A combined molecular dynamic and quantum mechanic study of the solvent and guest molecule effect on the stability and length of heterocyclic peptide nanotubes

2015 ◽  
Vol 17 (17) ◽  
pp. 11382-11391 ◽  
Author(s):  
Mohammad Izadyar ◽  
Mohammad Khavani ◽  
Mohammad Reza Housaindokht
Keyword(s):  
Quantum Mechanic ◽  
Molecular Dynamic ◽  
Electrostatic Interactions ◽  
Guest Molecule ◽  
Guest Molecules ◽  
Peptide Nanotubes ◽  
The Stability ◽  
Peptide Nanotube

Guest molecules and solvents affect the stability and length of the heterocyclic peptide nanotube through the electrostatic interactions.

Determination of Relative Stability of Urea Complexes from X-Ray Powder Diffraction Data

1960 ◽  
Vol 4 ◽  
pp. 140-150 ◽  
Author(s):  
Jack Radell ◽  
J.W. Connolly
Keyword(s):  
Dissociation Constant ◽  
Guest Molecule ◽  
Interplanar Spacing ◽  
Dynamic Equilibrium ◽  
Crystalline Complex ◽  
Guest Molecules ◽  
X Ray ◽  
Host Molecules ◽  
The Stability

AbstractUrea complexes consist of a channel made up of hydrogen-bonded urea host molecules into which a variety of guest molecules can fit to form a crystalline complex. The urea host can accommodate, one at a time, a variety of guests having the requisite size and shape. The stability of the resulting complex is a function of the properties of the guest molecule. A procedure has been devised which produces pure complex free of any uncomplexed urea or host molecules in solution. The insoluble crystalline complexes formed from the solution of urea and guest molecule in methanol established a dynamic equilibrium. When the crystals of complex are removed from the solution, dissociation to urea and guest occurs to an extent, depending upon the dissociation constant of the complex. If the dissociation constant, KD, is very low, undetectable quantities of uncomplexed urea form along with complex. If the dlissoclation constant is high, extensive amounts of urea form in the presence of complex. Characteristic interplanar spacing s are obtained for a urea complex irrespective of the guest molecule present. The pattern obtained for the hexagonal complex is completely different from the pattern obtained for tetragonal urea. X-ray examination of a homologous series of compounds gives, for each partially dissociated complex, spacings for both urea and complex. The relative intensities of urea and complex spacings permit the estimation of the stability of such a complex compared to that of other homologues.

scholarly journals Hydrogen Inter-Cage Hopping and Cage Occupancies inside Hydrogen Hydrate: Molecular-Dynamics Analysis

2020 ◽  
Vol 11 (1) ◽  
pp. 282
Author(s):  
Yogeshwaran Krishnan ◽  
Mohammad Reza Ghaani ◽  
Arnaud Desmedt ◽  
Niall J. English
Keyword(s):  
Molecular Dynamics ◽  
Energy Barrier ◽  
Guest Molecule ◽  
Arrhenius Equation ◽  
Dynamics Simulation ◽  
Type Ii ◽  
Large Cage ◽  
Guest Molecules ◽  
Simulation Time ◽  
Average Occupancy

The inter-cage hopping in a type II clathrate hydrate with different numbers of H2 and D2 molecules, from 1 to 4 molecules per large cage, was studied using a classical molecular dynamics simulation at temperatures of 80 to 240 K. We present the results for the diffusion of these guest molecules (H2 or D2) at all of the different occupations and temperatures, and we also calculated the activation energy as the energy barrier for the diffusion using the Arrhenius equation. The average occupancy number over the simulation time showed that the structures with double and triple large-cage H2 occupancy appeared to be the most stable, while the small cages remained with only one guest molecule. A Markov model was also calculated based on the number of transitions between the different cage types.

scholarly journals Contribution of engineered electrostatic interactions to the stability of cytosolic malate dehydrogenase

2001 ◽  
Vol 14 (11) ◽  
pp. 911-917 ◽  
Author(s):  
Francesca Trejo ◽  
Josep Ll. Gelpí ◽  
Albert Ferrer ◽  
Albert Boronat ◽  
Montserrat Busquets ◽  
...  
Keyword(s):  
Malate Dehydrogenase ◽  
Electrostatic Interactions ◽  
The Stability ◽  
Cytosolic Malate Dehydrogenase

