MeTA studio: a cross platform, programmable IDE for computational chemist

The development of a cross-platform, programmable integrated development environment (IDE), MeTA Studio, specifically tailored but not restricted to computational chemists working in the area of quantum chemistry with an emphasis on handling large molecules is presented. The IDE consists of a number of modules which include a visualizer and a programming and collaborative framework. The inbuilt viewer assists in visualizing molecules, their scalar fields, manually fragmenting a molecule, and introduces some innovative but simple techniques for handling large molecules. These include a simple Find language and simultaneous multiple camera views of the molecule. Basic tools needed to handle collaborative computing effectively are also included opening up new vistas for sharing ideas and information among computational chemists working on similar problems. MeTA Studio is an integrated programming environment that provides a rich set of application programming interfaces (APIs) which can be used to easily extend its functionality or build new applications as needed by the users. (http://code.google.com/p/metastudio/).

Enabling ab initio Hessian and frequency calculations of large molecules

A linear scaling method, termed as cardinality guided molecular tailoring approach, is applied for the estimation of the Hessian matrix and frequency calculations of spatially extended molecules. The method is put to test on a number of molecular systems largely employing the Hartree-Fock and density functional theory for a variety of basis sets. To demonstrate its ability for correlated methods, we have also performed a few test calculations at the Moller-Plesset second order perturbation theory. A comparison of central processing unit and memory requirements for medium-sized systems with those for the corresponding full ab initio computation reveals substantial gains with negligible loss of accuracy. The technique is further employed for a set of larger molecules, Hessian and frequency calculations of which are not possible on commonly available personal-computer-type hardware.

WebProp: Web interface for ab initio calculation of molecular one-electron properties

This note describes the features and implementation issues of WebProp, a web-based interface for evaluating ab initio quality one-electron properties. The interface code is written in HTML and Python, while the backend is handled using Python and our indigenously developed code INDPROP for property evaluation. A novel feature of this setup is that it provides a simple interface for computing first principle one-electron properties of small to medium sized molecules. To facilitate computation of otherwise expensive calculations on large molecular systems, we employ the Molecular Tailoring Approach (MTA) developed in our laboratory to obtain the density matrix (DM). This DM is then employed for computing the one-electron properties of these systems. The backend transparently handles jobs submitted by the user and runs them either on a single machine or over a grid of compute nodes. The results of the calculations, which include the summary and the files necessary for visualization of one-electron properties, are e-mailed to the user. The user can either directly use the data or visualize it using visualization tools such as UNIVIS-2000 or Drishti.

Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategies

A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including alpha-tocopherol, taxol, gamma-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.

Metal-mediated transport of electrons across molecular films

Electron transfer (ET) to a redox probe in solution across the self-assembled monolayers (SAMs) of a tris-(2-pyridylmethyl)amine-based ligand on gold electrodes is greatly enhanced by Cu-binding.

Self-assembled monolayers (SAMs) of alkoxycyanobiphenyl thiols on gold—A study of electron transfer reaction using cyclic voltammetry and electrochemical impedance spectroscopy

Self-assembled monolayers (SAMs) of liquid crystalline thiol-terminated alkoxycyanobiphenyl molecules with different alkyl chain lengths on Au surface have been studied for the first time using electrochemical techniques such as cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The barrier property of the SAM-modified surfaces was evaluated using two different redox probes, namely potassium ferro/ferri cyanide and hexaammineruthenium(III) chloride. It was found that for short-length alkyl chain thiol (C5) the electron transfer reaction of hexaammineruthenium(III) chloride takes place through tunneling mechanism. In contrast, redox reaction of potassium ferro/ferri cyanide is almost completely blocked by the SAM-modified Au surface. From the impedance data, a surface coverage value of >99.9% was calculated for all the thiol molecules.

Self-assembled monolayers of alkanethiols on gold prepared in a hexagonal lyotropic liquid crystalline phase of Triton X-100/water system

In this paper, we have reported a new method of preparing self-assembled monolayers (SAMs) of decanethiol and hexadecanethiol on gold surface by using a lyotropic liquid crystalline phase as an adsorbing medium. The stability and blocking ability of these SAMs were characterized using grazing angle Fourier transform infrared (FTIR) spectroscopy and electrochemical techniques such as cyclic voltammetry and electrochemical impedance spectroscopy. The lyotropic liquid crystalline medium possesses a hexagonal structure consisting of a nonionic surfactant Triton X-100, water, and the corresponding thiol, which provides a highly hydrophobic environment to solubilize the alkanethiols and later to facilitate their delivery to the gold surface. We find that the SAMs formed from the hexagonal liquid crystalline phase are highly compact and have excellent electrochemical blocking ability towards the redox probes compared to conventional SAMs prepared from commonly used organic solvents such as ethanol. From the impedance studies, we have determined the capacitance of the monolayer-coated electrodes and the surface coverage of the SAM, which has been found to be >99.98% on gold surface. We have also estimated the extent of ionic permeability through the film and measured the rate constants for the redox reactions on the SAM-modified electrodes. Our results show that the rate constants of [Fe(CN)6](3-/4-) and [Ru(NH3)6](2+/3+) redox couples are very much lower in the case of monolayers prepared in liquid crystalline phase compared to the SAM formed in 1 mM thiol in ethanol solution, suggesting a better blocking ability of the SAMs in the former case. From the grazing angle FTIR spectroscopic studies and capacitance measurements, we have ruled out any coadsorption of surfactant molecules on the Au surface. These results suggest that SAMs of very low defect density and extremely low ionic permeability can be obtained when a hexagonal lyotropic liquid crystalline phase is used as an adsorbing medium.

