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Interaction Potential (interaction + potential)
Kinds of Interaction Potential Selected AbstractsA Theoretical ab initio Study of the Capacity of Several Binding Units for the Molecular Recognition of AnionsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 1 2005Carolina Garau Abstract Noncovalent bonding between anions and the ,-cloud of electron-deficient aromatic rings has recently attracted considerable attention. Complexes of bromide with different electron-deficient aromatic rings and with other binding units based on hydrogen bonding (urea, thiourea and squaramide) have been studied and compared using high level B3LYP/6-31++G** ab initio and Molecular Interaction Potential with polarization (MIPp) calculations. Our findings reveal that electron-deficient aromatic rings are excellent candidates for constructing anion receptors and that the interaction strength can be modulated by the nature of the ring. Supporting experimental evidence has been obtained from X-ray structures retrieved from the Cambridge Structural Database. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Interplay between anion-, and hydrogen bonding interactionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2009Daniel Escudero Abstract The interplay between two important noncovalent interactions involving aromatic rings is studied by means of high level ab initio calculations. They demonstrate that synergistic effects are present in complexes where anion-, and hydrogen bonding interactions coexist. These synergistic effects have been studied using the "atoms-in-molecules" theory and the Molecular Interaction Potential with polarization partition scheme. The present study examines how these two interactions mutually influence each other. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Coherent state path integral and super-symmetry for condensates composed of bosonic and fermionic atomsFORTSCHRITTE DER PHYSIK/PROGRESS OF PHYSICS, Issue 9-10 2007B. Mieck Abstract A super-symmetric coherent state path integral on the Keldysh time contour is considered for bosonic and fermionic atoms which interact among each other with a common short-ranged two-body potential. We investigate the symmetries of Bose-Einstein condensation for the equivalent bosonic and fermionic constituents with the same interaction potential so that a super-symmetry results between the bosonic and fermionic components of super-fields. Apart from the super-unitary invariance U(L | S) of the density terms, we specialize on the examination of super-symmetries for pair condensate terms. Effective equations are derived for anomalous terms which are related to the molecular- and BCS- condensate pairs. A Hubbard-Stratonovich transformation from ,Nambu'-doubled super-fields leads to a generating function with super-matrices for the self-energy whose manifold is given by the orthosympletic super-group Osp(S,S | 2L). A nonlinear sigma model follows from the spontaneous breaking of the ortho-symplectic super-group Osp(S,S | 2L) to the coset decomposition Osp(S,S | 2L) \ U(L | S), U(L | S). The invariant subgroup U(L | S) for the vacuum or background fields is represented by the density terms in the self-energy whereas the super-matrices on the coset space Osp(S,S | 2L) \ U(L | S) describe the anomalous molecular and BCS- pair condensate terms. A change of integration measure is performed for the coset decomposition Osp(S,S | 2L) \ U(L | S) , U(L | S), including a separation of density and anomalous parts of the self-energy with a gradient expansion for the Goldstone modes. The independent anomalous fields in the actions can be transformed by the inverse square root of the metric tensor of Osp(S,S | 2L) \ U(L | S) so that the non-Euclidean integration measure with super-Jacobi-determinant can be removed from the coherent state path integral and Gaussian-like integrations remain. The variations of the independent coset fields in the effective actions result in classical field equations for a nonlinear sigma model with the anomalous terms. The dynamics of the eigenvalues of the coset matrices is determined by Sine-Gordon equations which have a similar meaning for the dynamics of the molecular- and BCS-pair condensates as the Gross-Pitaevskii equation for the coherent wave function in BEC phenomena. [source] Theory of tip-dependent imaging of adsorbates in the STM: CO on Cu(111)INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2006D. Drakova Abstract The processes of local electron injection or extraction in the scanning tunneling microscopy (STM) and spectroscopy (STS) lead to the creation of short-lived excited states localized at the electrode surfaces. The dynamic relaxation of the transient negative or positive ion resonances, due to both local and long-range interactions, is the clue to the understanding of numerous phenomena in STM/STS ranging from the "anomalously" large tip height corrugation amplitudes on clean metal surfaces to the observation of quantum mirages and features in the STS, which are not observed with the help of other surface spectroscopies. Quantum nanodynamics theory (QND) has been applied to calculate the interaction potential of a single CO molecule with the Cu(111) surface, with a transient negative ion resonance formed when an electron is injected from the tip, and the tunneling conductance on the clean and CO covered Cu(111) surface using a clean metal tip Al/Al(111) and a Pt(111) tip with an adsorbed CO molecule at the apex. Within QND and three-dimensional scattering theory, regarding the tunneling as an