Ab Initio Tools Research Articles

A Complete and Accurate Ab Initio Repeat Finding Algorithm.

It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy.

Theoretical Rovibronic Treatment of the X̃ (2)Σ(+) and à (2)Π States of C2H and the X̃ (1)Σ(+) State of C2H(-) from Quartic Force Fields.

Quartic force fields (QFFs) have been shown to be an effective ab initio tool for the generation of highly accurate anharmonic spectroscopic data but have only recently been extended to the description of electronically excited states using equation-of-motion (EOM) coupled cluster theory. In this study, rovibrational data are provided for the X̃ (2)Σ(+) ground state of the ethynyl radical as well as the X̃ (1)Σ(+) ground state of the acetylide anion using traditional QFF methods in conjunction with the new EOM-based QFF method to describe the ethynyl radical's à (2)Π excited state. These data sets include fundamental vibrational frequencies, rotational constants, and vibrationally averaged structures in addition to other spectroscopic constants. An anticipated theoretical correction (ATC) is shown to be an effective way of improving the accuracy of the fundamental modes of the ethynyl radical's à (2)Π electronically excited state, lowering the frequencies from 2 to 9%. The anharmonic fundamental vibrational frequencies of à (2)Π C2H are reported to be ν2 = 538.0 cm(-1) (bend), ν3 = 1832.2 cm(-1) (C-C stretch), and ν1 = 3008.1 cm(-1) (C-H stretch). These à (2)Π frequencies match closely to predicted transitions from previous theoretical work as well as observed transitions from matrix isolation results. Electron binding energies for the X̃ (2)Σ(+) C2H ← X̃ (1)Σ(+) C2H(-) and à (2)Π C2H ← X̃ (1)Σ(+) C2H(-) transitions are found to be 2.975 and 3.4 eV, respectively. Spectroscopic data are also provided for the (13)C and deuterated isotopologues of X̃ (2)Σ(+) C2H, à (2)Π C2H, and X̃ (1)Σ(+) C2H(-).

Development of a “Realistic” Model of the Dynamic Chromatin Fiber using an Integrated Computational Approach

DNA in eukaryotic cells is highly compacted into a hierarchical chromatin structure to fit inside the nucleus. Linker histones play an important role in this packing. Their interaction with the nucleosomes and intervening DNA linkers, in combination with linker length, are believed to affect chromatin folding and long-range interactions. The details of chromatin structure at this level of compaction are still an open question but have profound implications on biological processes, such as gene expression. Two major challenges are that linker histones contain a long intrinsically disordered C-terminal domain (CTD) and determination of high-resolution structures of chromatin has not been possible due to the large size of the system and its dynamic nature.We are taking advantage of the recently published 11-A resolution electron microscopy maps of two chromatin fibers (Song et al., 2014), to construct a complete low-resolution model of chromatin. High-resolution crystal structures of nucleosome core particles are fitted to the electron density maps and the intervening segments of linker DNA are modeled based on a sampling protocol that utilizes new DNA optimization methods. Situs is used to score all models against the density maps. Linker histones are modeled on the densities extracted after accounting for the nucleosomes and linker DNA. The modeled paths of the DNA linkers and the sites of the nucleosomes provide spatial constraints for positioning the globular core and modeling the folding of the disordered CTD of the linker histone. The pathways of the CTD are selected from ensembles of conformations obtained using ab initio structure prediction tools like Rosetta. We are using the model in coarse-grained Monte Carlo simulations of long-range interactions along arrays of precisely positioned nucleosomes in the presence of linker histones.

Computational Modeling of the N-Terminus of the Human Dopamine Transporter (hDAT)

