International Journal of Molecular Sciences

722 KiB

Open AccessArticle

A Velocity Extraction Method in Molecular Dynamic Simulation of Low Speed Nanoscale Flows

by Wenfei Zhang

Int. J. Mol. Sci. 2006, 7(9), 405-416; https://doi.org/10.3390/i7090405 - 28 Sep 2006

Cited by 2 | Viewed by 7636

A new algorithm to extract the velocity caused by the external forces inmolecular dynamic simulation of nanoscale flow problems is proposed. The flowvelocity, an important component in these type of problems, is usually obtained from theaverage value in the time space because the accumulation of the thermal velocity willapproach zero when the time period is large, but this method is not always suitable,especially when the flow velocity is much smaller than the thermal velocity. Based on theidea of the linear accumulation of the flow velocity, in this study a new algorithm isderived to extract the flow velocity. This algorithm can be used to calculate nanoscaleflow problem no matter whether the value of the flow velocity is big or small. Using thisnew algorithm, the 2-D liquid flow of argon in nanochannels was simulated. Thenumerical result demonstrates the effectiveness of the new algorithm. Full article

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606 KiB

Open AccessReview

In Silico Design in Homogeneous Catalysis Using Descriptor Modelling

by Enrico Burello and Gadi Rothenberg

Int. J. Mol. Sci. 2006, 7(9), 375-404; https://doi.org/10.3390/i7090375 - 28 Sep 2006

Cited by 73 | Viewed by 14719

Abstract

This review summarises the state-of-the-art methodologies used for designing homogeneous catalysts and optimising reaction conditions (e.g. choosing the right solvent). We focus on computational techniques that can complement the current advances in high-throughput experimentation, covering the literature in the period 1996-2006. The review assesses the use of molecular modelling tools, from descriptor models based on semiempirical and molecular mechanics calculations, to 2D topological descriptors and graph theory methods. Different techniques are compared based on their computational and time cost, output level, problem relevance and viability. We also review the application of various data mining tools, including artificial neural networks, linear regression, and classification trees. The future of homogeneous catalysis discovery and optimisation is discussed in the light of these developments. Full article

(This article belongs to the Special Issue Virtual Combinatorial Synthesis and Drug Design)

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139 KiB

Open AccessArticle

Prediction of Environmental Properties for Chlorophenols with Posetic Quantitative Super-Structure/Property Relationships (QSSPR)

by Teodora Ivanciuc, Ovidiu Ivanciuc and Douglas J. Klein

Int. J. Mol. Sci. 2006, 7(9), 358-374; https://doi.org/10.3390/i7090358 - 28 Sep 2006

Cited by 31 | Viewed by 9920

Abstract

Due to their widespread use in bactericides, insecticides, herbicides, andfungicides, chlorophenols represent an important source of soil contaminants. Theenvironmental fate of these chemicals depends on their physico-chemical properties. In theabsence of experimental values for these physico-chemical properties, one can use predictedvalues computed with quantitative structure-property relationships (QSPR). As analternative to correlations to molecular structure we have studied the super-structure of areaction network, thereby developing three new QSSPR models (poset-average, cluster-expansion, and splinoid poset) that can be applied to chemical compounds which can behierarchically ordered into a reaction network. In the present work we illustrate these posetQSSPR models for the correlation of the octanol/water partition coefficient (log K_ow) and thesoil sorption coefficient (log K_OC) of chlorophenols. Excellent results are obtained for allQSSPR poset models to yield: log K_ow, r = 0.991, s = 0.107, with the cluster-expansionQSSPR; and log K_OC, r = 0.938, s = 0.259, with the spline QSSPR. Thus, the poset QSSPRmodels predict environmentally important properties of chlorophenols. Full article

(This article belongs to the Special Issue POR Approximation in QSAR/QSPR Theory)

