Quantum topology phase diagrams for molecules,clusters, and solids

The need to make more quantitative use of the total electronic charge density distribution is demonstrated in this short perspective. This is framed in the perspective of the ground breaking early work of Bader and coworkers, along with mathematicians who captured the essential nature of a molecule in a suitably compact form in real space. We see that this simple form is the Poincaré–Hopf relation for molecules and clusters and the Euler–Hopf relation in solids. Thom's theory of elementary catastrophes combined with the Poincaré–Hopf relation provides the inspiration for the new quantum topology. An alternative use of the Poincaré–Hopf relation, molecular recognition, is discussed. Quantum topology is then used to create a topology phase diagram for both molecules and solids. The author adds their perspectives of the huge potential of the quantum topology approach by demonstrating the ease with which new theoretical ideas can be generated. © 2013 Wiley Periodicals, Inc.     

Isomer‐dependent reaction mechanisms of cyclic ether intermediates: cis‐2,3‐dimethyloxirane and trans‐2,3‐dimethyloxirane

Oxiranes are a class of cyclic ethers formed in abundance during low‐temperature combustion of hydrocarbons and biofuels, either via chain‐propagating steps that occur from unimolecular decomposition of β‐hydroperoxyalkyl radicals (β‐?QOOH) or from reactions of H?O with alkenes. The cis‐ and trans‐isomers of 2,3‐dimethyloxirane are intermediates of n‐butane oxidation, and while rate coefficients for β‐?QOOH → 2,3‐dimethyloxirane + ?OH are reported extensively, subsequent reaction mechanisms of the cyclic ethers are not. As a result, chemical kinetics mechanisms commonly adopt simplified chemistry to describe the consumption of 2,3‐dimethyloxirane by convoluting several elementary reactions into a single step, which may introduce mechanism truncation error—uncertainty derived from missing or incomplete chemistry. The present research examines the isomer dependence of 2,3‐dimethyloxirane reaction mechanisms in support of ongoing efforts to minimize mechanism truncation error. Reaction mechanisms are inferred via the detection of products from Cl‐initiated oxidation of both cis‐2,3‐dimethyloxirane and trans‐2,3‐dimethyloxirane using multiplexed photoionization mass spectrometry (MPIMS). The experiments were conducted at 10 Torr and temperatures of 650 K and 800 K. To complement the experiments, the enthalpies of stationary points on the ?R + O₂ surfaces were computed at the ccCA‐PS3 level of theory. In total, 28 barrier heights were computed on the 2,3‐dimethyloxiranylperoxy surfaces. Two notable aspects are low‐lying pathways that form resonance‐stabilized ketohydroperoxide‐type radicals caused by ?QOOH ring‐opening when the unpaired electron is localized adjacent to the ether group, and cis‐trans isomerization of ?R and ?QOOH radicals, via inversion, which enable reaction pathways otherwise restricted by stereochemistry. Several species were identified in the MPIMS experiments from ring opening of 2,3‐dimethyloxiranyl radicals. Neither of the two conjugate alkene isomers prototypical of ?R + O₂ reactions were detected. Products were also identified from decomposition of ketohydroperoxide‐type radicals. The present work provides the first analysis of 2,3‐dimethyloxirane oxidation chemistry and reveals that consumption pathways are complex and require the expansion of submechanisms in chemical kinetics mechanisms.     

Separation,interconversion, and insecticidal activity of the cis‐ and trans‐isomers of novel hydrazone derivatives

A series of cis‐ and trans‐isomers of hydrazone derivatives were separated and analyzed through HPLC with diode‐array detection and HPLC‐MS/MS using ESI and ion trap MS. Two single crystals (A‐5‐1 and C‐2‐1) of the trans‐isomers were obtained and determined using X‐ray crystallography data, and the cis‐ to trans‐isomerization under different conditions was discussed. Both of the cis‐ and trans‐isomers of A‐4 and A‐5 exhibited good insecticidal activities against Plutella xylostella.     

Water‐Promoted Kinetic Separation of trans‐ and cis‐Limonene Oxides

The efficient hydrolytic kinetic separation of trans/cis‐(R)‐(+)‐limonene oxides was realized in a 1:1 mixed solvent of water and 1,4‐dioxane without additional catalyst. Optically pure trans‐(R)‐(+)‐limonene oxide was recovered in high yield (77%).     

