Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules.

A detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and water clusters is presented. Recent work questioning the applicability of Kohn-Sham density-functional theory to proteins and large water clusters (E. Rudberg, J. Phys.: Condens. Mat. 2012, 24, 072202) has demonstrated vanishing HOMO-LUMO gaps for these systems, which is generally attributed to the treatment of exchange in the functional used. The present work shows that the vanishing gap is, in fact, an electrostatic artefact of the method used to prepare the system. Practical solutions for ensuring the gap is maintained when the system size is increased are demonstrated. This work has important implications for the use of large-scale density-functional theory in biomolecular systems, particularly in the simulation of photoemission, optical absorption and electronic transport, all of which depend critically on differences between energies of molecular orbitals.Comment: 13 pages, 4 figure

Significance testing testate amoeba water table reconstructions

Transfer functions are valuable tools in palaeoecology, but their output may not always be meaningful. A recently-developed statistical test ('randomTF') offers the potential to distinguish among reconstructions which are more likely to be useful, and those less so. We applied this test to a large number of reconstructions of peatland water table depth based on testate amoebae. Contrary to our expectations, a substantial majority (25 of 30) of these reconstructions gave non-significant results (P > 0.05). The underlying reasons for this outcome are unclear. We found no significant correlation between randomTF P-value and transfer function performance, the properties of the training set and reconstruction, or measures of transfer function fit. These results give cause for concern but we believe it would be extremely premature to discount the results of non-significant reconstructions. We stress the need for more critical assessment of transfer function output, replication of results and ecologically-informed interpretation of palaeoecological data

Viral forensic genomics reveals the relatedness of classic herpes simplex virus strains KOS, KOS63, and KOS79

Herpes simplex virus 1 (HSV-1) is a widespread global pathogen, of which the strain KOS is one of the most extensively studied. Previous sequence studies revealed that KOS does not cluster with other strains of North American geographic origin, but instead clustered with Asian strains. We sequenced a historical isolate of the original KOS strain, called KOS63, along with a separately isolated strain attributed to the same source individual, termed KOS79. Genomic analyses revealed that KOS63 closely resembled other recently sequenced isolates of KOS and was of Asian origin, but that KOS79 was a genetically unrelated strain that clustered in genetic distance analyses with HSV-1 strains of North American/European origin. These data suggest that the human source of KOS63 and KOS79 could have been infected with two genetically unrelated strains of disparate geographic origins. A PCR RFLP test was developed for rapid identification of these strains

Role of lattice distortion and A site cation in the phase transitions of methylammonium lead halide perovskites

The rapid increase in power conversion efficiencies of photovoltaic devices incorporating lead halide perovskites has resulted in intense interest in the cause of their excellent properties. In the present paper, resonant ultrasound spectroscopy has been used to determine the elastic and anelastic properties of CH3NH3PbX3(where X=Cl, Br, or I) and CD3ND3PbI3 perovskites in the 5–380 K temperature range. This is coupled with differential scanning calorimetry, variable temperature neutron powder diffraction, and variable temperature photoluminescence studies to provide insights into the underlying processes and structural instabilities in the crystal structure. By comparing measurements on CH3NH3PbI3 with the deuterated equivalent, it has been possible to distinguish processes which are related to the hydrogen bonding between the methylammonium cation and the perovskite framework. We observe that replacing hydrogen with deuterium has a significant impact on both the elastic and photophysical properties, which shows that hydrogen bonding plays a crucial role in the material performance. Temperature-dependent photoluminescence studies show that the light emission is unaffected by the tetragonal-orthorhombic phase transition, but a blueshift in the emission and a steep increase in photoluminescence quantum yield are seen at temperatures below 150 K. Finally, observations of peaks in acoustic loss occurring in CH3NH3PbCl3 have revealed freezing processes in the vicinity of ∼150−170K, with activation energies in the range of 300 to 650 meV. These processes are attributed to freezing of the motion of methylammonium cations, and could explain the changes in photoluminescence seen in CH3NH3PbI3 at the same temperature. © 2018 American Physical Society. This work has been made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at: https://doi.org/10.1103/PhysRevMaterials.2.06540

Role of lattice distortion and A site cation in the phase transitions of methylammonium lead halide perovskites

The rapid increase in power conversion efficiencies of photovoltaic devices incorporating lead halide perovskites has resulted in intense interest in the cause of their excellent properties. In the present paper, resonant ultrasound spectroscopy has been used to determine the elastic and anelastic properties of CH3NH3PbX3 (where X=Cl, Br, or I) and CD3ND3PbI3 perovskites in the 5–380 K temperature range. This is coupled with differential scanning calorimetry, variable temperature neutron powder diffraction, and variable temperature photoluminescence studies to provide insights into the underlying processes and structural instabilities in the crystal structure. By comparing measurements on CH3NH3PbI3 with the deuterated equivalent, it has been possible to distinguish processes which are related to the hydrogen bonding between the methylammonium cation and the perovskite framework. We observe that replacing hydrogen with deuterium has a significant impact on both the elastic and photophysical properties, which shows that hydrogen bonding plays a crucial role in the material performance. Temperature-dependent photoluminescence studies show that the light emission is unaffected by the tetragonal-orthorhombic phase transition, but a blueshift in the emission and a steep increase in photoluminescence quantum yield are seen at temperatures below 150 K. Finally, observations of peaks in acoustic loss occurring in CH3NH3PbCl3 have revealed freezing processes in the vicinity of ∼150−170K, with activation energies in the range of 300 to 650 meV. These processes are attributed to freezing of the motion of methylammonium cations, and could explain the changes in photoluminescence seen in CH3NH3PbI3 at the same temperature

