Jakub Kostal

Towards rational molecular design: derivation of property guidelines for reduced acute aquatic toxicity

One of the most elusive yet significant goals of green chemistry is the routine design of commercially useful chemicals with reduced toxicological hazard. The main objective of this study was to derive property guidelines for the design of chemicals with reduced acute aquatic toxicity to multiple species. The properties explored included chemical solubilities, size, shape and molecular orbital energies. Physicochemical properties were predicted using Schrodingers QikProp, while frontier orbital energies (HOMO, LUMO and HOMO–LUMO gap) were determined based on AM1 and DFT calculations using Gaussian03. Experimental toxicity data included acute toxicity thresholds (LC50) for the fathead minnow (Pimephales promelas; 570 compounds), the Japanese medaka (Oryzias latipes; 285 compounds), a cladoceran (Daphnia magna; 363 compounds) and green algae (Pseudokirchneriella subcapitata, 300 compounds). Mechanistically-driven qualitative and quantitative analyses between the in-silico predicted molecular properties and in vivo toxicity data were explored in order to propose property limits associated with higher probabilities of acutely safe chemicals. The analysis indicates that 70–80% of the compounds that have low or no acute aquatic toxicity concern by EPA guidelines to the four species have a defined range of values for octanol-water partition coefficient (logPo/w) and ΔE (LUMO–HOMO gap). Compounds with logPo/w values less than 2 and ΔE (AM1) greater than 9 eV are significantly more likely to have low acute aquatic toxicity compared to compounds that do not meet these criteria. These results are mechanistically rationalized. Our work proposes design guidelines that can be used to significantly increase the probability that a chemical will have low acute toxicity to the four species studied, and potentially other aquatic species.

Identifying and designing chemicals with minimal acute aquatic toxicity

Significance Two of the rigorous disciplines that have emerged over the last 20 y to empower sustainability science are industrial ecology and green chemistry. Robust assessment tools of industrial ecology identify the greatest opportunities to mitigate human health and environmental impacts resulting from human activity. Green chemistry designs and develops chemicals, materials, and processes that, throughout the life cycle, minimize hazard and maximize efficiency. This process often entails synthesizing new molecules while maintaining function and minimizing adverse outcomes, particularly toxicity. There is an urgent need to develop accurate and economical screening tools that predict potential toxicity and inform the design of safer alternatives. A computational approach is presented for the rational design of molecules for reduced acute aquatic toxicity. Industrial ecology has revolutionized our understanding of material stocks and flows in our economy and society. For this important discipline to have even deeper impact, we must understand the inherent nature of these materials in terms of human health and the environment. This paper focuses on methods to design synthetic chemicals to reduce their intrinsic ability to cause adverse consequence to the biosphere. Advances in the fields of computational chemistry and molecular toxicology in recent decades allow the development of predictive models that inform the design of molecules with reduced potential to be toxic to humans or the environment. The approach presented herein builds on the important work in quantitative structure–activity relationships by linking toxicological and chemical mechanistic insights to the identification of critical physical–chemical properties needed to be modified. This in silico approach yields design guidelines using boundary values for physiochemical properties. Acute aquatic toxicity serves as a model endpoint in this study. Defining value ranges for properties related to bioavailability and reactivity eliminates 99% of the chemicals in the highest concern for acute aquatic toxicity category. This approach and its future implementations are expected to yield very powerful tools for life cycle assessment practitioners and molecular designers that allow rapid assessment of multiple environmental and human health endpoints and inform modifications to minimize hazard.

Towards rational molecular design for reduced chronic aquatic toxicity

The routine rational design of commercial chemicals with minimal toxicological hazard to humans and the environment is a key goal of green chemistry. The development of such a design strategy requires an understanding of the interrelationships between physical–chemical properties, structure, mechanisms and modes of action. This study develops property-based guidelines for the design of chemicals with reduced chronic aquatic toxicity to multiple standardized species and endpoints by exploring properties associated with bioavailability, narcotic toxicity and reactive modes of action, such as electrophilic interactions. Two simple properties emerge as key parameters that distinguish chemicals in the Low EPA level of concern to three aquatic species from those in the High level of concern – octanol–water partition coefficient, (log Po–w) and ΔE (LUMO–HOMO energy gap). Physicochemical properties were predicted using Schrodingers QikProp, while frontier orbital energies were determined based on AM1 and DFT calculations using Gaussian03. Experimental toxicity data used consisted of chronic toxicity thresholds (NOEC) for Daphnia magna reproduction (317 compounds, 504 h-assay) and Oryzias latipes (Japanese medaka, 122 compounds in 336, 504 and 672 h assays) survival, and Pseudokirchneriella subcapitata, a green algae model (392 compounds). Results indicate that 92% of compounds of Low chronic concern have log Po–w values 9 eV. Chronically safe compounds to P. subcapitata meet similar criteria – 80% have log Po–w values < 3 and ΔE greater than 9 eV. Our work proposes design guidelines that can be used to significantly increase the probability that a chemical will have low chronic toxicity, based on the endpoints evaluated, to the three diverse aquatic species studied, and potentially to other aquatic species.

