On the structure of Si(100) surface: importance of higher order correlations for buckled dimer.
ABSTRACT: We revisit a dangling theoretical question of whether the surface reconstruction of the Si(100) surface would energetically favor the symmetric or buckled dimers on the intrinsic potential energy surfaces at 0 K. This seemingly simple question is still unanswered definitively since all existing density functional based calculations predict the dimers to be buckled, while most wavefunction based correlated treatments prefer the symmetric configurations. Here, we use the doubly hybrid density functional (DHDF) geometry optimizations, in particular, XYGJ-OS, complete active space self-consistent field theory, multi-reference perturbation theory, multi-reference configuration interaction (MRCI), MRCI with the Davidson correction (MRCI + Q), multi-reference average quadratic CC (MRAQCC), and multi-reference average coupled pair functional (MRACPF) methods to address this question. The symmetric dimers are still shown to be lower in energy than the buckled dimers when using the CASPT2 method on the DHDF optimized geometries, consistent with the previous results using B3LYP geometries [Y. Jung, Y. Shao, M. S. Gordon, D. J. Doren, and M. Head-Gordon, J. Chem. Phys. 119, 10917 (2003)]. Interestingly, however, the MRCI + Q, MRAQCC, and MRACPF results (which give a more refined description of electron correlation effects) suggest that the buckled dimer is marginally more stable than its symmetric counterpart. The present study underlines the significance of having an accurate description of the electron-electron correlation as well as proper multi-reference wave functions when exploring the extremely delicate potential energy surfaces of the reconstructed Si(100) surface.
Project description:It has been a long-standing puzzle why buckled dimers of the Si(001) surface appeared symmetric below ~20?K in scanning tunneling microscopy (STM) experiments. Although such symmetric dimer images were concluded to be due to an artifact induced by STM measurements, its underlying mechanism is still veiled. Here, we demonstrate, based on a first-principles density-functional theory calculation, that the symmetric dimer images are originated from the flip-flop motion of buckled dimers, driven by quantum tunneling (QT). It is revealed that at low temperature the tunneling-induced surface charging with holes reduces the energy barrier for the flipping of buckled dimers, thereby giving rise to a sizable QT-driven frequency of the flip-flop motion. However, such a QT phenomenon becomes marginal in the tunneling-induced surface charging with electrons. Our findings provide an explanation for low-temperature STM data that exhibits apparent symmetric (buckled) dimer structure in the filled-state (empty-state) images.
Project description:Halogen bonding is the noncovalent interaction of halogen atoms in which they act as electron acceptors. Whereas three-center hydrogen bond complexes, [D···H···D]+ where D is an electron donor, exist in solution as rapidly equilibrating asymmetric species, the analogous halogen bonds, [D···X···D]+, have been observed so far only to adopt static and symmetric geometries. Herein, we investigate whether halogen bond asymmetry, i.e., a [D-X···D]+ bond geometry, in which one of the D-X bonds is shorter and stronger, could be induced by modulation of electronic or steric factors. We have also attempted to convert a static three-center halogen bond complex into a mixture of rapidly exchanging asymmetric isomers, [D···X-D]+ ? [D-X···D]+, corresponding to the preferred form of the analogous hydrogen bonded complexes. Using 15N NMR, IPE NMR, and DFT, we prove that a static, asymmetric geometry, [D-X···D]+, is obtained upon desymmetrization of the electron density of a complex. We demonstrate computationally that conversion into a dynamic mixture of asymmetric geometries, [D···X-D]+ ? [D-X···D]+, is achievable upon increasing the donor-donor distance. However, due to the high energetic gain upon formation of the three-center-four-electron halogen bond, the assessed complex strongly prefers to form a dimer with two static and symmetric three-center halogen bonds over a dynamic and asymmetric halogen bonded form. Our observations indicate a vastly different preference in the secondary bonding of H+ and X+. Understanding the consequences of electronic and steric influences on the strength and geometry of the three-center halogen bond provides useful knowledge on chemical bonding and for the development of improved halonium transfer agents.
