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1.
Chem Res Toxicol ; 36(9): 1444-1450, 2023 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-37676849

RESUMO

The use of quantum mechanics (QM) has long been the norm to study covalent-binding phenomena in chemistry and biochemistry. The pharmaceutical industry leverages QM models explicitly in covalent drug discovery and implicitly to characterize short-range interactions in noncovalent binding. Predictive toxicology has resisted widespread adoption of QM, including in the pharmaceutical industry, despite its obvious relevance to the metabolic processes in the upstream of adverse outcome pathways and advances in both QM methods and computational resources, which support fit-for-purpose applications in reasonable timeframes. Here, we make the case for embracing QM as an indispensable part of a toxicologist's toolkit. We argue that QM provides the necessary orthogonality to alert-based expert systems and traditional QSARs, consistent with calls for animal-free integrated testing strategies for safety assessments of commercial chemicals. We outline existing roadblocks to this transition, including the need to train model developers in QM and the shift toward service-based toxicity models that utilize high-performance computing clusters. Lastly, we describe recent examples of successful implementations of QM in hazard assessments and propose how in silico toxicology can be further advanced by integrating QM with artificial intelligence.


Assuntos
Rotas de Resultados Adversos , Inteligência Artificial , Descoberta de Drogas , Indústria Farmacêutica , Relação Quantitativa Estrutura-Atividade
2.
Chem Res Toxicol ; 36(2): 291-304, 2023 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-36745540

RESUMO

N-Nitroso contaminants in medicinal products are of concern due to their high carcinogenic potency; however, not all these compounds are created equal, and some are relatively benign chemicals. Understanding the structure-activity relationships (SARs) that drive hazards in one molecule versus another is key to both protecting human health and alleviating costly and sometimes inaccurate animal testing. Here, we report on an extension of the CADRE (computer-aided discovery and REdesign) platform, which is used broadly by the pharmaceutical and personal care industries to assess environmental and human health endpoints, to predict the carcinogenic potency of N-nitroso compounds. The model distinguishes compounds in three potency categories with 77% accuracy in external testing, which surpasses the reproducibility of rodent cancer bioassays and constraints imposed by limited (high-quality) data. The robustness of predictions for more complex pharmaceuticals is maximized by capturing key SARs using quantum mechanics, that is, by hinging the model on the underlying chemistry versus chemicals in the training set. To this end, the present approach can be leveraged in a quantitative hazard assessment and to offer qualitative guidance using electronic structure comparisons between well-studied analogues and unknown contaminants.


Assuntos
Carcinógenos , Compostos Nitrosos , Animais , Humanos , Carcinógenos/toxicidade , Carcinógenos/química , Reprodutibilidade dos Testes , Compostos Nitrosos/toxicidade , Compostos Nitrosos/química , Relação Estrutura-Atividade , Preparações Farmacêuticas
3.
Chem Res Toxicol ; 35(11): 2097-2106, 2022 11 21.
Artigo em Inglês | MEDLINE | ID: mdl-36190799

RESUMO

Asthma is among the most common occupational diseases with considerable public health and economic costs. Chemicals that induce hypersensitivity in the airways can cause respiratory distress and comorbidities with respiratory infections such as COVID. Robust predictive models for this end point are still elusive due to the lack of an experimental benchmark and the over-reliance of existing in silico tools on structural alerts and structural (vs chemical) similarities. The Computer-Aided Discovery and REdesign (CADRE) platform is a proven strategy for providing robust computational predictions for hazard end points using a tiered hybrid system of expert rules, molecular simulations, and quantum mechanics calculations. The recently developed CADRE model for respiratory sensitization is based on a highly curated data set of structurally diverse chemicals with high-fidelity biological data. The model evaluates absorption kinetics in lung mucosa using Monte Carlo simulations, assigns reactive centers in a molecule and possible biotransformations via expert rules, and determines subsequent reactivity with cell proteins via quantum-mechanics calculations using a multi-tiered regression. The model affords an accuracy above 0.90, with a series of external validations based on literature data in the range of 0.88-0.95. The model is applicable to all low-molecular-weight organics and can inform not only chemical substitution but also chemical redesign to advance development of safer alternatives.