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142 KiB

Open AccessArticle

Interaction of Plant Epicuticular Waxes and Extracellular Esterases of Curvularia eragrostidis during Infection of Digitaria sanguinalis and Festuca arundinacea by the Fungus

by Fei Wang, Peng Zhang, Sheng Qiang and Lang-Lai Xu

Int. J. Mol. Sci. 2006, 7(9), 346-357; https://doi.org/10.3390/i7090346 - 27 Sep 2006

Cited by 15 | Viewed by 8961

Abstract

Curvularia eragrostidis, a causal agent of head blight on the weed (Digitariasanguinalis), did not cause disease on the turfgrass Festuca arundinacea. Differentextracellular esterase isoenzymes were detected in saprophytic and parasitic phases duringthe fungal germination. The epicuticular waxes of D. sanguinalis were more efficient toinduce the secretion of esterases from the fungus than that of F. arundinacea, but were morerapidly degraded by the fungal enzymes. Component analysis indicated that the epicuticularwaxes from D. sanguinalis were mostly composed of alcohols, with 54.3% being 9,12-Octadecadien-1-ol. The main component of F arundinacea waxes was alkyl compounds,with 49.8% being olefin, 9-Tricosence. More long-chained esters were found in D.sanguinalis waxes, which were easier to be digested than those in F. arundinacea waxes byextreacellular esterases of the fungus. Epicuticular waxes play a role in varyingpathogenicity of C. eragrostidis on D. sanguinalis and F arundinacea. Full article

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227 KiB

Open AccessArticle

Ballistic Protons and Microwave-induced Water Solitons in Bioenergetic Transformations

by Reuven Tirosh

Int. J. Mol. Sci. 2006, 7(9), 320-345; https://doi.org/10.3390/i7090320 - 26 Sep 2006

Cited by 6 | Viewed by 10699

Abstract

Active streaming (AS) of liquid water is considered to generate and overcomepressure gradients, so as to drive cell motility and muscle contraction by hydrauliccompression. This idea had led to reconstitution of cytoplasm streaming and musclecontraction by utilizing the actin-myosin ATPase system in conditions that exclude acontinuous protein network. These reconstitution experiments had disproved a contractileprotein mechanism and inspired a theoretical investigation of the AS hypothesis, aspresented in this article. Here, a molecular quantitative model is constructed for a chemicalreaction that might generate the elementary component of such AS within the pure waterphase. Being guided by the laws of energy and momentum conservation and by the physicalchemistry of water, a vectorial electro-mechano-chemical conversion is considered, asfollows: A ballistic H⁺ may be released from H₂O-H⁺ at a velocity of 10km/sec, carrying akinetic energy of 0.5 proton*volt. By coherent exchange of microwave photons during 10^-10sec, the ballistic proton can induce cooperative precession of about 13300 electrically-polarized water molecule dimers, extending along 0.5 μm. The dynamic dimers rearrangealong the proton path into a pile of non-radiating rings that compose a persistent rowing-likewater soliton. During a life-time of 20 msec, this soliton can generate and overcome amaximal pressure head of 1 kgwt/cm² at a streaming velocity of 25 μm/sec and intrinsicpower density of 5 Watt/cm³. In this view, the actin-myosin ATPase is proposed to catalyzestereo-specific cleavage of H₂O-H⁺ , so as to generate unidirectional fluxes of ballisticprotons and water solitons along each actin filament. Critical requirements and evidentialpredictions precipitate consistent implications to the physical chemistry of water, enzymatichydrolysis and synthesis of ATP, trans-membrane signaling, intracellular transport, cellmotility, intercellular interaction, and associated electro-physiological function. Sarcomerecontraction is described as hydraulic compression, driven by the suction power of centrally-oriented AS. This hydraulic mechanism anticipates structural, biochemical, mechanical and energetic aspects of striated muscle contraction, leading to quantitative formulation of a hydrodynamic power-balance equation yielding a general force-velocity relation. Full article

(This article belongs to the Special Issue Muscle Contraction Mechanism, Motor Proteins Function and Molecular Aspects of Water)

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Int. J. Mol. Sci., Volume 7, Issue 9 (September 2006) – 5 articles , Pages 320-416

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