DAT is a transmembrane protein in the family of Neurotransmitter:Sodium Symporters (NSS). The NSS are responsible for the clearance of neurotransmitters from the synaptic cleft, and for their translocation back into the presynaptic nerve terminal. In contrast to its bacterial homologue, the leucine transporter (LeuT), mammalian DAT contains long intracellular N- and C-terminal domains that are strongly implicated in the transporter function. The N-terminus (N-term), in particular, regulates the process of efflux, i.e. the reverse transport of the substrate (dopamine) through DAT. Currently, the molecular mechanisms of the efflux remain largely elusive due to lack of structural information on the N-terminal segment. To seek a valid prediction of the three-dimensional (3D) fold of the N-terminus from the human DAT (hDAT) we used a combination of ab initio structure prediction tools and extensive atomistic MD simulations. The ab initio modeling revealed structured regions within the first 57 residues of the N-term. The subsequent long (2.2 μs in total) atomistic MD simulations of the N-terminal in complex with a lipid membrane showed that the identified secondary structure elements were stable on the simulation timescales and were involved in specific interactions with pertinent models of the cell membrane. The N-term engages with lipid membranes through direct electrostatic interactions with the charged lipids PIP2 (phosphatidylinositol 4,5-biphosphate) and PS (phosphatidylserine). We identify specific motifs along the N-terminal domain that are implicated in such interactions and show that differential modes of N-term/membrane associations result in differential positioning of the structured segments on the membrane surface. The molecular insights we report regarding the preferred modes of interaction of the DAT N-term with model membranes provide a novel structural context for future explorations of the mechanistic questions related to the functional mechanisms of this transporter.

Modeling the Absorbance Properties of a Pyrene Chromophore Grafted onto a Au25 Nanocluster: A TD-DFT Study

Using ab initio spectroscopic tools, we have studied the structural and electronic properties of a pyrene chromophore grafted onto a Au25 nanocluster synthesized by Devadas and co-workers [J. Phys. Chem. Lett. 2010, 1, 1497]. To simulate the electronic absorption spectra of this hybrid metallic/organic structure, we relied on a three-step approach: (1) Molecular Dynamics simulations based on Force Field Classical Mechanics, (2) geometry optimizations at the ZORA-BP86/TZP level, and (3) TD-DFT calculations with the CAM-B3LYP functional. This procedure allowed us to reproduce and rationalize the experimental observations. Because of small spatial overlap and energy matching between the organic and metallic frontier orbitals, the absorption spectrum of the hybrid system is a simple addition of the pyrene and nanocluster optical spectra. To tune the optical properties of the organic moiety and enable the electronic communication within the hybrid system, a modification of the pyrene skeleton is proposed. This study thus paves the way toward the simulation of UV–visible absorption spectra of hybrid metallic–organic systems.

Prediction of potential novel microRNAs in soybean when in symbiosis.

MicroRNAs (miRNAs) are small molecules, noncoding proteins that are involved in many biological processes, especially in plants; among these processes is nodulation in the legume. Biological nitrogen fixation is a key process, with critical importance to the soybean crop. This study aimed to identify the potential of novel miRNAs to act during the root nodulation process. We utilized a set of transcripts that were differentially expressed in soybean roots 10 days after inoculation with Bradyrhizobium japonicum, which were obtained in a previous study, and performed a set of computational analyses that led us to select new miRNAs potentially involved in nodulation. Among these analyses, the set of transcripts were submitted to an in silico annotation of noncoding RNAs, including a search of similarity against miRNA public databases, ab initio tools for miRNA identification, structural search against miRNA families, prediction of the secondary structure of miRNA precursors, and prediction of the sequences of mature miRNAs. Subsequently, we applied filter procedures based on miRNA selections described in the literature (e.g., free energy value). In the next step, a manual curation inspection of the annotation was performed and the top candidates were selected and used for prediction of potential target genes, which were later checked manually in the database of the soybean genome. This prediction led us to the identification of 9 potential new miRNAs; among these, 4 were conserved in other plants. Moreover, we predicted their target genes might play important roles in the regulation of nodulation.

Modeling optical signatures and excited-state reactivities of substituted hydroxyphenylbenzoxazole (HBO) ESIPT dyes

The potential energy surfaces of dyes displaying strong excited-state intramolecular proton transfer (ESIPT) are investigated with the help of ab initio tools. It allows us to rationalize the interplay between the excited-state transition free energies and the observed optical signatures.