The search for formal electrostatic effects on molecular conformation and crystal packing: crystal structure of 2,2′′-disubstituted (HversusPPh2) 1,1′-(1,2-phenylene)bis(3-methyl-1H-imidazol-3-ium) bis(trifluoromethanesulfonate)

2016 ◽  
Vol 72 (3) ◽  
pp. 198-202
Author(s):  
Carine Duhayon ◽  
Yves Canac ◽  
Laurent Dubrulle ◽  
Carine Maaliki ◽  
Remi Chauvin
Keyword(s):  
Crystal Structure ◽  
Electrostatic Interactions ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Relative Orientation ◽  
Electron Delocalization ◽  
Electrostatic Effects ◽  
Conformational Freedom ◽  
The Stability ◽  
Bond Character

Electrostatic interactions between localized integral charges make the stability and structure of highly charged small and rigid organics intriguing. Can σ/π-electron delocalization compensate reduced conformational freedom by lowering the repulsion between identical charges? The crystal structure of the title salt, C14H16N42+·2CF3SO3−, (2), is described and compared with that of the 2,2′′-bis(diphenylphosphanyl) derivative, (4). The conformations of the dications and their interactions with neighbouring trifluoromethanesulfonate anions are first analyzed from the standpoint of formal electrostatic effects. Neither cation exhibits any geometrical strain induced by the intrinsic repulsion between the positive charges. In contrast, the relative orientation of the imidazolium rings [i.e. antifor (2) andsynfor (4)] is controlled by different configurations of the interactions with the closest trifluoromethanesulfonate anions. The long-range arrangement is also found to be specific: beyond the formal electrostatic packing, C—H...O and C—H...F contacts have no definite `hydrogen-bond' character but allow the delineation of layers, which are either pleated or flat in the packing of (2) or (4), respectively.

scholarly journals Calix[4]arene-Based MOFs Controlled by Length of Alkyldiammonium Guests

2014 ◽  
Vol 70 (a1) ◽  
pp. C1713-C1713
Author(s):  
Ki-Min Park ◽  
Eunji Lee ◽  
Huiyeong Ju ◽  
Suk-Hee Moon ◽  
Shim Sung Lee
Keyword(s):  
Electrostatic Interactions ◽  
Three Dimensional ◽  
Van Der Waals Interactions ◽  
Supramolecular Interactions ◽  
Solvothermal Reaction ◽  
Guest Molecules ◽  
Structural Framework ◽  
Guest Species ◽  
Dimensional Network ◽  
Alternative Conformation

Our interest in the development of MOFs with the cavities controlled by guest species has led us to investigate the MOFs based on calix[4]arene derivatives, in which metal ions link the calix unit to give the networks with the cavities accommodating several guest species, because the calix[4]arene-based MOFs contain porosity associated with both the ligand itself and the structural framework. In the present work, we employed a low rim-functionalized calix[4]arene tetraacetic acid (H4CTA) with 1,3-alternative conformation as a multidentate building block and alkyldiamines as the guest molecules. In the solvothermal reaction of H4CTA and Zn(II) ion in the presence of alkyldiamines, two types of new MOFs based on calix[4]arene tetraacetate (CTA4-) depending on the lengths of α,ω–alkyldiammonium guests have been synthesized by including suitable alkyldiammonium guests. Their single-crystal X-ray diffraction analyses reveal that the short alkyldiammonium guests such as ethyldiammonium, propyldiammonium, and butyldiammonium lead to form two-dimensional framework with the cavity consisting of two CTA4-and four Zn(II) ions whereas the alkyldiammonium guests such as heptyldiammonium, octyldiammonium, nonyldiammonium, and decyldiammonium give rise to generate three-dimensional network with the cavity surrounded by six CTA4-and four Zn(II) ions. The alkyldiammonium guests in both MOFs are well accommodated by each cavity via a variety of supramolecular interactions including electrostatic interactions, hydrogen bonds and van der Waals interactions. We will present and discuss a study on the syntheses and characterization of two new MOFs based on calix[4]arene derivative.