Assuntos
COVID-19 , Humanos , Simulação por Computador , Método de Monte Carlo , Pulmão , Computadores
4.
Chem Res Toxicol ; 35(6): 1011-1022, 2022 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-35532537

RESUMO

Peptide couplers (also known as amide bond-forming reagents or coupling reagents) are broadly used in organic chemical syntheses, especially in the pharmaceutical industry. Yet, occupational health hazards associated with this chemical class are largely unexplored, which is disconcerting given the intrinsic reactivity of these compounds. Several case studies involving occupational exposures reported adverse respiratory and dermal health effects, providing initial evidence of chemical sensitization. To address the paucity of toxicological data, a pharmaceutical cross-industry task force was formed to evaluate and assess the potential of these compounds to cause eye and dermal irritation as well as corrosivity and dermal sensitization. The goal of our work was to inform health and safety professionals as well as pharmaceutical and organic chemists of the occupational health hazards associated with this chemical class. To that end, 25 of the most commonly used peptide couplers and five hydrolysis products were selected for in vivo, in vitro, and in silico testing. Our findings confirmed that dermal sensitization is a concern for this chemical class with 21/25 peptide couplers testing positive for dermal sensitization and 15 of these being strong/extreme sensitizers. We also found that dermal corrosion and irritation (8/25) as well as eye irritation (9/25) were health hazards associated with peptide couplers and their hydrolysis products (4/5 were dermal irritants or corrosive and 4/5 were eye irritants). Resulting outcomes were synthesized to inform decision making in peptide coupler selection and enable data-driven hazard communication to workers. The latter includes harmonized hazard classifications, appropriate handling recommendations, and accurate safety data sheets, which support the industrial hygiene hierarchy of control strategies and risk assessment. Our study demonstrates the merits of an integrated, in vivo -in silico analysis, applied here to the skin sensitization endpoint using the Computer-Aided Discovery and REdesign (CADRE) and Derek Nexus programs. We show that experimental data can improve predictive models by filling existing data gaps while, concurrently, providing computational insights into key initiating events and elucidating the chemical structural features contributing to adverse health effects. This interactive, interdisciplinary approach is consistent with Green Chemistry principles that seek to improve the selection and design of less hazardous reagents in industrial processes and applications.


Assuntos
Irritantes , Saúde Ocupacional , Humanos , Peptídeos/farmacologia , Preparações Farmacêuticas , Pele
5.
Environ Sci Technol ; 55(17): 11713-11722, 2021 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-34428037

RESUMO

Development of high-performing pesticides with tunable degradation properties is vital to increasing the safety and effectiveness of tomorrow's analogs. Chromophoric dissolved organic matter in the excited triple state (3CDOM*) is known to play a key role in the removal of pesticides via indirect photodegradation. However, the potential of these transformations to guide the design of safer chemicals has not yet been fully realized. Here, we report a two-tier computational framework developed to probe and predict both kinetics and thermodynamics of 3CDOM*-pesticide interactions. In the first tier, robust in silico models were constructed by fitting free energies obtained from density functional theory (DFT) calculations to cell potentials and second-order rate constants for the 3CDOM*-pesticide electron transfer. In the second tier, Gibbs free energies and corresponding free energy barriers, determined in solution using the Marcus theory, were applied to develop a quick yet accurate screening approach based on the frontier molecular orbital (FMO) Theory. Being highly mechanistic and spanning ca. 1500 unique 3CDOM*-pesticide interactions, our approach is both robust and broadly applicable. To that end, the outcomes of our computational models were integrated into an easy-to-use decision framework that can guide structure-based design of less persistent pesticide analogs.


Assuntos
Praguicidas , Cinética , Fotólise
6.
J Am Chem Soc ; 142(2): 696-699, 2020 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-31884790

RESUMO

New atom-economical alternatives to Wittig chemistry are needed to construct olefins from carbonyl compounds, but none have been developed to-date. Here we report an atom-economical olefination of carbonyls via aldol-decarbonylative coupling of aldehydes using robust and recyclable supported Pd catalysts, producing only CO and H2O as waste. The reaction affords homocoupling of aliphatic aldehydes, as well as heterocoupling of aliphatic and aromatic ones. Computations provide insight into the selectivity and thermodynamics of the reaction. The tandem aldol-decarbonylation reaction opens the door to exploration of new carbonyl reactivity to construct olefins.