FFLUX: Transferability of polarizable machine‐learned electrostatics in peptide chains

The fully polarizable, multipolar, and atomistic force field protein FFLUX is being built from machine learning (i.e., kriging) models, each of which predicts an atomic property. Each atom of a given protein geometry needs to be assigned such a kriging model. Such a knowledgeable atom needs to be informed about a sufficiently large environment around it. The resulting complexity can be tackled by collecting the 20 natural amino acids into a few groups. Using substituted deca‐alanines, we present the proof‐of‐concept that a given atom's charge can be modeled by a few kriging models only. © 2017 Wiley Periodicals, Inc.     

Effect of trans‐ and cis‐isomeric defects on the localization of the charged excitations in π‐conjugated organic polymers

We use the long‐range‐corrected hybrid density functional theory models to study the effect of various conformational distortions of weak‐trans and strong‐cis nature on the spatial localization of charged states in poly(p‐phenylene vinylene) (PPV) and its derivative poly[2‐methoxy‐5‐(2′‐ethylhexyloxy)‐p‐phenylene vinylene] (MEH‐PPV). The extent of self‐trapping of positive (P⁺) and negative (P^?) polarons is observed to be highly sensitive to molecular conformation that, in turn, controls the distribution of atomic charges within the polymers. It is shown that, to reach good agreement with recent experimental data on lattice distortion for P⁺ and P^? excitations, the polarization of the medium plays a critical role. The introduction of weak‐trans defects along the MEH‐PPV chain breaks the observed symmetry for P⁺ and P^? excitations. The P^? states exhibit more spatial localization owing to lattice relaxation than their vacuum counterparts in contrast to P⁺. These observations suggest higher mobilities of holes than that of electrons in MEH‐PPV, in agreement with the experimental observations. The predicted binding, reorganization, and solvation energies for PPV and MEH‐PPV are analyzed for this difference in the response behavior of holes and electrons for trans and cis distortions. This study allows for a better understanding of charge‐transport and photophysical properties in π‐conjugated organic materials by analyzing their underlying structure–property correlations. © 2013 Wiley Periodicals, Inc. 1 1 This article is a U.S. Government work, and as such, is in the public domain in the United States of America.
J. Polym. Sci., Part B: Polym. Phys. 2013 , 51, 935–942     

Synthesis and characterization of novel poly(ester‐carbonate)s by copolymerization of trans‐4‐hydroxy‐L‐proline with cyclic carbonate

The melt ring‐opening/condensation reaction of trans‐4‐hydroxy‐N‐benzyloxycarbonyl‐L‐proline (N‐CBz‐Hpr) with cyclic carbonate [trimethylene carbonate (tri‐MC) or tetramethylene carbonate (tetra‐MC)] at a wide range of molar fractions in the feed produced new degradable poly(ester‐carbonate)s. The influence of reaction conditions such as polymerization time and temperature on the yield and inherent viscosity of the copolymers was investigated. The polymerizations were carried out in bulk at 140 °C with 1.5 wt % stannous octoate as a catalyst for 30 h. The poly(ester‐carbonate)s obtained were characterized by Fourier transform infrared spectroscopy, ¹H NMR, differential scanning calorimetry, gel permeation chromatography, and Ubbelohde viscometry. The copolymers synthesized exhibited moderate molecular weights with rather narrow molecular weight distributions. The values of the glass‐transition temperature (T_g) of the copolymers depend on the molar fractions of cyclic carbonate. For the poly(N‐CBz‐Hpr‐co‐tri‐MC) system, with a decreased tri‐MC content from 93 to 16 mol %, the T_g increased from ?10 to 60 °C. Similarly, for the poly(N‐CBz‐Hpr‐co‐tetra‐MC) system, when the tetra‐MC content decreased from 80 to 8 mol %, the T_g increased from ?18 to 52 °C. The relationship between the poly(N‐CBz‐Hpr‐co‐tri‐MC) T_g and the compositions was in approximation with the Fox equation. In vitro degradation of these poly(N‐CBz‐Hpr‐co‐tri‐MC)s was evaluated from weight‐loss measurements. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1435–1443, 2003     

Synthesis and structural characterization of syndiotactic trans‐1,2 and cis‐1,2 polyhexadienes

