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Dive into the research topics where Steven Trohalaki is active.

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Featured researches published by Steven Trohalaki.


Computational Biology and Chemistry | 2000

Improved QSARs for predictive toxicology of halogenated hydrocarbons

Steven Trohalaki; Eric M. Gifford; Ruth Pachter

In our continuing efforts to provide a predictive toxicology capability, we seek to improve QSARs (quantitative structure-activity relationships) for chemicals of interest. Currently, although semi-empirical molecular orbital methods are hardly the state of the art for studying small molecules, AM1 calculations appear to be the method of choice when calculating quantum-chemical descriptors. However, with the advent of modern computational capabilities and the development of fast algorithms, ab initio molecular orbital and first principles density functional methods can be expeditiously applied in current QSAR studies. We present a study on halogenated alkanes to assess whether more accurate quantum methods result in QSARs that correlate better with experimental data. Furthermore, improved QSARs can also be obtained through development of new descriptors with explicit physical interpretations that should lead to better understanding of the mechanisms involved in the toxic response. We show that descriptors calculated from chemical intermediates may be useful in future QSARs.


Polymer | 1995

Barrier to phenyl rotation in poly(p-phenylene benzobisthiazole) from ab initio molecular orbital calculations

Steven Trohalaki; Douglas S. Dudis

Abstract Optimal molecular geometry and the barrier to internal phenyl rotation were obtained from ab initio molecular orbital calculations of model compounds of poly( p -phenylene benzobisthiazole). Bond lengths and angles are in good agreement with those found from a previous X-ray crystallographic study of a similar model compound. Based on the calculated torsional potential, the discrepancy between theoretical and experimental phenyl torsions is attributed to crystal packing forces. The calculated torsion barrier is three to five times greater than in previous semi-empirical AM1 molecular orbital calculations. Calculations were performed with the 6 – 31 G ∗ basis set and the rotation barrier was corrected for electron correlation employing second-order Moller-Plesset perturbation theory.


Polymer | 1996

Molecular dynamics simulation of a single-component molecular composite: poly(p-phenylene benzobisthiazole)/meta-poly(aryl ether ketone) block copolymer

Steven Trohalaki

Molecular dynamics simulations were performed with a model of a single-component molecular composite in the form of a block copolymer composed of poly(p-phenylene benzobisthiazole) rigid-rod and flexible meta-poly(aryl ether ketone) subunits. The molecular composite concept, applied to improve the compressive strength of rigid-rod polymers and to improve their solubility, relies on a uniform distribution of rods in a coil-like matrix. Pair distribution functions, orientation correlation functions and correlation volumes calculated from equilibrium dynamics trajectories of bulk copolymer, coil homopolymer and rigid-rod homopolymer systems imply that, while inter-rod spacing is only slightly increased in the copolymer, correlation of rod orientation is greatly reduced but to a somewhat lesser extent than previously found for a graft copolymer composed of identical subunits. Conformations of the flexible blocks extend to accommodate the partial rod alignment. The block copolymer topology appears to be a viable alternative to the hairy-rod graft copolymer as a single-component molecular composite.


MRS Proceedings | 2004

Fluorophore Conformation in Green Fluorescent Protein: A Quantum Mechanics/Molecular Mechanics Study

Steven Trohalaki; Soumya S. Patnaik; Ruth Pachter

Green Fluorescent Protein (GFP) is a widely used fluorescent marker exhibiting two excitation peaks – a strong peak at 398 nm and a second at 475 nm, with the fluorescence at ca. 510 nm. Its molecular structure consists of a β-barrel composed of 11 β-strands and a central helix containing the fluorophore. Two different forms of the fluorophore – a protonated/neutral fluorophore and a de-protonated/anionic fluorophore – are thought to be responsible for the two distinct spectroscopic states. Notably, the isolated fluorophore in solution is efficiently quenched. Conformational flexibility within the protein cavity is an implicitly important factor that governs the photochemistry of GFP. However, the literature contains accounts of studies that reach conflicting conclusions, claiming that either the fluorophores barrier to internal rotation is negligibly small or that the protein cavity is not complementary to a planar fluorophore. In this work, we calculate the torsional potential of one of the two exocyclic bonds that connect the two rings in the fluorophore, taking into account its immediate environment by applying a quantum mechanics/molecular mechanics method, with the ultimate aim of evaluating the protein-environment effects on the fluorescence.


Energy & Fuels | 2005

Quantitative Structure−Property Relationships for Melting Points and Densities of Ionic Liquids

Steven Trohalaki; Ruth Pachter; Greg Drake; Tommy Hawkins


Qsar & Combinatorial Science | 2005

Prediction of Melting Points for Ionic Liquids

Steven Trohalaki; Ruth Pachter


ACS Applied Materials & Interfaces | 2013

Electronic properties of a graphene device with peptide adsorption : insight from simulation

Brahim Akdim; Ruth Pachter; Steve S. Kim; Rajesh R. Naik; Tiffany R. Walsh; Steven Trohalaki; Gongyi Hong; Zhifeng Kuang; Barry L. Farmer


Biopolymers | 2004

Molecular modeling of green fluorescent protein: Structural effects of chromophore deprotonation†

Soumya S. Patnaik; Steven Trohalaki; Ruth Pachter


Toxicological Sciences | 2002

Risk Assessment of High-Energy Chemicals by in Vitro Toxicity Screening and Quantitative Structure-Activity Relationships

Steven Trohalaki; Robert J. Zellmer; Ruth Pachter; Saber M. Hussain; John M. Frazier


Energy & Fuels | 1999

Modeling of fuel-system icing inhibitors

Steven Trohalaki; Ruth Pachter; John R. Cummings

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Ruth Pachter

Wright-Patterson Air Force Base

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Soumya S. Patnaik

Air Force Research Laboratory

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Rajesh R. Naik

Air Force Research Laboratory

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Barry L. Farmer

Wright-Patterson Air Force Base

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Brahim Akdim

Wright-Patterson Air Force Base

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Douglas S. Dudis

Air Force Research Laboratory

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Gary S. Kedziora

Wright-Patterson Air Force Base

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Gongyi Hong

Wright-Patterson Air Force Base

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Greg Drake

Air Force Research Laboratory

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