7.
Chem Res Toxicol ; 33(4): 880-888, 2020 04 20.
Artigo em Inglês | MEDLINE | ID: mdl-32166946

RESUMO

As vast numbers of new chemicals are introduced to market annually, we are faced with the grand challenge of protecting humans and the environment while minimizing economically and ethically costly animal testing. In silico models promise to be the solution we seek, but we find ourselves at crossroads of future development efforts that would ensure standalone applicability and reliability of these tools. A conscientious effort that prioritizes experimental testing to support the needs of in silico models (versus regulatory needs) is called for to achieve this goal. Using economic analogy in the title of this work, we argue that a prudent investment is to go all-in to support in silico model development, rather than gamble our future by keeping the status quo of a "balanced portfolio" of testing approaches. We discuss two paths to future in silico toxicology-one based on big-data statistics ("broadsword"), and the other based on direct modeling of molecular interactions ("scalpel")-and offer rationale that the latter approach is more transparent, is better aligned with our quest for fundamental knowledge, and has a greater potential to succeed if we are willing to transform our toxicity-testing paradigm.


Assuntos
Simulação por Computador , Testes de Toxicidade , Animais , Humanos , Modelos Moleculares
8.
Chem Res Toxicol ; 33(2): 426-435, 2020 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-31858786

RESUMO

The transcription factor Nrf2a induces a cellular antioxidant response and provides protection against chemical-induced oxidative stress, as well as playing a critical role in development and disease. Zebrafish are a powerful model to study the role of Nrf2a in these processes but have been limited by reliance on transient gene knockdown techniques or mutants with only partial functional alteration. We developed several lines of zebrafish carrying different null (loss of function, LOF) or hyperactive (gain of function, GOF) mutations to facilitate our understanding of the Nrf2a pathway in protecting against oxidative stress. The mutants confirmed Nrf2a dependence for induction of the antioxidant genes gclc, gstp, prdx1, and gpx1a and identified a role for Nrf2a in the baseline expression of these genes, as well as for sod1. Specifically, the 4-fold induction of gstp by tert-butyl hydroperoxide (tBHP) in wild type fish was abolished in LOF mutants. In addition, baseline gstp expression in GOF mutants increased by 12.6-fold and in LOF mutants was 0.8-fold relative to wild type. Nrf2a LOF mutants showed increased sensitivity to the acute toxicity of cumene hydroperoxide (CHP) and tBHP throughout the first 4 days of development. Conversely, GOF mutants were less sensitive to CHP toxicity during the first 4 days of development and were protected against the toxicity of both hydroperoxides after 4 dpf. Neither gain nor loss of Nrf2a modulated the toxicity of R-(-)-carvone (CAR), despite the ability of this compound to potently induce Nrf2a-dependent antioxidant genes. Similar to other species, GOF zebrafish mutants exhibited significant growth and survival defects. In summary, these new genetic tools can be used to facilitate the identification of downstream gene targets of Nrf2a, better define the role of Nrf2a in the toxicity of environmental chemicals, and further the study of diseases involving altered Nrf2a function.


Assuntos
Derivados de Benzeno/toxicidade , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/efeitos dos fármacos , Mutação com Ganho de Função , Mutação com Perda de Função , Fator 2 Relacionado a NF-E2/genética , Estresse Oxidativo/efeitos dos fármacos , Proteínas de Peixe-Zebra/genética , Peixe-Zebra/genética , terc-Butil Hidroperóxido/toxicidade , Animais , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Relação Dose-Resposta a Droga , Mutação com Ganho de Função/efeitos dos fármacos , Mutação com Perda de Função/efeitos dos fármacos , Fator 2 Relacionado a NF-E2/metabolismo , Estresse Oxidativo/genética , Proteínas de Peixe-Zebra/metabolismo
9.
Chem Res Toxicol ; 33(2): 367-380, 2020 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-31789507

