1
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Csizi KS, Reiher M. Automated preparation of nanoscopic structures: Graph-based sequence analysis, mismatch detection, and pH-consistent protonation with uncertainty estimates. J Comput Chem 2024; 45:761-776. [PMID: 38124290 DOI: 10.1002/jcc.27276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties. Molecular simulations of nanoscopic atomistic structures therefore require accurately resolved three-dimensional input structures. If extracted from experiment, these structures often suffer from severe uncertainties, of which the lack of information on hydrogen atoms is a prominent example. Hence, experimental structures require careful review and curation, which is a time-consuming and error-prone process. Here, we present a fast and robust protocol for the automated structure analysis and pH-consistent protonation, in short, ASAP. For biomolecules as a target, the ASAP protocol integrates sequence analysis and error assessment of a given input structure. ASAP allows for pK a prediction from reference data through Gaussian process regression including uncertainty estimation and connects to system-focused atomistic modeling described in Brunken and Reiher (J. Chem. Theory Comput. 16, 2020, 1646). Although focused on biomolecules, ASAP can be extended to other nanoscopic objects, because most of its design elements rely on a general graph-based foundation guaranteeing transferability. The modular character of the underlying pipeline supports different degrees of automation, which allows for (i) efficient feedback loops for human-machine interaction with a low entrance barrier and for (ii) integration into autonomous procedures such as automated force field parametrizations. This facilitates fast switching of the pH-state through on-the-fly system-focused reparametrization during a molecular simulation at virtually no extra computational cost.
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Affiliation(s)
- Katja-Sophia Csizi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Markus Reiher
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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2
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Tran TTV, Tayara H, Chong KT. Recent Studies of Artificial Intelligence on In Silico Drug Absorption. J Chem Inf Model 2023; 63:6198-6211. [PMID: 37819031 DOI: 10.1021/acs.jcim.3c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Absorption is an important area of research in pharmacochemistry and drug development, because the drug has to be absorbed before any drug effects can occur. Furthermore, the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profile of drugs can be directly and considerably altered by modulating factors affecting absorption. Many drugs in development fail because of poor absorption. The research and continuous efforts of researchers in recent years have brought many successes and promises in drug absorption property prediction, especially in silico, which helps to reduce the time and cost significantly for screening undesirable drug candidates. In this report, we explicitly provide an overview of recent in silico studies on predicting absorption properties, especially from 2019 to the present, using artificial intelligence. Additionally, we have collected and investigated public databases that support absorption prediction research. On those grounds, we also proposed the challenges and development directions of absorption prediction in the future. We hope this review can provide researchers with valuable guidelines on absorption prediction to facilitate the development of newer approaches in drug discovery.
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Affiliation(s)
- Thi Tuyet Van Tran
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Faculty of Information Technology, An Giang University, Long Xuyen 880000, Vietnam
- Vietnam National University, Ho Chi Minh City, Ho Chi Minh 700000, Vietnam
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Kil To Chong
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
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3
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Zhang CZ, Jin RH, Shen QQ, Liu LL. Synthesis of graphene oxide grafted by diazanyl groups and its application in recovery of lead from lead-acid wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:29844-29858. [PMID: 36418827 DOI: 10.1007/s11356-022-24319-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Heavy metal ion (HMI) in wastewater is a kind of resource that is wrongly placed. Recovery of heavy metal from lead-acid wastewater desires efficient and reusable functional materials. In this paper, graphene oxide-like with diazanyl groups (GOLA) was synthesized by a nucleophilic substitution reaction of graphene oxide-like with hydroxyl groups (GOLH) with diazane. GOLA exhibited good stability and recyclability in wastewater. The maximal adsorption capacity (qmax) values of GOLA for Pb(II), Cd(II), Cu(II), Ni(II), and Cr(III) ions were 505.80, 401.99, 83.48, 82.29, and 147.77 mg/g, respectively. The equilibrium time of GOLA adsorbing HMIs was 20 min. GOLA was employed to recover lead ions from lead-acid wastewater to give Pb(OH)2 and reusable water. Therefore, this paper provides a useful method of recycling lead from lead-acid wastewater.
