Nonbonded Attraction Research Articles

Emergent Sequence Biasing in Step-Growth Copolymerization: Influence of Non-Bonded Interactions and Comonomer Reactivities.

The phase behavior and material properties of copolymers are intrinsically dependent on their primary comonomer sequences. Achieving precise control over monomer sequence in synthetic copolymerizations is challenging, as sequence determination is influenced not only by the reaction conditions and the properties of the reactants but also by the statistical nature of the copolymerization process itself. Mayo-Lewis reactivity ratios are often used to predict copolymer composition and sequence and are based on ratios of static reactivity constants. However, prior results have demonstrated that in a generic, solution-based step-growth A,B-copolymerization, relatively weak non-bonded attractions between certain monomer pairs induce emergent microphase separations. Such polymerization-driven separations lead to deviations from standard kinetics due to the emergent heterogeneities in reactant concentrations, which can also cause significant shifts in the resulting copolymer sequences. Previously, these effects were observed in systems where the activation energies were equal for all reaction pathways, that is, between all monomer pair combinations. In this work, we explore the combined effects on copolymerization kinetics of differences in both activation energies and non-bonded attractions between monomers and examine the sequences produced within this same step-growth copolymerization model. Our results indicate that altering activation energies influences the kinetics and sequences in a manner that also depends on the non-bonded attractions, showing that these effects may work in concert or in opposition to one another to bias the sequences formed. Non-standard kinetic behaviors and long-range sequence biasing are observed under certain conditions, and the extent of each clearly shifts as the reaction proceeds. These findings provide insight into the complex interplay between sequence and nascent oligomer phase behavior, highlighting the potential for exploiting emergent phase properties in the informed design of advanced sequence-biased materials.

Insights into the intermolecular interactions and temperature-concentration dependence of transport in ionic liquid-based EMI–TFSI/LiTFSI electrolytes

DFT calculations and MD simulations show that the EMI–TFSI/LiTFSI system is stabilized by strong nonbonded attractions, and the lithium-ion conductivity depends on the LiTFSI concentration and system temperature.

The Sequence of a Step-Growth Copolymer Can Be Influenced by Its Own Persistence Length.

Synthetic copolymer sequences remain challenging to control, and there are features of even simple one-pot, solution-based copolymerizations that are not yet fully understood. In previous simulations on step-growth copolymerizations in solution, we demonstrated that modest variations in the attractions between type A and B monomers could significantly influence copolymer sequence through an emergent aggregation and phase separation initiated by the lengthening of nascent oligomers. Here we investigate how one aspect of a copolymer's geometry-its flexibility-can modulate those effects. Our simulations show the onset of strand alignment within the polymerization-induced aggregates as chain stiffness increases and demonstrate that this alignment can influence the resulting copolymer sequences. For less flexible copolymers, with persistence lengths ≥10 monomers, modest nonbonded attractions of ∼kBT between monomers of the same type yield A and B blocks of a characteristic length and result in a polydispersity index that grows rapidly, peaks, and then diminishes as the reaction proceeds. These results demonstrate that for copolymer systems with modest variations in intermonomer attractions and physically realistic flexibilities a nascent copolymer's persistence length can influence its own sequence.

The Anomeric Effect: It's Complicated.

The origin of the anomeric effect has been reexamined in a coordinated experimental and computational investigation. The results of these studies implicate a number of different, but correlated, interactions that in the aggregate are responsible for the anomeric effect. No single factor is uniquely responsible for the axial preference of a substituent that is the hallmark of the anomeric effect. A CH···G nonbonded attraction between a polar axial substituent (G) and the syn-axial hydrogen(s) in the heterocycle has been demonstrated experimentally. The hyperconjugation model involving electron transfer from a ring heteroatom to an excited state of an axial C-G bond was shown to be, at most, a minor contributor because of the very small changes in charge density at the ring heteroatom(s): the main charge transfer is from hydrogen to G in the H-C-G unit. This appears to result from lengthening the C-G bond to minimize repulsion with the ring atom lone pair(s) and the advantage of having a more positive hydrogen that leads to a stabilizing Coulombic interaction with the ring heteroatom(s). In short, the anomeric effect arises mainly from two separate CH···G nonbonded Coulombic attractions.

