Ab Initio Tools Research Articles

Hybrid dithienylethene-naphthopyran multi-addressable photochromes: an ab initio analysis

Using ab initio tools, we investigate the structural and electronic properties as well as the NMR spectra of hybrid dithienylethene-naphthopyran photochromes synthesised by Frigoli and Mehl (Angew. Chem. Int. Ed., 2005, 44, 5048). All possible closed/open structures have been considered and in each case several conformers could be characterised. Both UV/vis and NMR spectroscopic signatures have been compared to experimental references, and it was shown that the selected DFT/TD-DFT procedure is adequate not only to reproduce the measured spectral values but also to explain the observed photochromic pathways. Our work indicates that several conformers with different relative dithienylethene and naphthopyran orientations might be present experimentally.

Ab Initio Investigation of the Electronic Properties of Coupled Dithienylethenes

The design of more efficient photochromes does not stand as the only challenge in the field of molecular switches; more complex and refined structures, allowing one to pave the way toward multiply addressable structures, are highly sought after. In this framework, compounds containing several dithienylethenes have been recently proposed. In the present Letter, we investigate the spectral properties of photochromes made of two dithienylethene units linked through conjugated bridges to form meta and para switches. All combinations of closed and open forms have been modeled by using (time-dependent) density functional theory. With this ab initio tool, the coupling between the photochromic centers could be assessed. Such calculations are a step necessary to understand the parameters guiding the formation of the fully closed forms.

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data

Summary: W-ChIPMotifs is a web application tool that provides a user friendly interface for de novo motif discovery. The web tool is based on our previous ChIPMotifs program which is a de novo motif finding tool developed for ChIP-based high-throughput data and incorporated various ab initio motif discovery tools such as MEME, MaMF, Weeder and optimized the significance of the detected motifs by using a bootstrap resampling statistic method and a Fisher test. Use of a randomized statistical model like bootstrap resampling can significantly increase the accuracy of the detected motifs. In our web tool, we have modified the program in two aspects: (i) we have refined the P-value with a Bonferroni correction; (ii) we have incorporated the STAMP tool to infer phylogenetic information and to determine the detected motifs if they are novel and known using the TRANSFAC and JASPAR databases. A comprehensive result file is mailed to users.Availability: http://motif.bmi.ohio-state.edu/ChIPMotifs. Data used in the article may be downloaded from http://motif.bmi.ohio-state.edu/ChIPMotifs/examples.shtml.Contact: victor.jin@osumc.edu

How Many New Genes Are There?

How Many New Genes Are There?

Method of predicting Splice Sites based on signal interactions

BackgroundPredicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan.ResultsAccording to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE) and Intronic (ISE) Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments.ConclusionDesigned methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site.ReviewersThis article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand.

Correlated complex independent particle potential for calculating electronic resonances

We have formulated and applied an analytic continuation method for the recently formulated correlated independent particle potential [A. Beste and R. J. Bartlett J. Chem. Phys. 120, 8395 (2004)] derived from Fock space multireference coupled cluster theory. The technique developed is an advanced ab initio tool for calculating the properties of resonances in the low-energy electron-molecule collision problem. The proposed method quantitatively describes elastic electron-molecule scattering below the first electronically inelastic threshold. A complex absorbing potential is utilized to define the analytic continuation for the potential. A separate treatment of electron correlation and relaxation effects for the projectile-target system and the analytic continuation using the complex absorbing potential is possible, when an approximated form of the correlated complex independent particle potential is used. The method, which is referred to as complex absorbing potential-based correlated independent particle (CAP-CIP), is tested by application to the well-known (2)Pi(g) shape resonance of e-N(2) and the (2)B(2g) shape resonance of e-C(2)H(4) (ethylene) with highly satisfactory results.