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Affiliation(s)
- Chao-Zhi Zhang
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China.
- School of Chemistry and Materials Science, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China.
| | - Rui-Hua Jin
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China
| | - Qian-Qian Shen
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China
| | - Ling-Ling Liu
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China
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4
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Bosia F, Zheng P, Vaucher A, Weymuth T, Dral PO, Reiher M. Ultra-fast semi-empirical quantum chemistry for high-throughput computational campaigns with Sparrow. J Chem Phys 2023; 158:054118. [PMID: 36754821 DOI: 10.1063/5.0136404] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Semi-empirical quantum chemical approaches are known to compromise accuracy for the feasibility of calculations on huge molecules. However, the need for ultrafast calculations in interactive quantum mechanical studies, high-throughput virtual screening, and data-driven machine learning has shifted the emphasis toward calculation runtimes recently. This comes with new constraints for the software implementation as many fast calculations would suffer from a large overhead of the manual setup and other procedures that are comparatively fast when studying a single molecular structure, but which become prohibitively slow for high-throughput demands. In this work, we discuss the effect of various well-established semi-empirical approximations on calculation speed and relate this to data transfer rates from the raw-data source computer to the results of the visualization front end. For the former, we consider desktop computers, local high performance computing, and remote cloud services in order to elucidate the effect on interactive calculations, for web and cloud interfaces in local applications, and in world-wide interactive virtual sessions. The models discussed in this work have been implemented into our open-source software SCINE Sparrow.
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Affiliation(s)
- Francesco Bosia
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Peikun Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Alain Vaucher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Thomas Weymuth
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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5
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Udofia IA, Ekama T, Ogunbayo TB, Oloba-Whenu OA, Rhyman L, Isanbor C, Ramasami P. Experimental and theoretical calculation of pKa values of substituted-2,4,6-trinitrodiphenylamines. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Okumuş A, Elmas G, Binici A, Aydın B, Açık L, Kılıç Z, Hökelek T. Phosphorus-nitrogen compounds. Part 62. Preparation of tetraaminobis(4-fluorobenzyl)spiro(N/N)cyclotriphosphazenes: Chemical, structural characterizations, antimicrobial, antioxidant and DNA-binding activity studies. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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7
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Binici A, Elmas G, Okumuş A, Güzel R, Şimşek H, Kılıç Z. Phosphorus–nitrogen compounds: Part 60: Synthesis of hexaminomonoferrocenyl-spiro(N/O)cyclotetraphosphazenes: Spectral and electrochemical properties, tuning of redox feature, and antituberculosis activity. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2100888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Arzu Binici
- Department of Consumer Safety & Public Health Laboratories, Republic of Turkiye, Ministry of Health, Ankara, Türkiye
| | - Gamze Elmas
- Department of Chemistry, Ankara University, Ankara, Türkiye
| | - Aytuğ Okumuş
- Department of Chemistry, Ankara University, Ankara, Türkiye
| | - Remziye Güzel
- Department of Chemistry, Dicle University, Diyarbakır, Türkiye
| | - Hülya Şimşek
- Department of Medical Microbiology, Faculty of Medicine, Bozok University, Yozgat, Türkiye
| | - Zeynel Kılıç
- Department of Consumer Safety & Public Health Laboratories, Republic of Turkiye, Ministry of Health, Ankara, Türkiye
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8
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Zhu T, He Q, Wang Z, Zhang J, Li H, Fu H, Liao F. Self-driven in situ facile synthesis of CuO/Cu 2O for enhanced catalytic reduction of 4-nitrophenol by acetic acid. NEW J CHEM 2022. [DOI: 10.1039/d2nj02366k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of CuO, Cu2O and CuO/Cu2O catalyst structures with different morphologies are synthesized in situ by controlling the anionic species of the copper salts in the reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP).
