Ab initio relativistic effective potentials with spin‐orbit operators. I. Li through Ar

Molecular modeling and simulation of G-quadruplexes and quadruplex-ligand complexes

Methods for the molecular modeling and simulation of G-quadruplex structures and their drug/ligand complexes are discussed, and a range of protocols is presented for undertaking a variety of tasks including model-building, ligand docking, dynamics simulation, continuum solvent modeling, energetic calculations, principal component analysis, and quantum chemical computations. The scope and limitations of these approaches are discussed.

Theoretical studies of the low-lying states of GeSi+

Electronic structure and spectroscopic properties of the ground and low-lying excited states of GeSi+ have been studied by using multireference singles and doubles configuration interaction (MRDCI) method that includes relativistic effective core potentials of Ge and Si atoms. At least 17 Lambda-Sigma bound states of GeSi+ are reported within 5 eV. Potential energy curves of 24 Lambda-Sigma states which correlate with the lowest two dissociation limits, Ge+(2Pu)+Si(3Pg) and Ge(3Pg)+Si+ (2Pu) are constructed. The ground-state dissociation energy of GeSi+ is estimated to be 3.116 eV. The spin-orbit coupling among all states correlating the two dissociation limits is also included in the calculations. Spectroscopic constants of 27 Omega states of the ion are reported. Effects of the spin-orbit coupling on the spectroscopic properties are also studied. Potential energy curves of Omega states show several avoided crossings. Transition probabilities of many electric dipole allowed and spin-forbidden transitions are computed. Transitions such as 24Sigma(-)-X4Sigma- and 44Sigma(-)-X4Sigma- are found to be highly probable. Partial lifetimes for some weak spin-forbidden transitions to the ground-state components, X4Sigma(1/2)- and X4Sigma(3/2)- are also computed.

Components for integral evaluation in quantum chemistry

Sharing low-level functionality between software packages enables more rapid development of new capabilities and reduces the duplication of work among development groups. Using the component approach advocated by the Common Component Architecture Forum, we have designed a flexible interface for sharing integrals between quantum chemistry codes. Implementation of these interfaces has been undertaken within the Massively Parallel Quantum Chemistry package, exposing both the IntV3 and Cints/Libint integrals packages to component applications. Benchmark timings for Hartree-Fock calculations demonstrate that the overhead due to the added interface code varies significantly, from less than 1% for small molecules with large basis sets to nearly 10% for larger molecules with smaller basis sets. Correlated calculations and density functional approaches encounter less severe performance overheads of less than 5%. While these overheads are acceptable, additional performance losses occur when arbitrary implementation details, such as integral ordering within buffers, must be handled. Integral reordering is observed to add an additional overhead as large as 12%; hence, a common standard for such implementation details is desired for optimal performance.

Simple STM tip functionalization for rapid DNA sequencing: an Ab initio Green's function study

An ab initio nonequilibrium Green's function study of the electron-transport properties of the adenine, thymine, cytosine, and guanine DNA bases located between gold electrodes has been performed. One-electron transmission spectra were calculated for both gold and sulfur-modified gold electrodes, which are model conditions of scanning tunneling microscopy (STM) experiments with the different tips. It is shown that the nature of chemical bonding between molecules and metal electrodes plays the most significant role in the overall conductance of the systems. The distance between electrodes and the size of molecules are less important, at least when both sides of the molecule form chemical contact with the electrodes. On the basis of the obtained results, a simple two-pass DNA sequencing scheme is suggested.

An investigation of secondary ion yield enhancement using Bin2+ (n=1,3,5) primary ions

We have investigated secondary ion yield enhancement using Bin2+ (n=1, 3, 5) primary ions impacting phenylalanine, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), cholesterol, Irganox 1010, and polymer films adsorbed on silicon and aluminum. Secondary ion yields are increased using Bi2+and Bi3(2+) primary ions for the molecular layers and polymers that can undergo allyl cation rearrangements. For Irganox 1010, the deprotonated molecular ion yields (m/z 1175; [M-H]-) are one to two times larger for Bi2+ and Bi(3)2+ primary ions than for Bi+ and Bi3+ at the same primary ion velocities. In the positive ion mode, the largest fragment ion yield (m/z 899) is 1.5 times larger for Bi2+ ions than for Bi+. For Bi3(2+) the largest fragment ion yield is only 70% of the ion yield using Bi3+, but the secondary ion yields of the fragment ions at m/z 57 and 219 are enhanced. For polymers that can undergo allyl cation rearrangement reactions the secondary ion yield enhancements of the monomer ions range from 1.3 to 4.3. For Bi(5)2+ primary ions, secondary ion yields were the same or slightly larger than for Bi5+ in the negative ion mass spectra for Irganox 1010, but lower in the positive ion mode. No secondary ion yield enhancements were measured on polymer samples for Bi5(2+). For all polymer films studied, secondary ion intensities from the oligomer regions are substantially decreased using Bin2+ (n=1, 3, 5). We discuss differences in the ionization mechanisms for doubly and singly-charged Bi primary ion bombardment.