Linear phosphorus–boron chains: model system with huge electronic first hyperpolarizability

AbstractThe longitudinal electronic static first hyperpolarizability of model linear phosphorus–boron chains is investigated using ab initio tools, including dynamic electron correlation corrections. The polymer presents an extremely large first hyperpolarizability (1700 × 10−30 esu per unit cell) that can be rationalized in terms of delocalization and asymmetry (unit cell and chain‐ends contributions). © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Ab Initio Investigation of the Structures and Properties of Polyaminoborane

We have investigated the structures and the properties of polyaminoborane oligomers by using ab initio computational tools including dynamic electron correlation effects. It turned out that the PBE0/6-31G(2d) method provides a good agreement between experimental and theoretical structures. The key data include geometries, rotational profiles, infrared spectra, vertical excitation energies, atomic charges, and dipole moments. The variations of these properties upon conformation changes are studied. Our results are compared to available experimental measurements.

Effects of Chain Substitution on the Structures and Properties of Polyphosphinoborane

The impact of side-group substitution on the three-dimensional structure and on the properties of the homologuous series of polyphosphinoborane oligomers has been investigated by using ab initio computational tools, taking into account dynamic electron correlation effects. This includes the evaluation of the following: geometries, conformations, rotational profiles, infrared spectra, vertical excitations energies, atomic charges, and dipole moments.

Theoretical study of the longitudinal first hyperpolarizability of polysilaacetylene.

With the help of ab initio tools taking into account dynamic electron correlation effects, we study the longitudinal electronic first hyperpolarizability of carbon-silicon analogues to polyacetylene. It turns out that the MP2/6-31G(d)//HF/6-31G(d) scheme is suitable to obtain a semiquantitative accuracy for the first hyperpolarizability of long polysilaacetylene oligomers. The conformation of the chain has a crucial impact on its second-order nonlinear optical properties. We also show that, for some chain lengths, the frequency dispersion effects may have a huge impact, even when far away from resonance. These phenomena are rationalized in terms of delocalization and asymmetry.

Structures and Properties of Polyphosphinoborane: an Oligomeric Theoretical Study

We have investigated the structures and properties of polyphosphinoborane oligomers by using ab initio computational tools, including electron correlation effects. The key data evaluated include geometries, conformations, rotational profiles, infrared spectra, vertical excitation energies, atomic charges, and dipole moments which can significantly depend on the conformation adopted by polyphosphinoborane.

Vibrational energy levels for symmetric and asymmetric isotopomers of ammonia with an exact kinetic energy operator and new potential energy surfaces

A new vibrational Hamiltonian operator for ammonia is presented. The potential energy part is expressed in terms of symmetrized bond-angle valence coordinates and an inversion coordinate, which is a function of the bond angles. In the exact kinetic energy operator, the stretching part is instead given in terms of unsymmetrized bond displacement coordinates. Six-dimensional ammonia potential energy surfaces are calculated using high-level ab initio tools, the CCSD(T) method with aug-cc-pVQZ and aug-cc-pVTZ basis sets. The potential energy functions are constructed in two, two-dimensional steps. The surfaces are expressed as a Taylor-type series with respect to the doubly degenerate asymmetric stretching and bending coordinates. This representation is given along a two-dimensional surface of the totally symmetric stretching and inversion coordinates of ammonia. Vibrational energies are calculated variationally in a finite basis representation. Employing successive basis set contractions, it is possible to optimize some potential energy parameters simultaneously for seven symmetric and asymmetric isotopomers very effectively. The symmetric part of the surface is fitted to experimentally observed vibrational band centers up to 6000 cm−1. This reduces the mean absolute error from 7.84 cm−1 with a pure ab initio potential to 0.44 cm−1 compared to the experimental values for NH314. In addition, vibrational energy levels of NH314 have been calculated up to about 15 000 cm−1 using the pure ab initio surface obtained with the aug-cc-pVTZ basis set. The nuclear motion calculation converges all levels up to about 10 000 cm−1 to within 0.05 cm−1.