excited-state problem, we provide the explanation of the tip-dependent STM image of a single CO molecule on Cu(111). The appearance of the CO molecule as an indentation, using a clean metal tip and as a protrusion with a tip terminated by a CO molecule, is understood as a result of tunneling through two competing channels. Tunneling via adsorbate-induced ion resonances enhances the tunneling conductance. In contrast, tunneling via metal ion resonances only leads to attenuation of the conductance in the presence of the adsorbate. The current in the vicinity of the adsorbed CO molecule is reduced when a clean metal tip is used; i.e., CO appears dark in the STM image, because metal ion resonances on Cu(111) derive from the surface states with image state components coupling to plasmons and are therefore very diffuse. With a CO-terminated tip, the major current channel is, for symmetry reasons, from the 2,-derived orbital of the tip CO molecule, via the diffuse 2,-derived orbital of the CO molecule on the sample, hence adsorbed CO appears bright. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Accessing Time,Varying Forces on the Vibrating Tip of the Dynamic Atomic Force Microscope to Map Material CompositionISRAEL JOURNAL OF CHEMISTRY, Issue 2 2008Ozgur Sahin In dynamic atomic force microscopes the primary physical quantities being measured are the amplitude/phase or amplitude/frequency of the vibrating force probe. Topographic images with spatial resolutions down to the atomic scale can be obtained by mapping these measurements across the sample surface under feedback control. During the imaging process the vibrating tip is observing tip,sample interaction potentials (force,distance relationships) at every point on the surface. The interaction potential is a superposition of short- and long,distance interactions of various origins determined by the material compositions of the tip, sample, and the medium of imaging. In principle, measurement of tip,sample interaction potential should allow determination and mapping of material composition of the sample. However, a single measurement of amplitude/phase or amplitude/frequency in dynamic atomic force microscopes is not enough to characterize a complicated tip,sample interaction potential. Recent developments in the understanding of dynamics of the vibrating force probe (cantilever), together with specially designed cantilevers that utilize torsional vibrations in addition to conventional vertical vibrations, enable the recovery of tip,sample interaction potentials at a timescale less than a millisecond. Here, with theory and experiments, we discuss how these cantilevers recover the information about the tip,sample interaction forces and give an example of compositional mapping on a polymeric material system. [source] Small-angle X-ray scattering measurements of helium-bubble formation in borosilicate glassJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2006Alexander Y. Terekhov Small-angle X-ray scattering (SAXS) measurements have been performed to study helium-bubble formation in borosilicate glass. Helium was introduced by He+ implantation over an energy range of 1 to 2,MeV to give a uniform distribution over ,1,µm depth. The implanted dose was varied from 9 × 1013 to 2.8 × 1016,ions,cm,2, corresponding to a local concentration range of 40 to 11200 atomic parts per million (a.p.p.m.) averaged over the implantation depth. The SAXS response was fit with the Percus,Yevick hard-sphere interaction potential to account for interparticle interference. The fits yield helium-bubble radii and helium-bubble volume fractions that vary from 5 to 15,Å and from 10,3 to 10,1, respectively, as the dose increased from 9 × 1013 to 2.8 × 1016,cm,2. The SAXS data are also consistent with maximum helium solubility with respect to bubble formation between 40 and 200 a.p.p.m. in the borosilicate glass matrix. [source] A NEMO potential that includes the dipole,quadrupole and quadrupole,quadrupole polarizabilityJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Asbjørn Holt Abstract To increase the accuracy of molecular force fields a systematical and balanced improvement of the various terms included is needed. In this work, we have followed this strategy to improve the quality of the NEMO potential for the formaldehyde dimer by introducing local quadrupole moments and higher-order polarizabilities. It is found that inclusion of the quadrupole moment significantly improves the interaction potential. Furthermore, the inclusion of higher-order polarizabilities up to quadrupole,quadrupole polarizability is shown to give a better description of the intermolecular interaction. In addition, it is demonstrated that localized properties based on MP2 densities reproduces the BSSE corrected MP2 interaction energy at large intermolecular separations. This is not the case for HF,SCF based properties. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Monte Carlo Simulation of Polymer Reactions at InterfacesMACROMOLECULAR THEORY AND SIMULATIONS, Issue 4 2007Andreas John Abstract Adhesion of immiscible polymers during two-component injection moulding may be improved by transreactions of properly functionalised components. We performed MC simulations based on the three-dimensional coarse-grained bond fluctuation model (BFM) including a thermal interaction potential in with energy to characterise the behaviour of several selected types of chemical reactions, which are governed by activation energies of EA,=,0, 1, 3 and 5 kBT. The consumption of reactive monomers for all the reactions in the time interval below the Rouse time ,R exhibits a typical crossover from a kinetic-controlled to a diffusion-controlled behaviour and can be described by a bimolecular kinetic ansatz. [source] Role of drug metabolism in drug discovery and developmentMEDICINAL RESEARCH REVIEWS, Issue 5 2001Gondi N. Kumar Abstract Metabolism by the host organism is one of the most important determinants of the pharmacokinetic profile of a drug. High metabolic lability usually leads to poor bioavailability and high clearance. Formation of active or toxic metabolites will have an impact on the pharmacological and toxicological outcomes. There is also potential for drug,drug interactions with coadministered drugs due to inhibition and/or induction of drug metabolism pathways. Hence, optimization of the metabolic liability and drug,drug interaction potential of the new chemical entities are some of the most important steps during the drug discovery process. The rate and site(s) of metabolism of new chemical entities by drug metabolizing enzymes are amenable to modulation by appropriate structural changes. Similarly, the potential for drug,drug interactions can also be minimized by appropriate structural modifications to the drug candidate. However, the optimization of the metabolic stability and drug,drug interaction potential during drug discovery stage has been largely by empirical methods and by trial and error. Recently, a lot of effort has been applied to develop predictive methods to aid the optimization process during drug discovery and development. This article reviews the role of drug metabolism in drug discovery and development. © 2001 John Wiley & Sons, Inc. Med Res Rev, 21, No. 5, 397,411, 2001 [source] Utilization review of concomitant use of potentially interacting drugs in Thai patients using warfarin therapy,PHARMACOEPIDEMIOLOGY AND DRUG SAFETY, Issue 2 2007Surachai Kotirum PharmD Abstract Purpose In Thailand, there has been no study determining the concomitant use of medications, known to potentially interact with warfarin, in patients receiving warfarin therapy. This paper examined the frequency of which specific interacting drugs were concomitantly used in warfarin users. Methods We retrospectively examined the database of warfarin outpatient medical records from a regional 756-bed hospital located in the north of Thailand. All patients receiving warfarin from 10 June 1999 to 4 August 2004 were reviewed to identify all drugs possessing interaction potential with warfarin. The potential of significant interactions were divided into high, moderate and low, according to the extent of evidence documented in textbooks and literature. Results Among 1093 patients receiving warfarin therapy, 914 (84%) patients received at least one potentially interacting drug and half of them (457 patients) received at least one drug with high potential for interaction. The most frequently concomitant drug that increased INR was acetaminophen (63%, 316/457). Propylthiouracil was the most frequently concomitant drug that decreased INR response (4%, 19/457), while diclofenac was the most frequently concomitant drug that increased bleeding risk (16%, 73/457). Conclusions About a half of patients receiving warfarin therapy was prescribed concomitant drug(s) that has a high potential of interactions with warfarin. These patients should be closely monitored and counselled to watch for signs and symptoms of bleeding and thrombosis to avoid adverse events associated with drug interactions. Copyright © 2006 John Wiley & Sons, Ltd. [source] Preface: phys. stat. sol. (b) 245/3PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 3 2008Christopher W. Smith This is the third Special Issue of physica status solidi (b) focusing on materials with a negative Poisson's ratio or other ,anomalous' physical properties. This issue contains selected papers from the First International Conference on Auxetics and Anomalous Systems held at the University of Exeter, UK, on 4,6 September 2006. Around 50 participants from all over the world as well as from a wide range of scientific and engineering disciplines contributed to what was a highly successful conference. This conference follows in the footsteps of two previous workshops held at the Mathematical Research and Conference Centre in B,dlewo near Pozna,, Poland, in 2004 and 2005 [1, 2]. The papers selected for this issue publish recent results obtained for ,anomalous systems' in experiment, theory and computer simulations. In the following we summarize very briefly their contents. Alderson and Coenen compare the performance of auxetic composites to similar systems with conventional positive Poisson's ratios. They find that there are indeed differences which appear to arise from the change of the overall Poisson's ratio of the composite, some beneficial like a rise in impact tolerance at low impact rates, and others deleterious such as the reduced tolerance at higher impact rates. This is one of the first investigations of possible applications for auxetic materials. The two papers by Gaspar and Koenders both examine the effects of disorder upon anomalous properties, especially negative Poisson's ratio. In the first one Gaspar demonstrates how a mean strain estimate fails to predict negative values of Poisson's ratio because of an inability to account for local fluctuations in elastic properties. For instance it is shown that the volume fraction of auxetic regions in an globally auxetic material (measured experimentally) are smaller than a mean strain homogenisation would require. Koenders and Gaspar explore the elastic properties, and especially Poisson's