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We consider several molecules characterised by π-electron conjugation whose extent changes along a flexible torsional coordinate, and which represent the monomer units of polymorphic molecular crystals. Delocalisation error in density functional theory (DFT) adversely impacts conformational energies in these species, overstabilising the conformation that maximises conjugation length and leading to incorrect relative energies for the corresponding crystal polymorphs. We demonstrate that density-corrected (DC-)DFT, in which a DFT exchange-correlation functional is evaluated using a Hartree–Fock density, significantly reduces these conformational energy errors. When DC-DFT monomer energies are used as a low-cost intramolecular correction to a periodic DFT calculation of the molecular crystal, the resulting relative polymorph energies are within 1 kJ/mol of benchmark results. [ABSTRACT FROM AUTHOR]

We report an implementation of periodic boundary conditions for mixed quantum mechanics/molecular mechanics (QM/MM) simulations, in which atomic partial charges are used to represent periodic images of the QM region. These charges are incorporated into the Fock matrix in a manner that preserves the variational nature of the self-consistent field procedure, and their interactions with the MM charges are summed using the conventional Ewald technique. To ensure that the procedure is stable in arbitrary basis sets, the atomic charges are derived by least-squares fit to the electrostatic potential generated by the QM region. We formulate and implement analytic energy gradients for the QM/MM-Ewald method and demonstrate that stable molecular dynamics simulations are thereby obtained. As a proof-of-concept application, we perform QM/MM simulations of a hydrated electron in bulk liquid water at the level of Hartree-Fock theory plus empirical dispersion. These simulations demonstrate that the "cavity model" of the aqueous electron, in which the spin density of the anionic defect is localized within an excluded volume in the liquid, is stable at room temperature on a time scale of at least several picoseconds. These results validate cavity-forming pseudopotential models of e−(aq) that have previously been derived from static-exchange Hartree-Fock calculations, and cast doubt upon whether non-cavity-forming pseudopotentials are faithful to the underlying Hartree-Fock calculation from which they were obtained. [ABSTRACT FROM AUTHOR]

Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming ultrafast diffraction experiment on the photodynamics of cyclobutanone after excitation to the lowest lying Rydberg state (S2). A picosecond of nonadiabatic dynamics is described with ab initio multiple spawning. We use both time dependent density functional theory (TDDFT) and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) theory for the underlying electronic structure theory. We find that the lifetime of the S2 state is more than a picosecond (with both TDDFT and EOM-CCSD). The predicted ultrafast electron diffraction spectrum exhibits numerous structural features, but weak time dependence over the course of the simulations. [ABSTRACT FROM AUTHOR]

Here we demonstrate, compare and contrast relaxation- and correlation-driven charge migration dynamics in halogen, chalcogen, pnicogen and tetrel bonded clusters, following their vertical ionization. For this work, we have selected different isolated A–X:NH 3 clusters, where A represents F, Cl, CN and NH 2 substituents and X features Cl, SH, PH 2 and SiH 3 to exhibit specific noncovalent bonding interaction. The charge migration dynamics in these clusters is studied using the density functional theory (DFT) with the wB97XD functional and the 6-31+G(d,p) basis set. Approximately 400–600 attosecond time scale is predicted for charge migration in (1:1) AX:NH 3 complexes. Effects of basis set and intermolecular distance on the ultrafast charge migration dynamics through the halogen, chalcogen, pnicogen, and tetrel bonded clusters are also discussed. This is the first report on pure relaxation- and correlation-driven charge migration dynamics in chalcogen, pnicogen and tetrel bonded clusters. [ABSTRACT FROM AUTHOR]

A 3-year-old patient in India experiencing headaches and seizures was diagnosed with a fungal infection, initially misidentified as Cladophialophora bantiana. Follow-up sequencing identified the isolate to be Fonsecaea monophora fungus. This case demonstrates the use of molecular methods for the correct identification of F. monophora, an agent of fungal brain abscess. [ABSTRACT FROM AUTHOR]

Background: Bronchoalveolar lavage (BAL) galactomannan (GM) is commonly used to diagnose Aspergillus‐related lung diseases. However, unlike serum GM, which is measured in undiluted blood, BAL‐GM is estimated using variable aliquots and cumulative volume of instillates during bronchoscopy. Objective: Since different studies have reported varying diagnostic accuracy and cut‐offs for BAL‐GM in CPA, we hypothesized that the total volume of instillate and ‘order/label’ of aliquots significantly affects the BAL‐GM values, which was evaluated as part of this study. Patients & Methods: We obtained 250 BAL samples from 50 patients (five from each) with suspected chronic pulmonary aspergillosis. BAL fluid was collected after instilling sequential volumes of 40 mL of normal saline each for the first four labels and a fifth label was prepared by mixing 1 mL from each of the previous labels. The GM level of each label was measured by PLATELIA™ ASPERGILLUS Ag enzyme immunoassay. This study measured the discordance, level of agreement, diagnostic characteristics (sensitivity, specificity and AUROC) and best cut‐offs for BAL‐GM in the different aliquots of lavage fluid. Results: The study population, classified into CPA (28%) and non‐CPA (72%) groups, based on ERS/ESCMID criteria (excluding BAL‐GM) were not different with respect to clinico‐radiological characteristics. The discordance of BAL‐GM positivity (using a cut‐off of >1) between the serial labels for the same patient ranged between 10% and 22%, while the discordance between classification using BAL‐GM positivity (using a cut‐off of ≥1) and clinic‐radio‐microbiological classification ranged between 18% and 30%. The level of agreement for serial labels was at best fair (<0.6 for all except one ‘label’). The AUROC for the serial samples ranged between 0.595 and 0.702, with the ‘40 mL and the ‘mix’ samples performing the best. The best BAL‐GM cut‐off also showed significant variation between serial labels of varying dilutions (Range:1.01 ‐ 4.26). Interpretation: This study highlights the variation in BAL‐GM measured and the ‘positivity’ between different ‘labels’ of aliquots of BAL, with the first aliquot and the mixed sample showing the best performances for diagnosis of CPA. Future studies should attempt to ‘standardise’ the instilled volume for BAL‐GM estimation to standardise the diagnostic yield. [ABSTRACT FROM AUTHOR]