Interaction of local anesthetics with the K+ channel pore domain

Local anesthetics and related drugs block ionic currents of Na+, K+ and Ca2+ conducted across the cell membrane by voltage-dependent ion channels. Many of these drugs bind in the permeation pathway, occlude the pore and stop ion movement. However channel-blocking drugs have also been associated with decreased membrane stability of certain tetrameric K+ channels, similar to the destabilization of channel function observed at low extracellular K+ concentration. Such drug-dependent stability may result from electrostatic repulsion of K+ from the selectivity filter by a cationic drug molecule bound in the central cavity of the channel. In this study we used the pore domain of the KcsA K+ channel protein to test this hypothesis experimentally with a biochemical assay of tetramer stability and theoretically by computational simulation of local anesthetic docking to the central cavity. We find that two common local anesthetics, lidocaine and tetracaine, promote thermal dissociation of the KcsA tetramer in a K+-dependent fashion. Docking simulations of these drugs with open, open-inactivated and closed crystal structures of KcsA yield many energetically favorable drug-channel complexes characterized by nonbonded attraction to pore-lining residues and electrostatic repulsion of K+. The results suggest that binding of cationic drugs to the inner cavity can reduce tetramer stability of K+ channels.

Interaction of Local Anesthetics with KcsA K+ Channel: Tetramer Stability and Docking Simulations

Many local anesthetic and anti-arrhythmic drugs block voltage-dependent Na+ and K+ channels. In particular, cardiac Kv1.5 and Kv11.1 (hERG) exhibit drug- and K+-dependent membrane stability. Since thermal stability of the KscA K+ channel tetramer is K+-dependent and all K+ channels share a structurally conserved pore domain, we hypothesized that tetramer stability of KcsA may be sensitive to binding of local anesthetics. Using SDS-PAGE to monitor KcsA tetramer we found: 1. 20 mM Lidocaine (Lid) and 5 mM tetracaine (Tet) shift the temperature (T) dependence of tetramer stability to lower T in the presence of 5 mM K+. 2. KcsA tetramer in the presence of 5 mM K+ dissociates at 90° C as a function of [Lid] and [Tet]. 3. KscA tetramer completely dissociates in the presence of Tet (5 mM) but not Lid (20 mM) within 10 minutes at 22° C in the absence of K+. 4. [K+]-dependence of KcsA tetramer stability is shifted to higher [K+] in the presence of Lid and Tet suggesting antagonism between binding of local anesthetics to a site in the tetramer and K+ to the selectivity filter. These results are indicative of a negatively coupled interaction between local anesthetic drugs and K+ that perturbs the tetrameric quaternary structure of K+ channels. To investigate whether Lid and Tet could physically bind within the inner cavity of KcsA we carried out Monte Carlo-minimization docking of Lid and Tet to open, inactivated, and closed KcsA crystal structures. The results suggest that Lid and Tet binding within the inner cavity of KcsA involves electrostatic repulsion with K+ and non-bonded attraction to residues of the selectivity filter (Thr74, Thr75) and inner pore helix (Ile100, Phe103).

Supercritical carbon dioxide assisted dispersion and distribution of silica nanoparticles in polymers

Creating well-dispersed polymer nanocomposites is an important part of controlling composite properties. Nanoparticles have been shown to improve among others electrical, thermal, mechanical, and barrier properties of polymers if they can be dispersed and distributed within the polymer matrix effectively. In the current study, supercritical carbon dioxide is used to disperse and distribute silica nanoparticles in poly(methyl methacrylate), PMMA. It was found that processing silica/PMMA nanocomposite system with supercritical carbon dioxide led to drastic improvement of the dispersion and distribution of silica nanoparticles in PMMA. The state of dispersion and distribution was found to strongly depend on the carbon dioxide saturation pressure – the greater the saturation pressure was, the better the dispersion and distribution became. The dispersion and distribution of silica nanoparticles were quantified via radial distribution function (RDF), which was constructed from transmission electron micrographs. In addition, the non-bonded attraction and cohesive energy between almost-touching nanoparticles were calculated using the Hamaker theory and results were compared with the internal pressure of expanding pores.

Critical Buckling Length versus Persistence Length: What Governs Biofilament Conformation?

We numerically study the length dependence in the bending stiffness of alpha helices, coiled coils, and a linear chain model. As the length approaches what we named the critical buckling length lc, the chain appears to become increasingly more flexible. This is due to weak nonbonded attractions that eventually lead to buckling instability and alter the chain's conformational ensemble. For alpha helices and coiled coils, lc is much less than their respective persistence lengths, so lc is the defining length scale for their conformations. These results elucidate the importance of weak nonspecific attractions that are inherent in many biofilaments in physiological conditions.

Stochastic approach to force field evaluations: conformational analysis of raloxifene, a potential new therapeutic agent for post-menopausal osteoporosis

Three widely used force fields are compared with regard to their ability to describe conformer populations. The test molecule is raloxifene, an exciting new potential medicine for treating postmenopausal osteoporosis in women. The TRIPOS (Sybyl), MM3, and UFF force fields are used to sample the low energy conformations of the long piperidinium-containing side chain of this selective estrogen receptor modulator. In this test, the conformer populations are particularly affected by nonbonded interactions. MM3 gives reasonable results, as does the UFF force field, although the latter is sensitive to the setup of a conformational search calculation. The TRIPOS (Sybyl) force field overestimates nonbonded attractions, thus biasing the conformer population toward folded structures in which the cationic ring abuts the phenolic ring.