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Affiliation(s)
- Ting Zhu
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Qian He
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Ziwei Wang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Juan Zhang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Hanke Li
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, South China University of Technology, Guangzhou, Guangdong 510641, China
| | - Hongquan Fu
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Fang Liao
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
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9
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Pracht P, Grimme S. Efficient Quantum-Chemical Calculations of Acid Dissociation Constants from Free-Energy Relationships. J Phys Chem A 2021; 125:5681-5692. [PMID: 34142841 DOI: 10.1021/acs.jpca.1c03463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calculation of acid dissociation constants (pKa) is an important task in computational chemistry and chemoinformatics. Theoretically and with minimal empiricism, this is possible from computed acid dissociation free energies via so-called linear free-energy relationships. In this study some modifications are introduced to the latter, providing a straightforward, broadly applicable protocol with an adjustable degree of sophistication for quantum chemistry-based calculations of pKa in water. It targets a wide pKa range (∼70 units) and medium-sized, flexible molecules. Herein, a focus is set on the recently published r2SCAN-3c and related efficient composite density functionals and the semiempirical GFN2-xTB method, including a newly introduced energy correction for heterolytic dissociation, both in combination with implicit solvation models. The performance is evaluated in comparison with experimental data, showing mean errors often smaller than a targeted 1 pKa unit accuracy. Larger deviations are observed only upon inclusion of challenging highly negative (<-5) or positive (>15) pKa values. Among all those tested, it is found that B97-3c is the best performing functional, although rather independently of the density functional theory (DFT) method used; low root-mean-square errors of 0.8-1.0 pKa units for typical drugs are obtained. For optimal performance, it is recommended to employ DFT functional specific free-energy relationship parameters. Additionally, a significant conformational dependence of the pKa values is revealed and quantified for some nonrigid drug molecules.
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Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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10
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Gieseking RLM. A new release of MOPAC incorporating the INDO/S semiempirical model with CI excited states. J Comput Chem 2021; 42:365-378. [PMID: 33227163 DOI: 10.1002/jcc.26455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/28/2020] [Accepted: 11/05/2020] [Indexed: 11/10/2022]
Abstract
The semiempirical INDO/S Hamiltonian is incorporated into a new release of MOPAC2016. The MOPAC2016 software package has long been at the forefront of semiempirical quantum chemical methods (SEQMs) for small molecules, proteins, and solids and until this release has included only NDDO-type SEQMs. The new code enables the calculation of excited states using the INDO/S Hamiltonian combined with a configuration interaction (CI) approach using single excitations (CIS), single and double excitations (CISD), or multiple reference determinants (MRCI) where reference determinants are generated using a complete active space (CAS) approach. The capacity to perform excited-state calculations beyond the CIS level makes INDO/CI one of the few low-cost computational methods capable of accurately modeling states with substantial double-excitation character. Solvent corrections to the ground-state and excited-state energies can be computed using the COSMO implicit solvent model, incorporating state-specific corrections to the excited states based on the solvent refractive index. This code produces physically reasonable electronic structures, absorption spectra, and solvatochromic shifts at low computational costs for systems up to hundreds of atoms, and for both organic molecules and metal clusters.
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11
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Dutra FR, Silva CDS, Custodio R. On the Accuracy of the Direct Method to Calculate p Ka from Electronic Structure Calculations. J Phys Chem A 2020; 125:65-73. [PMID: 33356255 PMCID: PMC7872415 DOI: 10.1021/acs.jpca.0c08283] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
The
direct method (HA(soln) ⇌ A(soln)– + H(soln)+) for calculating
pKa of monoprotic acids is as efficient
as thermodynamic cycles. A selective adjustment of proton free energy
in solution was used with experimental pKa data. The procedure was analyzed at different levels of theory.
The solvent was described by the solvation model density (SMD) model,
including or not explicit water molecules, and three training sets
were tested. The best performance under any condition was obtained
by the G4CEP method with a mean absolute error close to 0.5 units
of pKa and an uncertainty around ±1
unit of pKa for any training set including
or excluding explicit solvent molecules. PM6 and AM1 performed very
well with average absolute errors below 0.75 units of pKa but with uncertainties up to ±2 units of pKa, using only the SMD solvent model. Density
functional theory (DFT) results were highly dependent on the basis
functions and explicit water molecules. The best performance was observed
for the local spin density approximation (LSDA) functional in almost
all calculations and under certain conditions, as high as those obtained
by G4CEP. Basis set complexity and explicit solvent molecules were
important factors to control DFT calculations. The training set molecules
should consider the diversity of compounds.
