The infuence of glycosidic linkage neighbors on disaccharide conformation in vacuum

Correct description of the free energy of conformation change of disaccharides is important in understanding a variety of biochemical processes and, ultimately, in the manufacture of better food and paper products. In this study, we determine the relative free energy of a series of 12 disaccharides in vacuum using replica exchange molecular dynamics (repMD) simulations. The chosen sugars and the novel application of this method allow the exploration of the role of glycosidic linkage neighbors in conformer stabilization. In line with expectations, we find that hydrogen bonding (and therefore energetically preferred conformations) are determined both by the nature of the glycosidic linkage (i.e., 1 f 2, 1 f 3, or 1 f 4), the C1 epimer of the of the nonreducing monosaccharide, and by the configuration of carbon atoms once removed from the glycosidic linkage. Contrary to suggestions by prior authors for repMD more generally, we also demonstrate that repMD provides enhanced sampling, relative to conventional MD simulations of equivalent length, for disaccharides in vacuum at 300 K.Fundação para a Ciência e a Tecnologia (FCT)SFRH/BPD/20555/2004/0GVLNational Science Foundation under Grant CHE-043132

Quantum mechanical calculation of aqueuous uranium complexes: carbonate, phosphate, organic and biomolecular species

<p>Abstract</p> <p>Background</p> <p>Quantum mechanical calculations were performed on a variety of uranium species representing U(VI), U(V), U(IV), U-carbonates, U-phosphates, U-oxalates, U-catecholates, U-phosphodiesters, U-phosphorylated N-acetyl-glucosamine (NAG), and U-2-Keto-3-doxyoctanoate (KDO) with explicit solvation by H₂O molecules. These models represent major U species in natural waters and complexes on bacterial surfaces. The model results are compared to observed EXAFS, IR, Raman and NMR spectra.</p> <p>Results</p> <p>Agreement between experiment and theory is acceptable in most cases, and the reasons for discrepancies are discussed. Calculated Gibbs free energies are used to constrain which configurations are most likely to be stable under circumneutral pH conditions. Reduction of U(VI) to U(IV) is examined for the U-carbonate and U-catechol complexes.</p> <p>Conclusion</p> <p>Results on the potential energy differences between U(V)- and U(IV)-carbonate complexes suggest that the cause of slower disproportionation in this system is electrostatic repulsion between UO₂[CO₃]₃^5-ions that must approach one another to form U(VI) and U(IV) rather than a change in thermodynamic stability. Calculations on U-catechol species are consistent with the observation that UO₂²⁺can oxidize catechol and form quinone-like species. In addition, outer-sphere complexation is predicted to be the most stable for U-catechol interactions based on calculated energies and comparison to ¹³C NMR spectra. Outer-sphere complexes (i.e., ion pairs bridged by water molecules) are predicted to be comparable in Gibbs free energy to inner-sphere complexes for a model carboxylic acid. Complexation of uranyl to phosphorus-containing groups in extracellular polymeric substances is predicted to favor phosphonate groups, such as that found in phosphorylated NAG, rather than phosphodiesters, such as those in nucleic acids.</p

Periodic density functional theory calculations of bulk and the (010) surface of goethite

<p>Abstract</p> <p>Background</p> <p>Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna <it>Ab Initio </it>Simulation Package (VASP).</p> <p>Results</p> <p>Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H₂O layer) and solvated (three H₂O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H₂O showed a significantly lower potential energy for the former.</p> <p>Conclusion</p> <p>Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H₂O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces.</p

The Center for Environmental Kinetics Analysis: an NSF- and DOE-funded Environmental Molecular Science Institute (EMSI) at Penn State

Physicochemical and microbiological processes taking place at environmental interfaces influence natural processes as well as the transport and fate of environmental contaminants, the remediation of toxic chemicals, and the sequestration of anthropogenic CO2. A team of scientists and engineers has been assembled to develop and apply new experimental and computational techniques to expand our knowledge of environmental kinetics. We are also training a cohort of talented and diverse students to work on these complex problems at multiple length scales and to compile and synthesize the kinetic data. Development of the human resources capable of translating molecular-scale information into parameters that are applicable in real world, field-scale problems of environmental kinetics is a major and relatively unique objective of the Institute's efforts. The EMSI team is a partnership among 10 faculty at The Pennsylvania State University (funded by the National Science Foundation Divisions of Chemistry and Earth Sciences), one faculty member at Juniata College, one faculty member at the University of Florida, and four researchers drawn from Los Alamos National Laboratory, Pacific Northwest National Laboratory, and Lawrence Berkeley National Laboratory (funded by the Department of Energy Division of Environmental Remediation Sciences). Interactions among the applied and academic scientists drives research approaches aimed toward solving important problems of national interest. The Institute is organized into three interest groups (IGs) focusing on the processes of dissolution (DIG), precipitation (PIG), and microbial reactions at surfaces (BIG). Some of the research activity from each IG is highlighted to the right. The IGs interact with each other as each interest group studies reactions across the molecular, microscopic, mesoscopic and, in most cases, field scales. For example, abiotic dissolution and precipitation reactions of Fe oxides as studied in the Dissolution IG provides the baseline for kinetic behavior as the BIG researches the interaction of microorganisms with these same minerals. The attachment of bacteria and redox chemistry that occurs between microorganisms and minerals are critical factors in maintaining groundwater quality and remediation of many toxic waste sites and is one of the main thrusts of research within our EMSI. The IGs also participate in using visualization tools to promote greater understanding of complex environmental data. As a whole, CEKA is also working to compile environmental kinetics data into a cyberinfrastructure and database. The database can be accessed at: http://keystone.ist.psu.edu/

Improving the predictive potential of diffusion MRI in schizophrenia using normative models-Towards subject-level classification.