Interaction of HOCl with a chlorinated ice surface to produce molecular chlorine: An ab-initio study

The reaction between molecular HOCl and a chlorinated surface of ice to produce molecular chlorine has been theoretically investigated. Ab initio quantum mechanical tools (GAUSSIAN 98 and EMBED01) have been used for this purpose, based on a molecular cluster and on an embedded cluster model, respectively. Different reaction paths have been explored, requiring a pre-activation of the substrate. In all cases, important activation barriers have been found. Only if certain types of structural defects are present at the surface, the reaction has been found to take place almost spontaneously.

Origins and Applications of London Dispersion Forces and Hamaker Constants in Ceramics

The London dispersion forces, along with the Debye and Keesom forces, constitute the long‐range van der Waals forces. London's and Hamaker's work on the point‐to‐point dispersion interaction and Lifshitz's development of the continuum theory of dispersion are the foundations of our understanding of dispersion forces. Dispersion forces are present for all materials and are intrinsically related to the optical properties and the underlying interband electronic structures of materials. The force law scaling constant of the dispersion force, known as the Hamaker constant, can be determined from spectral or parametric optical properties of materials, combined with knowledge of the configuration of the materials. With recent access to new experimental and ab initio tools for determination of optical properties of materials, dispersion force research has new opportunities for detailed studies. Opportunities include development of improved index approximations and parametric representations of the optical properties for estimation of Hamaker constants. Expanded databases of London dispersion spectra of materials will permit accurate estimation of both nonretarded and retarded dispersion forces in complex configurations. Development of solutions for generalized multilayer configurations of materials are needed for the treatment of more‐complex problems, such as graded interfaces. Dispersion forces can play a critical role in materials applications. Typically, they are a component with other forces in a force balance, and it is this balance that dictates the resulting behavior. The ubiquitous nature of the London dispersion forces makes them a factor in a wide spectrum of problems; they have been in evidence since the pioneering work of Young and Laplace on wetting, contact angles, and surface energies. Additional applications include the interparticle forces that can be measured by direct techniques, such as atomic force microscopy. London dispersion forces are important in both adhesion and in sintering, where the detailed shape at the crack tip and at the sintering neck can be controlled by the dispersion forces. Dispersion forces have an important role in the properties of numerous ceramics that contain intergranular films, and here the opportunity exists for the development of an integrated understanding of intergranular films that encompasses dispersion forces, segregation, multilayer adsorption, and structure. The intrinsic length scale at which there is a transition from the continuum perspective (dispersion forces) to the atomistic perspective (encompassing interatomic bonds) is critical in many materials problems, and the relationship of dispersion forces and intergranular films may represent an important opportunity to probe this topic. The London dispersion force is retarded at large separations, where the transit time of the electromagnetic interaction must be considered explicitly. Novel phenomena, such as equilibrium surficial films and bimodal wetting/dewetting, can result in materials systems when the characteristic wavelengths of the interatomic bonds and the physical interlayer thicknesses lead to a change in the sign of the dispersion force. Use of these novel phenomena in future materials applications provides interesting opportunities in materials design.

Hydrogen bonding at the diatomics-in-molecules level: Water clusters

Further developments of the intermolecular diatomics-in-molecules (DIM) theory towards construction of potential energy surfaces of hydrogen-bonded molecular aggregates are presented. Compared to the previously studied hydrogen fluoride clusters (HF)n [J. Chem. Phys. 111, 4442 (1999)], considerably more complicated and challenging systems, namely, water clusters (H2O)n (n=2–6) have been analyzed in this work. The present DIM, or more precisely, diatomics-in-ionic-systems, scheme is based on the balanced treatment of neutral and ionic contributions to the electronic properties of polyatomic species, and in this case takes into account the mixing of the OH and O−H+ electronic states within the valence bond description of water molecules. The potential curves of diatomic molecules required for the present application, including ionic species O−H, OH+, O2−, have been computed by ab initio quantum chemistry tools. The results of DIM calculations of equilibrium geometry configurations, binding energies, and relative energies for the low-lying isomers of (H2O)n (n=2–6) are compared to the reference data showing a good predictive power of this method.

