Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents

In this paper, the conformation and dynamics properties of polyethylene oxide (PEO) and polypropylene oxide (PPO) polymer chains at 298 K have been studied in the melt and at infinite dilution condition in water, methanol, chloroform, carbon tetrachloride, and n-heptane using molecular dynamics simulations. The calculated density of PEO melt with chain lengths of n = 2, 3, 4, 5 and, for PPO, n = 7 are in good agreement with the available experimental data. The conformational properties of PEO and PPO show an increasing gauche preference for the O-C-C-O dihedral in the following order water>methanol>chloroform>carbon tetrachloride = n-heptane. On the contrary, the preference for trans conformation has a maximum in carbon tetrachloride and n-heptane followed in the order by chloroform, methanol, and water. The PEO conformational preferences are in qualitative agreement with results of NMR studies. PEO chains formed different types of hydrogen bonds with polar solvent molecules. In particular, the occurrence of bifurcated hydrogen bonding in chloroform was also observed. Radii of gyration of PEO chains of length larger than n = 9 monomers showed a good agreement with light scattering data in water and in methanol. For the shorter chains the observed deviations are probably due to the enhanced hydrophobic effects caused by the terminal methyl groups. For PEO the fitting of end-to-end distance distributions with the semi-flexible chain model at 298 K provided persistence lengths of 0.375 and 0.387 nm in water and methanol, respectively. Finally, the radius of gyration of Pluronic P85 turned out to be 2.25 ± 0.4 nm at 293 K in water in agreement with experimental data.     

Intrinsic conformational preferences of C(alpha,alpha)-dibenzylglycine

The intrinsic conformational preferences of C (alpha,alpha)-dibenzylglycine, a symmetric alpha,alpha-dialkylated amino acid bearing two benzyl substituents on the alpha-carbon atom, have been determined using quantum chemical calculations at the B3LYP/6-31+G(d,p) level. A total of 46 minimum energy conformations were found for the N-acetyl- N'-methylamide derivative, even though only nine of them showed a relative energy lower than 5.0 kcal/mol. The latter involves C 7, C 5, and alpha' backbone conformations stabilized by intramolecular hydrogen bonds and/or N-H...pi interactions. Calculation of the conformational free energies in different environments (gas-phase, carbon tetrachloride, chloroform, methanol, and water solutions) indicates that four different minima (two C 5 and two C 7) are energetically accessible at room temperature in the gas phase, while in methanol and aqueous solutions one such minimum (C 5) becomes the only significant conformation. Comparison with results recently reported for C (alpha,alpha)-diphenylglycine indicates that substitution of phenyl side groups by benzyl enhances the conformational flexibility leading to (i) a reduction of the strain of the peptide backbone and (ii) alleviating the repulsive interactions between the pi electron density of the phenyl groups and the lone pairs of the carbonyl oxygen atoms.     

4-Methylpseudoproline derived from α-methylserine - synthesis and conformational studies

This paper presents the synthesis and solution conformational studies of the tripeptides Fmoc-Ala-(R)-(αMe)Ser(Ψ(H,H)Pro)-Ala-OBu(t) (6a) and Fmoc-Ala-(S)-(αMe)Ser(Ψ(H,H)Pro)-Ala-OBu(t) (6b). Additionally, the X-ray structure of 6a is given. NMR analysis corroborated by theoretical calculations (XPLOR) shows that in both peptides the amide bond between pseudoproline and the preceding amino acid is in the trans conformation. The same amide bond geometry was observed in the crystal state of 6a. The latter is additionally influenced by the presence of two symmetrically independent molecules in an asymmetric unit. Both molecules adopt a conformation which resembles β-turn type II, stabilized by hydrogen bonding. The conformational preferences and prolyl cis-trans isomerization of Ac-(αMe)Ser(Ψ(H,H)Pro)-NHMe (7) were explored at the IEFPCM/B3LYP/6-31+G(d) level of theory in vacuum, water and chloroform. It has been shown that the trans isomer predominates in water solutions and the cis isomer is preferred in chloroform. The conformation of 7 is down-puckered independently of the geometry of the amide bonds, with lower puckering in the transition state of the cis-trans isomerization.     

