. Willett, Carbohydrate Research, Vol. 326, pp 194,209 and 210,226), are applied to a periodic cell containing ten maltodecaose fragments and TIP3P water molecules. Simulations were carried out at 25 K intervals over a range of temperatures above and below the expected glass transition temperature, Tg, for different water concentrations. The amorphous cell was constructed through successive dynamic equilibration steps at temperatures above Tg and the temperature lowered until several points of reduced slope (1/T vs volume) were obtained. This procedure was carried out at each hydration level. Each dynamics simulation was continued until the volume remained constant without up or down drift for at least the last 100 ps. For a given temperature, most simulations required 400,600 ps to reach an equilibrium state, but longer times were necessary as the amount of water in the cell was reduced. A total of more than 30 ns of simulations were required for the complete study. The Tg for each hydrated cell was taken as that point at which a discontinuity in slope of the volume (V), potential energy (PE), or density (,) vs 1/T was observed. The average calculated Tg values were 311, 337, 386, and 477 K for hydration levels of 15.8, 10, 5, and 1%, respectively, in generally good agreement with experimental values. The Tg for anhydrous amylose is above the decomposition temperature for carbohydrates and so cannot be easily measured. However, it has also been difficult to obtain a value of Tg for anhydrous amylose using simulation methods. Other molecular parameters such as end-to-end distances, mean square distributions, and pair distributions are discussed. Published 2002 John Wiley & Sons, Inc. Biopolymers 63: 99,110, 2002 [source] A Heat-Integrated Reverse-Flow Reactor Concept for Endothermic High-Temperature Syntheses.CHEMICAL ENGINEERING & TECHNOLOGY (CET), Issue 9 2009Part II: Development of a Reformer Prototype for Hydrogen Production Abstract In the first part of the contribution, the asymmetric operation of a reverse-flow reactor for endothermic high-temperature syntheses has been introduced and front phenomena have been discussed. The current part presents the implementation of the concept to the production of hydrogen by methane steam reforming. A key element of the developed reformer is the integration of combustion chambers for in situ heat generation during reheating of the bed. To avoid local temperature peaks, the concept of flameless combustion is used. The concept was adapted to the requirements of the unsteady operation. A proper design of the combustion chamber was developed using computational fluid dynamics calculations, tracer experiments and tests in a single combustion chamber. The concept was further tested under periodic operation in a laboratory setup. The formation of the desired, axially extended high-temperature plateau in the center of the reactor could be shown experimentally. The results prove the adequacy of the reverse-flow reformer to attain a stable periodic operation without excess temperatures. [source] A Conjugated Thiophene-Based Rotaxane: Synthesis, Spectroscopy, and ModelingCHEMISTRY - A EUROPEAN JOURNAL, Issue 13 2010Leszek Zalewski Dr. Abstract A dithiophene rotaxane 1,,-CD and its shape-persistent corresponding dumbbell 1 were synthesized and fully characterized. 2D NOESY experiments, supported by molecular dynamics calculations, revealed a very mobile macrocycle (,-CD). Steady-state and time-resolved photoluminescence experiments in solution were employed to elucidate the excited-state dynamics for both systems and to explore the effect of cyclodextrin encapsulation. The photoluminescence (PL) spectrum of 1,,-CD was found to be blueshifted with respect to the dumbbell 1 (2.81 and 2.78,eV, respectively). Additionally, in contrast to previous observations, neither PL spectra nor the decay kinetics of both threaded and unthreaded systems showed changes upon increasing the concentration or changing the polarity of the solutions, thereby providing evidence for a lack of tendency toward aggregation of the unthreaded backbone. [source] Ionic Hydrogen Bonds Controlling Two-Dimensional Supramolecular Systems at a Metal SurfaceCHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2007Dietmar Payer Abstract Hydrogen-bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), self-assembles at low temperatures (250,300,K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420,K leads to a densely packed quartet structure consisting of flat-lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization. [source] Chiral Recognition by Resorcin[4]arene Receptors: Intrinsic Kinetics and DynamicsCHEMISTRY - A EUROPEAN JOURNAL, Issue 17 2004Andrea Tafi Prof. Abstract Molecular recognition of representative amino acids (A) by a chiral amido[4]resorcinarene receptor (1L) was investigated in the gas phase by ESI-FT-ICR mass spectrometry. The ligand displacement reaction between noncovalent diastereomeric [1L,H,A]+ complexes and the 2-aminobutane enantiomers (B) exhibits a distinct enantioselectivity with regard to both the leaving amino acid A and the amine reactant B. The emerging selectivity picture, discussed in the light of molecular mechanics and molecular dynamics calculations, points to chiral recognition by 1L, as determined by the effects of the host asymmetric frame on the structure, stability, and rearrangement dynamics of the diastereomeric [1L,H,A]+ complexes and the orientation of the amine reactant B in encounters with [1L,H,A]+. The results