Ab Initio Investigation of CO2 Adsorption on 13-Atom 4d Clusters.

Abstract:

:In this work, we report an ab initio investigation based on density functional theory calculations within van der Waals D3 corrections to investigate the adsorption properties and activation of CO2 on transition-metal (TM) 13-atom clusters (TM = Ru, Rh, Pd, Ag), which is a key step for the development of subnano catalysts for the conversion of CO2 to high-value products. From our analyses, which include calculations of several properties and the Spearman correlation analysis, we found that CO2 adopts two distinct structures on the selected TM13 clusters, namely, a bent CO2 configuration in which the OCO angle is about 125 to 150° (chemisorption), which is the lowest energy CO2/TM13 configuration for TM = Ru, Rh, Pd. As in the gas phase, the linear CO2 structure yields the lowest energy for CO2/Ag13 and several higher energy configurations for TM = Ru, Rh, Pd. The bent CO2 (activated) is driven by a chemisorption CO2-TM13 interaction due to the charge transfer from the TM13 clusters toward CO2, while a weak physisorption interaction is obtained for the linear CO2 on the TM13 clusters. Thus, the CO2 activation occurs only in the first case and it is driven by charge transfer from the TM13 clusters to the CO2 molecule (i.e., CO2-δ), which is confirmed by our Bader charge analysis and vibrational frequencies.

journal_name

J Chem Inf Model

authors

Batista KEA,Ocampo-Restrepo VK,Soares MD,Quiles MG,Piotrowski MJ,Da Silva JLF

doi

10.1021/acs.jcim.9b00792

subject

Has Abstract

pub_date

2020-02-24 00:00:00

pages

537-545

issue

2

eissn

1549-9596

issn

1549-960X

journal_volume

60

pub_type

杂志文章
  • De Novo Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization.

    abstract::Artificial intelligence and multiobjective optimization represent promising solutions to bridge chemical and biological landscapes by addressing the automated de novo design of compounds as a result of a humanlike creative process. In the present study, we conceived a novel pair-based multiobjective approach implement...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00517

    authors: Domenico A,Nicola G,Daniela T,Fulvio C,Nicola A,Orazio N

    更新日期:2020-10-26 00:00:00

  • Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.

    abstract::Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00877

    authors: Wakefield AE,Yueh C,Beglov D,Castilho MS,Kozakov D,Keserű GM,Whitty A,Vajda S

    更新日期:2020-12-28 00:00:00

  • How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?

    abstract::With continually increased computer power, molecular mechanics force field-based approaches, such as the endpoint methods of molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA), have been routinely applied in both drug lead identification and opt...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00934

    authors: Hao D,He X,Ji B,Zhang S,Wang J

    更新日期:2020-12-28 00:00:00

  • Including explicit water molecules as part of the protein structure in MM/PBSA calculations.

    abstract::Water is the natural medium of molecules in the cell and plays an important role in protein structure, function and interaction with small molecule ligands. However, the widely used molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method for binding energy calculation does not explicitly take account of wa...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci4001794

    authors: Zhu YL,Beroza P,Artis DR

    更新日期:2014-02-24 00:00:00

  • GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

    abstract::The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In th...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00148

    authors: Won J,Lee GR,Park H,Seok C

    更新日期:2018-06-25 00:00:00

  • Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors.

    abstract::Traditionally, a drug potency is expressed in terms of thermodynamic quantities, mostly Kd, and empirical IC50 values. Although binding affinity as an estimate of drug activity remains relevant, it is increasingly clear that it is also important to include (un)binding kinetic parameters in the characterization of pote...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00518

    authors: Bernetti M,Rosini E,Mollica L,Masetti M,Pollegioni L,Recanatini M,Cavalli A

    更新日期:2018-11-26 00:00:00

  • Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G-Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields.

    abstract::Human telomeric DNA G-quadruplex has been identified as a good therapeutic target in cancer treatment. G-quadruplex-specific ligands that stabilize the G-quadruplex have great potential to be developed as anticancer agents. Two crystal structures (an apo form of parallel stranded human telomeric G-quadruplex and its h...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00287

    authors: Machireddy B,Kalra G,Jonnalagadda S,Ramanujachary K,Wu C

    更新日期:2017-11-27 00:00:00

  • Development of an informatics platform for therapeutic protein and peptide analytics.

    abstract::The momentum gained by research on biologics has not been met yet with equal thrust on the informatics side. There is a noticeable lack of software for data management that empowers the bench scientists working on the development of biologic therapeutics. SARvision|Biologics is a tool to analyze data associated with b...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400333x

    authors: Hansen MR,Villar HO,Feyfant E

    更新日期:2013-10-28 00:00:00

  • Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations.

    abstract::Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most wid...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c01168

    authors: Rusu VH,Santos DES,Poleto MD,Galheigo MM,Gomes ATA,Verli H,Soares TA,Lins RD

