Biomedical subjects

Juan E Peralta

Publications and source records attributed to Juan E Peralta.

12 recordsLinked to original sources

PubMed2006

First-principles electronic transport calculations in finite elongated systems: a divide and conquer approach.

We present a first-principles method for the evaluation of the transmittance probability and the coherent conductance through elongated systems composed of a repeating molecular unit and terminated at both ends. Our method is based on a divide and conquer approach in which the Hamiltonian of the elongated system can be represented by a block tridiagonal matrix, and therefore can be readily inverted. This allows us to evaluate the transmittance and the conductance using first-principles electronic structure methods without explicitly performing calculations involving the entire system. A proof of concept model based on a trans-polyacetylene chain bridging two aluminum leads indicates that our divide and conquer approach is able to capture all the features appearing in the transmittance probability curves obtained by a full scale calculation.

Journal Article↗

PubMed2006

Screened exchange hybrid density-functional study of the work function of pristine and doped single-walled carbon nanotubes.

We present a detailed study of the work function of pristine and doped single-walled carbon nanotubes (SWCNTs) using a novel screened exchange hybrid density functional. We find that SWCNTs with diameters larger than 0.9 nm tend asymptotically and smoothly to the graphene limit of 4.6 eV. On the other hand, the work function of narrow tubes exhibits a strong dependence on their diameter and chiral angle. Boron or nitrogen doping, with concentrations from 1% to 2%, not only changes the electronic behavior by introducing new states around the Fermi level, but also produces a significant change of the work function that can vary between 3.9 (N doping) and 5.2 eV (B doping).

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PubMed2005

Relativistic calculation of indirect NMR spin-spin couplings using the Douglas-Kroll-Hess approximation.

We have employed the Douglas-Kroll-Hess approximation to derive the perturbative Hamiltonians involved in the calculation of NMR spin-spin couplings in molecules containing heavy elements. We have applied this two-component quasirelativistic approach using finite perturbation theory in combination with a generalized Kohn-Sham code that includes the spin-orbit interaction self-consistently and works with Hartree-Fock and both pure and hybrid density functionals. We present numerical results for one-bond spin-spin couplings in the series of tetrahydrides CH(4), SiH(4), GeH(4), and SnH(4). Our two-component Hartree-Fock results are in good agreement with four-component Dirac-Hartree-Fock calculations, although a density-functional treatment better reproduces the available experimental data.

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PubMed2005

Energy band gaps and lattice parameters evaluated with the Heyd-Scuseria-Ernzerhof screened hybrid functional.

This work assesses the Heyd-Scuseria-Ernzerhof (HSE) screened Coulomb hybrid density functional for the prediction of lattice constants and band gaps using a set of 40 simple and binary semiconductors. An extensive analysis of both basis set and relativistic effects is given. Results are compared with established pure density functionals. For lattice constants, HSE outperforms local spin-density approximation (LSDA) with a mean absolute error (MAE) of 0.037 A for HSE vs 0.047 A for LSDA. For this specific test set, all pure functionals tested produce MAEs for band gaps of 1.0-1.3 eV, consistent with the very well-known fact that pure functionals severely underestimate this property. On the other hand, HSE yields a MAE smaller than 0.3 eV. Importantly, HSE correctly predicts semiconducting behavior in systems where pure functionals erroneously predict a metal, such as, for instance, Ge. The short-range nature of the exchange integrals involved in HSE calculations makes their computation notably faster than regular hybrid functionals. The current results, paired with earlier work, suggest that HSE is a fast and accurate alternative to established density functionals, especially for solid state calculations.

Journal Article↗

PubMed2005

Scalar relativistic all-electron density functional calculations on periodic systems.

Scalar relativistic effects are included in periodic boundary conditions calculations with Gaussian orbitals. This approach is based on the third-order Douglas-Kroll-Hess approximation, allowing the treatment of all electrons on an equal footing. With this methodology, we are able to perform relativistic all-electron density functional calculations using the traditional local spin-density and generalized gradient approximations (GGA), as well as meta-GGA and hybrid density functionals. We present benchmark results for the bulk metals Pd, Ag, Pt, and Au, and the large band gap semiconductors AgF and AgCl.

Journal Article↗

PubMed2005

Density functional theory study of optical transitions in semiconducting single-walled carbon nanotubes.

We present a density functional theory study of optical transitions in semiconducting single-walled carbon nanotubes. We utilize recently developed exchange-correlation functionals in a set of 21 tubes that includes large and chiral nanotubes. The novel TPSSh meta-generalized gradient approximation hybrid functional accurately reproduces optical excitations with mean absolute errors of 0.024 and 0.065 eV for first and second transitions, respectively. We also report predictions for higher order optical transitions.