contribute to the development of a dynamic model of chiral recognition of biomolecules by enzyme mimics in the unsolvated state. La spettrometria di massa ESI-FT-ICR č stata impiegata per lo studio del riconoscimento chirale di alcuni amminoacidi rappresentativi (A) da parte di un ammido[4]resorcinarene chirale (1L). La reazione di rilascio dell,amminoacido A dai complessi diastereomerici non covalenti [1L,H,A]+ a seguito dell,attacco degli enantiomeri del 2-amminobutano (B) mostra una distinta enantioselettivitą sia per quanto riguarda la molecula uscente A che per quanto riguarda il reagente B. Il quadro di reattivitą ottenuto, discusso alla luce di calcoli di meccanica e dinamica molecolare, indica che il riconoscimento chirale da parte di 1L č determinato dall,effetto della struttura asimmetrica dell, ammido[4]resorcinarene sulla struttura, la stabilitą, e la dinamica di riarrangiamento dei suoi complessi diastereomerici [1L,H,A]+ e dall, orientamento dell,ammina reagente B nel complesso di collisione con [1L,H,A]+. I risultati ottenuti contribuiscono allo sviluppo di un modello dinamico per il riconoscimento chirale di biomolecole da parte di enzimi artificiali allo stato non solvatato. [source] Selective Adsorption of Polychlorinated Dibenzo- p -dioxins and Dibenzofurans by the Zeosils UTD-1, SSZ-24, and ITQ-4CHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2004Ralph Jäger Dr. Abstract Zeosils are microporous solids with a pure silica framework. Due to their hydrophobic properties, zeosils are ideal host materials for the adsorption of hydrophobic guest molecules. We tested zeosils with different pore diameters (UTD-1, SSZ-24 and ITQ-4 as well as CIT-5) for the selective adsorption of the polychlorinated dibenzo- p -dioxins and dibenzofurans. This group of highly toxic substances contains 210 congeners that possess similar chemical properties, but differ in their size and shape. In the experiment, polychlorinated dibenzo- p -dioxins and dibenzofurans were extracted from fly ash of a waste incinerator, adsorbed on amorphous silica, then thermally desorbed and flushed over a sequential arrangement of the zeosils at elevated temperature by a stream of nitrogen. ITQ-4 with the smallest pore diameter was placed first, followed by SSZ-24 and, finally, by UTD-1 with the largest pore diameter. After the experiment, the zeosils were analysed for their contents of the different congeners. The results show that the sorption of the congeners occurs selectively and that it is governed by the size and the shape of the dioxin molecules, which in turn depend on the number of chlorine atoms and the pattern of chlorine substitution (regioisomers). Geometrical reasoning as well as molecular dynamics calculations on the zeosil structures and on the dioxin molecules were helpful in rationalising the results. This work represents an especially complex case of the molecular sieving effect and may lead to a selective on-line monitoring of the concentrations of dioxin molecules in waste gases of industrial combustion processes. The size- and shape-selective sorption of dioxin molecules may also bear some resemblance to the molecular recognition process that occurs in nature at the aryl hydrocarbon receptor. [source] Discovery of Potent Vascular Endothelial Growth Factor Receptor-2 InhibitorsCHEMMEDCHEM, Issue 1 2010Athanasios Papakyriakou Dr. Abstract Substantial evidence over the last decades has implicated uncontrolled angiogenesis with various pathological states, including cancer. Vascular endothelial growth factor (VEGF) plays a critical role in its regulation. Because the tyrosine kinase VEGF receptor-2 (VEGFR-2) is the major mediator of the mitogenic, angiogenic, and permeability-enhancing effects of VEGF, it has become one of the most profound anti-angiogenesis targets. Inspired by the anthranilamide class of VEGFR-2 inhibitors, we performed a computational analysis of some potent representative members, using docking and molecular dynamics calculations. Based on the observations drawn from introducing the effect of the receptor's flexibility in implicit aqueous environment, we designed, synthesized, and characterized several new analogues of related scaffolds with modifications in their steric and electronic characteristics. In,vitro evaluation of these compounds revealed several novel VEGFR-2 inhibitors that are less cytotoxic and more potent than the parent compounds. [source] UV Spectra and Excitation Delocalization in DNA: Influence of the Spectral WidthCHEMPHYSCHEM, Issue 7 2005Emanuela Emanuele Abstract The singlet excited states of the model DNA duplex (dA)10.(dT)10 are studied. Calculations are performed in the exciton theory framework. Molecular dynamics calculations provide the duplex geometry. The dipolar coupling is determined using atomic transition charges. The monomer transition energies are simulated by Gaussian functions resembling the absorption bands of nucleosides in aqueous solutions. Most of the excited states are found to be delocalized over at least two bases and result from the mixing of different monomer states. Their properties are only weakly affected by conformational changes of the double helix. On average, the highest oscillator strength is carried by the upper eigenstates. The duplex absorption spectra are shifted a few nanometers to higher energies with respect to the spectra of noninteracting monomers. The states with larger spatial extent are located close to the maximum of the absorption spectrum. [source] | |||||||||||||||||||||||||