An NMR and quantum-mechanical investigation of tetrahydrofuran solvent effects on the conformational equilibria of 1,4-butanedioic acid and its salts

Vicinal proton-proton NMR couplings have been used to compare the influences of water and tetrahydrofuran (THF) as solvents on the conformational equilibria of 1,4-butanedioic (succinic) acid and its mono- and dianionic salts. An earlier NMR investigation (Lit, E. S.; Mallon, F. K.; Tsai, H. Y.; Roberts, J. D. J. Am Chem. Soc. 1993, 115, 9563-9567) showed that, in water, the conformational preferences for the gauche conformations for butanedioic acid and its monoanion and dianion were, respectively, approximately 84%, 66%, and 43%, essentially independent of the nature of the cation or concentration. We now report the corresponding gauche percentages calculated in the same way for 0.05 M solutions in THF to be 66%, 90-100%, and 46-64%. Substantial evidence was adduced for the rotational angle between the substituents in the monoanion being approximately 70 degrees. The positions of conformational equilibria of the salts in THF, particularly of the dianion, were found to be rather insensitive to concentration and temperature, but more sensitive to the amount of water present. Ab initio quantum-mechanical calculations for 1,4-butanedioate dianion indicate that, as expected for the gas phase, the trans conformation of the dianion should be heavily favored over the gauche, but, in both THF and water, the gauche conformation is calculated to predominate with rotational angles substantially less than 60 degrees. This conclusion is, in fact, generally consistent with the experimental vicinal proton couplings, which are wholly inconsistent with the trans conformation.     

Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid

We have used quantum mechanical calculations at the B3LYP/6-311G(d,p) level to determine the conformational preferences of the N-acetyl-N'-methylamide derivative of 1-aminocyclopentane-1-carboxylic acid in the gas phase, chloroform solution, and water solution. The backbone conformation of this dipeptide has been described through the dihedral angles varphi and psi, while the pseudorotational phase angle was used to define the conformation of the cyclopentane ring. Results indicate that the backbone flexibility of this amino acid is restricted by the cyclic nature of the side chain, the relative stability of the different conformations depending on the polarity of the environment. The potential energy of the pseudorotation was also studied as a function of the backbone conformation. Interestingly, the conformation of the cyclic side chain depends on the backbone arrangement. Furthermore, the number of pseudorotational states accessible at room temperature is high in all the investigated environments, especially in aqueous solution. Finally, a set of force-field parameters for classical molecular mechanics calculations was developed for the investigated amino acid. Molecular dynamics simulations in both chloroform and aqueous solutions were performed to demonstrate the reliability of such parameters.     

Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study

The conformational preferences of oligopeptides of an ϵ-amino acid (2-((1R,3S)-3-(aminomethyl)cyclopentyl)acetic acid, Amc₅a) with a cyclopentane substituent in the C^β−C^γ−C^δ sequence of the backbone were investigated using DFT methods in chloroform and water. The most preferred conformation of Amc₅a oligomers (dimer to hexamer) was the H₁₆ helical structure both in chloroform and water. Four residues were found to be sufficient to induce a substantial H₁₆ helix population in solution. The Amc₅a hexamer adopted a stable left-handed (M)-2.3₁₆ helical conformation with a rise of 4.8 Å per turn. The hexamer of Ampa (an analogue of Amc₅a with replacing cyclopentane by pyrrolidine) adopted the right-handed mixed (P)-2.9_18/16 helical conformation in chloroform and the (M)-2.4₁₆ helical conformation in water. Therefore, hexamers of ϵ-amino acid residues exhibited different preferences of helical structures depending on the substituents in peptide backbone and the solvent polarity as well as the chain length.     

Hydrophilic gold nanoparticles adaptable for hydrophobic solvents

Surface ligand molecules enabling gold nanoparticles to disperse in both polar and nonpolar solvents through changes in conformation are presented. Gold nanoparticles coated with alkyl-head-capped PEG derivatives were initially well dispersed in water through exposure of the PEG residue (bent form). When chloroform was added to the aqueous solution of gold nanoparticles, the gold nanoparticles were transferred from an aqueous to a chloroform phase through exposure of the alkyl-head residue (straight form). The conformational change (bent to straight form) of immobilized ligands in response to the polarity of the solvents was supported by NMR analyses and water contact angles.     

Solvent and substituent effects on the conformational equilibria and intramolecular hydrogen bonding of 4-substituted-2-hydroxybenzaldehydes

By applying the B3LYP/6-31G(d) method with the SCIPCM model on seven 4X substituted 2-hydroxybenzaldehydes, some structural characteristics related with their conformational equilibria and intramolecular hydrogen bonds have been clarified. The compounds are almost completely under the planar conformation characterized by a strong intramolecular hydrogen bond, which decreases in those solvents that possess a higher hydrogen bond donating capability and polarity. The substituents exert a marked influence on the conformational equilibrium constants and the strength of the IHB. Moreover, the excellent Hammett-type equations obtained support the proposed conformational reactions to quantify the IHB in the o-hydroxybenzaldehydes studied.     

