Hamiltonian and partition function of the generalized model of polypeptide chain in competing and non-competing solvents in the presence of interchain interactions

For the generalized model of polypeptide chain in competing and non-competing solvents, the Hamiltonian is constructed with allowance for interchain interactions. It is shown that the partition function for the model in a solvent coincides to inessential factor with the partition function without solvent, if redefinition is made of the reduced interaction energy J for a competing solvent and of the number of conformations Q for a non-competing solvent.     

Two-scale generalized model of polypeptide chain in combined solvent

The Hamiltonian of the two-scale generalized model of the polypeptide chain is constructed for the case of combined solvent. It is shown that the partition function for the model with solvent equals to within unessential factor the partition function without solvent with redefinition of the reduced energy of interaction, for competitive interaction between solvents and biopolymer, and of the number of conformations, for non-competitive interactions. Behavior of the correlation length at changes in contributions from different types of interaction is considered.     

Topology-dependent entropic differences for chiral polypeptides in solvents

The entropy of topological conformations of helical biopolymers in a solvent is determined as a function of the chirality of winding. Probability distributions are obtained by taking all possible winding conformations of a polypeptide. The results show that between mirror image distributions, there is a difference in entropy arising from a net topological winding number and the interaction of a chiral solute with its environment. This interaction is reflected in a drift coefficient which varies from segment to segment along the length of a biopolymer.     

Study by 1H NMR of the Influence of the Porosity and Solvent on the Conformations of Macromolecules at an Interface: Poly(Ethylene Oxide) Grafted on Silica

The ¹H NMR technique was used to study the behaviour of poly(ethylene oxide) chains grafted chemically on silica. A noticeable influence of the nature of the surface and solvent on the conformation of the grafted macromolecules was observed. For precipitated silica the chains adopted a disordered conformation whereas for pyrogenic silica they formed a more uniform layer. The grafting ratio and the solvent can both modify the conformations of the chains. The dependence of the relaxation times (T₁ and T₂) on the grafting ratios is discussed qualitatively from a phenomenological point of view. Different models are proposed for the two extreme grafting ratio levels in both the absence and the presence of solvent. Without solvent, for both grafting ratios, the macromolecules lie very flat on the silica and the layer is more organized, especially at high grafting ratio. In the presence of solvent the chains spread out in the solvent, adopt a more extended conformation and the local concentration of monomers at the surface decreases.     

Process-directed self-assembly of multiblock copolymers: Solvent casting <Emphasis Type="Italic">vs</Emphasis> spray coating

Using computer simulation of a soft, coarse-grained model and self-consistent field theory we investigate how collapsed, globular chain conformations in the initial stages of structure formation, which are produced by spray-coating, affect the single-chain structure and morphology of microphase-separated multiblock copolymers. Comparing spray-coated films with films that start from a disordered state of Gaussian chains, we observe that the collapsed molecular conformations in the initial stage give rise to (1) a smaller fraction of blocks that straddle domains (bridges), (2) a significant reduction of the molecular extension normal to the internal interfaces, and (3) a slightly larger lamellar domain spacing in the final morphology. The relaxation of molecular conformations towards equilibrium is very protracted for both processes – solvent casting and spray coating. These findings illustrate that the process conditions of the copolymer materials may significantly affect materials properties (such as mechanical properties) because the system does not reach thermal equilibrium on the relevant time scales.     

Nanoscale swimmers: hydrodynamic interactions and propulsion of molecular machines

Molecular machines execute nearly regular cyclic conformational changes as a result of ligand binding and product release. This cyclic conformational dynamics is generally non-reciprocal so that under time reversal a different sequence of machine conformations is visited. Since such changes occur in a solvent, coupling to solvent hydrodynamic modes will generally result in self-propulsion of the molecular machine. These effects are investigated for a class of coarse grained models of protein machines consisting of a set of beads interacting through pair-wise additive potentials. Hydrodynamic effects are incorporated through a configuration-dependent mobility tensor, and expressions for the propulsion linear and angular velocities, as well as the stall force, are obtained. In the limit where conformational changes are small so that linear response theory is applicable, it is shown that propulsion is exponentially small; thus, propulsion is nonlinear phenomenon. The results are illustrated by computations on a simple model molecular machine.     