Scanning Tunneling Microscopy, Fourier Transform Infrared Spectroscopy, and Electrochemical Characterization of 2-Naphthalenethiol Self-Assembled Monolayers on the Au Surface: A Study of Bridge-Mediated Electron Transfer in Ru(NH3)62+|Ru(NH3)63+ Redox Reactions

We have studied the structure, adsorption kinetics, and barrier properties of self-assembled monolayers of 2-naphthalenethiol on Au using electrochemical techniques, grazing-angle Fourier transform infrared (FTIR) spectroscopy, and scanning tunneling microscopy (STM). The results of cyclic voltammetric and impedance measurements using redox probes show that 2-naphthalenethiol on Au forms a stable and reproducible, but moderately blocking, monolayer. Annealing of the self-assembled monolayer (SAM)-modified surface at 72 +/- 2 degrees C remarkably improves the blocking property of the monolayer of 2-naphthalenethiol on Au. From the study of kinetics of SAM formation, we find that the self-assembly follows Langmuir adsorption isotherm. Our STM and FTIR results show that the molecules are adsorbed with the naphthalene ring tilted from the surface normal by forming a square root 3 x 3 R30 degrees overlayer structure. From our studies, we conclude that the electron-transfer reaction of ferro/ferricyanide in the freshly formed monolayer occurs predominantly through the pinholes and defects present in the monolayer. However, in the case of thermally annealed specimen, although the ferro/ferricyanide reaction is almost completely blocked, the electron-transfer reaction of hexaammineruthenium(III) chloride is not significantly inhibited. It is proposed that the electron-transfer reaction in the case of the ruthenium redox couple takes place by a tunneling mechanism through the high-electron-density aromatic naphthalene ring acting as a bridge between the monolayer-modified electrode and the ruthenium complex.

Filamin A mutations cause periventricular heterotopia with Ehlers-Danlos syndrome

OBJECTIVE

To define the clinical, radiologic, and genetic features of periventricular heterotopia (PH) with Ehlers-Danlos syndrome (EDS).

METHODS

Exonic sequencing and single stranded conformational polymorphism (SSCP) analysis was performed on affected individuals. Linkage analysis using microsatellite markers on the X-chromosome was performed on a single pedigree. Western blotting evaluated for loss of filamin A (FLNA) protein and Southern blotting assessed for any potential chromosome rearrangement in this region.

RESULTS

The authors report two familial cases and nine additional sporadic cases of the EDS-variant form of PH, which is characterized by nodular brain heterotopia, joint hypermobility, and development of aortic dilatation in early adulthood. MRI typically demonstrated bilateral nodular PH, indistinguishable from PH due to FLNA mutations. Exonic sequencing or SSCP analyses of FLNA revealed a 2762 delG single base pair deletion in one affected female. Another affected female harbored a C116 single point mutation, resulting in an A39G change. A third affected female had a 4147 delG single base pair deletion. One pedigree with no detectable exonic mutation demonstrated positive linkage to the FLNA locus Xq28, an affected individual in this family also had no detectable FLNA protein, but no chromosomal rearrangement was detected.

CONCLUSION

These results suggest that the Ehlers-Danlos variant of periventricular heterotopia (PH), in part, represents an overlapping syndrome with X-linked dominant PH due to filamin A mutations.

Many-body interaction analysis: Algorithm development and application to large molecular clusters

A completely automated algorithm for performing many-body interaction energy analysis of clusters (MBAC) [M. J. Elrodt and R. J. Saykally, Chem. Rev. 94, 1975 (1994); S. S. Xantheas, J. Chem. Phys. 104, 8821 (1996)] at restricted Hartree-Fock (RHF)/MA Plesset 2nd order perturbation theory (MP2)/density functional theory (DFT) level of theory is reported. Use of superior guess density matrices (DM's) for smaller fragments generated from DM of the parent system and elimination of energetically insignificant higher-body combinations, leads to a more efficient performance (speed-up up to 2) compared to the conventional procedure. MBAC approach has been tested out on several large-sized weakly bound molecular clusters such as (H(2)O)(n), n=8, 12, 16, 20 and hydrated clusters of amides and aldehydes. The MBAC results indicate that the amides interact more strongly with water than aldehydes in these clusters. It also reconfirms minimization of the basis set superposition error for large cluster on using superior quality basis set. In case of larger weakly bound clusters, the contributions higher than four body are found to be repulsive in nature and smaller in magnitude. The reason for this may be attributed to the increased random orientations of the interacting molecules separated from each other by large distances.