Conformational preference and cis-trans isomerization of 4(R)-substituted proline residues

We report here the conformational preference and prolyl cis-trans isomerization of 4(R)-substituted proline dipeptides, N-acetyl-N'-methylamides of 4(R)-hydroxy-L-proline and 4(R)-fluoro-L-proline (Ac-Hyp-NHMe and Ac-Flp-NHMe, respectively), studied at the HF/6-31+G(d), B3LYP/6-31+G(d), and B3LYP/6-311++G(d,p) levels of theory. The 4(R)-substitution by electron-withdrawing groups did not result in significant changes in backbone torsion angles as well as endocyclic torsion angles of the prolyl ring. However, the small changes in backbone torsion angles phi and psi and the decrease of bond lengths r(Cbeta-Cgamma) or r(Cgamma-Cdelta) appear to induce the increase of the relative stability of the trans up-puckered conformation and to alter the relative stabilities of transition states for prolyl cis-trans isomerization. Solvation free energies of local minima and transition states in chloroform and water were calculated using the conductor-like polarizable continuum model at the HF/6-31+G(d) level of theory. The population of trans up-puckered conformations increases in the order Ac-Pro-NHMe < Ac-Hyp-NHMe < Ac-Flp-NHMe in chloroform and water. The increase in population for trans up-puckered conformations in solution is attributed to the increase in population for the polyproline-II-like conformations with up puckering. The barriers DeltaGct++ to prolyl cis-to-trans isomerization for Ac-Hyp-NHMe and Ac-Flp-NHMe increase as the solvent polarity increases, as seen for Ac-Pro-NHMe. In particular, it was identified that the cis-trans isomerization proceeds through the clockwise rotation about the prolyl peptide bond for Ac-Hyp-NHMe and Ac-Flp-NHMe in chloroform and water, as seen for Ac-Pro-NHMe.     

Peptide backbone folding induced by the C(alpha)-tetrasubstituted cyclic alpha-amino acids 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) and 1-aminocyclopentane-1-carboxylic acid (Ac5c). A joint computational and experimental study

The conformational study of a new group of synthetic peptides containing 4-amino-1,2-dithiolane-4-carboxylic acid (Adt), a cysteine-related achiral residue, has been carried out through a joint application of computational and experimental methodologies. Molecular Dynamics simulations clearly suggest the tendency of this molecule to adopt a gamma-turn conformation in vacuum and help in analyzing the complex and crucial conformational behaviour of the dithiolane ring which appears to preferentially adopt a C(S)-like structure. Electronic structure calculations carried out in solution using the Density Functional Theory also indicate the preservation of the gamma-like folding in apolar solvents and the helix-like one in more polar solvents. A comparison with the achiral 1-aminocycloalkane-1-carboxylic acid (Ac5c) has been carried out using the same computational tools. NMR and IR data on dipeptide derivatives containing the Adt or Ac5c residue show that in chloroform solution all the models prefer a gamma-turn structure, centered at the cyclic residue, stabilized by an intramolecular H-bond, whereas in a more polar solvent, i.e. dimethyl sulfoxide, this folding is not maintained. The experimental conformational studies, extended to N-Boc protected tripeptides, clearly indicate the remarkable tendency of both the five-membered C(alpha)-tetrasubstituted cyclic amino acids Adt and Ac5c to induce the gamma-turn structure also in models able to adopt the beta-bend conformation.     

Solvent Extraction of Sodium and Potassium Ions by Dicarboxylated Calix[4]arenes

The extraction of sodium and potassium ions by 25,27-dicarboxymethyl-26,28-dimethoxy-5,11,17,23-tetra-tert-butyl calix[4]arene (L1H2) in chloroform shows the formation of MLIH and M2LI complexes (M = Na, K). In 1,2-dichloroethane, the MLIH species are formed in the acidic pH range, while only the Na2LI species is found at high pH values. The corresponding extraction equilibrium constants K11 (M) and K21 (M) have been evaluated and show a selectivity in favour of Na+ as compared to K+, whatever the nature of the complexes. In chloroform, this selectivity is much more pronounced considering the 2 : 1 complexes: K11(Na)/K11(K) K21(Na)/K21(K).The coexistence of 1 : 1 and 2 : 1 metal : ligand complexes is also shown in the extraction of sodium in 1,2-dichloroethane by the 25,27-dicarboxymethyl-26,28-dimethoxyethoxy-5,11,17,23-tetra-tertbutyl calix[4]arene (LIIH2), locked in the cone conformation.Structural data of the complexes are discussed on the basis of 1H-NMR spectra. In particular, for LIH2, a conformational change from cone to partial cone upon metal complexation has been evidenced for the complexes KLIH, K2LI and Na2LI.     

