scholarly journals A Kinetic and Thermodynamic Behavioral Comparison of Observable Secondary and Tertiary 2-Norbornyl Cations

1975 ◽  
Vol 53 (13) ◽  
pp. 1891-1900 ◽  
Author(s):  
R. Haseltine ◽  
N. Wong ◽  
T. S. Sorensen ◽  
A. J. Jones
Keyword(s):  
Model Systems ◽  
Suitable Model ◽  
Absolute Rate ◽  
Free Energies ◽  
Ion Structure ◽  
Hydride Shift ◽  
Carbonium Ion ◽  
Carbenium Ion ◽  
Rearrangement Processes ◽  
Rate Comparison

By analyzing various rearrangement processes, one can deduce the relative stabilities of the following 2-norbornyl cations (kcal/mol): 1,2-dimethyl, 0; 2-methyl, 1; 1-methyl, 6.5; and the parent 2-norbornyl, 8.5. Secondary 2-norbornyl cations have been assigned a "carbonium ion" structure and tertiary a "carbenium ion" structure. Using suitable model systems, an absolute rate comparison has been made of all three common rearrangement processes in the tertiary systems ("carbenium") with those already measured for the 2-norbornyl cation ("carbonium"). The activation free energies, ΔG≠, (in kcal/mol) were: Wagner–Meerwein (WM) shift: tertiary, < 4; secondary, < 4; endo-6,2-hydride shift: tertiary, 7.2; secondary, 5.8; exo-3,2-hydride shift: tertiary, 6.6; secondary, 11.4. A discussion of the structure of tertiary and secondary 2-norbornyl cations emphasizes the following points: (i) a rationalization of the rapid endo-6,2-hydride shift observed in norbornyl cations does not necessitate a protonated nortricyclene ("carbonium ion") postulate; (ii) on the basis of the results for acyclic cations and the 1,2-dimethyl-2-norbornyl cation, one would not expect to "freeze out" the WM shift in an equilibrating 2-norbornyl cation structure; (iii) the formation of nortricyclenes may be related to a partial C6—C2 bond in the ions; and (iv) the structure of the observable secondary 2-norbornyl cation probably involves partial C6—C2 bonding but, in our opinion, this does not require a symmetrical static formulation.

Visual control of orientation behaviour in the fly: Part I. A quantitative analysis

1976 ◽  
Vol 9 (3) ◽  
pp. 311-375 ◽  
Author(s):  
Werner Reichardt ◽  
Tomaso Poggio
Keyword(s):  
Information Processing ◽  
Quantitative Analysis ◽  
Visual System ◽  
Sensory Information ◽  
Model Systems ◽  
Suitable Model ◽  
Logical Organization ◽  
Integrative Level ◽  
Processing Properties ◽  
Different Levels

An understanding of sensory information processing in the nervous system will probably require investigations with a variety of ‘model’ systems at different levels of complexity.Our choice of a suitable model system was constrained by two conflicting requirements: on one hand the information processing properties of the system should be rather complex, on the other hand the system should be amenable to a quantitative analysis. In this sense the fly represents a compromise.In these two papers we explore how optical information is processed by the fly's visual system. Our objective is to unravel the logical organization of the fly's visual system and its underlying functional and computational principles. Our approach is at a highly integrative level. There are different levels of analysing and ‘understanding’ complex systems, like a brain or a sophisticated computer.

On the transferability of electron density in binary vanadium borides VB, V3B4 and VB2

2015 ◽  
Vol 71 (6) ◽  
pp. 777-787 ◽  
Author(s):  
Bürgehan Terlan ◽  
Lev Akselrud ◽  
Alexey I. Baranov ◽  
Horst Borrmann ◽  
Yuri Grin
Keyword(s):  
Quantum Theory ◽  
Crystal Structures ◽  
Electron Density ◽  
Critical Points ◽  
Atoms In Molecules ◽  
Model Systems ◽  
Suitable Model ◽  
Interatomic Distances ◽  
Systematic Analysis ◽  
A Charge

Binary vanadium borides are suitable model systems for a systematic analysis of the transferability concept in intermetallic compounds due to chemical intergrowth in their crystal structures. In order to underline this structural relationship, topological properties of the electron density in VB, V3B4 and VB2 reconstructed from high-resolution single-crystal X-ray diffraction data as well as derived from quantum chemical calculations, are analysed in terms of Bader's Quantum Theory of Atoms in Molecules [Bader (1990). Atoms in Molecules: A Quantum Theory, 1st ed. Oxford: Clarendon Press]. The compounds VB, V3B4 and VB2 are characterized by a charge transfer from the metal to boron together with two predominant atomic interactions, the shared covalent B—B interactions and the polar covalent B—M interactions. The resembling features of the crystal structures are well reflected by the respective B—B interatomic distances as well as by ρ(r) values at the B—B bond critical points. The latter decrease with an increase in the corresponding interatomic distances. The B—B bonds show transferable electron density properties at bond critical points depending on the respective bond distances.