The (E) isomer in mixtures of (E) and (Z) 1,3‐hexadiene was polymerized with the system CoCl₂(PⁱPrPh₂)₂‐MAO, a highly active and stereospecific catalyst for the preparation of 1,2 syndiotactic polybutadiene. A new crystalline polymer with a melting point of 109 °C was obtained. The polymer was characterized by IR, NMR (¹³C, ¹H in solution and ¹³C in the solid‐state), X‐ray diffraction, DSC, GPC and it was found to have a trans‐1,2 syndiotactic structure with a 5.18 ± 0.04 Å fiber periodicity. Since only the (E) isomer was polymerized, at the end of the reaction we were able to separate the (Z) isomer, which was ultimately polymerized with CpTiCl₃‐MAO at low temperature, obtaining a low molecular weight, stereoregular polymer that, characterized by IR and NMR methods, was found to exhibit a cis‐1,2 syndiotactic structure, never reported before. Molecular mechanics calculations were carried out on the trans‐1,2 syndiotactic polymer and structural models consistent with the X‐ray diffraction data are proposed. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5339–5353, 2007     

Interconversion of cis‐ and trans‐Fused Oxabicyclo[5.2.0]nonan‐2‐ones

On irradiation (350 nm) in the presence of alkenes (2,3‐dimethylbut‐2‐ene, 1,1‐dimethoxyethene, and 2,4,4‐trimethylpent‐1‐ene), benzoxepinone 1 and dioxepinone 2 are converted into mixtures of cis‐ and trans‐fused oxabicyclo[5.2.0]nonan‐2‐ones. Their relative thermodynamic stabilities (as reflected by the observed diastereoisomer ratios after equilibration with basic alumina) depend on the substitution pattern of the alkene moiety.     

Poly(styrene‐co‐glycerol dimethacrylate): Synthesis,characterization, and application as a resin for gel‐phase peptide synthesis

An efficient cross‐linked polymer support for solid‐phase synthesis was prepared by introducing glycerol dimethacrylate cross‐linker to polystyrene network using free radical aqueous suspension polymerization. The support was characterized by various spectroscopic methods. Morphological feature of the resin was analyzed by microscopy. The polymerization reaction was investigated with respect to the effect of amount of cross‐linking agent, which in turn vary the swelling, loading, and the mechanical stability of the resin. The solvent uptake of the polymer was studied in relation to cross‐linking and compared with Merrifield resin. The stability of the resin was tested in different synthetic conditions used for solid‐phase peptide synthesis. Hydroxy group of the support was derivatized to chloro and then amino groups using different reagents and reaction conditions. Efficiency of the support was tested and compared with TentaGel? resin by following different steps involved in the synthesis of the 65–74 fragment of acyl carrier protein. The results showed that the poly(styrene‐co‐glycerol dimethacrylate) (GDMA‐PS) is equally efficient as TentaGel resin in peptide synthesis. The purity of the peptides was analyzed by HPLC and identities were determined by mass spectroscopy and amino acid analysis. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4382–4392, 2005     

Cationic ring‐opening polymerization behavior of a five‐membered cyclic thiocarbonate having a spiro‐linked adamantane moiety

This work deals with the synthesis and cationic ring‐opening polymerization behavior of a novel five‐membered cyclic thiocarbonate bearing a spiro‐linked adamantane moiety, tricyclo[3.3.1.1^3,7]decane‐2‐spiro‐4′‐(1′,3′‐dioxolane‐2′‐thione) ( TC2 ). The cationic ring‐opening polymerization of TC2 did not proceed with trifluoromethanesulfonic acid, methyl trifluoromethanesulfonate, triethyloxonium tetrafluoroborate (Et₃OBF₄), boron trifluoride etherate (BF₃OEt₂), titanium tetrachloride, or methyl iodide as the initiator, presumably because of the steric hindrance of the adamantane moiety. However, the cationic ring‐opening copolymerization of TC2 with five‐ or six‐membered cyclic thiocarbonates, that is, 1,3‐dioxolane‐2‐thione, 1,3‐dioxane‐2‐thione, 5‐methyl‐1,3‐dioxane‐2‐thione, or 5,5‐dimethyl‐1,3‐dioxane‐2‐thione, initiated by BF₃OEt₂ or Et₃OBF₄, proceeded to afford the corresponding copolymer via a selective ring‐opening direction. The increase in the feed ratio of TC2 in the copolymerization increased the unit ratio derived from TC2 in the copolymer; however, the molecular weight of the copolymer decreased. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 699–707, 2003     