RESUMO

Sustainable molecular design of less hazardous chemicals promises to reduce risks to public health and the environment. Computational chemistry modeling coupled with alternative toxicology models (e.g., larval fish) present unique high-throughput opportunities to understand structural characteristics eliciting adverse outcomes. Numerous environmental contaminants with reactive properties can elicit oxidative stress, an important toxicological response associated with diverse adverse outcomes (i.e., cancer, diabetes, neurodegenerative disorders, etc.). We examined a common chemical mechanism (bimolecular nucleophilic substitution (SN2)) associated with oxidative stress using property-based computational modeling coupled with acute (mortality) and sublethal (glutathione, photomotor behavior) responses in the zebrafish (Danio rerio) and the fathead minnow (Pimephales promelas) models to identify whether relationships exist among biological responses and molecular attributes of industrial chemicals. Following standardized methods, embryonic zebrafish and larval fathead minnows were exposed separately to eight different SN2 compounds for 96 h. Acute and sublethal responses were compared to computationally derived in silico chemical descriptors. Specifically, frontier molecular orbital energies were significantly related to acute LC50 values and photomotor response (PMR) no observed effect concentrations (NOECs) in both fathead minnow and zebrafish. This reactivity index, LC50 values, and PMR NOECs were also significantly related to whole body glutathione (GSH) levels, suggesting that acute and chronic toxicity results from protein adduct formation for SN2 electrophiles. Shared refractory locomotor response patterns among study compounds and two alternative vertebrate models appear informative of electrophilic properties associated with oxidative stress for SN2 chemicals. Electrophilic parameters derived from frontier molecular orbitals were predictive of experimental in vivo acute and sublethal toxicity. These observations provide important implications for identifying and designing less hazardous industrial chemicals with reduced potential to elicit oxidative stress through bimolecular nucleophilic substitution.


Assuntos
Modelos Animais de Doenças , Substâncias Perigosas/toxicidade , Locomoção/efeitos dos fármacos , Teoria Quântica , Animais , Biomarcadores/análise , Cyprinidae , Dose Letal Mediana , Estresse Oxidativo , Testes de Toxicidade , Peixe-Zebra
10.
Environ Sci Technol ; 54(19): 12262-12270, 2020 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-32845620

RESUMO

Whether conducting a risk, hazard, or alternatives assessment, one invariably struggles with the task of reconciling multiple available values of toxicological thresholds into a single outcome. When combining multiple pieces of evidence from many different sources, it is important to consider the role of data uncertainty. Uncertainty is inherent to all scientific data. However, in toxicological assessments, controversies and uncertainties are typically understated; they lack methodological transparency; or they poorly integrate qualitative and quantitative sources of information. Similarly, in model development, data curation is rarely performed with sufficient rigor, particularly when applying big data statistics. To overcome the hurdles of a decision process that must reconcile divergent data, we developed an uncertainty scoring tool that can be trained to reproduce specific decision-making paradigms and ensure consistency in the practitioner's judgment across complex scenarios. While designed to aid with ecotoxicological assessments and predictive model development, the tool's applicability extends to any decision-making process that calls for synthesis of incongruent data. Here, we highlight the development process, as well as demonstrate the method's utility in several prototypical ecotoxicological case studies.


Assuntos
Ecotoxicologia , Medição de Risco , Incerteza
11.
Chem Res Toxicol ; 32(3): 421-436, 2019 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-30547568