scholarly journals Emergent colloidal currents across ordered and disordered landscapes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Dominik Lips ◽  
Ralph L. Stoop ◽  
Philipp Maass ◽  
Pietro Tierno
Keyword(s):  
Magnetic Particles ◽  
Lattice Gas ◽  
Solvable Model ◽  
Model Systems ◽  
Suitable Model ◽  
Many Body ◽  
Emergent Phenomena ◽  
Density Relationship ◽  
Far From Equilibrium ◽  
Experimental Findings

AbstractMany-particle effects in driven systems far from equilibrium lead to a rich variety of emergent phenomena. Their classification and understanding often require suitable model systems. Here we show that microscopic magnetic particles driven along ordered and defective lattices by a traveling wave potential display a nonlinear current-density relationship, which arises from the interplay of two effects. The first one originates from particle sizes nearly commensurate with the substrate in combination with attractive pair interactions. It governs the colloidal current at small densities and leads to a superlinear increase. We explain such effect by an exactly solvable model of constrained cluster dynamics. The second effect is interpreted to result from a defect-induced breakup of coherent cluster motion, leading to jamming at higher densities. Finally, we demonstrate that a lattice gas model with parallel update is able to capture the experimental findings for this complex many-body system.

SIMPLE, BASIC, MECHANISMS THAT ENHANCE OR DIMINISH THE CONCENTRATION OF SELECTED METABOLITES WITHIN METABOLISING BIOLOGICAL SYSTEMS

2005 ◽  
Vol 13 (01) ◽  
pp. 23-30
Author(s):  
JUKKA TIENARI
Keyword(s):  
Internal Control ◽  
Random Distribution ◽  
Biological Systems ◽  
Biological Molecules ◽  
Reciprocal Effects ◽  
Control Mechanisms ◽  
Absolute Rate ◽  
Free Energies ◽  
Biochemical Control ◽  
Selection Of

An attempt is made for pedagogical purposes to construct a model as simple as possible for analyzing biochemical control mechanisms that participate in the selection of molecules in biological systems. The analysis is simplified by an assumption that the system is in a steady state. The mechanisms result from the principle that in an open system the absolute rate constants determine the proportions of components. Reactions producing or consuming substances that influence the rates of other reactions in the system also influence the amounts of participating substances. Reciprocal effects result in internal control which selects some substances by increasing their relative amounts. Similar mechanisms also control processes other than chemical reactions. The selection contributes to the maintenance of the non-random distribution of molecules in the biosphere that allows certain biological molecules to be more abundant than other molecules consisting of the same elements and having comparable standard free energies of formation.

Acetolytic cleavage of 2β,19-Epoxy-5α-cholestane involving a 1,2-Hydride shift to C2

1977 ◽  
Vol 30 (10) ◽  
pp. 2249 ◽  
Author(s):  
RE Gall ◽  
J Taylor
Keyword(s):  
Acetic Anhydride ◽  
Boron Trifluoride ◽  
Shift Reagent ◽  
Deuterium Exchange ◽  
Paramagnetic Shift ◽  
Nucleophilic Attack ◽  
Rearrangement Product ◽  
Hydride Shift ◽  
Carbonium Ion

Acetolytic cleavage of 2β,19-epoxy-5α-cholestane (1a) with boron trifluoride and acetic anhydride followed by hydrolysis gave the 2α,19- diol (2b), the only rearrangement product the 1α,19-diol (3b) and a mixture of olefins (4b). Deuterium exchange studies and the use of a paramagnetic shift reagent have shown that the reaction leading to the rearranged diol(3b) is not concerted and appears to involve an intermediate carbonium ion since hydride shift from both C 1 and C 3 occur. The formation of the 1α,19-diol (3b) as the only rearranged product can be rationalized as nucleophilic attack on the acetoxonium ion (8).

scholarly journals Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

2019 ◽  
Author(s):  
David Slochower ◽  
Niel Henriksen ◽  
Lee-Ping Wang ◽  
John Chodera ◽  
David Mobley ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Small Molecule ◽  
Force Fields ◽  
Free Energy Calculations ◽  
Model Systems ◽  
Conformational Space ◽  
Free Energies ◽  
Binding Thermodynamics ◽  
Binding Free Energies