Project description:The partitioning of lipids among different microenvironments in a bilayer is of considerable relevance to characterization of composition variations in biomembranes. Atomistic simulation has been ill-suited to model equilibrated lipid mixtures because the time required for diffusive exchange of lipids among microenvironments exceeds typical submicrosecond molecular dynamics trajectories. A method to facilitate local composition fluctuations, using Monte Carlo mutations to change lipid structures within the semigrand-canonical ensemble (at a fixed difference in component chemical potentials, Deltamu), was recently implemented to address this challenge. This technique was applied here to mixtures of dimyristoylphosphatidylcholine and a shorter-tail lipid, either symmetric (didecanoylphosphatidylcholine (DDPC)) or asymmetric (hexanoyl-myristoylphosphatidylcholine), arranged in two types of structure: bilayer ribbons and buckled bilayers. In ribbons, the shorter-tail component showed a clear enrichment at the highly curved rim, more so for hexanoyl-myristoylphosphatidylcholine than for DDPC. Results on buckled bilayers were variable. Overall, the DDPC content of buckled bilayers tended to exceed by several percent the DDPC content of flat ones simulated at the same Deltamu, but only for mixtures with low overall DDPC content. Within the buckled bilayer structure, no correlation could be resolved between the sign or magnitude of the local curvature of a leaflet and the mean local lipid composition. Results are discussed in terms of packing constraints, surface area/volume ratios, and curvature elasticity.
Project description:The possibility of carbon tetravalence in geometries other than tetrahedral and of carbon hypervalence has been taken seriously since the 1970s. Computational modeling and subsequent experimental validation have established the existence of molecules with carbon atoms with planar tetravalence and as many as six objects in carbon's coordination sphere. In this work, we develop insight into the nature of bonding to carbon in these unusual environs as provided by Bader's Atoms in Molecules (AIM) analysis of the electron density, along with the electron localization function (ELF) and the non-covalent index (NCI). We review several well-established systems (spiropentadiene dication, hexamethyl benzene dication, dimethanospiro[2.2]octaplane dication, and 1,8-dimethoxy-9-dimethoxyanthracene cation) and propose new D2d-symmetric variants of a hexacoordinated species.
Project description:To adapt and automate the medication regimen complexity index (MRCI) within the structure of a commercial medication database in the post-acute home care setting.In phase 1, medication data from 89 645 electronic health records were abstracted to line up with the components of the MRCI: dosage form, dosing frequency, and additional administrative directions. A committee reviewed output to assign index weights and determine necessary adaptations. In phase 2 we examined the face validity of the modified MRCI through analysis of automatic tabulations and descriptive statistics.The mean number of medications per patient record was 7.6 (SD 3.8); mean MRCI score was 16.1 (SD 9.0). The number of medications and MRCI were highly associated, but there was a wide range of MRCI scores for each number of medications. Most patients (55%) were taking only oral medications in tablet/capsule form, although 16% had regimens with three or more medications with different routes/forms. The biggest contributor to the MRCI score was dosing frequency (mean 11.9). Over 36% of patients needed to remember two or more special instructions (eg, take on alternate days, dissolve).Medication complexity can be tabulated through an automated process with some adaptation for local organizational systems. The MRCI provides a more nuanced way of measuring and assessing complexity than a simple medication count.An automated MRCI may help to identify patients who are at higher risk of adverse events, and could potentially be used in research and clinical decision support to improve medication management and patient outcomes.
Project description:The gating ring of cyclic nucleotide-modulated channels is proposed to be either a two-fold symmetric dimer of dimers or a four-fold symmetric tetramer based on high-resolution structure data of soluble cyclic nucleotide-binding domains and functional data on intact channels. We addressed this controversy by obtaining structural data on an intact, full-length, cyclic nucleotide-modulated potassium channel, MloK1, from Mesorhizobium loti, which also features a putative voltage-sensor. We present here the 3D single-particle structure by transmission electron microscopy and the projection map of membrane-reconstituted 2D crystals of MloK1 in the presence of cAMP. Our data show a four-fold symmetric arrangement of the CNBDs, separated by discrete gaps. A homology model for full-length MloK1 suggests a vertical orientation for the CNBDs. The 2D crystal packing in the membrane-embedded state is compatible with the S1-S4 domains in the vertical "up" state.