RESUMO

Here we report a vertically integrated in vitro - in silico study that aims to elucidate the molecular initiating events involved in the induction of oxidative stress (OS) by seven diverse chemicals (cumene hydroperoxide, t-butyl hydroperoxide, hydroquinone, t-butyl hydroquinone, bisphenol A, Dinoseb, and perfluorooctanoic acid). To that end, we probe the relationship between chemical properties, cell viability, glutathione (GSH) depletion, and antioxidant gene expression. Concentration-dependent effects on cell viability were assessed by MTT assay in two Hepa-1 derived mouse liver cell lines: a control plasmid vector transfected cell line (Hepa-V), and a cell line with increased glutamate-cysteine ligase (GCL) activity and GSH content (CR17). Changes to intracellular GSH content and mRNA expression levels for the Nrf2-driven antioxidant genes Gclc, Gclm, heme oxygenase-1 ( Hmox1), and NADPH quinone oxidoreductase-1 ( Nqo1) were monitored after sublethal exposure to the chemicals. In silico models of covalent and redox reactivity were used to rationalize differences in activity of quinones and peroxides. Our findings show CR17 cells were generally more resistant to chemical toxicity and showed markedly attenuated induction of OS biomarkers; however, differences in viability effects between the two cell lines were not the same for all chemicals. The results highlight the vital role of GSH in protecting against oxidative stress-inducing chemicals as well as the importance of probing molecular initiating events in order to identify chemicals with lower potential to cause oxidative stress.


Assuntos
Antioxidantes/metabolismo , Expressão Gênica/efeitos dos fármacos , Glutationa/biossíntese , Glutationa/metabolismo , Hepatócitos/efeitos dos fármacos , Hepatócitos/metabolismo , 2,4-Dinitrofenol/análogos & derivados , 2,4-Dinitrofenol/química , 2,4-Dinitrofenol/farmacologia , Animais , Derivados de Benzeno/química , Derivados de Benzeno/farmacologia , Compostos Benzidrílicos/química , Compostos Benzidrílicos/farmacologia , Caprilatos/química , Caprilatos/farmacologia , Sobrevivência Celular/efeitos dos fármacos , Células Cultivadas , Fluorocarbonos/química , Fluorocarbonos/farmacologia , Hidroquinonas/química , Hidroquinonas/farmacologia , Cinética , Camundongos , Estrutura Molecular , Estresse Oxidativo/efeitos dos fármacos , Fenóis/química , Fenóis/farmacologia , terc-Butil Hidroperóxido/química , terc-Butil Hidroperóxido/farmacologia
12.
Proc Natl Acad Sci U S A ; 112(20): 6289-94, 2015 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-24639521

RESUMO

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.


Assuntos
Organismos Aquáticos/efeitos dos fármacos , Ecologia/métodos , Química Verde/métodos , Substâncias Perigosas/toxicidade , Indústrias/métodos , Testes de Toxicidade Aguda/métodos , Animais , Cyprinidae , Daphnia , Análise Discriminante , Ecologia/tendências , Química Verde/tendências , Humanos , Indústrias/normas , Dose Letal Mediana , Modelos Lineares
13.
Chem Res Toxicol ; 30(4): 893-904, 2017 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-27750016

RESUMO

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.


Assuntos
Substâncias Perigosas/toxicidade , Estresse Oxidativo/efeitos dos fármacos , Animais , Antioxidantes/metabolismo , Biomarcadores/metabolismo , Cyprinidae/metabolismo , Dano ao DNA/efeitos dos fármacos , Glutationa/metabolismo , Glutationa Transferase/genética , Glutationa Transferase/metabolismo , Substâncias Perigosas/química , Substâncias Perigosas/metabolismo , Modelos Animais , Fator 2 Relacionado a NF-E2/genética , Fator 2 Relacionado a NF-E2/metabolismo , Teoria Quântica , Superóxido Dismutase/genética , Superóxido Dismutase/metabolismo , Peixe-Zebra/metabolismo
14.
Chem Res Toxicol ; 29(1): 58-64, 2016 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-26650775

RESUMO

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.


Assuntos
Simulação por Computador , Modelos Moleculares , Compostos Orgânicos/química , Compostos Orgânicos/toxicidade , Testes de Irritação da Pele/métodos , Pele/efeitos dos fármacos , Animais , Humanos , Método de Monte Carlo , Permeabilidade/efeitos dos fármacos , Absorção Cutânea/efeitos dos fármacos
15.
J Comput Chem ; 36(27): 2064-74, 2015 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-26311531

RESUMO

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.


Assuntos
Compostos Heterocíclicos com 3 Anéis/química , Simulação de Dinâmica Molecular , Nitrocompostos/química , Metilação , Método de Monte Carlo , Distribuição Normal , Teoria Quântica , Eletricidade Estática , Termodinâmica
16.
Chem Res Toxicol ; 25(12): 2780-7, 2012 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-23106682

RESUMO

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.


