277 research outputs found
Time-dependent density functional theory calculation of van der Waals coefficient of sodium clusters
In this paper we employ all-electron \textit{ab-initio} time-dependent
density functional theory based method to calculate the long range
dipole-dipole dispersion coefficient (van der Waals coefficient) of
sodium atom clusters containing even number of atoms ranging from 2 to 20
atoms. The dispersion coefficients are obtained via Casimir-Polder relation.
The calculations are carried out with two different exchange-correlation
potentials: (i) the asymptotically correct statistical average of orbital
potential (SAOP) and (ii) Vosko-Wilk-Nusair representation of
exchange-correlation potential within local density approximation. A comparison
with the other theoretical results has been performed. We also present the
results for the static polarizabilities of sodium clusters and also compare
them with other theoretical and experimental results. These comparisons reveal
that the SAOP results for C_{6} and static polarizability are quite accurate
and very close to the experimental results. We examine the relationship between
volume of the cluster and van der Waals coefficient and find that to a very
high degree of correlation C_{6} scales as square of the volume. We also
present the results for van der Waals coefficient corresponding to cluster-Ar
atom and cluster-N_{2} molecule interactions.Comment: 22 pages including 6 figures. To be published in Journal of Chemical
Physic
Calculation of valence electron momentum densities using the projector augmented-wave method
We present valence electron Compton profiles calculated within the
density-functional theory using the all-electron full-potential projector
augmented-wave method (PAW). Our results for covalent (Si), metallic (Li, Al)
and hydrogen-bonded ((H_2O)_2) systems agree well with experiments and
computational results obtained with other band-structure and basis set schemes.
The PAW basis set describes the high-momentum Fourier components of the valence
wave functions accurately when compared with other basis set schemes and
previous all-electron calculations.Comment: Submitted to Journal of Physics and Chemistry of Solids on September
17 2004. Revised version submitted on December 13 200
Network equilibration and first-principles liquid water.
Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD), following the Born-Oppenheimer forces obtained from density-functional theory (DFT). The linear-scaling capability of our method allows the consideration of larger system sizes (up to 128 molecules in this study), even if the main emphasis of this work is in the time scale. We obtain diffusivities that are substantially lower than the experimental values, in agreement with recent findings using similar methods. A fairly good agreement with D(T) experiments is obtained if the simulation temperature is scaled down by approximately 20%. It is still an open question whether the deviation is due to the limited accuracy of present density functionals or to quantum fluctuations, but neither technical approximations (basis set, localization for linear scaling) nor the system size (down to 32 molecules) deteriorate the DFT description in an appreciable way. We find that the need for long equilibration times is consequence of the slow process of rearranging the H-bond network (at least 20 ps at AIMDs room temperature). The diffusivity is observed to be very directly linked to network imperfection. This link does not appear an artifact of the simulations, but a genuine property of liquid water
SCN1A variants from bench to bedside-improved clinical prediction from functional characterization
Variants in the SCN1A gene are associated with a wide range of disorders including genetic epilepsy with febrile seizures plus (GEFS+), familial hemiplegic migraine (FHM), and the severe childhood epilepsy Dravet syndrome (DS). Predicting disease outcomes based on variant type remains challenging. Despite thousands of SCN1A variants being reported, only a minority has been functionally assessed.
We review the functional SCN1A work performed to date, critically appraise electrophysiological measurements, compare this to in silico predictions, and relate our findings to the clinical phenotype.
Our results show, regardless of the underlying phenotype, that conventional in silico software correctly predicted benign from pathogenic variants in nearly 90%, however was unable to differentiate within the disease spectrum (DS vs. GEFS+ vs. FHM). In contrast, patch‐clamp data from mammalian expression systems revealed functional differences among missense variants allowing discrimination between disease severities. Those presenting with milder phenotypes retained a degree of channel function measured as residual whole‐cell current, whereas those without any whole‐cell current were often associated with DS (p = .024).