Electron spin localisation and correlation effects for point defects in semi-ionic solids

Point defects strongly influence the electrical, catalytic and optical properties of important industrial materials such as silica, aluminosilicates and aluminophosphates. We concentrate here on the predictive ability of modern ab initio solid-state tools to describe electron localised states in these materials. We apply a periodic boundary conditions approach to investigate equilibrium configurations and electronic structures of oxygen vacancies in the form of diamagnetic VO and paramagnetic E′ centres. Localisation of the electronic states at the defect is studied using both Hartree–Fock (HF) and Density Functional theories. Thus, we are able to characterise the effect of electron correlation on spin polarisation and electron trapping. Geometries and energetics of defect formation are investigated, along with the one-electron spectra and spin/charge density distributions, which allow us to gather a comprehensive representation of the defect ground state.

Systematic study of the lowest energy states of Pd, Pd2, and Pd3

A systematic study has been carried out for the determination and characterization of the lowest states of Pd, Pd2, and Pd3 using some of the best ab initio tools available at present (conventional and DFT). Full electron ab initio calculations using the HF, MP2, MP3, MP4, and QCI methods were compared with DFT methods using several gradient-corrected functionals as well as the hybrid B3LYP functional that performed very well for the energetics studies of these small clusters. A suitable basis set has been found to perform considerably well with palladium atoms, another of double-ζ quality has been found insufficient to reproduce basic characteristics of the smallest palladium clusters. The results indicate that the ground state for Pd is a singlet. The dimer is a triplet; however, it is very difficult to ascertain due to the closeness between singlet and triplet states (0.9 kcal/mol). The trimer ground state was found to be a triplet with a separation from the lowest singlet of 3.2 kcal/mol. The lowest triplet and singlet of Pd3 were practically equilateral triangles. © 1997 John Wiley & Sons, Inc.

Systematic study of the lowest energy states of Pd, Pd2, and Pd3

A systematic study has been carried out for the determination and characterization of the lowest states of Pd, Pd , and Pd using some of the best ab initio tools available at 23 . present conventional and DFT . Full electron ab initio calculations using the HF, MP2, MP3, MP4, and QCI methods were compared with DFT methods using several gradient- corrected functionals as well as the hybrid B3LYP functional that performed very well for the energetics studies of these small clusters. A suitable basis set has been found to perform considerably well with palladium atoms, another of double-z quality has been found insufficient to reproduce basic characteristics of the smallest palladium clusters. The results indicate that the ground state for Pd is a singlet. The dimer is a triplet; however, it is very difficult to ascertain due to the closeness between singlet and triplet . states 0.9 kcalrmol . The trimer ground state was found to be a triplet with a separation from the lowest singlet of 3.2 kcalrmol. The lowest triplet and singlet of Pd were 3 practically equilateral triangles. Q 1997 John Wiley & Sons, Inc.

A relativistic C.I. study on theJ=1/2 even spectrum of Sr II

We present a method for performing relativistic CI calculations in ground and excited atomic and ionic levels. An electron occupying a relativistic shellnκ in a given electronic configuration is described by a single numerical four-component Dirac-Fock orbital having the samen and κ quantum numbers to those of the shellnκ. Application of this method yields estimates for the I.P. (88 741 cm−1) and the core correlation energy (−30916 cm−1) for Sr II and for the total correlation energy in Sr III (−30916 cm−1). Core-valence correlation energies for the |core 5s〉 (−4379 cm−1), |core 6s〉 (−1191 cm−1) and |core 13s〉 (−32 cm−1) levels have been calculated for Sr II. Estimates for the total relativistic, Breit, vacuum polarization and self energy corrections for these levels are also reported. Configurations in which the core is not fully occupied have been found to yield significant contributions to the correlation energies of both ground and excited levels. Our results show that full scale relativistic CI calculations using numerical four-component Dirac-Fock orbitals are feasible and provide a useful ab-initio tool for the investigation of atomic properties within the framework of fully relativistic theories.