Assuntos
Alcenos/toxicidade , Carcinógenos/toxicidade , Compostos de Epóxi/toxicidade , Modelos Biológicos , Mutagênicos/toxicidade , Alcenos/química , Carcinógenos/química , Compostos de Epóxi/química , Halogênios/química , Mutagênicos/química
17.
iScience ; 25(11): 105256, 2022 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-36281453

RESUMO

Antiquated and inefficient data-sharing practices represent one of the key obstacles to advancing sustainability goals through green chemistry. To this end, we need to robustly link data on chemical impacts with new chemical design strategies, which requires the development of next-generation data-sharing platforms to harmonize both data and efforts. These decentralized and interactive programs should be structured as live ecosystems for data generation and exchange, inviting conversations about the reliability and relevance of information used to make decisions regarding chemical performance and safety.

18.
Sci Adv ; 8(13): eabn2058, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35353571

RESUMO

Rational design of pesticides with tunable degradation properties and minimal ecotoxicity is among the grand challenges of green chemistry. While computational approaches have gained traction in predictive toxicology, current methods lack the necessary multifaceted approach and design-vectoring tools needed for system-based chemical development. Here, we report a tiered computational framework, which integrates kinetics and thermodynamics of indirect photodegradation with predictions of ecotoxicity and performance, based on cutoff values in mechanistically derived physicochemical properties and electronic parameters. Extensively validated against experimental data and applied to 700 pesticides on the U.S. Environmental Protection Agency's registry, our simple yet powerful approach can be used to screen existing molecules to identify application-ready candidates with desirable characteristics. By linking structural attributes to process-based outcomes and by quantifying trade-offs in safety, depletion, and performance, our method offers a user-friendly roadmap to rational design of novel pesticides.

19.
Environ Toxicol Chem ; 40(6): 1740-1749, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33492718

RESUMO

Threshold of toxicological concern (TTC) is a concept that has been around for decades in human health sciences. Ecotoxicology recently adopted a variant of this concept as eco-TTC. Adoption of the concept of TTC considerably reduces the amount of animal testing required for regulatory purposes. We provide an application of a universal TTC for the entirety of acute fish toxicity data (i.e., establishment of an exposure level below which there would be minimal probability of acute fish toxicity for any chemical, without consideration of mechanism of action). We calculated TTC values for a number of subgroups using various approaches. These approaches were evaluated using data from a cohort of 69 999 acute fish toxicological assays. This database was normalized/curated for units, exposure duration, quality assurance/control, and duplicates, which reduced it to 47 694 assays. Data were not normally but log-normally distributed, making geometric means the most appropriate statistical parameter. Thus, we developed descriptive statistics using geometric means with 95, 99, and 99.9% confidence intervals. Various assessment factors (akin to predicted-no-effect concentration derivation) were applied to the geometric means to derive TTCs. Other approaches employed were the calculation of y = 0 intercepts as well as development of 95 and 99.75% cutoffs of cumulative data as well as modular uncertainty scoring tool (MUST) analysis. All of the methodologies derived highly congruent TTCs ranging from to 2 to 8 µg/L except for the 99.75th percentile cutoff of 0.3 µg/L. The data would be most useful in making a binary testing/no testing required decision. For acute fish toxicity, a TTC value of 2 µg/L was most appropriate, based on the 95th percentile of data distribution without any assessment factor. Environ Toxicol Chem 2021;40:1740-1749. © 2021 SETAC.


Assuntos
Ecotoxicologia , Peixes , Animais , Humanos , Medição de Risco/métodos
20.
J Am Chem Soc ; 132(25): 8766-73, 2010 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-20524660

RESUMO

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.


Assuntos
Óxido de Etileno/química , Solventes/química , Cloridrinas/química , Ciclização , Concentração de Íons de Hidrogênio , Cinética , Modelos Moleculares , Conformação Molecular , Método de Monte Carlo , Teoria Quântica , Termodinâmica
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