These findings demonstrate that electrophysiological data from mammalian expression systems can serve as useful disease biomarker when evaluating SCN1A variants, particularly in view of new and emerging treatment options in DS
A new approach to local hardness
The applicability of the local hardness as defined by the derivative of the
chemical potential with respect to the electron density is undermined by an
essential ambiguity arising from this definition. Further, the local quantity
defined in this way does not integrate to the (global) hardness - in contrast
with the local softness, which integrates to the softness. It has also been
shown recently that with the conventional formulae, the largest values of local
hardness do not necessarily correspond to the hardest regions of a molecule.
Here, in an attempt to fix these drawbacks, we propose a new approach to define
and evaluate the local hardness. We define a local chemical potential,
utilizing the fact that the chemical potential emerges as the additive constant
term in the number-conserving functional derivative of the energy density
functional. Then, differentiation of this local chemical potential with respect
to the number of electrons leads to a local hardness that integrates to the
hardness, and possesses a favourable property; namely, within any given
electron system, it is in a local inverse relation with the Fukui function,
which is known to be a proper indicator of local softness in the case of soft
systems. Numerical tests for a few selected molecules and a detailed analysis,
comparing the new definition of local hardness with the previous ones, show
promising results.Comment: 30 pages (including 6 figures, 1 table
Work functions, ionization potentials, and in-between: Scaling relations based on the image charge model
We revisit a model in which the ionization energy of a metal particle is
associated with the work done by the image charge force in moving the electron
from infinity to a small cut-off distance just outside the surface. We show
that this model can be compactly, and productively, employed to study the size
dependence of electron removal energies over the range encompassing bulk
surfaces, finite clusters, and individual atoms. It accounts in a
straightforward manner for the empirically known correlation between the atomic
ionization potential (IP) and the metal work function (WF), IP/WF2. We
formulate simple expressions for the model parameters, requiring only a single
property (the atomic polarizability or the nearest neighbor distance) as input.
Without any additional adjustable parameters, the model yields both the IP and
the WF within 10% for all metallic elements, as well as matches the size
evolution of the ionization potentials of finite metal clusters for a large
fraction of the experimental data. The parametrization takes advantage of a
remarkably constant numerical correlation between the nearest-neighbor distance
in a crystal, the cube root of the atomic polarizability, and the image force
cutoff length. The paper also includes an analytical derivation of the relation
of the outer radius of a cluster of close-packed spheres to its geometric
structure.Comment: Original submission: 8 pages with 7 figures incorporated in the text.
Revised submission (added one more paragraph about alloy work functions): 18
double spaced pages + 8 separate figures. Accepted for publication in PR
Proton transfer or hemibonding? The structure and stability of radical cation clusters
The basin hopping search algorithm in conjunction with second-order Moller-Plesset perturbation theory is used to determine the lowest energy structures of the radical cation clusters (NH_3)_n^+, (H_2O)_n^+, (HF)_n^+, (PH_3)_n^+, (H_2S)_n^+ and (HCl)_n^+, where n=2-4. The energies of the most stable structures are subsequently evaluated using coupled cluster theory in conjunction with the aug-cc-pVTZ basis set. These cationic clusters can adopt two distinct structural types, with some clusters showing an unusual type of bonding, often referred to as hemibonding, while other clusters undergo proton transfer to give an ion and radical. It is found that proton transfer based structures are preferred by the (NH_3)_n+, (H_2O)_n^+, and (HF)_n^+ clusters while hemibonded structures are favoured by (PH_3)_n^+, (H_2S)_n^+ and (HCl)_n^+. These trends can be attributed to the relative strengths of the molecules and molecular cations as Brønsted bases and acids, respectively, and the strength of the interaction between the ion and radical in the ion-radical clusters
First-Principles Investigation of Ag-Doped Gold Nanoclusters
Gold nanoclusters have the tunable optical absorption property, and are promising for cancer cell imaging, photothermal therapy and radiotherapy. First-principle is a very powerful tool for design of novel materials. In the present work, structural properties, band gap engineering and tunable optical properties of Ag-doped gold clusters have been calculated using density functional theory. The electronic structure of a stable Au20 cluster can be modulated by incorporating Ag, and the HOMO–LUMO gap of Au20−nAgn clusters is modulated due to the incorporation of Ag electronic states in the HOMO and LUMO. Furthermore, the results of the imaginary part of the dielectric function indicate that the optical transition of gold clusters is concentration-dependent and the optical transition between HOMO and LUMO shifts to the low energy range as the Ag atom increases. These calculated results are helpful for the design of gold cluster-based biomaterials, and will be of interest in the fields of radiation medicine, biophysics and nanoscience
Ab initio studies of structures and properties of small potassium clusters
We have studied the structure and properties of potassium clusters containing
even number of atoms ranging from 2 to 20 at the ab initio level. The geometry
optimization calculations are performed using all-electron density functional
theory with gradient corrected exchange-correlation functional. Using these
optimized geometries we investigate the evolution of binding energy, ionization
potential, and static polarizability with the increasing size of the clusters.