Thorpe-Ingold Acceleration of Oxirane Formation is Mostly a Solvent Effect

The Thorpe-Ingold hypothesis for the gem-dimethyl effect in the cyclization reactions of 2-chloroethoxide derivatives has been investigated computationally in the gas phase and in aqueous solution. Ab initio MP2/6-311+G(d,p) and CBS-Q calculations reveal little intrinsic difference in reactivity with increasing alpha-methylation for the series of reactants 1-3. However, inclusion of continuum hydration or of explicit hydration through mixed quantum and statistical mechanics (MC/FEP) simulations does reproduce the substantial, experimentally observed rate increases with increasing alpha-methylation. Analysis of the MC/FEP results provides clear evidence that the rate increases stem primarily from increased steric hindrance to hydration of the nucleophilic oxygen atom with increasing alpha-methylation. Thus, the gem-dimethyl acceleration of oxirane formation for 1-3 is found to be predominantly a solvent effect.

CADRE-SS, an in Silico Tool for Predicting Skin Sensitization Potential Based on Modeling of Molecular Interactions

Using computer models to accurately predict toxicity outcomes is considered to be a major challenge. However, state-of-the-art computational chemistry techniques can now be incorporated in predictive models, supported by advances in mechanistic toxicology and the exponential growth of computing resources witnessed over the past decade. The CADRE (Computer-Aided Discovery and REdesign) platform relies on quantum-mechanical modeling of molecular interactions that represent key biochemical triggers in toxicity pathways. Here, we present an external validation exercise for CADRE-SS, a variant developed to predict the skin sensitization potential of commercial chemicals. CADRE-SS is a hybrid model that evaluates skin permeability using Monte Carlo simulations, assigns reactive centers in a molecule and possible biotransformations via expert rules, and determines reactivity with skin proteins via quantum-mechanical modeling. The results were promising with an overall very good concordance of 93% between experimental and predicted values. Comparison to performance metrics yielded by other tools available for this endpoint suggests that CADRE-SS offers distinct advantages for first-round screenings of chemicals and could be used as an in silico alternative to animal tests where permissible by legislative programs.

Investigation of solvent effects on the rate and stereoselectivity of the Henry reaction.

A combined computational and experimental kinetic study on the Henry reaction is reported. The effects of solvation on the transition structures and the rates of reaction between nitromethane and formaldehyde, and between nitropropane and benzaldehyde are elucidated with QM/MM calculations.

A free energy approach to the prediction of olefin and epoxide mutagenicity and carcinogenicity.

The mutagenic and carcinogenic effects of strong alkylating agents, such as epoxides, have been attributed to their ability to covalently bind DNA in vivo. Most olefins are readily oxidized to reactive epoxides by CytP450. In an effort to develop predictive models for olefin and epoxide mutagenicity, the ring openings of 15 halogen-, alkyl-, alkenyl-, and aryl-substituted epoxides were modeled by quantum-mechanical transition state calculations using MP2/6-31+G(d,p) in the gas phase and in aqueous solution. Free energies of activation (ΔG(‡)) and free energies of reaction (ΔG(rxn)) were computed for each epoxide in the series. This study finds that an aqueous solution ΔG(rxn) threshold value of approximately -14.7 kcal/mol can be used to discern mutagenic/carcinogenic epoxides (ΔG(rxn) < -14.7 kcal/mol) from nonmutagens/noncarcinogens (ΔG(rxn) > -14.7 kcal/mol). The computed reaction thermodynamics are appropriate regardless of ring-opening mechanism in vivo and are thus proposed as an effective in silico screen and design guideline for decreasing potential mutagenicity and carcinogenicity of olefins and their respective epoxides.

Toward the Design of Less Hazardous Chemicals: Exploring Comparative Oxidative Stress in Two Common Animal Models.

Sustainable molecular design of less hazardous chemicals presents a potentially transformative approach to protect public health and the environment. Relationships between molecular descriptors and toxicity thresholds previously identified the octanol-water distribution coefficient, log D, and the HOMO-LUMO energy gap, ΔE, as two useful properties in the identification of reduced aquatic toxicity. To determine whether these two property-based guidelines are applicable to sublethal oxidative stress (OS) responses, two common aquatic in vivo models, the fathead minnow (Pimephales promelas) and zebrafish (Danio rerio), were employed to examine traditional biochemical biomarkers (lipid peroxidation, DNA damage, and total glutathione) and antioxidant gene activation following exposure to eight structurally diverse industrial chemicals (bisphenol A, cumene hydroperoxide, dinoseb, hydroquinone, indene, perfluorooctanoic acid, R-(-)-carvone, and tert-butyl hydroperoxide). Bisphenol A, cumene hydroperoxide, dinoseb, and hydroquinone were consistent inducers of OS. Glutathione was the most consistently affected biomarker, suggesting its utility as a sensitivity response to support the design of less hazardous chemicals. Antioxidant gene expression (changes in nrf2, gclc, gst, and sod) was most significantly (p < 0.05) altered by R-(-)-carvone, cumene hydroperoxide, and bisphenol A. Results from the present study indicate that metabolism of parent chemicals and the role of their metabolites in molecular initiating events should be considered during the design of less hazardous chemicals. Current empirical and computational findings identify the need for future derivation of sustainable molecular design guidelines for electrophilic reactive chemicals (e.g., SN2 nucleophilic substitution and Michael addition reactivity) to reduce OS related adverse outcomes in vivo.

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on‐the‐fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C‐shell linker script facilitates the interprogram communication. The BOSS–Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS–Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free‐energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.