Looking for treasure in stereochemistry-land. A path marked by curiosity, obstinacy, and serendipity

Over the past 40 years, much of my research has evolved around various topics of conformational analysis and asymmetric synthesis. This Perspective describes some of my salient contributions in eight different areas of organic stereochemistry: (1) conformational analysis of six-membered rings, (2) evaluation of stereoelectronic interactions in (1)J(C-H) one-bond coupling constants in six-membered rings, (3) eclipsed conformation in cis-2-tert-butyl-5-(tert-butylsulfonyl)-1,3-dioxane, (4) determination of enthalpic and entropic contributions to ΔG°(CH(2)Ph) and ΔG°(t-Bu), (5) study of the "attractive gauche effect" in O-C-C-O segments, (6) examination of salt effects on conformational equilibria, (7) asymmetric synthesis of β-amino acids, and (8) asymmetric organocatalysis and "Green" chemistry. It will be appreciated that a basic understanding of the principles of physical organic chemistry has been essential in all projects. Furthermore, curiosity, enthusiasm, obstinacy, and paying attention to unexpected observations will lead to many new (stereo)chemical discoveries.     

A combined NMR, DFT, and X-ray investigation of some cinchona alkaloid O-ethers

Structures and conformational behavior of several cinchona alkaloid O-ethers in the solid state (X-ray), in solution (NMR and DFT), and in the gas phase (DFT) were investigated. In the crystal, O-phenylcinchonidine adopts the Open(3) conformation similar to cinchonidine, whereas the O-methyl ether derivatives of both cinchonidine and cinchonine are packed in the Closed(1) conformation. Dynamic equilibria in solutions of the alkaloids were revealed by combined experimental-theoretical spin simulation/iteration techniques for the first time. In the (1)H NMR spectra in CDCl3 and toluene-d8 at room temperature, Closed(1) conformation was observed for the O-silyl ethers as a separate set of signals. For O-methyl ether derivatives Closed(1) could be separated only at -30 degrees C in CDCl3 or toluene-d8 and for O-phenylcinchonidine at -70 degrees C in CDCl3/CD2Cl2. The ratio between the Closed(2) and Open(3) conformers was estimated by analyzing the vicinal coupling constant (3)J(H9,H8) at ambient and low temperatures. The observed conformational equilibria of O-(tert-butyldimethylsilyl)cinchonidine in CDCl 3 and toluene-d8 are in good agreement with the theoretically estimated equilibrium populations of the conformations according to Boltzmann statistics. The conformational equilibria of four cinchona alkaloid O-ether solutes in CDCl3 and toluene-d8 are discussed in the light of their relevance to the mechanism of 1-phenyl-1,2-propanedione (PPD) hydrogenation over cinchona alkaloid modified heterogeneous platinum catalysts. It was demonstrated that the conformation found to be abundant in the liquid phase has no direct correlation with the enantioselectivity of the PPD hydrogenation reaction.     

On the Conformation of Bilirubin Ditaurate

Summary.  The first optically active taurine conjugate of a bilirubin was prepared by reaction of taurine sodium salt with the mixed anhydride formed from reaction of (βS,β′S)-dimethylmesobilirubin-XIIIα with isobutyl chloroformate. Analysis of the circular dichroism spectra of the conjugate in water and chloroform indicate a conformational preference for the (M)-helical ridge-tile conformation, thus providing the first spectroscopic evidence on the conformation of ditaurobilirubins. Corresponding author. E-mail: lightner@scs.unr.edu Received July 5, 2002; accepted July 15, 2002     

NMR conformational analysis of antide, a potent antagonist of the gonadotropin releasing hormone