The polarizabilities are calculated by employing Moller-Plesset perturbation
theory and time dependent density functional theory. The polarizabilities of
dimer and tetramer are also calculated by employing large basis set coupled
cluster theory with single and double excitations and perturbative triple
excitations. The time dependent density functional theory calculations of
polarizabilities are carried out with two different exchange-correlation
potentials: (i) an asymptotically correct model potential and (ii) within the
local density approximation. A systematic comparison with the other available
theoretical and experimental data for various properties of small potassium
clusters mentioned above has been performed. These comparisons reveal that both
the binding energy and the ionization potential obtained with gradient
corrected potential match quite well with the already published data.
Similarly, the polarizabilities obtained with Moller-Plesset perturbation
theory and with model potential are quite close to each other and also close to
experimental data.Comment: 33 pages including 10 figure
Genotype–phenotype associations in 1018 individuals with SCN1A‐related epilepsies
Objective:
SCN1A variants are associated with epilepsy syndromes ranging from mild genetic epilepsy with febrile seizures plus (GEFS+) to severe Dravet syndrome (DS). Many variants are de novo, making early phenotype prediction difficult, and genotype–phenotype associations remain poorly understood.
Methods:
We assessed data from a retrospective cohort of 1018 individuals with SCN1A-related epilepsies. We explored relationships between variant characteristics (position, in silico prediction scores: Combined Annotation Dependent Depletion (CADD), Rare Exome Variant Ensemble Learner (REVEL), SCN1A genetic score), seizure characteristics, and epilepsy phenotype.
Results:
DS had earlier seizure onset than other GEFS+ phenotypes (5.3 vs. 12.0 months, p < .001). In silico variant scores were higher in DS versus GEFS+ (p < .001). Patients with missense variants in functionally important regions (conserved N-terminus, S4–S6) exhibited earlier seizure onset (6.0 vs. 7.0 months, p = .003) and were more likely to have DS (280/340); those with missense variants in nonconserved regions had later onset (10.0 vs. 7.0 months, p = .036) and were more likely to have GEFS+ (15/29, χ2 = 19.16, p < .001). A minority of protein-truncating variants were associated with GEFS+ (10/393) and more likely to be located in the proximal first and last exon coding regions than elsewhere in the gene (9.7% vs. 1.0%, p < .001). Carriers of the same missense variant exhibited less variability in age at seizure onset compared with carriers of different missense variants for both DS (1.9 vs. 2.9 months, p = .001) and GEFS+ (8.0 vs. 11.0 months, p = .043). Status epilepticus as presenting seizure type is a highly specific (95.2%) but nonsensitive (32.7%) feature of DS.
Significance:
Understanding genotype–phenotype associations in SCN1A-related epilepsies is critical for early diagnosis and management. We demonstrate an earlier disease onset in patients with missense variants in important functional regions, the occurrence of GEFS+ truncating variants, and the value of in silico prediction scores. Status epilepticus as initial seizure type is a highly specific, but not sensitive, early feature of DS
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