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Affiliation(s)
- Felipe Ribeiro Dutra
- Instituto de Química, Universidade Estadual de Campinas, P.O. Box 6154, Barão Geraldo, 13083-970 Campinas, São Paulo, Brazil
| | - Cleuton de Souza Silva
- Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, Campus de Itacoatiara, 69100-021 Itacoatiara, Amazonas, Brazil
| | - Rogério Custodio
- Instituto de Química, Universidade Estadual de Campinas, P.O. Box 6154, Barão Geraldo, 13083-970 Campinas, São Paulo, Brazil
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12
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Mohebi N, Kassaee MZ. Predicting novel strong acids of plumbylene at theoretical levels. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nazanin Mohebi
- Department of Chemistry Tarbiat Modares University Tehran Iran
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13
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Laribi A, Allegra S, Souiri M, Mzoughi R, Othmane A, Girardot F. Legionella pneumophila sg1-sensing signal enhancement using a novel electrochemical immunosensor in dynamic detection mode. Talanta 2020; 215:120904. [PMID: 32312449 DOI: 10.1016/j.talanta.2020.120904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/20/2023]
Abstract
This work presents a comparison between static and dynamic modes of biosensing using a novel microfluidic assay for continuous and quantitative detection of Legionella pneumophila sg1 in artificial water samples. A self-assembled monolayer of 16-amino-1-hexadecanethiol (16-AHT) was covalently linked to a gold substrate, and the resulting modified surface was used to immobilize an anti-Legionella pneumophila monoclonal antibody (mAb). The modified surfaces formed during the biosensor functionalization steps were characterized using electrochemical measurements and microscopic imaging techniques. Under static conditions, the biosensor exhibited a wide linear response range from 10 to 108 CFU/mL and a detection limit of 10 CFU/mL. Using a microfluidic system, the biosensor responses exhibited a linear relationship for low bacterial concentrations ranging from 10 to 103 CFU/mL under dynamic conditions and an enhancement of sensing signals by a factor of 4.5 compared to the sensing signals obtained under static conditions with the same biosensor for the detection of Legionella cells in artificially contaminated samples.
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Affiliation(s)
- Ahlem Laribi
- Environments, Territories, Societies (EVS) Lab, Mixed Research Unit (Jean Monnet University - French National Centre for Scientific Research) 5600, University of Lyon, F42023, France; Laboratory of Advanced Materials and Interfaces, Faculty of Medicine, University of Monastir, 5019, Monastir, Tunisia.
| | - Séverine Allegra
- Environments, Territories, Societies (EVS) Lab, Mixed Research Unit (Jean Monnet University - French National Centre for Scientific Research) 5600, University of Lyon, F42023, France
| | - Mina Souiri
- Laboratory of Advanced Materials and Interfaces, Faculty of Medicine, University of Monastir, 5019, Monastir, Tunisia
| | - Ridha Mzoughi
- Regional Laboratory of Hygiene, University Hospital Farhat Hached, 4000 Sousse, Tunisia and Laboratory of Analysis Treatment and Valorization of Pollutants and Products, Faculty of Pharmacy, 5000, Monastir, Tunisia
| | - Ali Othmane
- Laboratory of Advanced Materials and Interfaces, Faculty of Medicine, University of Monastir, 5019, Monastir, Tunisia
| | - Françoise Girardot
- Environments, Territories, Societies (EVS) Lab, Mixed Research Unit (Jean Monnet University - French National Centre for Scientific Research) 5600, University of Lyon, F42023, France
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14
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Pracht P, Bohle F, Grimme S. Automated exploration of the low-energy chemical space with fast quantum chemical methods. Phys Chem Chem Phys 2020; 22:7169-7192. [PMID: 32073075 DOI: 10.1039/c9cp06869d] [Citation(s) in RCA: 861] [Impact Index Per Article: 215.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated minimum energy structures normally form the basis of further, mostly DFT computational work, such as the calculation of spectra or macroscopic properties. By using basic quantum chemical methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chemical methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized molecules) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chemistry and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.