    更新日期:2020-12-28 00:00:00

  • Use of 3D QSAR models for database screening: a feasibility study.

    abstract::The applicability and scope of 3D QSAR methods (CoMFA, CoMSIA) to screen databases are examined. A protocol requiring minimal user intervention has been established to align training and test set molecules using FlexS. As model system isozymes of human carbonic anhydrase (hCA) are used, all results are exemplified stu...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci7002945

    authors: Hillebrecht A,Klebe G

    更新日期:2008-02-01 00:00:00

  • OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods.

    abstract::Side-chain modeling is critical for protein structure prediction since the uniqueness of the protein structure is largely determined by its side-chain packing conformation. In this paper, differing from most approaches that rely on rotamer library sampling, we first propose a novel side-chain rotamer prediction method...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00951

    authors: Xu G,Wang Q,Ma J

    更新日期:2020-12-28 00:00:00

  • Phytochemical informatics of traditional Chinese medicine and therapeutic relevance.

    abstract::Distribution patterns of 8411 compounds from 240 Chinese herbs were analyzed in relation to the herbal categories of traditional Chinese medicine (TCM), using Random Forest (RF) and self-organizing maps (SOM). RF was used first to construct TCM profiles of individual compounds, which describe their affinities for 28 m...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci700155t

    authors: Ehrman TM,Barlow DJ,Hylands PJ

    更新日期:2007-11-01 00:00:00

  • Exploring Alternative Strategies for the Identification of Potent Compounds Using Support Vector Machine and Regression Modeling.

    abstract::Support vector regression (SVR) is a premier approach for the prediction of compound potency. Given the conceptual link between support vector machine (SVM) and SVR modeling, SVR is capable of accounting for continuous and discontinuous structure-activity relationships (SARs) in potency prediction, which further exten...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00584

    authors: Miyao T,Funatsu K,Bajorath J

    更新日期:2019-03-25 00:00:00

  • Advantages of Relative versus Absolute Data for the Development of Quantitative Structure-Activity Relationship Classification Models.

    abstract::The appropriate selection of a chemical space represented by the data set, the selection of its chemical data representation, the development of a correct modeling process using a robust and reproducible algorithm, and the performance of an exhaustive training and external validation determine the usability and reprod...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00492

    authors: Ruiz IL,Gómez-Nieto MÁ

    更新日期:2017-11-27 00:00:00

  • Improving classical substructure-based virtual screening to handle extrapolation challenges.

    abstract::Target-oriented substructure-based virtual screening (sSBVS) of molecules is a promising approach in drug discovery. Yet, there are doubts whether sSBVS is suitable also for extrapolation, that is, for detecting molecules that are very different from those used for training. Herein, we evaluate the predictive power of...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200472s

    authors: Biniashvili T,Schreiber E,Kliger Y

    更新日期:2012-03-26 00:00:00

  • Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics.

    abstract::The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structur...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00009

    authors: Dahanayake JN,Shahryari E,Roberts KM,Heikes ME,Kasireddy C,Mitchell-Koch KR

    更新日期:2019-05-28 00:00:00

  • Conformational analysis of macrocycles: finding what common search methods miss.

    abstract::As computational drug design becomes increasingly reliant on virtual screening and on high-throughput 3D modeling, the need for fast, robust, and reliable methods for sampling molecular conformations has become greater than ever. Furthermore, chemical novelty is at a premium, forcing medicinal chemists to explore more...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900238a

    authors: Bonnet P,Agrafiotis DK,Zhu F,Martin E

    更新日期:2009-10-01 00:00:00

  • Prediction of pH-dependent aqueous solubility of druglike molecules.

    abstract::In the present work, the Henderson-Hasselbalch (HH) equation has been employed for the development of a tool for the prediction of pH-dependent aqueous solubility of drugs and drug candidates. A new prediction method for the intrinsic solubility was developed, based on artificial neural networks that have been trained...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600292q

    authors: Hansen NT,Kouskoumvekaki I,Jørgensen FS,Brunak S,Jónsdóttir SO

    更新日期:2006-11-01 00:00:00

  • GalaxyDock: protein-ligand docking with flexible protein side-chains.

    abstract::An important issue in developing protein-ligand docking methods is how to incorporate receptor flexibility. Consideration of receptor flexibility using an ensemble of precompiled receptor conformations or by employing an effectively enlarged binding pocket has been reported to be useful. However, direct consideration ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300342z

    authors: Shin WH,Seok C

    更新日期:2012-12-21 00:00:00

  • SARANEA: a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets.