Conformation of Symmetric Bilirubin Analogs from 13C-Nuclear Magnetic Resonance Spin Lattice T1 Relaxation Times

Symmetric analogs of bilirubin with propionic acid groups shortened and lengthened (and esterified as methyl esters) adopt similar conformations in deuterated dimethylsulfoxide solvent, as determined from their ¹³C-NMR spin lattice relaxation times. Segmental motion of the alkanoic acid chain carbons indicates internal hydrogen bonding with solvent participation.     

Role of geometrical prodan structures in the determination of possible centers of hydrogen bond formation

Using the method of intermediate neglect of differential overlap (INDO), quantum-chemical investigations of geometrical prodan structures with different rotation and deflection angles of methyl groups in the dimethylaminogroup of the molecule are performed. The charge distribution is studied for different conformations of the molecule. The possible centers of prodan interaction with proton-donor solvents are estimated. It is demonstrated that in addition to the oxygen and nitrogen atoms, the carbon atoms of the hydrocarbon chain and the aromatic prodan ring can interact with the solvent. __________ Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 1, pp. 10–16, January, 2008.     

Hydrophobicity and unique folding of selected polymers

In a suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in terms of individual properties of monomers, which model exposure to the solvent and the steric factor. Received: 4 June 1998     

Hydrodynamic effect on the correlation functions of a gaussian polymer chain

Time-dependent correlation functions of the conformations of a single gaussian polymer chain immersed in a solvent are calculated renormalization-group theoretically. As a byproduct is is confirmed that to order ? (=4-d, d being the spatial dimensionality) the translational diffusion constant obtained fully dynamically (i.e. by the Green-Kubo formalism) is identical to that obtained by the Kirkwood theory (or the Kirkwood-Riseman formalism) even with the self-avoiding interaction.     

The Solvent Effect on Spin Exchange in Long-Chain Nitroxide Biradicals

Intramolecular electron spin exchange, as a function of temperature and the solvent viscosity, polarity and relaxation properties of the solvent molecules, has been studied by X-band electron paramagnetic resonance (EPR) spectroscopy in two long-chain flexible nitroxide biradicals existing in fluid solutions in three spectroscopically different spatial conformations. Certain thermodynamic parameters of the conformational rearrangements were calculated from the EPR spectra. Spin exchange in two biradicals dissolved in five different alcohols was compared with that in a nonpolar solvent (toluene), polar protic (water) and aprotic (acetonitrile), and with thermodynamic characteristics of the solvents. Distinct correlations were found between macroscopic (solvent viscosity, polarity) and microscopic (solvent longitudinal relaxation time) characteristics of solvents, and thermodynamic parameters of the intramolecular conformational transitions. Authors' address: Van Anh Tran, Institute of Physical and Theoretical Chemistry, Graz University of Technology, Technikerstrasse 4, 8010 Graz, Austria     

Extensive stretch of polysiloxane network chains with random- and super-coiled conformations

The stress-elongation relations at large deformations for the polymer network chains with randomcoiled and supercoiled conformations are investigated using the polysiloxane networks with high elongations at break far over 10. Supercoil is the conformation of network chains in deswollen polymer networks which are made by removing solvent from the networks crosslinked in solutions at low polymer concentrations. The validity of the scaling concept of Pincus blob for the mechanical response of a polymer chain is experimentally confirmed for the network composed of randomcoiled chains. The analysis of the stress- relations for the deswollen networks comprised of supercoiled chains on the basis of the Pincus blob concept suggests that supercoil is a much more contracted conformation relative to randomcoil. Received: 25 August 1997 / Received in final form: 13 October 1997 / Accepted: 22 January 1998     

头孢菌素类化合物的核磁共振谱研究

应用¹H NMR、¹³C NMR和DEPT135°技术以及¹H-¹H COSY、HMBC、HMQC二维核磁共振技术，对头孢菌素类抗生素头孢替坦二钠、头孢曲松钠及头孢噻肟钠的质子信号和碳信号进行了全归属，并指出其核磁共振谱特征.     