Total molecular photoionization cross-sections by algebraic diagrammatic construction-Stieltjes-Lanczos method: Benchmark calculations

In [K. Gokhberg, V. Vysotskiy, L. S. Cederbaum, L. Storchi, F. Tarantelli, and V. Averbukh, J. Chem. Phys. 130, 064104 (2009)] we introduced a new L(2) ab initio method for the calculation of total molecular photoionization cross-sections. The method is based on the ab initio description of discretized photoionized molecular states within the many-electron Green's function approach, known as algebraic diagrammatic construction (ADC), and on the application of Stieltjes-Chebyshev moment theory to Lanczos pseudospectra of the ADC electronic Hamiltonian. Here we establish the accuracy of the new technique by comparing the ADC-Lanczos-Stieltjes cross-sections in the valence ionization region to the experimental ones for a series of eight molecules of first row elements: HF, NH3, H2O, CO2, H2CO, CH4, C2H2, and C2H4. We find that the use of the second-order ADC technique [ADC(2)] that includes double electronic excitations leads to a substantial systematic improvement over the first-order method [ADC(1)] and to a good agreement with experiment for photon energies below 80 eV. The use of extended second-order ADC theory [ADC(2)x] leads to a smaller further improvement. Above 80 eV photon energy all three methods lead to significant deviations from the experimental values which we attribute to the use of Gaussian single-electron bases. Our calculations show that the ADC(2)-Lanczos-Stieltjes technique is a reliable and efficient ab initio tool for theoretical prediction of total molecular photo-ionization cross-sections in the valence region.

Insight into Group 4 Metallocenium-Mediated Olefin Polymerization Reaction Coordinates Using a Metadynamics Approach.

We report here the first application of the computationally efficient metadynamics approach for analyzing single-site olefin polymerization mechanisms. The mechanism of group 4 metallocenium catalysis for ethylene homopolymerization is investigated by modeling the ethylene insertion step at the cationic (η(5)-C5H5)Zr(CH3)2(+) center using molecular dynamics simulations within the Density Functional Theory (DFT) framework. In particular, the metadynamics formalism is adopted to enable theoretical characterization of covalent bond forming/breaking processes using molecular dynamics ab initio tools. Analysis of the ethylene insertion step free energy surface indicates a slightly exoergic process (-3.2 kcal/mol) with a barrier of 8.6 kcal/mol, in good agreement with conventional ab initio static calculations. Analysis of the structural and dynamic aspects of the simulated reaction coordinate reveals a preferred olefin configuration which aligns parallel to the Zr-CH3 vector in concert with insertion and a slightly bent conformation of the product n-propyl chain to avoid nonbonded repulsion between methylene groups. It is found that the unsaturated/electrophilic CpZr(CH3)2(+) center drives the insertion step, thus promoting the formation of the Zr-alkyl bond. The metadynamics analysis uniquely encompasses all energetically possible reaction coordinates, thus providing a more detailed mechanistic picture. These results demonstrate the potential of metadynamics in the conformational and geometrical analysis of transition metal-centered homogeneous catalytic processes.

Ab Initio Electronic Gaps of Ge Nanodots: The Role of Self-Energy Effects

Nanostructuring of a material leads to enormous effects on its excited state properties. This study, through the application of different state-of-the-art ab initio theoretical tools, investigates the effect of size on the electronic gap of germanium nanocrystals highlighting similarities and differences with respect to equivalent silicon nanostructures. We performed both GW and ΔSCF calculations for the determination of their electronic structure. While it is known that ΔSCF corrections to the Kohn–Sham gap vanish for extended systems, the two approaches were expected to be equivalent in the limit of small clusters. However, it has been recently found that for hydrogenated Si clusters the ΔSCF gaps are systematically smaller than the GW ones, while the opposite is true for Ag clusters. In this work we find that the GW gaps are larger than the ΔSCF ones for all the Ge dots, with the exception of the smallest one. Such crossing between the ΔSCF and the GW gap values was not expected and has never been obse...

Crystal structure prediction for supersaturated AZO: the case of Zn3Al2O6

Increasing the Al concentration in Al-doped ZnO (AZO) is one way of improving the conductivity of this transparent conductive oxide (TCO). Beyond a certain concentration, an unwanted secondary phase develops with a low conductivity. Its stoichiometry is Zn3Al2O6, and its crystal structure has not yet been convincingly determined. By applying unbiased ab initio structure prediction tools, we predict the crystal structure of Zn3Al2O6 to be monoclinic with space group Pm. It can be described as a nanofabric, with one-dimensional Al2O3 wires penetrating a ZnO matrix. This crystal has a formation energy that is lower than any structure proposed before, and is consistent with all available experimental information. Knowledge of the nature of this phase can help to avoid its formation and therefore to engineer AZO crystals with an increased level of Al-doping and associated increased conductivity.