ratio, of a heterogeneous 2D network of bending beams. They predict auxetic behaviour arising from localised disorder in the packing, and therefore effective locally aggregated elastic properties of the beams. In the three articles by Gatt et al. and Grima et al. models based on simple geometry are used to explain the behaviour of seemingly disparate systems, i.e. 2D honeycombs systems and zeolite SiO2 networks. Two papers concerning honeycombs demonstrate relationships between elastic properties and structure and the bounds for auxetic behaviour. The paper concerning the zeolite Natrolite uses numerical force field based energy minimisation methods to simulate the response of this particular zeolite to applied forces and then simplifies the predicted properties even further by considering structural units as rigid 2D polyhedra linked by flexible hinges. In a similar vein, though using a different approach and concerning a very different form of matter, Heyes shows how the heterogeneity in an assembly of particles in a liquid can affect the elastic properties of a liquid and notably the infinite frequency Poisson's ratio. Heyes uses the Molecular Dynamics approach to simulate a Lennard,Jones fluid under various pressures, notably comparing behaviour under positive and negative pressures. In their first paper Jasiukiewicz and co-authors derive elastic constants of 2D crystals for all four classes of 2D crystalline solids: hexagonal (isotropic), quadratic, rectangular, and oblique systems. In their second paper they demonstrate conditions required for auxetic behaviour of 2D crystals. Auxetic solids are further divided into those with some negative Poisson's ratios (auxetic), all negative Poisson's ratios (completely auxetic) and no negative Poisson's ratios (non-auxetic). Lakes and Wojciechowski consider counterintuitive properties of matter, like negative compressibility, negative Poisson's ratio, negative thermal expansion, negative specific heat, and negative pressure. They present and interpret experimental observations of negative bulk modulus in pre-strained foams. They propose also a constrained microscopic model which exhibits negative compressibility. Finally, they solve a very simple thermodynamic model with negative thermal expansion. Martin et al. take a long stride toward a real world application of auxetic materials with a wide ranging study starting with numerical modelling of a wingbox section to experimental testing in a wind tunnel. They show that an auxetic core in a wing box section can allow a passive aero-elastic response which can be tailored by careful design of the core so that camber, and thus drag, is reduced with increasing airspeed but without sacrificing structural integrity. Miller et al. consider another anomalous physical property, negative thermal expansivity, and its application in the form of particulate composites for amelioration of stresses arising from thermal mismatch. They show via experiments that particles with a negative coefficient of thermal expansion may be used as a composite reinforcer to reduce overall thermal expansion and behave according to the standard volume fraction based models. Narojczyk and Wojciechowski examine the effects of disorder upon the bulk elastic properties of 3D fcc soft sphere systems in terms of particle size. Systems, such as colloids, can be thought of in such terms. The study shows that higher order moments of probability distribution do not influence the bulk elastic properties much, but that lower moments such as the standard deviation of particle size influence the elastic properties greatly. The "hardness" of the particle interaction potential is also important in this context. In general, it is shown that the effect of increasing polydispersity is to increase the Poisson's ratio, except the [110] [10] directions. Scarpa and Malischewsky in their paper on Rayleigh waves in auxetic materials show how the Rayleigh wave speed is affected by the Poisson's ratio. The behaviour is complex and depends upon the homogeneity within the material, for instance slowing with decreasing Poisson's ratio in isotropic solids, but showing the reverse trend and increased sensitivity to Poisson's ratio in laminate composites. Scarpa et al. explore the buckling behaviour of auxetic tubes via three types of model, a simple beam mechanics and Eulerian buckling model, a 3D linear elastic FE model and a bespoke non-linear continuum model. The more sophisticated models provide increasing insight into the buckling behaviour though the simple beam model predicts reasonably well in the pre-buckling linear region. Some unexpected and interesting behaviour is predicted by the continuum model as the Poisson's ratio approaches the isotropic limit of ,1, including increasing sensitivity to Poisson's ratio and rapid mode jumping between integer wave numbers. The paper by Shilko et al. presents an analysis of a particular kind of friction joint, a double lap joint, and explores the effects of altering the elastic properties of one component, in particular it's Poisson's ratio. The manuscript introduces the evolution of smart materials from monolithic materials, and the classification of composites exhibiting negative Poisson's ratios. The paper then presents the case of a double lap joint and performs a sensitivity type study, via a 2D FE model, of the effects of changing the elastic properties and degree of anisotropy of one section of the model on various parameters defining the limits of functionality of the joint. The main finding is that an enhanced shear modulus, via a negative Poisson's