Theoretical simulation of thermally induced phase separation in a main‐chain liquid‐crystalline polymer solution

Phase diagrams of main‐chain liquid‐crystalline polymer (MCLCP) solutions have been calculated self‐consistently on the basis of a simple addition of the Flory–Huggins free energy for isotropic mixing, the Maier–Saupe free energy for nematic ordering, and the Flory free energy for chain rigidity of the MCLCP backbone. The calculated phase diagram is an upper critical solution type overlapping with the nematic–isotropic transition. The phase diagram consists of liquid–liquid, liquid–nematic, and pure nematic regions. Subsequently, the dynamics of thermally induced phase separation and morphology development have been investigated by the incorporation of the combined free energy density into the coupled time‐dependent Ginzburg–Landau (model C) equations, which involve conserved compositional and nonconserved orientational order parameters. The numerical calculations reveal a variety of the morphological patterns arising from the competition between liquid–liquid phase separation and nematic ordering of the liquid‐crystalline polymer. Of particular interest is the observation of an inflection in the growth dynamic curve, which may be attributed to the nematic ordering of the MCLCP component, which leads to the breakdown of the interconnected domains. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 913–926, 2003     

Interactions of Molecules with cis and trans Double Bonds: A Theoretical Study of cis‐ and trans‐2‐Butene

Noncovalent interactions of cis‐ and trans‐2‐butene, as the smallest model systems of molecules with cis and trans double bonds, were studied to find potential differences in interactions of these molecules. The study was performed using quantum chemical methods including very accurate CCSD(T)/CBS method. We studied parallel and displaced parallel interactions in 2‐butene dimers, in butane dimers, and between 2‐butene and saturated butane. The results show the trend that interactions of 2‐butene with butane are the strongest, followed by interactions in butane dimers, whereas the interaction in 2‐butene dimers are the weakest. The strongest calculated interaction energy is between trans‐2‐butene and butane, with a CCSD(T)/CBS energy of ?2.80 kcal mol^?1. Interactions in cis‐2‐butene dimers are stronger than interactions in trans‐2‐butene dimers. Interestingly, some of the interactions involving 2‐butene are as strong as interactions in a benzene dimer. These insights into interactions of cis‐ and trans‐2‐butene can improve understanding of the properties and processes that involve molecules with cis and trans double bonds, such as fatty acids and polymers.     

Two‐dimensional liquid chromatography analysis of all‐trans‐, 9‐cis‐, and 13‐cis‐astaxanthin in raw extracts from Phaffia rhodozyma

An effective two‐dimensional liquid chromatography method has been established for the analysis of all‐trans‐astaxanthin and its geometric isomers from Phaffia rhodozyma employing a C18 column at the first dimension and a C30 column in the second dimension, connected by a 10‐port valve using the photo‐diode array detector. The regression equation of astaxanthin calibration curve was established, and the precision and accuracy values were found to be in the range of 0.32–1.14% and 98.21–106.13%, respectively. By using two‐dimensional liquid chromatography, it was found that day light, ultrasonic treatment, and heat treatment have significant influence on the content of all‐trans‐astaxanthin in the extract from P. rhodozyma due to the transformation of all‐trans‐astaxanthin to cis‐astaxanthin. The day light and ultrasonic treatments more likely transform all‐trans‐astaxanthin to 9‐cis‐astaxanthin, and the thermal treatment transforms all‐trans‐astaxanthin to 13‐cis‐astaxanthin. These results indicate that the two‐dimensional liquid chromatography method can facilitate monitoring astaxanthin isomerization in the raw extract from P. rhodozyma. In addition, the study will provide a general reference for monitoring other medicals and bioactive chemicals with geometric isomers.     