Antide is a decapeptide [(N-Ac-D-Nal(1)-D-Cpa(2)-D-Pal(3)-Ser(4)-Lys(Nic)(5)-D-Lys(Nic)(6)-Leu(7)-Ilys(8)-Pro(9)-D-Ala(10)-NH(2)] that acts in vivo as an antagonist of GnRH (gonadotropin-releasing hormone). The conformational behavior of antide has been studied in water, TFE, DMF, and DMSO solutions by means of 2D-NMR spectroscopy and molecular dynamics calculations. Antide adopts in aqueous solution a delta-shaped backbone conformation, which is characterized by an irregular turn around residues D-Pal(3)-Ser(4) and by the close spatial proximity of the side chains belonging to D-Nal(1) and Ilys(8) (as many as 17 NOE peaks were detected between these side chains). The side-chain protons of Ilys(8) (especially the H(gamma) ones) present remarkably upfield shifted resonances, because of ring current effects induced by the naphthyl moiety. The upfield shifted resonances of the Ilys(8) H(gamma) hydrogen atoms are strictly characteristic of the water delta-shaped conformation and can be considered as structure markers. The observation of ring current shifted Ilys(8) H(gamma) resonances under different conditions (temperature, pH, solvent) indicates a remarkable stability of the water delta-shaped conformation. Such a conformation is at least partially disrupted in solvent mixtures containing high percentages of organic solvents. TFE can induce a well-defined conformation, which is characterized by an S-shaped backbone conformation. In DMF and DMSO solution, the molecule is basically endowed with a random coil conformation and high fluxionality. Antide fulfills the conformational requirements that are known to play a crucial role in receptor recognition, namely (i) the presence of a turn in the backbone and (ii) the all-trans nature of peptide bonds. In addition, the structural rigidity of antide likely adds a further contribution to the receptor binding affinity.     

An NMR investigation of the importance of intramolecular hydrogen bonding in determining the conformational equilibrium of ethylene glycol in solution

Although conformational analysis by NMR of ethylene glycol indicates generally strong preferences for the gauche conformation in solvents ranging from water to chloroform, the bulk of the NMR evidence indicates that intramolecular hydrogen bonding between the hydroxyl groups is unlikely to be a significant factor in determining that preference, except possibly in fairly non-polar solvents. The 'gauche effect' is clearly very important, especially in aqueous solution.     

Configurational and conformational control of chemical modification and thermal degradation of poly(vinyl chloride)

In the light of some earlier works on nucleophilic substitution on poly(vinyl chloride) (PVC) in solution, a conformational mechanism is proposed. It considers the TT isotactic diad conformation to be the only reactive species and the reaction to be controlled by the conformational equilibria that make such conformation available. As a result all the isotactic and the heterotactic triads are capable of reacting provided that they adopt the GTTG⁻ and the GTTT conformation, respectively. Since the replacement of a definite fraction of isotactic triads, which are assumed to be of the GTTG⁻ conformation, results in an enhanced thermal and photochemical stability, the lability of some chlorines at such triads is proved. Further arguments in favour of the conformational mechanism are afforded through recent results of i) substitution studies in the melt and in aqueous suspension with phase transfer catalysts, ii) accurate ¹³C NMR measurements of triad variation with degree of substitution.     

Conformational study of super-active analogues of somatostatin with reduced ring size by XXXH nmr

The conformational properties of five cyclic analogues related to somatostatin, and derived from the highly potent

(SMS 201-995) were investigated in DMSO-d6 and/or aqueous solution by ¹H NMR spectroscopy. The results were compared with those previously obtained with the three closely related analogues SMS 201-995, Sandoz 204-090 and CTC. The eight compounds are active in inhibiting the secretion of growth hormone. In water, we found the possibility of conformational equilibria involving γ turns. In DMSO, the N.M.R. results are in favour of a predominant conformation with a type II' β turn involving residues 3 to 6.     

Conformational preferences of non-prolyl and prolyl residues

The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis-trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C(7) hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the alpha-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis-trans isomerization increases. It is found that the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about the non-prolyl and prolyl peptide bonds in both the gas phase and the solutions. The pertinent distance d(N...H-N(NHMe)) can successfully describe the increase in the rotational barriers for the non-prolyl and prolyl trans-cis isomerization as the solvent polarity increases and the higher barriers for the non-prolyl residue than for the prolyl residue, as seen in experimental and calculated results. By analysis of the contributions to rotational barriers, the cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. The calculated cis populations and rotational barriers to the cis-trans isomerization for both the dipeptides in chloroform and/or water accord with the experimental values.     

Dielectric studies of conformational equilibria in acetylpyridines

Results of both linear and non-linear dielectric studies of the tautomeric equilibria in benzene solutions of 2- and 4-acetylpyridines are presented. The suggestion that 2-acetylpyridine occurs only in its trans conformation has been confirmed. The analysis for 4-acetylpyridine has shown the correctness and specific utility of the dielectric methods (particularly the non-linear) to studies of conformational equilibria.