ratio, can endow such a friction joint with superior performance. Manufacturing of auxetic materials on a commercial scale has proved to be the largest obstacle to their fuller exploitation. The paper by Simkins et al. explores one route for post processing of auxetic polymers fibres produced by a conventional melt extrusion route. Simkins et al. showed that a post process thermal annealing treatment, with carefully optimised parameters, was able to even out otherwise inhomogenous auxetic properties, and moreover improve other elastic and fracture properties often sacrificed for auxetic behaviour. We gratefully acknowledge the support given by the sponsors of the conference, namely the EPSRC of the UK and Auxetic Technologies Ltd. (UK). We also thank the Scientific Committee, the Organising Committee, and all the participants of the conference. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Vibrational properties of InP under pressure: a molecular-dynamics studyPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 1 2007Paulo S. Branício Abstract Dynamical properties of InP in the zincblende (ZB) are investigated using isothermal,isobaric molecular-dynamics simulations based on a proposed interaction potential for InP consisting of two- and three-body terms. The two-body term represents steric repulsion, Coulomb interactions due to charge transfer, induced charge,dipole interaction, and van der Waals dipole,dipole interaction. The three-body term represents covalent bond bending and stretching. The model is fitted to reproduce crystalline lattice constant, cohesive energy, and the structural transition pressure from ZB to rocksalt. The effects of hydro- static pressure and temperature on the vibrational density-of-states, phonon anharmonicity, dynamic Debye,Waller factor, thermal expansion coefficient are described as well as the pressure induced structural phase transformation. Results are consistent with available experimental data, in particular the calculated equation of state and phonon density-of-states have very good agreement. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Study on the pharmacokinetics drug,drug interaction potential of glycyrrhiza uralensis, a traditional Chinese medicine, with lidocaine in ratsPHYTOTHERAPY RESEARCH, Issue 5 2009Jingcheng Tang Abstract Drug,drug interaction potentials of an herbal medicine named Glycyrrhiza uralensis was investigated in rats via in vitro and in vivo pharmacokinetic studies. P450 levels and the metabolic rate of lidocaine in the liver microsomes prepared from different treatment groups were measured. In a separate in vivo pharmacokinetic study, the pharmacokinetic parameters of lidocaine in plasma and urine were estimated. P450 levels in the rats pretreated by Glycyrrhiza uralensis were significant higher than that in the non-treatment control. The increase in P450 levels was dose-dependent. Glycyrrhiza uralensis (1 and 3 g/kg) increased P450 levels by 62% and 91%, respectively, compared with the non-treatment control (0.695 nmol/mg protein). The metabolic rate of lidocaine in the liver microsomes was significantly higher in the herb pretreated rats. The pharmacokinetic profile of lidocaine was significantly modified in the rats with the herbal pretreatment. Elimination half-lives were shortened by 39%, and total clearances were increased by 59% with the pretreatment of Glycyrrhiza uralensis. In conclusion, Glycyrrhiza uralensis showed induction effect on P450 isozymes. Efficacy and safety profiles of a drug may be affected when the herbal products or herbal prescriptions containing the plant medicine were concomitantly used. Copyright © 2009 John Wiley & Sons, Ltd. [source] Echinacea purpurea and P-glycoprotein drug transport in Caco-2 cellsPHYTOTHERAPY RESEARCH, Issue 1 2009Torstein Schrøder Hansen Abstract Echinacea is widely used as a medical herbal product, but its interaction potential with the drug efflux transporter P-glycoprotein (P-gp) has not yet been evaluated. The interaction potential of Echinacea purpurea towards P-gp mediated drug transport was studied in human intestinal Caco-2 cells. Digoxin (30 nm) was used as a substrate and verapamil as a control inhibitor. Ethanol, 0.8%, needed for herbal extraction and compatibility with the commercial products, inhibited the net digoxin flux by 18%. E. purpurea influenced to a higher degree the B,A transport of digoxin than the A,B transport. A minor increase in net digoxin flux was observed at low concentrations of E. purpurea, an effect anticipated to be allosteric in nature. At higher concentrations, from 0.4 to 6.36 mg dry weight/mL, a statistically significant linear dose-related decrease was observed in the net digoxin flux, indicating a dose dependent E. purpurea inhibition of P-gp. Both Vmax and Km of the net digoxin flux, calculated to 23.7 nmol/cm2/h and 385 µm, respectively, decreased in the presence of E. purpurea in an uncompetitive fashion. Although the effects of Echinacea purpurea on systemic P-gp mediated drug transport are probably limited, an influence on drug bioavailability can not be excluded. Copyright © 2008 John Wiley & Sons, Ltd. [source] Irinotecan and its active metabolite, SN-38: review of bioanalytical methods and recent update from clinical pharmacology perspectivesBIOMEDICAL CHROMATOGRAPHY, Issue 1 2010Mullangi Ramesh Abstract The introduction of irinotecan has revolutionized the applicability of camptothecins as predominant topoisomerase I inhibitor for anti-cancer therapy. The potent anti-tumor activity of irinotecan is due to rapid formation of an in vivo active