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Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
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15
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Ayoubi-Chianeh M, Kassaee MZ. Novel silicon super bases at DFT level of theory: effects of fused benzene rings on the basicity of 2,4,6-cycloheptatrienesilylene. RESEARCH ON CHEMICAL INTERMEDIATES 2019. [DOI: 10.1007/s11164-019-03856-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Dral PO, Wu X, Thiel W. Semiempirical Quantum-Chemical Methods with Orthogonalization and Dispersion Corrections. J Chem Theory Comput 2019; 15:1743-1760. [PMID: 30735388 PMCID: PMC6416713 DOI: 10.1021/acs.jctc.8b01265] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/31/2022]
Abstract
We present two new semiempirical quantum-chemical methods with orthogonalization and dispersion corrections: ODM2 and ODM3 (ODM x). They employ the same electronic structure model as the OM2 and OM3 (OM x) methods, respectively. In addition, they include Grimme's dispersion correction D3 with Becke-Johnson damping and three-body corrections E ABC for Axilrod-Teller-Muto dispersion interactions as integral parts. Heats of formation are determined by adding explicitly computed zero-point vibrational energy and thermal corrections, in contrast to standard MNDO-type and OM x methods. We report ODM x parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine that are optimized with regard to a wide range of carefully chosen state-of-the-art reference data. Extensive benchmarks show that the ODM x methods generally perform better than the available MNDO-type and OM x methods for ground-state and excited-state properties, while they describe noncovalent interactions with similar accuracy as OM x methods with a posteriori dispersion corrections.
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Affiliation(s)
- Pavlo O. Dral
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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17
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Prediction of pK(a) values of neutral and alkaline drugs with particle swarm optimization algorithm and artificial neural network. Neural Comput Appl 2019. [DOI: 10.1007/s00521-018-3956-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Pracht P, Wilcken R, Udvarhelyi A, Rodde S, Grimme S. High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge. J Comput Aided Mol Des 2018; 32:1139-1149. [PMID: 30141103 DOI: 10.1007/s10822-018-0145-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022]
Abstract
Recent advances in the development of low-cost quantum chemical methods have made the prediction of conformational preferences and physicochemical properties of medium-sized drug-like molecules routinely feasible, with significant potential to advance drug discovery. In the context of the SAMPL6 challenge, macroscopic pKa values were blindly predicted for a set of 24 of such molecules. In this paper we present two similar quantum chemical based approaches based on the high accuracy calculation of standard reaction free energies and the subsequent determination of those pKa values via a linear free energy relationship. Both approaches use extensive conformational sampling and apply hybrid and double-hybrid density functional theory with continuum solvation to calculate free energies. The blindly calculated macroscopic pKa values were in excellent agreement with the experiment.
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Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Rainer Wilcken
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland.
| | - Anikó Udvarhelyi
- Novartis Pharma AG, Technical Research and Development, 4002, Basel, Switzerland
| | - Stephane Rodde
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany.
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19
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Zeng Q, Jones MR, Brooks BR. Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge. J Comput Aided Mol Des 2018; 32:1179-1189. [PMID: 30128926 DOI: 10.1007/s10822-018-0150-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/09/2018] [Indexed: 12/25/2022]
Abstract
In this work, quantum mechanical methods were used to predict the microscopic and macroscopic pKa values for a set of 24 molecules as a part of the SAMPL6 blind challenge. The SMD solvation model was employed with M06-2X and different basis sets to evaluate three pKa calculation schemes (direct, vertical, and adiabatic). The adiabatic scheme is the most accurate approach (RMSE = 1.40 pKa units) and has high correlation (R2 = 0.93), with respect to experiment. This approach can be improved by applying a linear correction to yield an RMSE of 0.73 pKa units. Additionally, we consider including explicit solvent representation and multiple lower-energy conformations to improve the predictions for outliers. Adding three water molecules explicitly can reduce the error by 2-4 pKa units, with respect to experiment, whereas including multiple local minima conformations does not necessarily improve the pKa prediction.