Stochastic approach to force field evaluations: conformational analysis of raloxifene, a potential new therapeutic agent for post-menopausal osteoporosis

Three widely used force fields are compared with regard to their ability to describe conformer populations. The test molecule is raloxifene, an exciting new potential medicine for treating postmenopausal osteoporosis in women. The TRIPOS (Sybyl), MM3, and UFF force fields are used to sample the low energy conformations of the long piperidinium-containing side chain of this selective estrogen receptor modulator. In this test, the conformer populations are particularly affected by nonbonded interactions. MM3 gives reasonable results, as does the UFF force field, although the latter is sensitive to the setup of a conformational search calculation. The TRIPOS (Sybyl) force field overestimates nonbonded attractions, thus biasing the conformer population toward folded structures in which the cationic ring abuts the phenolic ring.

Intramolecular coordination of silicon in silyl formates: spectroscopic evidence confirmed by ab initio calculations

The increased value of the SiOC bending force constant ( f SiOC), obtained in normal coordinate treatment of experimental vibrational spectra of trimethylsilyl formate, was regarded as evidence for the existence of non-bonded attraction between silicon and carbonyl oxygen in this molecule. The results of normal coordinate calculations were checked by ab initio studies of equilibrium geometries and f SiOC values of H 3SiOCHO conformers. Positive overlap population of Si⋯O contact and a 73% increase in the calculated f SiOC value in the most stable cis conformer compared with the trans form confirm formation of an intramolecular coordinate bond. The influence of such attraction on geometrical parameters of cis silyl formate, especially on SiH bond lengths, is analysed. Si⋯O attraction may be strengthened substitution of one hydrogen in the CH 3 group by fluorine. The optimized equilibrium structure of H 2FSiOCHO and the ab initio value of f SiOC force constant of this molecule were calculated and it was shown that although non-bonded attraction increases in this molecule, it does not lead to an increase in f SiOC.

Molecular mechanics and molecular shape: Part VI. The response of simple molecules to bimolecular association

A molecular-mechanical force field, originally developed to calculate the structure and conformation of single molecules, has been applied to pairs of identical molecules lying at close proximity. The prototypes examined are very simple - short alkanes and short haloalkanes - but do include cases with conformational diversity and possible electrostatic effects. The optimized mutual orientations include the parallel alignment of linear alkanes, head-to-tail orientations of haloalkanes, as well as the head-to-head association, known from the crystallographic literature. The effect of aggregation on the conformation of the separate partners has been studied, and the intramolecular response characterized: in all cases examined, the partners contract. The computed energy gains are of the expected order of magnitude, the main contribution coming always from what molecular-mechanists label “non-bonded attraction”. Graphical representations of optimized orientations show the “protrusion-in-cleft” matching of molecular surfaces.

The crystal and solution structure of 2,4-dinitrophenyl phenylsulfide determined by X-ray crystallography and13C-NMR spin-lattice relaxation measurements

The crystal structure of 2,4-dinitrophenyl phenylsulfide, C12H8N2O4S, has been determined by single crystal X-ray diffraction. The crystals are monoclinic, space groupP21/n, Z = 8, witha = 10.670(2),b = 8.381(4),c = 27.998(18) A, and β = 100.44(4) °. There are two crystallographically independent molecules per asymmetric unit. All intensity measurements were made at room temperature on an Enraf-Nonius CAD-4 automatic diffractometer using monochromatized MoKα radiation. The structure was solved by direct methods and refined to a finalR value of 0.032. The two independent molecules have nearly identical geometries, with the most notable difference being the torsion angles involving the sulfur atoms. Thepara-nitro groups are more nearly in the planes of the central phenyl rings than are theortho-nitro groups although there may be nonbonded attractions between the latter. The two phenyls of each molecule are nearly at right angles to each other, as necessitated by steric forces involvingortho hydrogens. The characteristic distortions of the central phenyl rings caused by differing substituent electronegativities and degrees of conjugation are noted. The13C-NMR spectrum of the compound was assigned by comparison of calculated with observed chemical shift data. Calculated chemical shifts were obtained by incrementation of the chemical shifts of diphenylsulfide with standard nitro group additivities which were adjusted for the sulfur-nitro group interaction. Where necessary, assignments were confirmed with selective excitation spin-coupled subspectra. Solution behavior of the molecule was determined from spin-lattice (T1) relaxation measurements which showed the unsubstituted ring to reorient anisotropically about the C(21)-C(24) bond axis while the substituted ring appears to be governed by the overall isotropic reorientation of the molecular framework, indicating that the sulfur-nitro group interaction restricts anisotropic reorientation about the C(11)-C(14) bond axis.