Theoretical study of the ArH+ photodissociation

The multireference Spin-Orbit (SO) Configuration Interaction (CI) method in its Lambda-S Contracted SO-CI (LSC-SO-CI) version is employed to calculate potential energy curves for the ground and low-lying excited states of the ArH(+) cation. For the first time, electric dipole moments are also computed in the approach, including SO coupling for transitions to the states responsible for the first absorption continuum (A-band) of ArH(+). On this basis, the partial and total absorption spectra in this energy range are obtained. It is shown that absorption in the A-band is dominated by the parallel A(1)Sigma(+)<--X(1)Sigma(+) transition. In the low-energy part of the band (<95 x 10(3) cm(-1)) the absorption is caused by the perpendicular B(1)Pi<--X(1)Sigma(+) excitation, but transitions to the b(3)Pi(0(+),1) states are also not negligible. The branching ratio Gamma for the final photodissociation products is calculated and it is shown to increase smoothly from 0 in the red tail of the band to 1 at E>or= 10(5) cm(-1). The latter value corresponds to the exclusive formation of the spin-excited Ar(+)((2)P(1/2)) ions, and thus leads to the inverse population of the Ar(+)((2)P(1/2)-(2)P(3/2)) ion states.

LANL2DZ basis sets recontracted in the framework of density functional theory

In this paper we report recontracted LANL2DZ basis sets for first-row transition metals. The valence-electron shell basis functions were recontracted using the PWP86 generalized gradient approximation functional and the hybrid B3LYP one. Starting from the original LANL2DZ basis sets a cyclic method was used in order to optimize variationally the contraction coefficients, while the contraction scheme was held fixed at the original one of the LANL2DZ basis functions. The performance of the recontracted basis sets was analyzed by direct comparison between calculated and experimental excitation and ionization energies. Results reported here compared with those obtained using the original basis sets show clearly an improvement in the reproduction of the corresponding experimental gaps.

Energy-consistent pseudopotentials for quantum Monte Carlo calculations

The authors present scalar-relativistic energy-consistent Hartree-Fock pseudopotentials for the main-group elements. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculations. They demonstrate their transferability through extensive benchmark calculations of atomic excitation spectra as well as molecular properties. In particular, they compute the vibrational frequencies and binding energies of 26 first- and second-row diatomic molecules using post-Hartree-Fock methods, finding excellent agreement with the corresponding all-electron values. They also show their pseudopotentials give superior accuracy than other existing pseudopotentials constructed specifically for QMC. Finally, valence basis sets of different sizes (VnZ with n=D,T,Q,5 for first and second rows, and n=D,T for third to fifth rows) optimized for our pseudopotentials are also presented.

Spectroscopic constants and potential energy curves of yttrium carbide (YC)

The potential energy curves of the low-lying electronic states of yttrium carbide (YC) and its cation are calculated at the complete active space self-consistent field and the multireference single and double excitation configuration interaction (MRSDCI) levels of theory. Fifteen low-lying electronic states of YC with different spin and spatial symmetries were identified. The X (4)Sigma- state prevails as the ground state of YC, and a low-lying excited A (4)Pi state is found to be 1661 cm(-1) higher at the MRSDCI level. The computations of the authors support the assignment of the observed spectra to a B (4)Delta(Omega=72)<--A (4)Pi(Omega=52) transition with a reinterpretation that the A (4)Pi state is appreciably populated under the experimental conditions as it is less than 2000 cm(-1) of the X (4)Sigma- ground state, and the previously suggested (4)Pi ground state is reassigned to the first low-lying excited state of YC. The potential energy curves of YC+ confirm a previous prediction by Seivers et al. [J. Chem. Phys. 105, 6322 (1996)] that the ground state of YC+ is formed through a second pathway at higher energies. The calculated ionization energy of YC is 6.00 eV, while the adiabatic electron affinity is 0.95 eV at the MRSDCI level. The computed ionization energy of YC and dissociation energy of YC+ confirm the revised experimental estimates provided by Seivers et al. although direct experimental measurements yielded results with greater errors due to uncertainty in collisional cross sections for YC+ formation.

Infrared Spectrum and Bonding in Uranium Methylidene Dihydride, CH2UH2

Uranium atoms activate methane upon ultraviolet excitation to form the methyl uranium hydride CH3-UH, which undergoes alpha-H transfer to produce uranium methylidene dihydride, CH2=UH2. This rearrangement most likely occurs on an excited-quintet potential-energy surface and is followed by relaxation in the argon matrix. These simple U+CH4 reaction products are identified through isotopic substitution (13CH4, CD4, CH2D2) and density functional theory frequency and structure calculations for the strong U-H stretching modes. Relativistic multiconfiguration (CASSCF/CASPT2) calculations substantiate the agostic distorted C1 ground-state structure for the triplet CH2=UH2 molecule. We find that uranium atoms are less reactive in methane activation than thorium atoms. Our calculations show that the CH2=UH2 complex is distorted more than CH2=ThH2. A favorable interaction between the low energy open-shell U(5f) sigma orbital and the agostic hydrogen contributes to the distortion in the uranium methylidene complexes.

Ab Initio Spin−Orbit Configuration Interaction Calculations for High-Lying States of the HeNe Quasimolecule

Multireference configuration interaction (MRD-CI) calculations are reported for a large series of electronic states of the HeNe quasimolecule up to 170000 cm(-1) excitation energy, including those that dissociate to the 3S1 and 2 1S0 excited states of the He atom. Spin-orbit coupling is included through the use of relativistic effective core potentials (RECPs). Good agreement is obtained with experimental spectroscopic data for the respective atomic levels, although there is a tendency to systematically underestimate the energies of the Ne atom by 1000-1500 cm(-1) because of differences in the correlation effects associated with its ground and Rydberg excited states. Potential curves are calculated for each of these states, and a number of relatively deep minima are found. The CI Omega-state wave functions are sufficiently diabatic until r = 4-5 a0 to allow for a clear identification of the He 1s-2s excited states. Electric dipole transition moments are computed between these states and the HeNe X 0+ ground state up to r = 4.0 a0, and it is found that the 2 (1)S0 - X maximum value is over an order of magnitude larger than that for the corresponding (3)S1 - X excitation process.