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Affiliation(s)
- Qiao Zeng
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA.
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA
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20
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Lu J, Lu T, Zhao X, Chen X, Zhan CG. Correlations between the 1H NMR chemical shieldings and the pK a values of organic acids and amines. J Mol Model 2018; 24:146. [PMID: 29858663 DOI: 10.1007/s00894-018-3690-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/22/2018] [Indexed: 01/18/2023]
Abstract
The acid dissociation constants and 1H NMR chemical shieldings of organic compounds are important properties that have attracted much research interest. However, few studies have explored the relationship between these two properties. In this work, we theoretically studied the NMR chemical shifts of a series of carboxylic acids and amines in the gas phase and in aqueous solution. It was found that the negative logarithms of the experimental acid dissociation constants (i.e., the pKa values) of the organic acids and amines in aqueous solution correlate almost linearly with the corresponding calculated NMR chemical shieldings. Key factors that affect the theoretically predicted pKa values are discussed in this paper. The present work provides a new way to predict the pKa values of organic/biochemical compounds. Graphical abstract The chemical shielding values of organic acids and amines correlate near linearly with their corresponding pKa values.
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Affiliation(s)
- Juanfeng Lu
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Tingting Lu
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Xinyun Zhao
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Xi Chen
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, 430074, People's Republic of China.
| | - Chang-Guo Zhan
- College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
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21
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Kromann JC, Jensen JH, Kruszyk M, Jessing M, Jørgensen M. Fast and accurate prediction of the regioselectivity of electrophilic aromatic substitution reactions. Chem Sci 2018; 9:660-665. [PMID: 29629133 PMCID: PMC5869546 DOI: 10.1039/c7sc04156j] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
While computational prediction of chemical reactivity is possible it usually requires expert knowledge and there are relatively few computational tools that can be used by a bench chemist to help guide synthesis. The RegioSQM method for predicting the regioselectivity of electrophilic aromatic substitution reactions of heteroaromatic systems is presented in this paper. RegioSQM protonates all aromatic C-H carbon atoms and identifies those with the lowest free energies in chloroform using the PM3 semiempirical method as the most nucleophilic center. These positions are found to correlate qualitatively with the regiochemical outcome in a retrospective analysis of 96% of more than 525 literature examples of electrophilic aromatic halogenation reactions. The method is automated and requires only a SMILES string of the molecule of interest, which can easily be generated using chemical drawing programs such as ChemDraw. The computational cost is 1-10 minutes per molecule depending on size, using relatively modest computational resources and the method is freely available via a web server at ; http://www.regiosqm.org. RegioSQM should therefore be of practical use in the planning of organic synthesis.
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Affiliation(s)
- Jimmy C Kromann
- Department of Chemistry , University of Copenhagen , Copenhagen , Denmark . ; http://www.twitter.com/janhjensen
| | - Jan H Jensen
- Department of Chemistry , University of Copenhagen , Copenhagen , Denmark . ; http://www.twitter.com/janhjensen
| | - Monika Kruszyk
- Discovery Chemistry , DMPK , Neuroscience Drug Discovery , H. Lundbeck A/S, Valby , Denmark .
- Department of Drug Design and Pharmacology , University of Copenhagen , Copenhagen , Denmark
| | - Mikkel Jessing
- Discovery Chemistry , DMPK , Neuroscience Drug Discovery , H. Lundbeck A/S, Valby , Denmark .
| | - Morten Jørgensen
- Discovery Chemistry , DMPK , Neuroscience Drug Discovery , H. Lundbeck A/S, Valby , Denmark .