13C nuclear magnetic resonance studies on the conformation of substituted hydantoins

A number of hydantoins were synthesized and their 13C n.m.r. spectra were studied using special solvents and shift reagents. Some interesting features of their conformation were deduced. In the case of hydantoins derived from phenylalanine evidence was found for non-bonded attraction between the hydantoin ring and the phenyl group in the side chain.

Non-bonded aromatic–amide attraction in 5-benzyl-3-arylhydantoins

Proton and 13C n.m.r. and X-ray diffraction evidence has been presented for non-bonded aromatic-amide attraction leading to a folded structure for hydantoin derivatives of phenylalanine in solution and in the solid state.

ChemInform Abstract: NON‐BONDED ATTRACTION AND THE CONFORMATION OF AROMATIC AMINO ACID DERIVATIVES

Chemischer InformationsdienstVolume 9, Issue 26 Physical Organic Chemistry ChemInform Abstract: NON-BONDED ATTRACTION AND THE CONFORMATION OF AROMATIC AMINO ACID DERIVATIVES A. K. BOSE, A. K. BOSESearch for more papers by this authorM. S. MANHAS, M. S. MANHASSearch for more papers by this authorR. F. TAVARES, R. F. TAVARESSearch for more papers by this authorJ. M. VAN DER VEEN, J. M. VAN DER VEENSearch for more papers by this authorH. FUJIWARA, H. FUJIWARASearch for more papers by this author A. K. BOSE, A. K. BOSESearch for more papers by this authorM. S. MANHAS, M. S. MANHASSearch for more papers by this authorR. F. TAVARES, R. F. TAVARESSearch for more papers by this authorJ. M. VAN DER VEEN, J. M. VAN DER VEENSearch for more papers by this authorH. FUJIWARA, H. FUJIWARASearch for more papers by this author First published: June 27, 1978 https://doi.org/10.1002/chin.197826089AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume9, Issue26June 27, 1978 RelatedInformation

Crystal and molecular structure of 1-phenyl-6-(phenylthio)-3H-2,1,3-benzoxathiazolium-3-olate

The crystal structure of 1-phenyl-6-(phenylthio)-3H-2,1,3-benzoxathiazolium-3-olate, C18H13NO2S2, has been determined by X-ray single crystal diffraction. The crystals are monoclinic, space groupP21,Z = 2, witha = 8.757(2),b = 8.428(2),c = 11.332(3) A, and β = 101.34(2) °. All intensity measurements were made at room temperature on an Enraf-Nonius CAD-4 automatic diffractometer using monochromatized, MoKα radiation. The final agreement factorR was 0.029 for 1465 contributing reflections. The nitrophenyl moiety is essentially planar, and the two phenylthio rings are canted at 74 ° and 87 ° to it. There is a possible nonbonded attraction between the nitro group and theortho-sulfur.

The manifestation of non-bonded attraction in the physical properties of cis and trans olefins

Non-bonded attraction is suggested to account for a host of differences in the physical properties of cis and trans olefins of the type XHCCHX. The main predictions are: (i) The cis isomer is more stable than the trans isomer; (ii) The CC bond is longer and the C-X bonds are shorter for the cis isomer; (iii) The π MO's orbital energies of the two isomers differ such that the trans isomer is a better electron donor and electron acceptor than the cis isomer. Ab initio calculations at the STO-3G and the 4-31G levels in support of the model are presented. The photoelectron spectra of cis and trans difluoro, dichloro and dibromoethylene are discussed, and found to be in accord with our qualitative model.

Non-bonded Attraction and the Conformation of Aromatic Amino Acid Derivatives

Non-bonded Attraction and the Conformation of Aromatic Amino Acid Derivatives

ChemInform Abstract: Conformational Control in Substituted Allyl Radicals by Nonbonded Attraction.

Chemischer InformationsdienstVolume 7, Issue 40 Physical Organic Chemistry ChemInform Abstract: Conformational Control in Substituted Allyl Radicals by Nonbonded Attraction. WOLFGANG W. SCHOELLER, WOLFGANG W. SCHOELLERSearch for more papers by this author WOLFGANG W. SCHOELLER, WOLFGANG W. SCHOELLERSearch for more papers by this author First published: October 5, 1976 https://doi.org/10.1002/chin.197640058Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume7, Issue40October 5, 1976 RelatedInformation