metabolite, SN-38. Therefore, irinotecan is considered as a pro-drug to generate SN-38. Over the past decade, side-by-side with the clinical advancement of the use of irinotecan in the oncology field, a plethora of bioanalytical methods have been published to quantify irinotecan, SN-38 and other metabolites. Because of the availability of HPLC, LC-MS and LC-MS/MS methods, the pharmacokinetic profiling of irinotecan and its metabolites has been accomplished in multiple species, including cancer patients. The developed assays continue to find use in the optimization of newly designed delivery systems with regard to pharmacokinetics to promote safe and effective use of either irinotecan or SN-38. This review intends to: firstly, provide an exhaustive compilation of the published assays for irinotecan, SN-38 and other metabolite(s) of irinotecan, as applicable; secondly, to enumerate the validation parameters and applicable conclusions; and thirdly, provide some recent perspectives in the clinical pharmacology arena pertaining to efflux transporters, pediatric profiling, role of kidney function in defining toxicity, drug,drug interaction potential of irinotecan, etc. Copyright © 2009 John Wiley & Sons, Ltd. [source] Protein,Protein Interactions in Complex Cosolvent Solutions,CHEMPHYSCHEM, Issue 5 2007Nadeem Javid Abstract The effects of various kosmotropic and chaotropic cosolvents and salts on the intermolecular interaction potential of positively charged lysozyme is evaluated at varying protein concentrations by using synchrotron small-angle X-ray scattering in combination with liquid-state theoretical approaches. The experimentally derived static structure factors S(Q) obtained without and with added cosolvents and salts are analysed with a statistical mechanical model based on the Derjaguin,Landau,Verwey,Overbeek (DLVO) potential, which accounts for repulsive and attractive interactions between the protein molecules. Different cosolvents and salts influence the interactions between protein molecules differently as a result of changes in the hydration level or solvation, in charge screening, specific adsorption of the additives at the protein surface, or increased hydrophobic interactions. Intermolecular interaction effects are significant above protein concentrations of 1 wt,%, and with increasing protein concentration, the repulsive nature of the intermolecular pair potential V(r) increases markedly. Kosmotropic cosolvents like glycerol and sucrose exhibit strong concentration-dependent effects on the interaction potential, leading to an increase of repulsive forces between the protein molecules at low to medium high osmolyte concentrations. Addition of trifluoroethanol exhibits a multiphasic effect on V(r) when changing its concentration. Salts like sodium chloride and potassium sulfate exhibit strong concentration-dependent changes of the interaction potential due to charge screening of the positively charged protein molecules. Guanidinium chloride (GdmCl) at low concentrations exhibits a similar charge-screening effect, resulting in increased attractive interactions between the protein molecules. At higher GdmCl concentrations, V(r) becomes more repulsive in nature due to the presence of high concentrations of Gdm+ ions binding to the protein molecules. Our findings also imply that in calculations of thermodynamic properties of proteins in solution and cosolvent mixtures, activity coefficients may not generally be neglected in the concentration range above 1 wt,% protein. [source] Anomalously Low Probabilities for Rotational Excitation in HD,Surface Scattering,CHEMPHYSCHEM, Issue 5 2006Antonio, iber Dr. The H2,Cs surface interaction potential is directly investigated by scattering a rotationally cold beam of HD molecules from a Cs surface (see angular distribution diagram). The probability of rotational excitation is two orders of magnitude smaller than for Cu and other metal surfaces. Coupled channel calculations interpret the results, and the anomalous behaviour is linked to the peculiarities of the closed-shell alkali surface interactions. [source] Theoretical Study on Co3+ in Aqueous Solution in Terms of ABEEM/MM ModelCHINESE JOURNAL OF CHEMISTRY, Issue 6 2007Qing-Mei Guan Abstract A detailed theoretical investigation on Co3+ hydration in aqueous solution has been carried out by means of molecular dynamics (MD) simulations based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The effective Co3+ ion-water potential has been constructed by fitting to ab initio structures and binding energies for ionic clusters. And then the ion-water interaction potential was applied in combination with the ABEEM-7P water model to molecular dynamics simulations of single Co3+(aq.) solution, managing to reproduce many experimental structural and dynamical properties of the solution. Here, not only the common properties (radial distribution function, angular distribution function and solvation energy) obtained for Co3+ in ABEEM-7P water solution were in good agreement with those from the experimental methods and other molecular dynamics simulations but also very interesting properties of charge distributions, geometries of water molecules, hydrogen bond, diffusion coefficients, vibrational spectra are investigated by ABEEM/MM model. [source] Trends in use of herbal and nutritional supplements in cardiovascular patientsCLINICAL CARDIOLOGY, Issue 2 2004Tomasz Stys M.D. Abstract Background: Use of herbs and nutritional supplements (known as naturoceuticals) is increasing in the USA, with about 50% of Americans taking naturoceuticals and spending over $10 billion