<div><div><div><p>Designing ligands that bind their target biomolecules with high affinity and specificity is a key step in small- molecule drug discovery, but accurately predicting protein-ligand binding free energies remains challenging. Key sources of errors in the calculations include inadequate sampling of conformational space, ambiguous protonation states, and errors in force fields. Noncovalent complexes between a host molecule with a binding cavity and a drug-like guest molecules have emerged as powerful model systems. As model systems, host-guest complexes reduce many of the errors in more complex protein-ligand binding systems, as their small size greatly facilitates conformational sampling, and one can choose systems that avoid ambiguities in protonation states. These features, combined with their ease of experimental characterization, make host-guest systems ideal model systems to test and ultimately optimize force fields in the context of binding thermodynamics calculations.</p><p><br></p><p>The Open Force Field Initiative aims to create a modern, open software infrastructure for automatically generating and assessing force fields using data sets. The first force field to arise out of this effort, named SMIRNOFF99Frosst, has approximately one tenth the number of parameters, in version 1.0.5, compared to typical general small molecule force fields, such as GAFF. Here, we evaluate the accuracy of this initial force field, using free energy calculations of 43 α and β-cyclodextrin host-guest pairs for which experimental thermodynamic data are available, and compare with matched calculations using two versions of GAFF. For all three force fields, we used TIP3P water and AM1-BCC charges. The calculations are performed using the attach-pull-release (APR) method as implemented in the open source package, pAPRika. For binding free energies, the root mean square error of the SMIRNOFF99Frosst calculations relative to experiment is 0.9 [0.7, 1.1] kcal/mol, while the corresponding results for GAFF 1.7 and GAFF 2.1 are 0.9 [0.7, 1.1] kcal/mol and 1.7 [1.5, 1.9] kcal/mol, respectively, with 95% confidence ranges in brackets. These results suggest that SMIRNOFF99Frosst performs competitively with existing small molecule force fields and is a parsimonious starting point for optimization.</p></div></div></div>

Microbes and Microbial Toxins: Paradigms for Microbial- Mucosal Interactions I. Pathophysiological aspects of enteric infections with the lumen-dwelling protozoan pathogenGiardia lamblia

2001 ◽  
Vol 280 (1) ◽  
pp. G1-G6 ◽  
Author(s):  
Lars Eckmann ◽  
Frances D. Gillin
Keyword(s):  
Small Intestine ◽  
B Cell ◽  
Diarrheal Disease ◽  
Clinical Symptoms ◽  
Experimental Studies ◽  
Model Systems ◽  
Mucosal Inflammation ◽  
Suitable Model ◽  
Host Defenses ◽  
Giardia Infection

Giardia lamblia is one of the most important causes of waterborne diarrheal disease worldwide, and giardiasis is the most common protozoan infection of the human small intestine. Symptomatic infection is characterized by diarrhea, abdominal pain, and malabsorption, leading to malnutrition and weight loss, particularly in children. The pathogen resides strictly in the lumen of the small intestine, and infection is typically not accompanied by significant mucosal inflammation. Clinical and experimental studies indicate that B cell-dependent host defenses, particularly IgA, are important for controlling and clearing Giardia infection, although B cell-independent mechanisms also contribute to this outcome. In contrast to antigiardial host defenses, much less is known about the pathophysiological mechanisms underlying the clinical symptoms of giardiasis, partly because of the current lack of suitable model systems. In addition to being an important human enteric pathogen, Giardia is an interesting model organism for gaining basic insights into genetic innovations that led to evolution of eukaryotic cells, since it belongs to the earliest diverging eukaryotic lineage known. The completion of the giardial genome project will increase understanding of the basic biology of the protozoan and will help us to better understand host pathogen-interactions as a basis for developing new vaccination and therapeutic strategies.

scholarly journals Comparisons Between DT40 Wild Type and DT40-Cre1 Cells as Suitable Model Systems for Studying the DNA Damage Response

Cell Cycle ◽  
2007 ◽  
Vol 6 (18) ◽  
pp. 2310-2313 ◽  
Author(s):  
Ronan T. Bree ◽  
Xian-Yang Lai ◽  
Lynn E. Canavan ◽  
Noel F. Lowndes
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Model Systems ◽  
Suitable Model ◽  
Wild Type ◽  
Damage Response

scholarly journals Cancer in the parasitic protozoans Trypanosoma brucei and Toxoplasma gondii

2015 ◽  
Vol 112 (29) ◽  
pp. 8835-8842 ◽  
Author(s):  
Zhao-Rong Lun ◽  
De-Hua Lai ◽  
Yan-Zi Wen ◽  
Ling-Ling Zheng ◽  
Ji-Long Shen ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Trypanosoma Brucei ◽  
Severe Disease ◽  
Life Cycles ◽  
Model Systems ◽  
Suitable Model ◽  
Complex Life Cycles ◽  
Obligate Intracellular ◽  
Obligate Intracellular Pathogen ◽  
Made In

Cancer is a general name for more than 100 malignant diseases. It is postulated that all cancers start from a single abnormal cell that grows out of control. Untreated cancers can cause serious consequences and deaths. Great progress has been made in cancer research that has significantly improved our knowledge and understanding of the nature and mechanisms of the disease, but the origins of cancer are far from being well understood due to the limitations of suitable model systems and to the complexities of the disease. In view of the fact that cancers are found in various species of vertebrates and other metazoa, here, we suggest that cancer also occurs in parasitic protozoans such as Trypanosoma brucei, a blood parasite, and Toxoplasma gondii, an obligate intracellular pathogen. Without treatment, these protozoan cancers may cause severe disease and death in mammals, including humans. The simpler genomes of these single-cell organisms, in combination with their complex life cycles and fascinating life cycle differentiation processes, may help us to better understand the origins of cancers and, in particular, leukemias.

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