On the photochromic properties of dithienylethenes grafted on gold clusters

Using ab initio spectroscopic tools, we have investigated the structural and electronic properties of a photochromic molecule grafted on a Au13 cluster. To simulate the electronic absorption spectra of this hybrid system, we relied on a (Time-Dependent) Density Functional Theory protocol. It is shown that this TD-DFT procedure combined with an analysis of the virtual molecular orbitals implied in the UV absorption bands provide insights into the loss or preservation of the photochromic properties of the organic switch after attachment to the metallic cluster.

Obtaining models suitable for Rietveld refinement: the EXPO2011 techniques

Abstract Rietveld refinement succeeds if the model is sufficiently close to the target structure. Severe distortions in the structural parameters or relatively high percentage of missed atoms do not allow the refinement to converge. Ab initio techniques like Direct or Patterson methods may rely only on the reflection intensities provided by full pattern decomposition algorithms. Owing to the relevant errors in the intensity estimates, the structural models provided by such phasing techniques are poor and require supplementary improvements before being submitted to Rietveld refinement. The situation is more favorable for non-ab initio techniques, when they can exploit the prior information on the full molecular geometry: their models can be easily submitted to Rietveld refinement, but often the accuracy of the refined model relies on the geometrical information rather than on the experiment. In this paper ab initio and non-ab initio phasing tools of EXPO2011, the updated and more powerful version of EXPO2009 [1], are described together with ancillary techniques for improving and completing the structural models.

Excited-state nature in benzodifuranone dyes: Insights from ab initio simulations

Using ab initio theoretical tools simultaneously accounting for electron correlation and environmental effects, we have simulated the optical spectra of benzodifuranone dyes. In a first step, a valuable computational protocol has been defined and it turned out that a PCM-TD-M06-2X/6-311+G(2d,p)//PCM-PBE0/6-311G(d,p) approach provides an adequate balance between computational requirements and accuracy (deviations of ca. 10 nm with respect to experiment). In a second stage, we have calculated the spectrum of a large series of push-pull structures, and it turned out that the benzodifuranone core is a strong electron capturing group at the excited-state. Indeed, strong auxochroms like the nitro and cyano groups fall short to significantly perturb the LUMO of this series of chromogens. Eventually, in a last phase, the implications of these results are discussed for a series of organic dyes of potential interest for solar cells (DSSC).

Photochromic properties of a dithienylethene–indolinooxazolidine switch: A theoretical investigation

Using ab initio spectroscopic tools, we have studied the structural and electronic properties of an hybrid dithienylethene–indolinooxazolidine switch synthesized by Pozzo and coworkers [Photochem. Photobiol. Sci. 9 (2010) 131]. To simulate the electronic absorption spectra of this mixed photochrome, we relied on a PCM-TD-DFT approach. Several functionals have been considered, namely the PBE0 global hybrid as well as four range-separated hybrids (CAM-B3LYP, LC- ωPBE, ωB97X and ωB97XD). On average, considering all four closed/open structures, ωB97XD provides the best compromise for estimating the transition wavelengths. It is shown that the TD-DFT procedure combined with an analysis of the molecular orbitals implied in the absorption bands provide insights into the observed photochromic pathways.

ChemInform Abstract: From Relative to Absolute Configuration of Complex Natural Products. Interplay Between NMR, ECD, VCD, and ORD Assisted by ab initio Calculations

AbstractReview: 162 refs.

An ab initio simulation of a dithienylethene/phenoxynaphthacenequinone photochromic hybrid

We simulate the properties of a photochromic blend synthesized by Myles, Wigglesworth and Branda [Adv. Mater. 15 (2003) 745] using ab initio tools. This hybrid multi-addressable molecular switch contains a dithienylethene moiety linked to a phenoxynaphthacenequinone group and exhibits four isomers with distinguishable excited-state features. In the first part of this work, we investigate the properties of model (isolated) dithienylethene and phenoxynaphthacenequinone photochromes, with a focus on the second family that was not fully characterized theoretically previously. In the second stage, the spectral properties of the blend are evaluated with the help of (Time-Dependent) Density Functional Theory.