per year for them. This raises concerns regarding their use instead of proven therapies, their side effects, and drug interaction potential. Hypothesis: The study sought to characterize cardiology patients who used supplements and to examine whether their use was diagnosis or doctor dependent, whether it affected patients' compliance, and what supplements were used. Methods: In all, 187 patients attending our cardiology clinic were interviewed, examined, and followed for up to 1 year. The users and nonusers of naturoceuticals were compared. Results: Supplements were used in 106 patients (an average of 3.1 naturoceutical per patient). There were no significant differences in their use by gender, age, primary care doctor specialty, or cardiovascular medications prescribed (except for statins). Patients with a history of myocardial infarction, coronary revascularization, hyperlipidemia, and a family history of coronary artery disease were more likely to use the supplements. Average low-density lipoprotein (106 vs. 108 mg/dl), average blood pressure (132/77 vs. 138/78 mmHg), and average hemoglobin (Hb)A1c (8.7 vs. 7.7%) showed no statistically significant differences between users and nonusers. Patients most commonly took multivitamins, vitamin E, vitamin C, vitamin B, folate, garlic, calcium, coenzyme Q10, and gingko. Conclusion: This study indicates that naturoceutical use is widespread among cardiovascular patients and it is difficult to predict clinically who the users are. Fortunately, according to our limited compliance measures, it appears that the naturoceutical use has not affected patients' compliance with traditional medications. Also, possibly a detrimental interaction potential between traditional medications and naturoceuticals has been demonstrated. [source] Finite element investigation of the ground states of the helium trimers 4He3 and 4He2,3HeINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2007Moses Salci Abstract A three-dimensional finite element method is applied to the ground states of the symmetric and asymmetric atomic helium trimers 4He3 and 4He2,3He. Three different He,He interaction potentials of hard-core nature were studied. Two extrapolation procedures based on the convergence properties of the finite element method are investigated. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Accessing Time,Varying Forces on the Vibrating Tip of the Dynamic Atomic Force Microscope to Map Material CompositionISRAEL JOURNAL OF CHEMISTRY, Issue 2 2008Ozgur Sahin In dynamic atomic force microscopes the primary physical quantities being measured are the amplitude/phase or amplitude/frequency of the vibrating force probe. Topographic images with spatial resolutions down to the atomic scale can be obtained by mapping these measurements across the sample surface under feedback control. During the imaging process the vibrating tip is observing tip,sample interaction potentials (force,distance relationships) at every point on the surface. The interaction potential is a superposition of short- and long,distance interactions of various origins determined by the material compositions of the tip, sample, and the medium of imaging. In principle, measurement of tip,sample interaction potential should allow determination and mapping of material composition of the sample. However, a single measurement of amplitude/phase or amplitude/frequency in dynamic atomic force microscopes is not enough to characterize a complicated tip,sample interaction potential. Recent developments in the understanding of dynamics of the vibrating force probe (cantilever), together with specially designed cantilevers that utilize torsional vibrations in addition to conventional vertical vibrations, enable the recovery of tip,sample interaction potentials at a timescale less than a millisecond. Here, with theory and experiments, we discuss how these cantilevers recover the information about the tip,sample interaction forces and give an example of compositional mapping on a polymeric material system. [source] Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentialsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2009Shih-Wei Chao Abstract Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon,carbon separation was sampled in a step 0.1 Å for a range of 3,9 Å, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen,hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Inverse Monte Carlo procedure for conformation determination of macromoleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003Mark Bathe Abstract A novel numerical method for determining the conformational structure of macromolecules is applied to idealized biomacromolecules in solution. The method computes effective inter-residue interaction potentials solely from the corresponding radial distribution functions, such as would be obtained from experimental data. The interaction potentials generate conformational ensembles that reproduce thermodynamic properties of the macromolecule (mean energy and heat capacity) in addition to the target radial distribution functions. As an evaluation of its utility in structure determination, we apply the method to a homopolymer and a heteropolymer model of a three-helix bundle protein [Zhou, Y.; Karplus, M. Proc Natl Acad Sci USA 1997, 94, 14429; Zhou, Y. et al. J Chem Phys 1997, 107, 10691] at various thermodynamic state points, including the ordered globule, disordered globule, and random coil states. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 876,890, 2003 [source] Study on the pharmacokinetics drug,drug interaction potential of glycyrrhiza uralensis, a traditional Chinese medicine, with lidocaine in ratsPHYTOTHERAPY RESEARCH, Issue 5 2009Jingcheng Tang Abstract Drug,drug interaction potentials of an herbal medicine named Glycyrrhiza uralensis was investigated in rats via in vitro and in vivo pharmacokinetic studies. P450 levels and the metabolic rate of lidocaine in the liver microsomes prepared from different treatment groups were measured. In a separate in vivo pharmacokinetic study, the pharmacokinetic parameters of lidocaine in plasma and urine were estimated. P450 levels in the rats pretreated by Glycyrrhiza uralensis were significant higher than that in the non-treatment control. The increase in P450 levels was dose-dependent. Glycyrrhiza uralensis (1 and 3 g/kg) increased P450 levels by 62% and 91%, respectively, compared with the non-treatment control (0.695 nmol/mg protein). The metabolic rate of lidocaine in the liver microsomes was significantly higher in the herb pretreated rats. The pharmacokinetic profile of lidocaine was significantly modified in the rats with the herbal pretreatment. Elimination half-lives were shortened by 39%, and total clearances were increased by 59% with the pretreatment of Glycyrrhiza uralensis. In conclusion, Glycyrrhiza uralensis showed induction effect on P450 isozymes. Efficacy and safety profiles of a drug may be affected when the herbal products or herbal prescriptions containing the plant medicine were concomitantly used. Copyright © 2009 John Wiley & Sons, Ltd. [source] X-ray study and structure simulation of amorphous tungsten oxideACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002L. A. Lugovskaya In this work, X-ray studies of the amorphous oxide films obtained by thermal evaporation of WO3 powder in a vacuum and by anodic oxidation were carried out. X-ray diffraction patterns were obtained in the symmetric reflection geometry on a DRON-4 diffractometer (Mo K, radiation, LiF monochromator) in automatic mode. Molecular dynamics simulation of amorphous tungsten oxide atomic configurations has been carried out in the micro-canonical ensemble (NVE) for N,=,208 atoms and N,=,624 atoms, in a cubic cell, using pairwise Born,Mayer interaction potentials and periodic boundary conditions. One of the purposes of the present work is to analyze the influence of the parameters and the cutoff of the interaction potentials on the interatomic distances. The values obtained in the molecular dynamics simulation for the pair functions D(r) are compared with the experimental data for amorphous oxides in order to choose the most convenient aforesaid values. The values of the average interatomic distances and the coordination numbers obtained by both methods are also compared. The result shows that the tungsten subsystem can be well reproduced using the potential cutoff radius of about 4,Å, but the oxygen subsystem can be well reproduced when the cutoff of the potential for the W,O pairs is equal to 2.8,Å. The configuration built during the molecular dynamics experiment consists of distorted octahedra. These octahedra form chains, as in the WO3 phases of type ReO3, and hexagonal rings, of the same type as in the WO3(1/3)H2O phase, when we extract (1/3)O at every WO3 unit. The pair function D(r) and scattering intensity I(s) distribution curves calculated for simulation configurations show a satisfactory agreement with experiment. [source] On the Generation of Catalytic Antibodies by Transition State AnaloguesCHEMBIOCHEM, Issue 4 2003Montserrat Barbany Abstract The effective design of catalytic antibodies represents a major conceptual and practical challenge. It is implicitly assumed that a proper transition state analogue (TSA) can elicit a catalytic antibody (CA) that will catalyze the given reaction in a similar way to an enzyme that would evolve (or was evolved) to catalyze this reaction. However, in most cases it was found that the TSA used produced CAs with relatively low rate enhancement as compared to the corresponding enzymes, when these exist. The present work explores the origin of this problem, by developing two approaches that examine the similarity of the TSA and the corresponding transition state (TS). These analyses are used to assess the proficiency of the CA generated by the given TSA. Both approaches focus on electrostatic effects that have been found to play a major role in enzymatic reactions. The first method uses molecular interaction potentials to look for the similarity between the TSA and the TS and, in principle, to help in designing new haptens by using 3D quantitative struture,activity relationships. The second and more quantitative approach generates a grid of Langevin dipoles, which are polarized by the TSA, and then uses the grid to bind the TS. Comparison of the resulting binding energy with the binding energy of the TS to the grid that was polarized by the TS provides an estimate of the proficiency of the given CA. Our methods are used in examining the origin of the difference between the catalytic power of the 1F7 CA and chorismate mutase. It is demonstrated that the relatively small changes in charge and structure between the TS and TSA are sufficient to account for the difference in proficiency between the CA and the enzyme. Apparently the environment that was preorganized to stabilize the TSA charge distribution does not provide a sufficient stabilization to the TS. The general implications of our findings and the difficulties in designing a perfect TSA are discussed. Finally, the possible use of our approach in screening for an optimal TSA is pointed out. [source] | |||||||||||||||||||||||||