Theoretical analysis of the anomalous spectral splitting of tetracene in 4He droplets

We present a theoretical analysis of the electronic absorption spectra of tetracene in (4)He droplets based on many-body quantum simulations. Using the path integral ground state approach, we calculate one- and two-body reduced density matrices of the most strongly localized He atoms near the molecule surface and use these to investigate the helium ground-state quantum coherence and correlations when tetracene is in its electronic ground and excited states. We identify a trio of quasi-one-dimensional, strongly localized atoms adsorbed along the long axis of the molecule that show some quantum coherence among themselves but far less with the remaining solvating helium. We evaluate the single-particle natural orbitals of the localized He atoms by diagonalization of the one-body density matrix and use these to construct single- and many-particle solvating helium basis states with which the zero-phonon spectral features of the tetracene-(4)He(N) absorption spectrum are then calculated. The absorption spectrum resulting from the three-body density matrix for the strongly bound trio of helium atoms is in very good agreement with the experimental data, accounting quantitatively for the anomalous splitting of the zero-phonon line [Hartmann, M.; Lindinger, A.; Toennies, J. P.; Vilesov, A. F. Chem. Phys. 1998, 239, 139; Krasnokutski, S.; Rouillé, G.; Huisken, F. Chem. Phys. Lett. 2005, 406, 386]. Our results indicate that the combination of strong localization and the quasi-one-dimensional nature of trios of helium atoms adsorbed along the long axis of tetracene leads to a quantum coherent, yet highly correlated ground state for the helium density closest to the molecule. The spectroscopic analysis shows that this feature accounts quantitatively for the anomalous splittings and hitherto unexplained fine structure observed in the absorption spectra of tetracene and suggests that it may be responsible for the corresponding zero-phonon splittings in other quasi-one-dimensional planar aromatic molecules.     

Molecular dynamics calculation of activation volumes

We propose a novel approach toward calculating activation and reaction volumes based on MD simulations of reaction systems. The accuracy of the calculated volumes, verified by the comparison to the experimental data, is suitable for quantitative analysis of the experimental volumes of activations in terms of structural parameters of the corresponding transition states.     

Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges

Absolute free energies of hydration have been computed for 13 diverse organic molecules using partial charges derived from ab initio 6-31G* wave functions. Both Mulliken charges and charges fit to the electrostatic potential surface (EPS) were considered in conjunction with OPLS Lennard–Jones parameters for the organic molecules and the TIP4P model of water. Monte Carlo simulations with statistical perturbation theory yielded relative free energies of hydration. These were converted to absolute quantities through perturbations to reference molecules for which absolute free energies of hydration had been obtained previously in TIP4P water. The average errors in the computed absolute free energies of hydration are 1.1 kcal/mol for the 6-31G* EPS charges and 4.0 kcal/mol for the Mulliken charges. For the EPS charges, the largest individual errors are under 2 kcal/mol except for acetamide, in which case the error is 3.7 kcal/mol. The hydrogen bonding between the organic solutes and water has also been characterized. © John Wiley & Sons, Inc.     

Simultaneous determination of estrogenic and androgenic hormones in water by isotope dilution gas chromatography-tandem mass spectrometry

A rapid gas chromatography-tandem mass spectrometry (GC-MS/MS) analytical method was developed for the simultaneous analysis of 7 estrogenic hormones (17α-estradiol, 17β-estradiol, estrone, mestranol, 17α-ethynylestradiol, levonorgestrel, estriol) and 5 androgenic hormones (testosterone, androsterone, etiocholanolone, dihydrotestosterone, androstenedione) in aqueous matrices. This method is unique in its inclusion of all 12 of these estrogens and androgens and is of particular value due to its very short chromatographic run time of 15 min. The use of isotope dilution for all analytes ensures the accurate quantification, accounting for analytical variabilities that may be introduced during sample processing and instrumental analysis. Direct isotopically labelled analogues were used for 8 of the 12 hormones and satisfactory isotope standards were identified for the remaining 4 hormones. Method detection levels (MDLs) were determined to describe analyte concentrations sufficient to provide a signal with 99% certainty of detection. The established MDLs for most analytes were 1-5 ngL(-1) in a variety of aqueous matrices. However, slightly higher MDLs were observed for etiocholanolone, androstenedione, testosterone, levonorgestrel and dihydrotestosterone in some aqueous matrices. Sample matrices were observed to have only a minor impact on MDLs and the method validation confirmed satisfactory method stability over intra-day and inter-day analyses of surface water and tertiary treated effluent samples.     

Determining the chromophore in the amylopectin–iodine complex by theoretical and experimental studies

A partial hydrolysis of amylose followed by the addition of iodine provides a spectrum almost identical to that of the amylopectin–iodine (API) complex suggesting the involvement of smaller “amylose-like” units in the API complex. Our theoretical studies on different polyiodine and polyiodide species suggest that a nearly linear I₄ unit stabilized within the cavity of a small “amylose-like” helix is responsible for the characteristic API spectrum. Since there are 2.75 anhydroglucose residues (AGU) for every iodine atom in the amylose–iodine (AI) complex and a structural similarity exists between the API and the AI (amylose–iodine) complexes, we identify (C₆H₁₀O₅)₁₁I₄ to be the chromophore in the API complex. © 1994 John Wiley & Sons, Inc.     

molSimplify: A toolkit for automating discovery in inorganic chemistry

We present an automated, open source toolkit for the first‐principles screening and discovery of new inorganic molecules and intermolecular complexes. Challenges remain in the automatic generation of candidate inorganic molecule structures due to the high variability in coordination and bonding, which we overcome through a divide‐and‐conquer tactic that flexibly combines force‐field preoptimization of organic fragments with alignment to first‐principles‐trained metal‐ligand distances. Exploration of chemical space is enabled through random generation of ligands and intermolecular complexes from large chemical databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from density functional theory (DFT), which are around 0.02 Ha/au across a large 150 molecule test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, preparation and execution of electronic structure calculations, and post‐processing for each generated structure aids interpretation of underlying chemical and energetic trends. © 2016 Wiley Periodicals, Inc.     

Modulation of fluorescence through coassembly of molecules in organic nanostructures

This paper describes the fluorescence of bimolecular coassemblies that form one-dimensional nanostructures. One molecule is a fluorescent peptide amphiphile containing its branched stilbene chromophore covalently linked to the hydrophilic end of the amphiphile, and the second molecule is a shorter, nonfluorescent peptide amphiphile of complementary charge. Using circular dichroism we observe that mixing both molecules results in coassemblies that exhibit a beta-sheet signature in the peptide region indicative of these types of nanostructures. The nature of the coassembly is dependent on the molar ratio of each component, and the changing CD spectra suggest the formation of domains along the length of the nanofibers with decreasing concentrations of the fluorescent component. In coassemblies with dilute concentrations of the fluorophore, we observe an increase in fluorescence intensity and quantum yield, as well as chiral transfer to the achiral segment of the fluorescent peptide amphiphile. The coassemblies studied containing a fluorescent component at a low molar ratio exhibit fluorescence resonance energy transfer to fluorescent acceptors in solution. When the nonfluorescent peptide amphiphile component is designed to bind the important bioactive polysaccharide heparin, a selective transfer of energy is observed between fluorescein-tagged heparin and the coassemblies in both dilute solution and in macroscopic gels.