Household Transmission of Rotavirus in a Community with Rotavirus Vaccination in Quininde, Ecuador

Background: We studied the transmission of rotavirus infection in households in peri-urban Ecuador in the vaccination era. Methods: Stool samples were collected from household contacts of child rotavirus cases, diarrhea controls and healthy controls following presentation of the index child to health facilities. Rotavirus infection status of contacts was determined by RT-qPCR. We examined factors associated with transmissibility (index-case characteristics) and susceptibility (householdcontact characteristics). Results: Amongst cases, diarrhea controls and healthy control household contacts, infection attack rates (iAR) were 55%, 8% and 2%, (n = 137, 130, 137) respectively. iARs were higher from index cases with vomiting, and amongst siblings. Disease ARs were higher when the index child was ,18 months and had vomiting, with household contact ,10 years and those sharing a room with the index case being more susceptible. We found no evidence of asymptomatic infections leading to disease transmission. Conclusion: Transmission rates of rotavirus are high in households with an infected child, while background infections are rare. We have identified factors associated with transmission (vomiting/young age of index case) and susceptibility (young age/sharing a room/being a sibling of the index case). Vaccination may lead to indirect benefits by averting episodes or reducing symptoms in vaccinees

Pushing property limits in materials discovery via boundless objective-free exploration

Materials chemists develop chemical compounds to meet often conflicting demands of industrial applications. This process may not be properly modeled by black-box optimization because the target property is not well defined in some cases. Herein, we propose a new algorithm for automated materials discovery called BoundLess Objective-free eXploration (BLOX) that uses a novel criterion based on kernel-based Stein discrepancy in the property space. Unlike other objective-free exploration methods, a boundary for the materials properties is not needed; hence, BLOX is suitable for open-ended scientific endeavors. We demonstrate the effectiveness of BLOX by finding light-absorbing molecules from a drug database. Our goal is to minimize the number of density functional theory calculations required to discover out-of-trend compounds in the intensity–wavelength property space. Using absorption spectroscopy, we experimentally verified that eight compounds identified as outstanding exhibit the expected optical properties. Our results show that BLOX is useful for chemical repurposing, and we expect this search method to have numerous applications in various scientific disciplines

Estimation of Enantiomeric Excess Based on Rapid Host–Guest Exchange

Chiral molecules possess enantiomers that have non-superimposable chemical structures but exhibit identical nuclear magnetic resonance (NMR) spectra. This feature prevents the use of NMR spectroscopic methods for the determination of enantiomeric excesses (ee) of chiral molecules, using simple mixtures of their enantiomers. Recently, however, it was reported that the addition of a symmetrical prochiral molecule (a reporter or host) into a solution of chiral analyte can lead to estimation of ee through interactions involving rapid exchange of the chiral analyte (guest) in the formed host–guest complex. This is due to the ee-dependent splitting of NMR resonances of the prochiral host molecule based on averaging the chemical shift non-equivalency caused by the presence of a chiral guest. The mechanism is not dependent on diastereomer formation, and 1:1 host–guest complexes can also show ee-dependent NMR peak splitting. Prochiral molecules capable of ee sensing using the NMR technique are now referred to as so-called prochiral solvating agents (pro-CSAs). pro-CSAs represent a family of reagents distinct from the commonly used NMR chiral derivatizing reagents (where chiral auxiliaries are used to derivatize enantiomers to diastereomers) or chiral solvating agents (where chiral auxiliaries interact in an asymmetric manner with analyte enantiomers). pro-CSA methods are unique since neither pro-CSA nor NMR contains chiral factors, making the technique neutral with respect to chirality. Here, we review our recent work on this matter involving several different nominally achiral receptor molecules whose unique guest binding properties and solution characteristics (especially with regard to NMR spectroscopy) allow for the estimation of ee in the corresponding chiral guests

Transiting Disintegrating Planetary Debris around WD 1145+017

More than a decade after astronomers realized that disrupted planetary material likely pollutes the surfaces of many white dwarf stars, the discovery of transiting debris orbiting the white dwarf WD 1145+017 has opened the door to new explorations of this process. We describe the observational evidence for transiting planetary material and the current theoretical understanding (and in some cases lack thereof) of the phenomenon.Comment: Invited review chapter. Accepted March 23, 2017 and published October 7, 2017 in the Handbook of Exoplanets. 15 pages, 10 figure