    abstract::We introduce SARANEA, an open-source Java application for interactive exploration of structure-activity relationship (SAR) and structure-selectivity relationship (SSR) information in compound sets of any source. SARANEA integrates various SAR and SSR analysis functions and utilizes a network-like similarity graph data...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900416a

    authors: Lounkine E,Wawer M,Wassermann AM,Bajorath J

    更新日期:2010-01-01 00:00:00

  • FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes.

    abstract::In this work we present the third generation of FAst MEtabolizer (FAME 3), a collection of extra trees classifiers for the prediction of sites of metabolism (SoMs) in small molecules such as drugs, druglike compounds, natural products, agrochemicals, and cosmetics. FAME 3 was derived from the MetaQSAR database ( Pedre...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00376

    authors: Šícho M,Stork C,Mazzolari A,de Bruyn Kops C,Pedretti A,Testa B,Vistoli G,Svozil D,Kirchmair J

    更新日期:2019-08-26 00:00:00

  • Knowledge-based scoring functions in drug design: 2. Can the knowledge base be enriched?

    abstract::Fast and accurate predicting of the binding affinities of large sets of diverse protein−ligand complexes is an important, yet extremely challenging, task in drug discovery. The development of knowledge-based scoring functions exploiting structural information of known protein−ligand complexes represents a valuable con...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci100343j

    authors: Shen Q,Xiong B,Zheng M,Luo X,Luo C,Liu X,Du Y,Li J,Zhu W,Shen J,Jiang H

    更新日期:2011-02-28 00:00:00

  • Prediction and Experimental Confirmation of Novel Peripheral Cannabinoid-1 Receptor Antagonists.

    abstract::Small molecules targeting peripheral CB1 receptors have therapeutic potential in a variety of disorders including obesity-related, hormonal, and metabolic abnormalities, while avoiding the psychoactive effects in the central nervous system. We applied our in-house algorithm, iterative stochastic elimination, to produc...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00577

    authors: El-Atawneh S,Hirsch S,Hadar R,Tam J,Goldblum A

    更新日期:2019-09-23 00:00:00

  • Protein Preparation Automatic Protocol for High-Throughput Inverse Virtual Screening: Accelerating the Target Identification by Computational Methods.

    abstract::Structure-based virtual screening is highly used in the early stages of drug discovery to identify new putative lead compounds for a given target. However, when a small molecule elicits a biological effect, but its target is unknown, or the side effects it causes arise from its undesired interaction with unknown count...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00428

    authors: De Vita S,Lauro G,Ruggiero D,Terracciano S,Riccio R,Bifulco G

    更新日期:2019-11-25 00:00:00

  • Multidimensional Drift of Sequence Attributes and Functional Profiles in the Superfamily of the Three-Finger Proteins and Their Structural Homologues.

    abstract::Functional diversity of the three-finger-protein domain (TFPD) had been acquired via hypervariability of some sequence positions and extensive insertion/deletion of short AA-segments that caused multidimensional drift of several sequence attributes such as the overall (HI) and local hydrophobicity levels, the isoelect...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00322

    authors: Galat A

    更新日期:2015-09-28 00:00:00

  • Customizable Generation of Synthetically Accessible, Local Chemical Subspaces.

    abstract::Screening large libraries of chemicals has been an efficient strategy to discover bioactive compounds; however a portion of the potential for success is limited to the available libraries. Synergizing combinatorial and computational chemistries has emerged as a time-efficient strategy to explore the chemical space mor...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.6b00648

    authors: Pottel J,Moitessier N

    更新日期:2017-03-27 00:00:00

  • PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.

    abstract::Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrization. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of inter...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00096

    authors: Graham JA,Essex JW,Khalid S

    更新日期:2017-04-24 00:00:00

  • Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches.

    abstract::Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of r...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050395b

    authors: Gilis D,Biot C,Buisine E,Dehouck Y,Rooman M

    更新日期:2006-03-01 00:00:00

  • Growth of ligand-target interaction data in ChEMBL is associated with increasing and activity measurement-dependent compound promiscuity.

    abstract::Compounds with high-confidence target annotations and activity measurements in the original and current release of the ChEMBL database have been compared to better understand how the growth of compound activity data might influence the spectrum of ligand-target interactions and the degree of target promiscuity among a...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci3003304

    authors: Hu Y,Bajorath J

    更新日期:2012-10-22 00:00:00

  • Binding of Cytotoxic Aβ25-35 Peptide to the Dimyristoylphosphatidylcholine Lipid Bilayer.

    abstract::Aβ25-35 is a short, cytotoxic, and naturally occurring fragment of the Alzheimer's Aβ peptide. To map the molecular mechanism of Aβ25-35 binding to the zwitterionic dimyristoylphosphatidylcholine (DMPC) bilayer, we have performed replica exchange with solute tempering molecular dynamics simulations using all-atom expl...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00045

    authors: Smith AK,Klimov DK

    更新日期:2018-05-29 00:00:00