Using one‐step perturbation to predict the effect of changing force‐field parameters on the simulated folding equilibrium of a β‐peptide in solution

Computer simulation using molecular dynamics is increasingly used to simulate the folding equilibria of peptides and small proteins. Yet, the quality of the obtained results depends largely on the quality of the force field used. This comprises the solute as well as the solvent model and their energetic and entropic compatibility. It is, however, computational very expensive to perform test simulations for each combination of force‐field parameters. Here, we use the one‐step perturbation technique to predict the change of the free enthalpy of folding of a β‐peptide in methanol solution due to changing a variety of force‐field parameters. The results show that changing the solute backbone partial charges affects the folding equilibrium, whereas this is relatively insensitive to changes in the force constants of the torsional energy terms of the force field. Extending the cut‐off distance for nonbonded interactions beyond 1.4 nm does not affect the folding equilibrium. The same result is found for a change of the reaction‐field permittivity for methanol from 17.7 to 30. The results are not sensitive to the criterion, e.g., atom‐positional RMSD or number of hydrogen bonds, that is used to distinguish folded and unfolded conformations. Control simulations with perturbed Hamiltonians followed by backward one‐step perturbation indicated that quite large perturbations still yield reliable results. Yet, perturbing all solvent molecules showed where the limitations of the one‐step perturbation technique are met. The evaluated methodology constitutes an efficient tool in force‐field development for molecular simulation by reducing the number of required separate simulations by orders of magnitude. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Polypeptide folding on a conformational‐space network: Dependence of network topology on the structural discretization procedure

Mapping the conformational space of a polypeptide onto a network of conformational states involves a number of subjective choices, mostly in relation to the definition of conformation and its discrete nature in a network framework. Here, we evaluate the robustness of the topology of conformational‐space networks derived from Molecular Dynamics (MD) simulations with respect to the use of different discretization (clustering) methods, variation of their parameters, simulation length and analysis time‐step, and removing high‐frequency motions from the coordinate trajectories. In addition, we investigate the extent to which polypeptide dynamics can be reproduced on the resulting networks when assuming Markovian behavior. The analysis is based on eight 500 ns and eight 400 ns MD simulations in explicit water of two 10‐residue peptides. Three clustering algorithms were used, two of them based on the pair‐wise root‐mean‐square difference between structures and one on dihedral‐angle patterns. A short characteristic path length and a power‐law behavior of the probability distribution of the node degree are obtained irrespective of the clustering method or the value of any of the tested parameters. The average cliquishness is consistently one or two orders of magnitude larger than that of a random realization of a network of corresponding size and connectivity. The cliquishness as function of node degree and the kinetic properties of the networks are found to be most dependent on clustering method and/or parameters. Although Markovian simulations on the networks reproduce cluster populations accurately, their kinetic properties most often differ from those observed in the MD simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Conformational analysis. Part 40: a theoretical and NMR investigation of the conformations of cis‐ and trans‐cyclopentane‐1,3‐diol

The conformations of cis‐ ( 1 ) and trans‐cyclopentane‐1,3‐diol ( 2 ) have been studied by ab initio (Gaussian 98) and molecular mechanics (PCMODEL) calculations and by NMR spectroscopy. The calculations gave two low‐energy conformations for ( 1 ), 1A and 1B , both with axial hydroxyl groups. Two conformations with equatorial hydroxyl groups ( 1C and 1D ) were found but with much higher energy (ca 4.0 kcal mol^?1). Five low‐energy conformers were found for 2 . Four were envelope conformations and one a half‐chair. The complete analysis of the 400 MHz ¹H NMR spectra of 1 in a variety of solvents and 2 in chloroform was performed by extensive decoupling experiments, iterative computer analysis and spectral simulation. This gave all the H,H couplings in the molecule, including in 1 a long‐range ⁴J(H,H) coupling between H‐2cis and H‐4,5cis. The ³J(H,H) couplings were used to determine the conformer populations in these molecules. This was initially achieved using the Haasnoot, de Leeuw and Altona equation. to obtain the conformer couplings. It was found that this equation was not accurate for the C·CH₂·CH₂·C fragment in these molecules and the following equation was derived for this fragment from five‐ and six‐ membered cyclic compounds in fixed conformations: (1) The conformer populations were obtained by calculating the conformer couplings which were then compared with the observed couplings. Compound 1 in benzene solution is an approximately equal mixture of conformers 1A and 1B with small (<4%) amounts of 1C and 1D . In the polar solvents acetone and acetonitrile the populations of 1A and 1B are again equal, with 20% of 1C and <2% of 1D . In 2 the major conformers are 2B and 2D with small amounts of 2C , 2E and 2A . These novel findings are considered with previous data on cyclopentanol and cis‐ and trans‐cyclopentane‐1,2‐diol and it is shown that the axial hydroxyl substituent at the fold of the envelope appears to be a major factor in determining the conformational energies of these compounds. Copyright © 2003 John Wiley & Sons, Ltd.