Aging of thin polymer films cast from a near-theta solvent

We have examined the aging behavior of spin-cast thin polymer films as a function of their processing history. Films prepared from solutions close to the Θ?temperature were aged for varying times at room temperature, followed by a dewetting experiment above the glass transition temperature of the polymer. The characteristic aging time varied strongly with the quality of the solvent, which is attributed to distorted chain conformations in the as-cast films. This is an indication for the nonequilibrium nature of thin polymer films, possibly causing some of their unexplained properties.     

Solvent complexes of jet-cooled β-phenylethylamine

Laser-induced fluorescence spectroscopy was used to investigate -phenylethylamine molecules that were cooled via supersonic gas expansions. The bare molecule spectra reveal 0-0 transitions that can be attributed to four separate conformers. Upon the addition of water or alcohol solvents, a series of new peaks is induced that appear to be built off separate bare molecule transitions. This is a pattern that is markedly different from the one seen for solvent addition to tyramine, which includes an-OH in the para position. As a result, definite hypotheses can be made to explain the influence of the para-OH in affecting solvent induced conformations.     

Defined-sector explicit solvent in the continuum model approach for computational prediction of pK a

Accurate prediction of the acidity dissociation constant (K _a) is a challenge for the theory of proton-transfer reactions, making first-principles prediction of pK _a within 0.5?pK units of experimental values a benchmark of broad interest. In the present contribution, the defined-sector explicit solvent in continuum cluster model, which considers the structure-to-chemical affinity relationship of the carboxyl functional group, is presented. The model demonstrates predictable solvent networks based on established ‘preferred’ conformations found in a training set. Predictability within 1?kcal?mol^–1 accuracy is shown for a full set of carboxylic acid systems with varying functionality.     

Conformations of isolated ampholytic dendrimers in solutions

We study the conformations of isolated trifunctional ampholytic dendrimers in solutions. For the previously homo-dendrimer case studied in the literature, we discuss the issues of density profiles, the existence of a cavity, backfolding, bond stretching and scaling laws for the dendrimer size across the good-to-poor solvent transition. We then consider the effect of introducing monomer charges in the outermost generation opposite to those in the interior generations in an electrically neutral overall ampholytic co-dendrimer.     

Enhanced near-neighbour aggregation of dichloro- and trichloromethane in liquid methane solution from molecular dynamics simulation of radial site–site distribution functions: a simple predictor of solute–solvent compatibility

Molecular dynamics simulations have been performed for a range of equi-site and site–site radial distribution functions for the five-atom halomethane species dichloro-, trichloro-, and tetrachloromethane dissolved in the low-molecular weight hydrocarbons liquefied methane and cyclopropane, with the general aim of using this approach to predict good or bad solvent characteristics. It was found that methane solutions of dichloro- and trichloromethane showed an enhancement of near-neighbour occupancy, the methane solvent seemingly exhibiting a phobic, structure-promoting solvation behaviour towards the two solutes by increasing the number of nearest neighbours above the values that would result from a pure dilution effect caused by the solvent. It was verified that there were no significant regions of solid-like conformations nor remnants of imperfect average homogeneity within the system at the necessarily low temperature (183?K). On the other hand, simulated site–site radial functions with solvents tetrachloromethane and cyclopropane indicate normal solution characteristics towards solutes dichloro- and trichloromethane. The cause of the phobic solvation behaviour of solvent liquid methane towards di- and trichloromethane is not obvious, except that it seemingly involves the presence of hydrogen atoms on the solute species because the site–site centre-of-mass radial distribution functions of tetrachloromethane in liquid methane implied normal solution behaviour.