Diffusion MRI studies consistently report group differences in white matter between individuals diagnosed with schizophrenia and healthy controls. Nevertheless, the abnormalities found at the group-level are often not observed at the individual level. Among the different approaches aiming to study white matter abnormalities at the subject level, normative modeling analysis takes a step towards subject-level predictions by identifying affected brain locations in individual subjects based on extreme deviations from a normative range. Here, we leveraged a large harmonized diffusion MRI dataset from 512 healthy controls and 601 individuals diagnosed with schizophrenia, to study whether normative modeling can improve subject-level predictions from a binary classifier. To this aim, individual deviations from a normative model of standard (fractional anisotropy) and advanced (free-water) dMRI measures, were calculated by means of age and sex-adjusted z-scores relative to control data, in 18 white matter regions. Even though larger effect sizes are found when testing for group differences in z-scores than are found with raw values (p < .001), predictions based on summary z-score measures achieved low predictive power (AUC < 0.63). Instead, we find that combining information from the different white matter tracts, while using multiple imaging measures simultaneously, improves prediction performance (the best predictor achieved AUC = 0.726). Our findings suggest that extreme deviations from a normative model are not optimal features for prediction. However, including the complete distribution of deviations across multiple imaging measures improves prediction, and could aid in subject-level classification

Quantum Mechanical Modeling of the Vibrational Spectra of Minerals with a Focus on Clays

We present an overview of how to use quantum mechanical calculations to predict vibrational frequencies of molecules and materials such as clays and silicates. Other methods of estimating vibrational frequencies are mentioned, such as classical molecular dynamics simulations; references are given for additional information on these approaches. Herein, we discuss basic vibrational theory, calculating Raman and infrared intensities, steps for creating realistic models, and applications to spectroscopy, thermodynamics, and isotopic fractionation. There are a wide variety of programs and methods that can be employed to model vibrational spectra, but this work focuses on hybrid density functional theory (DFT) approaches. Many of the principles are the same when used in other programs and DFT methods, so a novice can benefit from simple examples that illustrate key points to consider when modeling vibrational spectra. Other methods and programs are listed to give the beginner a starting point for exploring and choosing which approach will be best for a given problem. The modeler should also be aware of the numerous analytical methods available for obtaining information on vibrations of atoms in molecules and materials. In addition to traditional infrared and Raman spectroscopy, sum-frequency generation (SFG) and inelastic neutron scattering (INS) are also excellent techniques for obtaining vibrational frequency information in certain circumstances

Integrating Density Functional Theory Modeling with Experimental Data to Understand and Predict Sorption Reactions: Exchange of Salicylate for Phosphate on Goethite

Density functional theory (DFT) calculations are a quantum mechanical approach that can be used to model chemical reactions on an atomistic scale. DFT provides predictions on structures, thermodynamics, spectroscopic parameters and kinetics that can be compared against experimentally determined data. This paper is a primer on the basics of utilizing DFT for applications in mineral-water interfaces. In our case-study, we use DFT to model the surface complexes of phosphate and salicylate adsorbed onto the (101) and (210) surfaces of &alpha;-FeOOH (goethite), as an example of combining DFT and experiment. These three components are important in the phosphorus-organic matter interactions in soils, and by comparing the energies of the two surface complexes, the exchange energy of salicylate for phosphate onto goethite can be estimated. The structures of the surface complexes are predicted and the resulting vibrational frequencies calculated based on these structures are compared to previous observations. Upon verification of reasonable surface complex models, the potential energy of exchanging salicylate for phosphate is calculated and shown to be significantly exothermic. This model result is consistent with observations of plant exudates, such as salicylate freeing adsorbed phosphate in soils under P-limited conditions

Molecular models of benzene and selected polycyclic aromatic hydrocarbons in the aqueous and adsorbed states

Energy gaps between the highest-occupied molecular orbital and lowest-unoccupied molecular orbital (ΔE_(HOMO-LUMO)) for a suite of common polycyclic aromatic hydrocarbons (PAHs) in the gas-phase were calculated with three different molecular modeling methods: semiempirical, ab initio Hartree-Fock, and density functional calculations. Results indicate that semiempirical, Hartree-Fock, and density functional calculations may provide useful relative HOMO-LUMO gap information, but these methods overestimate the actual ΔE_(HOMO-LUMO). Based on vibrational frequency analyses, density functional calculations reliably produce dynamically stable structures that can be used to predict model ΔE_(HOMO-LUMO) values. Both the semiempirical and ab initio Hartree-Fock methods were unreliable in predicting dynamically stable structures; hence prediction of ΔE_(HOMO-LUMO) values was not possible for several PAHs. Changes in the HOMO-LUMO gap of benzene and selected PAHs due to solvation effects were calculated using self-consistent reaction field methods and explicit solvation. Self-consistent isodensity polarized continuum model calculations modeling water and octanol solvation do not change calculated ΔEHOMO-LUMO values enough to affect predicted phototoxicities; thus, gas-phase values may be used for PAHs in solution and in vivo. Energetics of PAH bonding to mineral surface groups were also modeled. In some cases, interaction of PAHs with model aluminate surface defects suggests that ΔE_(HOMO-LUMO) values may be lowered significantly by adsorption that would lower chemical stabilities. Significant increases in calculated ΔE_(HOMO-LUMO) that would increase chemical stability of the compounds were not predicted