Computer Simulation↗

PubMed2005

Optical transitions in metallic single-walled carbon nanotubes.

We report vertical electronic transitions of 20 metallic single-walled carbon nanotubes calculated as band energy differences from Kohn-Sham density functional theory. Our first-order transitions (E11) calculated with hybrid functionals (containing a portion of exact exchange) are in very good agreement with available experimental data. Recently, we have reported similar agreement between experiment and theory for semiconducting tubes. We find that the trigonal warping splitting in the band structure of metallic tubes is about 1.5 to 2 times larger than that reported previously.

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PubMed2004

Density functional investigations of the properties and thermochemistry of UF6 and UF5 using valence-electron and all-electron approaches.

The structural properties and thermochemistry of UF6 and UF5 have been investigated using both Hartree-Fock and density functional theory (DFT) approximations. Within the latter approach, the local spin-density approximation, the generalized gradient approximation, and hybrid density functionals were considered. To describe the uranium atom we employed small-core (60 electrons) and large-core (78 electrons) relativistic effective core potentials (RECPs), as well as the all-electron approximation based on the two-component third-order Douglas-Kroll-Hess Hamiltonian. For structural properties, we obtained very good agreement with experiment with DFT and both large and small-core RECPs. The best match with experiment is given by the hybrid functionals with the small-core RECP. The bond dissociation energy (BDE) was obtained from the relative energies of the fragments [UF6 --> UF5 + F], corrected for zero-point energy and spin-orbit interaction. Very good agreement was found between the BDE obtained from all-electron calculations and those calculated with the small-core RECP, while those from the large-core RECP are off by more than 50%. In order to obtain good agreement with experiment in the BDE it is imperative to work with hybrid density functionals and a small-core RECP.

Journal Article↗

PubMed2004

Density functional theory calculation of indirect nuclear magnetic resonance spin-spin coupling constants in C(70).

We calculate NMR spin-spin coupling constants in the C70 fullerene by means of density functional theory. We show that using a hybrid density functional (B3LYP) and an adequate basis set (cc-pCVDZ-sd), excellent agreement with experimental values can be achieved for one-bond couplings. These benchmark calculations suggest that theoretical predictions of NMR spin-spin couplings can be extremely valuable for discerning structural information of fullerenes.

Journal Article↗

PubMed2004

Relativistic all-electron two-component self-consistent density functional calculations including one-electron scalar and spin-orbit effects.

We have implemented a Gaussian basis-set two-component self-consistent field method based on the fourth-order nuclear-only Douglas-Kroll-Hess approximation. Two-electron spin-orbit effects are included using Boettger's screened-nuclear spin-orbit approximation. In our two-component approach, the spin-orbit interaction is taken into account in a variational fashion employing a generalized Kohm-Sham scheme which allows one to work with hybrid density functionals. For open-shell systems we adopt the noncollinear spin-density approximation. Results are presented for equilibrium bond lengths, harmonic vibrational frequencies, and bond dissociation energies with local spin-density, generalized gradient approximation, and hybrid functionals in a set of benchmark molecules.

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PubMed2004

Substituent effects on scalar J(13C, 13C) couplings in pyrimidines. An experimental and DFT study.

One- two- and three 13C, 13C (n = 1, 2, 3) scalar couplings, (n)J(C,C) in a set of pyrimidine derivatives were studied both experimentally at natural abundance and theoretically by their DFT calculation of all four contributions. Trends of non-contact terms are discussed and substituent effects are rationalized, comparing some of them with the corresponding values in benzene and pyridine. Although substituent effects on non-contact terms are relatively important, the whole trend is dominated by the Fermi contact term. According to the current literature, substituent effects on 1J(C,C) couplings in benzene derivatives are dominated by the inductive effect, which, apparently, is also the case in nitrogen heteroaromatic compounds. However, some differences observed in this work for substituent effects on 1J(C,C) couplings in pyrimidine derivatives suggest that in the latter type of compounds substituent effects can be affected by the orientation of the ring nitrogen lone pairs.

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PubMed2002

On the capriciousness of the FCCF Karplus curve.

Numerous well-behaved Karplus curves correlating dihedral angle (phi) and NMR coupling constants (3JXY) exist for X-C-Z-Y fragments with X or Y = H, C, F, and P. Absent is the enigmatic F-C-C-F moiety. By calculating the four Ramsey contributions to 3JFF for F-CH2-CH2-F, a pleasing phi/3JFF curve with both positive and negative regions arises. Unlike the H-C-C-H curve, F-C-C-F is PSO vs FC dominated. The latter and the F lone electron pairs cause both the negative J values and the substituent-induced J-leveling effect.

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