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22
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Meloun M, Pilařová L, Pekárek T, Javůrek M. Overlapping pK
a of the Multiprotic Hemostyptic Eltrombopag using UV–Vis Multiwavelength Spectroscopy and Potentiometry. J SOLUTION CHEM 2017. [DOI: 10.1007/s10953-017-0682-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Jensen JH, Swain CJ, Olsen L. Prediction of pK a Values for Druglike Molecules Using Semiempirical Quantum Chemical Methods. J Phys Chem A 2017; 121:699-707. [PMID: 28054775 DOI: 10.1021/acs.jpca.6b10990] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid yet accurate pKa prediction for druglike molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48 druglike compounds. The approach uses an isodesmic reaction where the pKa value is computed relative to a chemically related reference compound for which the pKa value has been measured experimentally or estimated using a standard empirical approach. The AM1- and PM3-based methods perform best with RMSE values of 1.4-1.6 pH units that have uncertainties of ±0.2-0.3 pH units, which make them statistically equivalent. However, for all but PM3/SMD and AM1/SMD the RMSEs are dominated by a single outlier, cefadroxil, caused by proton transfer in the zwitterionic protonation state. If this outlier is removed, the RMSE values for PM3/COSMO and AM1/COSMO drop to 1.0 ± 0.2 and 1.1 ± 0.3, whereas PM3/SMD and AM1/SMD remain at 1.5 ± 0.3 and 1.6 ± 0.3/0.4 pH units, making the COSMO-based predictions statistically better than the SMD-based predictions. For pKa calculations where a zwitterionic state is not involved or proton transfer in a zwitterionic state is not observed, PM3/COSMO or AM1/COSMO is the best pKa prediction method; otherwise PM3/SMD or AM1/SMD should be used. Thus, fast and relatively accurate pKa prediction for 100-1000s of druglike amines is feasible with the current setup and relatively modest computational resources.
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Affiliation(s)
- Jan H Jensen
- Department of Chemistry, University of Copenhagen , 1165 Copenhagen, Denmark
| | | | - Lars Olsen
- Section of Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen , 1165 Copenhagen, Denmark
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24
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Bochevarov AD, Watson MA, Greenwood JR, Philipp DM. Multiconformation, Density Functional Theory-Based pKa Prediction in Application to Large, Flexible Organic Molecules with Diverse Functional Groups. J Chem Theory Comput 2016; 12:6001-6019. [PMID: 27951674 DOI: 10.1021/acs.jctc.6b00805] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Art D. Bochevarov
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark A. Watson
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jeremy R. Greenwood
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Dean M. Philipp
- Schrödinger, Inc., 101 SW Main Street, Suite 1300, Portland, Oregon 97204, United States
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25
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Kromann JC, Larsen F, Moustafa H, Jensen JH. Prediction of pKa values using the PM6 semiempirical method. PeerJ 2016; 4:e2335. [PMID: 27602298 PMCID: PMC4991863 DOI: 10.7717/peerj.2335] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/16/2016] [Indexed: 12/11/2022] Open
Abstract
The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using isodesmic reactions and compared to published ab initio results. The pKa values of pyridines, alcohols, phenols, and benzoic acids considered in this study can generally be predicted with PM6 and ab initio methods to within the same overall accuracy, with average mean absolute differences (MADs) of 0.6-0.7 pH units. For carboxylic acids, the accuracy (0.7-1.0 pH units) is also comparable to ab initio results if a single outlier is removed. For primary, secondary, and tertiary amines the accuracy is, respectively, similar (0.5-0.6), slightly worse (0.5-1.0), and worse (1.0-2.5), provided that di- and tri-ethylamine are used as reference molecules for secondary and tertiary amines. When applied to a drug-like molecule where an empirical pKa predictor exhibits a large (4.9 pH unit) error, we find that the errors for PM6-based predictions are roughly the same in magnitude but opposite in sign. As a result, most of the PM6-based methods predict the correct protonation state at physiological pH, while the empirical predictor does not. The computational cost is around 2-5 min per conformer per core processor, making PM6-based pKa prediction computationally efficient enough to be used for high-throughput screening using on the order of 100 core processors.
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Affiliation(s)
- Jimmy C Kromann
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
| | - Frej Larsen
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
| | - Hadeel Moustafa
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
| | - Jan H Jensen
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
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