From Relative to Absolute Configuration of Complex Natural Products: Interplay Between NMR, ECD, VCD, and ORD Assisted by ab initio Calculations

This minireview is addressed to readers with a background in basic organic chemistry and spectroscopy, but without a specific knowledge of NMR, ECD, VCD and ORD. Herein we summarize the role of quantum mechanical ab initio prediction of spectral properties in NMR and chiroptical spectroscopies. Illustrative examples of the application of prediction of chemical shifts and scalar couplings to the determination of chemical constitution and relative configurations of natural products are presented. Once the relative configuration is determined, the absolute configuration can be established with the help of ECD, VCD and ORD spectroscopies assisted by quantum mechanical prediction of the corresponding spectra. The scope, limitations and advantages of these chiroptical spectroscopies are presented, in order to help the reader in choosing a suitable combination of ab initio and spectroscopic tools when facing a particular problem. Keywords: Relative configuration determination, absolute configuration determination, NMR, ECD, VCD, ORD, ab initio, natural products, quantum mechanical (QM) modeling, Optical rotation (OR), Chiroptical method, Potential energy surface (PES), Hierarchical organization of spherical environments (HOSE), Chemical shielding, Non hybrid generalized gradient functionals (GGA), Fermi-Contact term (FC), Spindipolar term (SD), Paramagnetic (PSO), Diamagnetic (DSO) spin-orbit terms, Hartree, –, Fock methods, X-ray crystal analysis, IR-silent solvents

Doubly Closing or Not? Theoretical Analysis for Coupled Photochromes

In the course of developing elaborate molecular switches allowing logic operations more evolved than the “on/off” effect, multiply addressable structures containing several dithienylethenes have been recently proposed. Using an ab initio spectroscopic tool, we investigate the structural and electronic properties of two dithienylethenes connected with four types of bridging units (phenyl, silyl, covalent, and ethynylene links). In each case, doubly closed, doubly open, and mixed open/closed structures have been considered. Combining a range-separated hybrid functional (CAM-B3LYP) to an extended basis set and a well-known solvent model, we accurately reproduced the position of the measured optical transitions of the different photochromes. This level of theory also allows to understand the presence or the absence of the fully closed form in most cases. Indeed, for three out of the four bridging units, a careful analysis of the molecular orbitals implied in the low-wavelength bands of the mixed open/closed c...

Low spin moment due to hidden multipole order from spin-orbital ordering in LaFeAsO

This work presents new development and applications of ab-initio simulation tools for material science. Focus lies on materials with strong electronic correlation and strong spin-orbit coupling. Improvements on methods for solving the impurity problem in LDA+DMFT is presented, as well as a reliant method for charge self-consistency in a LMTO based electronic structure code. A new adaptive scheme for Brillouin zone integration is developed, where we show a strong reduction of numerical noise compared to standard techniques. A reformulation of the standard LDA+U method aiming to reduce the number of free parameters is introduced. Fast and realistic reduction of the number of free parameters provides the possibility of high throughput calculations and enabled us to study a large number of compounds. An analysis method for polarization in terms of coupled multipoles, and their corresponding energy contributions is developed and applied. This led to the formulation of Katt's rules, a set of rules complementary to Hund's rules. Katt's rules applies for occupying the orbitals of an electronic shell with strong spin-orbit coupling. The analysis is also used to investigate the unconventional Uranium based superconductors URu2Si2, UPt3, UPd2Al3 and UNi2Al3, as well as the high temperature superconductor LaOFeAs. We also investigate the non-magnetic delta-phase of Plutonium, providing insight to the electronic structure and the branching ratios of 4d to 5f transitions seen in photo emission spectra.The influence of surface reconstruction on the magneto crystalline anisotropy is investigated in multilayer Fe/ZnSe, showing that Fe deposited on an unreconstructed interface strongly reduces the uniaxial component of the MAE. We provide a detailed understanding of the magnetic properties of Fe2P, opening possible routes for enhancing the MAE in this system. A general route to strong MAE in nano-laminates is presented, we apply this to propose a candidate with extremely strong anisotropy energy density, 5Fe/2W1-xReX for x=[0.6-0.8].