Inclusion compounds of plant growth regulators in cyclodextrins. V. 4-Chlorophenoxyacetic acid encapsulated in β-cyclodextrin and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin

2005 ◽  
Vol 61 (2) ◽  
pp. 207-217 ◽  
Author(s):  
Frantzeska Tsorteki ◽  
Kostas Bethanis ◽  
Nikos Pinotsis ◽  
Petros Giastas ◽  
Dimitris Mentzafos
Keyword(s):  
Guest Molecule ◽  
Crystal Packing ◽  
Host Molecule ◽  
X Ray Diffraction ◽  
Guest Molecules ◽  
Space Group ◽  
X Ray ◽  
Dimeric Complexes ◽  
The Mean ◽  
Chlorophenoxyacetic Acid

The crystal structures of 4-chlorophenoxyacetic acid (4CPA) included in β-cyclodextrin (β-CD) and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMβCD) have been studied by X-ray diffraction. The 4CPA/β-CD complex crystallizes as a head-to-head dimer in the space group C2 in the Tetrad packing mode. The packing modes of some β-CD dimeric complexes, having unique stackings, are also discussed. The 4CPA/TMβCD inclusion complex crystallizes in the space group P21 and its asymmetric unit contains two crystallographically independent complexes, complex A and complex B, exhibiting different conformations. The host molecule of complex A is significantly distorted, as a glucosidic residue rotated about the O4′—C1 and C4—O4 bonds forms an aperture where the guest molecule is accommodated. The phenyl moiety of the guest molecule of complex B is nearly perpendicular to the mean plane of the O4n atoms. The conformations of the guest molecules of the two complexes are similar. The crystal packing consists of antiparallel columns as in the majority of the TMβCD complexes published so far.

scholarly journals Exploiting directional long range secondary forces for regulating electrostatics-dominated noncovalent interactions

2017 ◽  
Vol 8 (2) ◽  
pp. 1378-1390 ◽  
Author(s):  
Mrityunjay K. Tiwari ◽  
Kumar Vanka
Keyword(s):  
Long Range ◽  
Electrostatic Interactions ◽  
Noncovalent Interactions ◽  
Supramolecular Complexes ◽  
The Stability

It has been well established that long range secondary electrostatic interactions (SEIs) have a significant effect on the stability of supramolecular complexes.

Sequence, Salt, Charge, and the Stability of DNA at High Pressure

1996 ◽  
Author(s):  
Robert B. Macgregor Jr ◽  
John Q. Wu
Keyword(s):  
Molar Volume ◽  
Volume Change ◽  
Salt Concentration ◽  
Electrostatic Interactions ◽  
Proposed Model ◽  
Dna Strands ◽  
Positive Volume ◽  
Ion Radius ◽  
The Stability ◽  
Kinetics Of

The effect of pressure on the helix-coil transition temperature (Tm) is reported for the double-stranded polymers poly(dA)poly(dT), poly[d(A-T)], poly[d(l-C], and poly[d(G-C] and triple-stranded poly(dA)2poly(dT). The Tm increases as a function of pressure, implying a positive volume change for the transition and leading to the conclusion that the molar volume of the coil form is larger than the molar volume of the helix. From the change in Tm as a function of pressure, molar volume changes of the transition (ΔVt) are calculated using the Clapeyron equation and calorimetrically determined enthalpies. For the doublestranded polymers, ΔVt, increases in the order poly[d(l-C] < polyt[d(A-T)] < poly(dA)-poly(dT) < polylcl(G-C)]. The value of ΔVt, for the triple-stranded to single-stranded transition of poly(dA) 2poly(dT) is larger than that of poly[d(G-C)I. The magnitude of ΔVt increases with salt concentration in all cases studied; however, the change of ΔVt with salt concentration depends on the sequence of the DNA and the number of strands involved in the transition. In the model proposed to explain the results, the overall molar volume change of the transition is a function of a negative volume change arising from changes in the electrostatic interactions of the DNA strands, and a positive volume change due to unstacking the bases. The model predicted the direction of the change in the ΔVt for several experiments. The magnitude of AVJ increases with counter ion radius, thus for polyld(A-T)], ΔVt, increases in the series Na+ , K+, Cs+, The ΔVt also increases if the charge on the phosphodiester groups is removed. The kinetics of the formation of double-stranded (dA)19(dT)19 in 50 mM NaCI are slowed approximately 14-fold at 200 MPa relative to atmospheric pressure. The implied volume of activation of +37 ml mol−l in the direction of this change is also in agreement with the proposed model. The stability of double- and triple-stranded DNA helices in water around neutral pH depends on the base composition and sequence, as well as on the ionic strength of the solution. Each of these dependencies also defines how DNA interacts with water.

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