Project description:The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.
Project description:We report the modulation of emission energy, exciton dynamics and lasing properties in a single buckled CdS nanoribbon (NR) by strain-engineering. Inspired by ordered structure fabrication on elastomeric polymer, we develop a new method to fabricate uniform buckled NRs supported on polydimethylsiloxane (PDMS). Wavy structure, of which compressive and tensile strain periodically varied along the CdS NR, leads to a position-dependent emission energy shift as large as 14?nm in photoluminescence (PL) mapping. Both micro-PL and micro-reflectance reveal the spectral characteristics of broad emission of buckled NR, which can be understood by the discrepancy of strain-induced energy shift of A- and B-exciton of CdS. Furthermore, the dynamics of excitons under tensile strain are also investigated; we find that the B-exciton have much shorter lifetime than that of redshifted A-exciton. In addition, we also present the lasing of buckled CdS NRs, in which the strain-dominated mode selection in multi-mode laser and negligible mode shifts in single-mode laser are clearly observed. Our results show that the strained NRs may serve as new functional optical elements for flexible light emitter or on-chip all-optical devices.
Project description:BACKGROUND: The Medication Regimen Complexity Index (MRCI) is a 65-item instrument that can be used to quantify medication regimen complexity at the patient level, capturing all prescribed and over-the-counter medications. Although the MRCI has been used in several studies, the narrow scope of the initial validation limits application at a population or clinical practice level. PURPOSE: To conduct a MRCI validation pertinent to the desired clinical use to identify patients for medication therapy management interventions. METHODS: An expert panel of clinical pharmacists ranked medication regimen complexity for two samples of cases: a single-disease cohort (diabetes mellitus) and a multiple-disease cohort (diabetes mellitus, hypertension, human immunodeficiency virus infection, geriatric depression). Cases for expert panel review were selected from 400 ambulatory clinic patients, and each case description included data that were available via claims or electronic medical records (EMRs). Construct validity was assessed using patient-level MRCI scores, medication count, and additional patient data. Concordance was evaluated using weighted ? agreement statistic, and correlations were determined using Spearman rank-order correlation coefficient (?) or Kendall ?. RESULTS: Moderate to good concordance between patient-level MRCI scores and expert medication regimen complexity ranking was observed (claims data, consensus ranking: single-disease cohort 0.55, multiple disease cohort 0.63). In contrast, only fair to moderate concordance was observed for medication count (single-disease cohort 0.33, multiple-disease cohort 0.48). Adding more-detailed administration directions from EMR data did not improve concordance. MRCI convergent validity was supported by strong correlations with medication count (all cohorts 0.90) and moderate correlations with morbidity measures (e.g., all cohorts; number of comorbidities 0.46, Chronic Disease Score 0.46). Nonsignificant correlation of MRCI scores with age and gender (all cohorts 0.08 and 0.06, respectively) supported MRCI divergent validity. LIMITATIONS: This study used cross-sectional, retrospective patient data for a small number of patients and clinical pharmacists from only two universities; therefore, results may have limited generalizability. CONCLUSIONS: The patient-level MRCI is a valid tool for assessing medication regimen complexity that can be applied by using data commonly found in claims and EMR databases and could be useful to identify patients who may benefit from medication therapy management.
Project description:Diffraction-limited optical microscopy lacks the resolution to directly characterize nanoscale features of single nanoparticles. This paper describes how structural features of gold nanostars can be identified using differential interference contrast (DIC) microscopy. First, we established structure-property relationships between categories of nanoparticle shapes and DIC optical images and then validated the correlation with electrodynamic simulations and electron microscopy. We found that DIC image patterns of single nanostars could be differentiated between 2D and 3D geometries. DIC images were also used to distinguish asymmetric and 4-fold symmetric structures and track nanoparticle orientation. Finally, we demonstrated how this wide-field optical technique can be used for in situ characterization of single nanoparticles rotating at a glass-water interface.